---
_id: '1047'
abstract:
- lang: eng
text: Particles in a perfect lattice potential perform Bloch oscillations when subject
to a constant force, leading to localization and preventing conductivity. For
a weakly interacting Bose-Einstein condensate of Cs atoms, we observe giant center-of-mass
oscillations in position space with a displacement across hundreds of lattice
sites when we add a periodic modulation to the force near the Bloch frequency.
We study the dependence of these "super" Bloch oscillations on lattice
depth, modulation amplitude, and modulation frequency and show that they provide
a means to induce linear transport in a dissipation-free lattice.
acknowledgement: We thank A. R. Kolovsky, A. Zenesini, and A. Wacker for discussions
and R. Grimm for generous support. We acknowledge funding by the Austrian Ministry
of Science and Research and the Austrian Science Fund and by the European Union
within the framework of the EuroQUASAR collective research project QuDeGPM. R. H.
is supported by a Marie Curie Action within FP7.
article_processing_charge: No
arxiv: 1
author:
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Lukas
full_name: Reichsöllner, Lukas
last_name: Reichsöllner
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Nägerl H. Inducing transport
in a dissipation-free lattice with super bloch oscillations. Physical Review
Letters. 2010;104(20). doi:10.1103/PhysRevLett.104.200403
apa: Haller, E., Hart, R., Mark, M., Danzl, J. G., Reichsöllner, L., & Nägerl,
H. (2010). Inducing transport in a dissipation-free lattice with super bloch oscillations.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.104.200403
chicago: Haller, Elmar, Russell Hart, Manfred Mark, Johann G Danzl, Lukas Reichsöllner,
and Hanns Nägerl. “Inducing Transport in a Dissipation-Free Lattice with Super
Bloch Oscillations.” Physical Review Letters. American Physical Society,
2010. https://doi.org/10.1103/PhysRevLett.104.200403.
ieee: E. Haller, R. Hart, M. Mark, J. G. Danzl, L. Reichsöllner, and H. Nägerl,
“Inducing transport in a dissipation-free lattice with super bloch oscillations,”
Physical Review Letters, vol. 104, no. 20. American Physical Society, 2010.
ista: Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Nägerl H. 2010. Inducing
transport in a dissipation-free lattice with super bloch oscillations. Physical
Review Letters. 104(20).
mla: Haller, Elmar, et al. “Inducing Transport in a Dissipation-Free Lattice with
Super Bloch Oscillations.” Physical Review Letters, vol. 104, no. 20, American
Physical Society, 2010, doi:10.1103/PhysRevLett.104.200403.
short: E. Haller, R. Hart, M. Mark, J.G. Danzl, L. Reichsöllner, H. Nägerl, Physical
Review Letters 104 (2010).
date_created: 2018-12-11T11:49:52Z
date_published: 2010-05-21T00:00:00Z
date_updated: 2021-01-12T06:47:54Z
day: '21'
doi: 10.1103/PhysRevLett.104.200403
extern: '1'
external_id:
arxiv:
- '1001.1206'
intvolume: ' 104'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1001.1206
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6343'
status: public
title: Inducing transport in a dissipation-free lattice with super bloch oscillations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2010'
...
---
_id: '1049'
abstract:
- lang: eng
text: Quantum many-body systems can have phase transitions even at zero temperature;
fluctuations arising from Heisenbergĝ€™s uncertainty principle, as opposed to
thermal effects, drive the system from one phase to another. Typically, during
the transition the relative strength of two competing terms in the systemĝ€™s
Hamiltonian changes across a finite critical value. A well-known example is the
Mottĝ€" Hubbard quantum phase transition from a superfluid to an insulating
phase, which has been observed for weakly interacting bosonic atomic gases. However,
for strongly interacting quantum systems confined to lower-dimensional geometry,
a novel type of quantum phase transition may be induced and driven by an arbitrarily
weak perturbation to the Hamiltonian. Here we observe such an effectĝ€"the
sineĝ€"Gordon quantum phase transition from a superfluid Luttinger liquid
to a Mott insulatorĝ€ "in a one-dimensional quantum gas of bosonic caesium
atoms with tunable interactions. For sufficiently strong interactions, the transition
is induced by adding an arbitrarily weak optical lattice commensurate with the
atomic granularity, which leads to immediate pinning of the atoms. We map out
the phase diagram and find that our measurements in the strongly interacting regime
agree well with a quantum field description based on the exactly solvable sineĝ€"Gordon
model. We trace the phase boundary all the way to the weakly interacting regime,
where we find good agreement with the predictions of the one-dimensional Boseĝ€"Hubbard
model. Our results open up the experimental study of quantum phase transitions,
criticality and transport phenomena beyond Hubbard-type models in the context
of ultracold gases.
acknowledgement: We thank W. Zwerger for discussions. We are indebted to R. Grimm
for generous support. We gratefully acknowledge funding by the Austrian Ministry
of Science and Research (Bundesministerium für Wissenschaft und Forschung) and the
Austrian Science Fund (Fonds zur Förderung der wissenschaftlichen Forschung) in
the form of a START prize grant, and by the European Union through the STREP FP7-ICT-2007-C
project NAME-QUAM (Nanodesigning of Atomic and Molecular Quantum Matter) and within
the framework of the EuroQUASAR collective research project QuDeGPM. R.H. is supported
by a Marie Curie International Incoming Fellowship within the 7th European Community
Framework Programme.
article_processing_charge: No
arxiv: 1
author:
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Lukas
full_name: Reichsöllner, Lukas
last_name: Reichsöllner
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Marcello
full_name: Dalmonte, Marcello
last_name: Dalmonte
- first_name: Guido
full_name: Pupillo, Guido
last_name: Pupillo
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Haller E, Hart R, Mark M, et al. Pinning quantum phase transition for a Luttinger
liquid of strongly interacting bosons. Nature. 2010;466(7306):597-600.
doi:10.1038/nature09259
apa: Haller, E., Hart, R., Mark, M., Danzl, J. G., Reichsöllner, L., Gustavsson,
M., … Nägerl, H. (2010). Pinning quantum phase transition for a Luttinger liquid
of strongly interacting bosons. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09259
chicago: Haller, Elmar, Russell Hart, Manfred Mark, Johann G Danzl, Lukas Reichsöllner,
Mattias Gustavsson, Marcello Dalmonte, Guido Pupillo, and Hanns Nägerl. “Pinning
Quantum Phase Transition for a Luttinger Liquid of Strongly Interacting Bosons.”
Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature09259.
ieee: E. Haller et al., “Pinning quantum phase transition for a Luttinger
liquid of strongly interacting bosons,” Nature, vol. 466, no. 7306. Nature
Publishing Group, pp. 597–600, 2010.
ista: Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Gustavsson M, Dalmonte
M, Pupillo G, Nägerl H. 2010. Pinning quantum phase transition for a Luttinger
liquid of strongly interacting bosons. Nature. 466(7306), 597–600.
mla: Haller, Elmar, et al. “Pinning Quantum Phase Transition for a Luttinger Liquid
of Strongly Interacting Bosons.” Nature, vol. 466, no. 7306, Nature Publishing
Group, 2010, pp. 597–600, doi:10.1038/nature09259.
short: E. Haller, R. Hart, M. Mark, J.G. Danzl, L. Reichsöllner, M. Gustavsson,
M. Dalmonte, G. Pupillo, H. Nägerl, Nature 466 (2010) 597–600.
date_created: 2018-12-11T11:49:52Z
date_published: 2010-07-29T00:00:00Z
date_updated: 2021-01-12T06:47:54Z
day: '29'
doi: 10.1038/nature09259
extern: '1'
external_id:
arxiv:
- '1004.3168'
intvolume: ' 466'
issue: '7306'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.3168
month: '07'
oa: 1
oa_version: Preprint
page: 597 - 600
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6341'
status: public
title: Pinning quantum phase transition for a Luttinger liquid of strongly interacting
bosons
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 466
year: '2010'
...
---
_id: '9485'
abstract:
- lang: eng
text: 'Cytosine methylation silences transposable elements in plants, vertebrates,
and fungi but also regulates gene expression. Plant methylation is catalyzed by
three families of enzymes, each with a preferred sequence context: CG, CHG (H
= A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis
thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally
hypomethylated in the CG context while retaining high non-CG methylation. Global
methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition
remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all
sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas
CG hypomethylation is localized. CHH methylation of small transposable elements
is increased in embryos, suggesting that endosperm demethylation enhances transposon
silencing. Genes preferentially expressed in endosperm, including those coding
for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated
in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm
biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is
conserved among angiosperms and has a profound effect on gene expression in cereal
crops.'
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Bradley
full_name: Dotson, Bradley
last_name: Dotson
- first_name: Matthew D.
full_name: Brooks, Matthew D.
last_name: Brooks
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes
in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734.
doi:10.1073/pnas.1009695107
apa: Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M.
D., & Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice
endosperm. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1009695107
chicago: Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley
Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates
Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107.
ieee: A. Zemach et al., “Local DNA hypomethylation activates genes in rice
endosperm,” Proceedings of the National Academy of Sciences, vol. 107,
no. 43. National Academy of Sciences, pp. 18729–18734, 2010.
ista: Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D.
2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings
of the National Academy of Sciences. 107(43), 18729–18734.
mla: Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 107, no. 43, National
Academy of Sciences, 2010, pp. 18729–34, doi:10.1073/pnas.1009695107.
short: A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D.
Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.
date_created: 2021-06-07T09:31:01Z
date_published: 2010-10-26T00:00:00Z
date_updated: 2021-12-14T08:40:02Z
day: '26'
department:
- _id: DaZi
doi: 10.1073/pnas.1009695107
extern: '1'
external_id:
pmid:
- '20937895'
intvolume: ' 107'
issue: '43'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1009695107
month: '10'
oa: 1
oa_version: Published Version
page: 18729-18734
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local DNA hypomethylation activates genes in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 107
year: '2010'
...
---
_id: '9489'
abstract:
- lang: eng
text: Cytosine methylation is an ancient process with conserved enzymology but diverse
biological functions that include defense against transposable elements and regulation
of gene expression. Here we will discuss the evolution and biological significance
of eukaryotic DNA methylation, the likely drivers of that evolution, and major
remaining mysteries.
article_processing_charge: No
article_type: review
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit
of safer sex. Current Biology. 2010;20(17):R780-R785. doi:10.1016/j.cub.2010.07.007
apa: Zemach, A., & Zilberman, D. (2010). Evolution of eukaryotic DNA methylation
and the pursuit of safer sex. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2010.07.007
chicago: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology. Elsevier, 2010. https://doi.org/10.1016/j.cub.2010.07.007.
ieee: A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the
pursuit of safer sex,” Current Biology, vol. 20, no. 17. Elsevier, pp.
R780–R785, 2010.
ista: Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the
pursuit of safer sex. Current Biology. 20(17), R780–R785.
mla: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology, vol. 20, no. 17, Elsevier,
2010, pp. R780–85, doi:10.1016/j.cub.2010.07.007.
short: A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.
date_created: 2021-06-07T09:45:27Z
date_published: 2010-09-14T00:00:00Z
date_updated: 2021-12-14T08:52:34Z
day: '14'
department:
- _id: DaZi
doi: 10.1016/j.cub.2010.07.007
extern: '1'
external_id:
pmid:
- '20833323'
intvolume: ' 20'
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2010.07.007
month: '09'
oa: 1
oa_version: Published Version
page: R780-R785
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of eukaryotic DNA methylation and the pursuit of safer sex
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 20
year: '2010'
...
---
_id: '3430'
abstract:
- lang: eng
text: These are notes for a set of 7 two-hour lectures given at the 2010 Summer
School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa,
Japan. The emphasis is on understanding how biological systems process information.
We take a physicist's approach of looking for simple phenomenological descriptions
that can address the questions of biological function without necessarily modeling
all (mostly unknown) microscopic details; the example that is developed throughout
the notes is transcriptional regulation in genetic regulatory networks. We present
tools from information theory and statistical physics that can be used to analyze
noisy nonlinear biological networks, and build generative and predictive models
of regulatory processes.
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Tkačik G. Lecture notes for 2010 summer school on Quantitative Evolutionary
and Comparative Genomics. In: Elsevier; 2010.'
apa: Tkačik, G. (2010). Lecture notes for 2010 summer school on Quantitative Evolutionary
and Comparative Genomics. Presented at the Summer School on Quantitative Evolutionary
and Comparative Genomics, Elsevier.
chicago: Tkačik, Gašper. “Lecture Notes for 2010 Summer School on Quantitative Evolutionary
and Comparative Genomics.” Elsevier, 2010.
ieee: G. Tkačik, “Lecture notes for 2010 summer school on Quantitative Evolutionary
and Comparative Genomics,” presented at the Summer School on Quantitative Evolutionary
and Comparative Genomics, 2010.
ista: Tkačik G. 2010. Lecture notes for 2010 summer school on Quantitative Evolutionary
and Comparative Genomics. Summer School on Quantitative Evolutionary and Comparative
Genomics.
mla: Tkačik, Gašper. Lecture Notes for 2010 Summer School on Quantitative Evolutionary
and Comparative Genomics. Elsevier, 2010.
short: G. Tkačik, in:, Elsevier, 2010.
conference:
name: Summer School on Quantitative Evolutionary and Comparative Genomics
date_created: 2018-12-11T12:03:17Z
date_published: 2010-06-22T00:00:00Z
date_updated: 2021-01-12T07:43:25Z
day: '22'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/pdf/1006.4291
month: '06'
oa: 1
publication_status: published
publisher: Elsevier
publist_id: '2970'
quality_controlled: 0
status: public
title: Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative
Genomics
type: conference
year: '2010'
...
---
_id: '3538'
abstract:
- lang: eng
text: How seizures start is a major question in epilepsy research. Preictal EEG
changes occur in both human patients and animal models, but their underlying mechanisms
and relationship with seizure initiation remain unknown. Here we demonstrate the
existence, in the hippocampal CA1 region, of a preictal state characterized by
the progressive and global increase in neuronal activity associated with a widespread
buildup of low-amplitude high-frequency activity (HFA) (> 100 Hz) and reduction
in system complexity. HFA is generated by the firing of neurons, mainly pyramidal
cells, at much lower frequencies. Individual cycles of HFA are generated by the
near-synchronous (within similar to 5 ms) firing of small numbers of pyramidal
cells. The presence of HFA in the low-calcium model implicates nonsynaptic synchronization;
the presence of very similar HFA in the high-potassium model shows that it does
not depend on an absence of synaptic transmission. Immediately before seizure
onset, CA1 is in a state of high sensitivity in which weak depolarizing or synchronizing
perturbations can trigger seizures. Transition to seizure is characterized by
a rapid expansion and fusion of the neuronal populations responsible for HFA,
associated with a progressive slowing of HFA, leading to a single, massive, hypersynchronous
cluster generating the high-amplitude low-frequency activity of the seizure.
author:
- first_name: Premysl
full_name: Jiruska, Premysl
last_name: Jiruska
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Andrew
full_name: Powell, Andrew
last_name: Powell
- first_name: John
full_name: Fox, John
last_name: Fox
- first_name: Wei
full_name: Chang, Wei
last_name: Chang
- first_name: Martin
full_name: Vreugdenhil, Martin
last_name: Vreugdenhil
- first_name: Xiaoli
full_name: Li, Xiaoli
last_name: Li
- first_name: Milan
full_name: Palus, Milan
last_name: Palus
- first_name: Alejandro
full_name: Bujan, Alejandro
last_name: Bujan
- first_name: Richard
full_name: Dearden, Richard
last_name: Dearden
- first_name: John
full_name: Jefferys, John
last_name: Jefferys
citation:
ama: Jiruska P, Csicsvari JL, Powell A, et al. High-frequency network activity,
global increase in neuronal activity, and synchrony expansion precede epileptic
seizures in vitro. Journal of Neuroscience. 2010;30(16):5690-5701. doi:10.1523/JNEUROSCI.0535-10.2010
apa: Jiruska, P., Csicsvari, J. L., Powell, A., Fox, J., Chang, W., Vreugdenhil,
M., … Jefferys, J. (2010). High-frequency network activity, global increase in
neuronal activity, and synchrony expansion precede epileptic seizures in vitro.
Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0535-10.2010
chicago: Jiruska, Premysl, Jozsef L Csicsvari, Andrew Powell, John Fox, Wei Chang,
Martin Vreugdenhil, Xiaoli Li, et al. “High-Frequency Network Activity, Global
Increase in Neuronal Activity, and Synchrony Expansion Precede Epileptic Seizures
in Vitro.” Journal of Neuroscience. Society for Neuroscience, 2010. https://doi.org/10.1523/JNEUROSCI.0535-10.2010.
ieee: P. Jiruska et al., “High-frequency network activity, global increase
in neuronal activity, and synchrony expansion precede epileptic seizures in vitro,”
Journal of Neuroscience, vol. 30, no. 16. Society for Neuroscience, pp.
5690–5701, 2010.
ista: Jiruska P, Csicsvari JL, Powell A, Fox J, Chang W, Vreugdenhil M, Li X, Palus
M, Bujan A, Dearden R, Jefferys J. 2010. High-frequency network activity, global
increase in neuronal activity, and synchrony expansion precede epileptic seizures
in vitro. Journal of Neuroscience. 30(16), 5690–5701.
mla: Jiruska, Premysl, et al. “High-Frequency Network Activity, Global Increase
in Neuronal Activity, and Synchrony Expansion Precede Epileptic Seizures in Vitro.”
Journal of Neuroscience, vol. 30, no. 16, Society for Neuroscience, 2010,
pp. 5690–701, doi:10.1523/JNEUROSCI.0535-10.2010.
short: P. Jiruska, J.L. Csicsvari, A. Powell, J. Fox, W. Chang, M. Vreugdenhil,
X. Li, M. Palus, A. Bujan, R. Dearden, J. Jefferys, Journal of Neuroscience 30
(2010) 5690–5701.
date_created: 2018-12-11T12:03:51Z
date_published: 2010-04-21T00:00:00Z
date_updated: 2021-01-12T07:44:10Z
day: '21'
doi: 10.1523/JNEUROSCI.0535-10.2010
extern: '1'
intvolume: ' 30'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.jneurosci.org/content/30/16/5690
month: '04'
oa: 1
oa_version: None
page: 5690 - 5701
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2848'
quality_controlled: '1'
status: public
title: High-frequency network activity, global increase in neuronal activity, and
synchrony expansion precede epileptic seizures in vitro
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2010'
...
---
_id: '3719'
abstract:
- lang: eng
text: The induction of a signaling pathway is characterized by transient complex
formation and mutual posttranslational modification of proteins. To faithfully
capture this combinatorial process in a math- ematical model is an important challenge
in systems biology. Exploiting the limited context on which most binding and modification
events are conditioned, attempts have been made to reduce the com- binatorial
complexity by quotienting the reachable set of molecular species, into species
aggregates while preserving the deterministic semantics of the thermodynamic limit.
Recently we proposed a quotienting that also preserves the stochastic semantics
and that is complete in the sense that the semantics of individual species can
be recovered from the aggregate semantics. In this paper we prove that this quotienting
yields a sufficient condition for weak lumpability and that it gives rise to a
backward Markov bisimulation between the original and aggregated transition system.
We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.
acknowledgement: Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL
ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National
Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support
from SystemsX.ch, the Swiss Initiative in Systems Biology.
alternative_title:
- EPTCS
arxiv: 1
author:
- first_name: Jérôme
full_name: Feret, Jérôme
last_name: Feret
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Heinz
full_name: Koeppl, Heinz
last_name: Koeppl
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based
systems. In: Vol 40. Open Publishing Association; 2010:142-161.'
apa: 'Feret, J., Henzinger, T. A., Koeppl, H., & Petrov, T. (2010). Lumpability
abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC:
Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open
Publishing Association.'
chicago: Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability
Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.
ieee: 'J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions
of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically
Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.'
ista: 'Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions
of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process
Calculi, EPTCS, vol. 40, 142–161.'
mla: Feret, Jérôme, et al. Lumpability Abstractions of Rule-Based Systems.
Vol. 40, Open Publishing Association, 2010, pp. 142–61.
short: J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association,
2010, pp. 142–161.
conference:
end_date: 2010-08-23
location: Jena, Germany
name: 'MECBIC: Membrane Computing and Biologically Inspired Process Calculi'
start_date: 2010-08-23
date_created: 2018-12-11T12:04:47Z
date_published: 2010-10-30T00:00:00Z
date_updated: 2023-02-23T11:15:19Z
day: '30'
ddc:
- '570'
department:
- _id: ToHe
- _id: CaGu
external_id:
arxiv:
- '1011.0496'
file:
- access_level: open_access
checksum: eaaba991a86fff37606b0eb5196878e8
content_type: application/pdf
creator: kschuh
date_created: 2019-01-31T12:09:09Z
date_updated: 2020-07-14T12:46:14Z
file_id: '5904'
file_name: Lumpability_abstractions_of_rule-based_systems.pdf
file_size: 907155
relation: main_file
file_date_updated: 2020-07-14T12:46:14Z
has_accepted_license: '1'
intvolume: ' 40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 142-161
publication_status: published
publisher: Open Publishing Association
publist_id: '2511'
quality_controlled: '1'
related_material:
record:
- id: '3168'
relation: later_version
status: public
scopus_import: 1
status: public
title: Lumpability abstractions of rule-based systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2010'
...
---
_id: '3743'
abstract:
- lang: eng
text: These are notes for a set of 7 two-hour lectures given at the 2010 Summer
School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa,
Japan. The emphasis is on understanding how biological systems process information.
We take a physicist's approach of looking for simple phenomenological descriptions
that can address the questions of biological function without necessarily modeling
all (mostly unknown) microscopic details; the example that is developed throughout
the notes is transcriptional regulation in genetic regulatory networks. We present
tools from information theory and statistical physics that can be used to analyze
noisy nonlinear biological networks, and build generative and predictive models
of regulatory processes.
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Tkačik G. From statistical mechanics to information theory: understanding
biophysical information-processing systems. ArXiv. 2010;q-MN:1-52.'
apa: 'Tkačik, G. (2010). From statistical mechanics to information theory: understanding
biophysical information-processing systems. ArXiv. ArXiv.'
chicago: 'Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding
Biophysical Information-Processing Systems.” ArXiv. ArXiv, 2010.'
ieee: 'G. Tkačik, “From statistical mechanics to information theory: understanding
biophysical information-processing systems,” ArXiv, vol. q-MN. ArXiv, pp.
1–52, 2010.'
ista: 'Tkačik G. 2010. From statistical mechanics to information theory: understanding
biophysical information-processing systems. ArXiv, q-MN, 1–52, .'
mla: 'Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding
Biophysical Information-Processing Systems.” ArXiv, vol. q-MN, ArXiv, 2010,
pp. 1–52.'
short: G. Tkačik, ArXiv q-MN (2010) 1–52.
date_created: 2018-12-11T12:04:55Z
date_published: 2010-06-22T00:00:00Z
date_updated: 2021-01-12T07:51:53Z
day: '22'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1006.4291v1
month: '06'
oa: 1
page: 1 - 52
publication: ArXiv
publication_status: published
publisher: ArXiv
publist_id: '2487'
quality_controlled: 0
status: public
title: 'From statistical mechanics to information theory: understanding biophysical
information-processing systems'
type: preprint
volume: q-bio.MN
year: '2010'
...
---
_id: '3748'
abstract:
- lang: eng
text: The chemotaxis signalling network in Escherichia coli that controls the locomotion
of bacteria is a classic model system for signal transduction1, 2. This pathway
modulates the behaviour of flagellar motors to propel bacteria towards sources
of chemical attractants. Although this system relaxes to a steady state in response
to environmental changes, the signalling events within the chemotaxis network
are noisy and cause large temporal variations of the motor behaviour even in the
absence of stimulus3. That the same signalling network governs both behavioural
variability and cellular response raises the question of whether these two traits
are independent. Here, we experimentally establish a fluctuation–response relationship
in the chemotaxis system of living bacteria. Using this relationship, we demonstrate
the possibility of inferring the cellular response from the behavioural variability
measured before stimulus. In monitoring the pre- and post-stimulus switching behaviour
of individual bacterial motors, we found that variability scales linearly with
the response time for different functioning states of the cell. This study highlights
that the fundamental relationship between fluctuation and response is not constrained
to physical systems at thermodynamic equilibrium4 but is extensible to living
cells5. Such a relationship not only implies that behavioural variability and
cellular response can be coupled traits, but it also provides a general framework
within which we can examine how the selection of a network design shapes this
interdependence
author:
- first_name: Heungwon
full_name: Park, Heungwon
last_name: Park
- first_name: William
full_name: Pontius, William
last_name: Pontius
- first_name: Calin C
full_name: Calin Guet
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: John
full_name: Marko, John F
last_name: Marko
- first_name: Thierry
full_name: Emonet,Thierry
last_name: Emonet
- first_name: Philippe
full_name: Cluzel,Philippe
last_name: Cluzel
citation:
ama: Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. Interdependence of
behavioural variability and response to small stimuli in bacteria. Nature.
2010;468:819-823. doi:10.1038/nature09551
apa: Park, H., Pontius, W., Guet, C. C., Marko, J., Emonet, T., & Cluzel, P.
(2010). Interdependence of behavioural variability and response to small stimuli
in bacteria. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09551
chicago: Park, Heungwon, William Pontius, Calin C Guet, John Marko, Thierry Emonet,
and Philippe Cluzel. “Interdependence of Behavioural Variability and Response
to Small Stimuli in Bacteria.” Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature09551.
ieee: H. Park, W. Pontius, C. C. Guet, J. Marko, T. Emonet, and P. Cluzel, “Interdependence
of behavioural variability and response to small stimuli in bacteria,” Nature,
vol. 468. Nature Publishing Group, pp. 819–823, 2010.
ista: Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. 2010. Interdependence
of behavioural variability and response to small stimuli in bacteria. Nature.
468, 819–823.
mla: Park, Heungwon, et al. “Interdependence of Behavioural Variability and Response
to Small Stimuli in Bacteria.” Nature, vol. 468, Nature Publishing Group,
2010, pp. 819–23, doi:10.1038/nature09551.
short: H. Park, W. Pontius, C.C. Guet, J. Marko, T. Emonet, P. Cluzel, Nature 468
(2010) 819–823.
date_created: 2018-12-11T12:04:57Z
date_published: 2010-12-09T00:00:00Z
date_updated: 2021-01-12T07:51:55Z
day: '09'
doi: 10.1038/nature09551
extern: 1
intvolume: ' 468'
main_file_link:
- open_access: '1'
url: http://europepmc.org/articles/pmc3230254
month: '12'
oa: 1
page: 819 - 823
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '2480'
quality_controlled: 0
status: public
title: Interdependence of behavioural variability and response to small stimuli in
bacteria
type: journal_article
volume: 468
year: '2010'
...
---
_id: '3749'
abstract:
- lang: eng
text: 'In E. coli, chemotactic behavior exhibits perfect adaptation that is robust
to changes in the intracellular concentration of the chemotactic proteins, such
as CheR and CheB. However, the robustness of the perfect adaptation does not explicitly
imply a robust chemotactic response. Previous studies on the robustness of the
chemotactic response relied on swarming assays, which can be confounded by processes
besides chemotaxis, such as cellular growth and depletion of nutrients. Here,
using a high-throughput capillary assay that eliminates the effects of growth,
we experimentally studied how the chemotactic response depends on the relative
concentration of the chemotactic proteins. We simultaneously measured both the
chemotactic response of E. coli cells to L: -aspartate and the concentrations
of YFP-CheR and CheB-CFP fusion proteins. We found that the chemotactic response
is fine-tuned to a specific ratio of [CheR]/[CheB] with a maximum response comparable
to the chemotactic response of wild-type behavior. In contrast to adaptation in
chemotaxis, that is robust and exact, capillary assays revealed that the chemotactic
response in swimming bacteria is fined-tuned to wild-type level of the [CheR]/[CheB]
ratio.'
acknowledgement: "P50 GM081892-04/GM/NIGMS NIH HHS/United States\nR01 AI059195-01A1/AI/NIAID
NIH HHS/United States\nR01 AI059195-02/AI/NIAID NIH HHS/United States\nR01 AI059195-03/AI/NIAID
NIH HHS/United States\nR01AI059195-03/AI/NIAID NIH HHS/United States\n\n\nPMCID:
PMC3230253 "
author:
- first_name: Heungwon
full_name: Park, Heungwon
last_name: Park
- first_name: Calin C
full_name: Calin Guet
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Thierry
full_name: Emonet,Thierry
last_name: Emonet
- first_name: Philippe
full_name: Cluzel,Philippe
last_name: Cluzel
citation:
ama: Park H, Guet CC, Emonet T, Cluzel P. Fine-tuning of chemotactic response in
E. coli determined by high-throughput capillary assay. Current Microbiology.
2010;62(3):764-769. doi:10.1007/s00284-010-9778-z
apa: Park, H., Guet, C. C., Emonet, T., & Cluzel, P. (2010). Fine-tuning of
chemotactic response in E. coli determined by high-throughput capillary assay.
Current Microbiology. Springer. https://doi.org/10.1007/s00284-010-9778-z
chicago: Park, Heungwon, Calin C Guet, Thierry Emonet, and Philippe Cluzel. “Fine-Tuning
of Chemotactic Response in E. Coli Determined by High-Throughput Capillary Assay.”
Current Microbiology. Springer, 2010. https://doi.org/10.1007/s00284-010-9778-z.
ieee: H. Park, C. C. Guet, T. Emonet, and P. Cluzel, “Fine-tuning of chemotactic
response in E. coli determined by high-throughput capillary assay,” Current
Microbiology, vol. 62, no. 3. Springer, pp. 764–769, 2010.
ista: Park H, Guet CC, Emonet T, Cluzel P. 2010. Fine-tuning of chemotactic response
in E. coli determined by high-throughput capillary assay. Current Microbiology.
62(3), 764–769.
mla: Park, Heungwon, et al. “Fine-Tuning of Chemotactic Response in E. Coli Determined
by High-Throughput Capillary Assay.” Current Microbiology, vol. 62, no.
3, Springer, 2010, pp. 764–69, doi:10.1007/s00284-010-9778-z.
short: H. Park, C.C. Guet, T. Emonet, P. Cluzel, Current Microbiology 62 (2010)
764–769.
date_created: 2018-12-11T12:04:57Z
date_published: 2010-10-23T00:00:00Z
date_updated: 2021-01-12T07:51:55Z
day: '23'
doi: 10.1007/s00284-010-9778-z
extern: 1
intvolume: ' 62'
issue: '3'
main_file_link:
- open_access: '1'
url: http://europepmc.org/articles/pmc3230253
month: '10'
oa: 1
page: 764 - 769
publication: Current Microbiology
publication_status: published
publisher: Springer
publist_id: '2479'
quality_controlled: 0
status: public
title: Fine-tuning of chemotactic response in E. coli determined by high-throughput
capillary assay
type: journal_article
volume: 62
year: '2010'
...
---
_id: '3772'
article_number: e1000987
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Understanding adaptation in large populations. PLoS Genetics.
2010;6(6). doi:10.1371/journal.pgen.1000987
apa: Barton, N. H. (2010). Understanding adaptation in large populations. PLoS
Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000987
chicago: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS
Genetics. Public Library of Science, 2010. https://doi.org/10.1371/journal.pgen.1000987.
ieee: N. H. Barton, “Understanding adaptation in large populations,” PLoS Genetics,
vol. 6, no. 6. Public Library of Science, 2010.
ista: Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics.
6(6), e1000987.
mla: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS
Genetics, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:10.1371/journal.pgen.1000987.
short: N.H. Barton, PLoS Genetics 6 (2010).
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-17T00:00:00Z
date_updated: 2021-01-12T07:52:05Z
day: '17'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pgen.1000987
file:
- access_level: open_access
checksum: 5c14de2680ab483cb835096c99ee734d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:24Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5075'
file_name: IST-2016-524-v1+1_journal.pgen.1000987.PDF
file_size: 349965
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '2454'
pubrep_id: '524'
quality_controlled: '1'
scopus_import: 1
status: public
title: Understanding adaptation in large populations
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
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2010'
...
---
_id: '3773'
abstract:
- lang: eng
text: If distinct biological species are to coexist in sympatry, they must be reproductively
isolated and must exploit different limiting resources. A two-niche Levene model
is analysed, in which habitat preference and survival depend on underlying additive
traits. The population genetics of preference and viability are equivalent. However,
there is a linear trade-off between the chances of settling in either niche, whereas
viabilities may be constrained arbitrarily. With a convex trade-off, a sexual
population evolves a single generalist genotype, whereas with a concave trade-off,
disruptive selection favours maximal variance. A pure habitat preference evolves
to global linkage equilibrium if mating occurs in a single pool, but remarkably,
evolves to pairwise linkage equilibrium within niches if mating is within those
niches--independent of the genetics. With a concave trade-off, the population
shifts sharply between a unimodal distribution with high gene flow and a bimodal
distribution with strong isolation, as the underlying genetic variance increases.
However, these alternative states are only simultaneously stable for a narrow
parameter range. A sharp threshold is only seen if survival in the 'wrong' niche
is low; otherwise, strong isolation is impossible. Gene flow from divergent demes
makes speciation much easier in parapatry than in sympatry.
acknowledgement: "The author thanks the Werner-Gren Foundation and the Royal Swedish
Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He
also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n"
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. What role does natural selection play in speciation? Philosophical
Transactions of the Royal Society of London Series B, Biological Sciences.
2010;365(1547):1825-1840. doi:10.1098/rstb.2010.0001
apa: Barton, N. H. (2010). What role does natural selection play in speciation?
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0001
chicago: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?”
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0001.
ieee: N. H. Barton, “What role does natural selection play in speciation?,” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.
ista: Barton NH. 2010. What role does natural selection play in speciation? Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547),
1825–1840.
mla: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?”
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:10.1098/rstb.2010.0001.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 1825–1840.
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-12T00:00:00Z
date_updated: 2021-01-12T07:52:06Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0001
external_id:
pmid:
- '20439284'
intvolume: ' 365'
issue: '1547'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pubmed/20439284
month: '06'
oa: 1
oa_version: Submitted Version
page: 1825 - 1840
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2455'
quality_controlled: '1'
scopus_import: 1
status: public
title: What role does natural selection play in speciation?
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3776'
abstract:
- lang: eng
text: 'The prevalence of recombination in eukaryotes poses one of the most puzzling
questions in biology. The most compelling general explanation is that recombination
facilitates selection by breaking down the negative associations generated by
random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of
HRI owing to: deleterious mutation, balancing selection and selective sweeps on:
neutral diversity, rates of adaptation and the mutation load. These effects are
mediated primarily by the density of deleterious mutations and of selective sweeps.
Sequence polymorphism and divergence suggest that these rates may be high enough
to cause significant interference even in genomic regions of high recombination.
However, neither seems able to generate enough variance in fitness to select strongly
for high rates of recombination. It is plausible that spatial and temporal fluctuations
in selection generate much more fitness variance, and hence selection for recombination,
than can be explained by uniformly deleterious mutations or species-wide selective
sweeps.'
acknowledgement: "Royal Society and Wolfson Foundation for their support\r\nWe would
like to thank Brian Charlesworth and Sally Otto for their helpful comments."
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Genetic linkage and natural selection. Philosophical Transactions
of the Royal Society of London Series B, Biological Sciences. 2010;365(1552):2559-2569.
doi:10.1098/rstb.2010.0106
apa: Barton, N. H. (2010). Genetic linkage and natural selection. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society. https://doi.org/10.1098/rstb.2010.0106
chicago: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0106.
ieee: N. H. Barton, “Genetic linkage and natural selection,” Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences, vol. 365, no.
1552. Royal Society, pp. 2559–2569, 2010.
ista: Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.
mla: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:10.1098/rstb.2010.0106.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 2559–2569.
date_created: 2018-12-11T12:05:06Z
date_published: 2010-08-27T00:00:00Z
date_updated: 2021-01-12T07:52:07Z
day: '27'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0106
file:
- access_level: open_access
checksum: 4d8aade10db030124ab158b622e337e0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:40Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5093'
file_name: IST-2016-555-v1+1_RS2009_revised.pdf
file_size: 250255
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 365'
issue: '1552'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 2559 - 2569
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2450'
pubrep_id: '555'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genetic linkage and natural selection
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3777'
abstract:
- lang: eng
text: 'Under the classical view, selection depends more or less directly on mutation:
standing genetic variance is maintained by a balance between selection and mutation,
and adaptation is fuelled by new favourable mutations. Recombination is favoured
if it breaks negative associations among selected alleles, which interfere with
adaptation. Such associations may be generated by negative epistasis, or by random
drift (leading to the Hill-Robertson effect). Both deterministic and stochastic
explanations depend primarily on the genomic mutation rate, U. This may be large
enough to explain high recombination rates in some organisms, but seems unlikely
to be so in general. Random drift is a more general source of negative linkage
disequilibria, and can cause selection for recombination even in large populations,
through the chance loss of new favourable mutations. The rate of species-wide
substitutions is much too low to drive this mechanism, but local fluctuations
in selection, combined with gene flow, may suffice. These arguments are illustrated
by comparing the interaction between good and bad mutations at unlinked loci under
the infinitesimal model.'
acknowledgement: I would like to thank W. G. Hill and L. Loewe for organizing this
special issue, and the Royal Society and Wolfson Foundation for their support. Also,
A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Mutation and the evolution of recombination. Philosophical Transactions
of the Royal Society of London Series B, Biological Sciences. 2010;365(1544):1281-1294.
doi:10.1098/rstb.2009.0320
apa: Barton, N. H. (2010). Mutation and the evolution of recombination. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society. https://doi.org/10.1098/rstb.2009.0320
chicago: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, 2010. https://doi.org/10.1098/rstb.2009.0320.
ieee: N. H. Barton, “Mutation and the evolution of recombination,” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.
ista: Barton NH. 2010. Mutation and the evolution of recombination. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544),
1281–1294.
mla: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:10.1098/rstb.2009.0320.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 1281–1294.
date_created: 2018-12-11T12:05:07Z
date_published: 2010-04-27T00:00:00Z
date_updated: 2021-01-12T07:52:07Z
day: '27'
department:
- _id: NiBa
doi: 10.1098/rstb.2009.0320
external_id:
pmid:
- '20308104'
intvolume: ' 365'
issue: '1544'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pubmed/20308104
month: '04'
oa: 1
oa_version: Submitted Version
page: 1281 - 1294
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2451'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mutation and the evolution of recombination
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3779'
abstract:
- lang: eng
text: Crosses between closely related species give two contrasting results. One
result is that species hybrids may be inferior to their parents, for example,
being less fertile [1]. The other is that F1 hybrids may display superior performance
(heterosis), for example with increased vigour [2]. Although various hypotheses
have been proposed to account for these two aspects of hybridisation, their biological
basis is still poorly understood [3]. To gain further insights into this issue,
we analysed the role that variation in gene expression may play. We took a conserved
trait, flower asymmetry in Antirrhinum, and determined the extent to which the
underlying regulatory genes varied in expression among closely related species.
We show that expression of both genes analysed, CYC and RAD, varies significantly
between species because of cis-acting differences. By making a quantitative genotype-phenotype
map, using a range of mutant alleles, we demonstrate that the species lie on a
plateau in gene expression-morphology space, so that the variation has no detectable
phenotypic effect. However, phenotypic differences can be revealed by shifting
genotypes off the plateau through genetic crosses. Our results can be readily
explained if genomes are free to evolve within an effectively neutral zone in
gene expression space. The consequences of this drift will be negligible for individual
loci, but when multiple loci across the genome are considered, we show that the
variation may have significant effects on phenotype and fitness, causing a significant
drift load. By considering these consequences for various gene-expression-fitness
landscapes, we conclude that F1 hybrids might be expected to show increased performance
with regard to conserved traits, such as basic physiology, but reduced performance
with regard to others. Thus, our study provides a new way of explaining how various
aspects of hybrid performance may arise through natural variation in gene activity.
acknowledgement: "This was supported by a Marie Curie grant for early stage training
and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank
X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green,
A. Bangham and J. Pateman for advice and assistance on shape model procedures; F.
Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols
and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n"
article_number: e1000429
author:
- first_name: Ulises
full_name: Rosas, Ulises
last_name: Rosas
- 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: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Pierre
full_name: Barbier De Reuille, Pierre
last_name: Barbier De Reuille
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation
between species and the basis of hybrid performance. PLoS Biology. 2010;8(7).
doi:10.1371/journal.pbio.1000429
apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E.
(2010). Cryptic variation between species and the basis of hybrid performance.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429
chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille,
and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.”
PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429.
ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic
variation between species and the basis of hybrid performance,” PLoS Biology,
vol. 8, no. 7. Public Library of Science, 2010.
ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic
variation between species and the basis of hybrid performance. PLoS Biology. 8(7),
e1000429.
mla: Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid
Performance.” PLoS Biology, vol. 8, no. 7, e1000429, Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000429.
short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology
8 (2010).
date_created: 2018-12-11T12:05:07Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2023-02-23T14:07:34Z
day: '20'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.1000429
file:
- access_level: open_access
checksum: ee1ce2fb283a6b4127544ae532d0b4a1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:11Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5060'
file_name: IST-2015-366-v1+1_journal.pbio.1000429.pdf
file_size: 1089530
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '2448'
pubrep_id: '366'
quality_controlled: '1'
related_material:
record:
- id: '9764'
relation: research_data
status: public
scopus_import: 1
status: public
title: Cryptic variation between species and the basis of hybrid performance
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
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2010'
...
---
_id: '3787'
abstract:
- lang: eng
text: DNA samples were extracted from ethanol and formalin-fixed decapod crustacean
tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown
that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors
impede PCR success when dealing with formalin-fixed material. Instead, amplification
success from formalin-fixed tissue appears to depend on the presence of unmodified
DNA in the extracted sample. A staining method that facilitates the targeting
of samples with a high content of unmodified DNA is provided.
acknowledgement: "The authors would like to thank two anonymous reviewers for their
remarks, which helped to improve the manuscript. This project was supported by the
Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract
no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology
Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal
Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government
of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS
Project http://www.synthesys. info/ which is financed by European Community Research
Infrastructure Action under the FP6 “Structuring the European Research Area” Programme.
Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical
point drying, P.Crabb for helping with the UV-light photography setting and our
colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology
NHM \r\n\r\n"
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Sally
full_name: Hall, Sally
last_name: Hall
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: David
full_name: Johnston, David
last_name: Johnston
- first_name: Jackie
full_name: Mackenzie Dodds, Jackie
last_name: Mackenzie Dodds
- first_name: Sven
full_name: Thatje, Sven
last_name: Thatje
citation:
ama: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction
from formalin-fixed tissue: new light from the deep sea. Scientia Marina.
2010;74(3):465-470. doi:10.3989/scimar.2010.74n3465'
apa: 'Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., &
Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the
deep sea. Scientia Marina. Consejo Superior de Investigaciones Científicas.
https://doi.org/10.3989/scimar.2010.74n3465'
chicago: 'Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie
Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light
from the Deep Sea.” Scientia Marina. Consejo Superior de Investigaciones
Científicas, 2010. https://doi.org/10.3989/scimar.2010.74n3465.'
ieee: 'F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje,
“DNA extraction from formalin-fixed tissue: new light from the deep sea,” Scientia
Marina, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp.
465–470, 2010.'
ista: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010.
DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia
Marina. 74(3), 465–470.'
mla: 'Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light
from the Deep Sea.” Scientia Marina, vol. 74, no. 3, Consejo Superior de
Investigaciones Científicas, 2010, pp. 465–70, doi:10.3989/scimar.2010.74n3465.'
short: F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje,
Scientia Marina 74 (2010) 465–470.
date_created: 2018-12-11T12:05:10Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-01-12T07:52:11Z
day: '01'
department:
- _id: NiBa
doi: 10.3989/scimar.2010.74n3465
intvolume: ' 74'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprints.soton.ac.uk/68731/
month: '09'
oa: 1
oa_version: Submitted Version
page: 465 - 470
publication: Scientia Marina
publication_status: published
publisher: Consejo Superior de Investigaciones Científicas
publist_id: '2440'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'DNA extraction from formalin-fixed tissue: new light from the deep sea'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2010'
...
---
_id: '3790'
abstract:
- lang: eng
text: Cell shape and motility are primarily controlled by cellular mechanics. The
attachment of the plasma membrane to the underlying actomyosin cortex has been
proposed to be important for cellular processes involving membrane deformation.
However, little is known about the actual function of membrane-to-cortex attachment
(MCA) in cell protrusion formation and migration, in particular in the context
of the developing embryo. Here, we use a multidisciplinary approach to study MCA
in zebrafish mesoderm and endoderm (mesendoderm) germ layer progenitor cells,
which migrate using a combination of different protrusion types, namely, lamellipodia,
filopodia, and blebs, during zebrafish gastrulation. By interfering with the activity
of molecules linking the cortex to the membrane and measuring resulting changes
in MCA by atomic force microscopy, we show that reducing MCA in mesendoderm progenitors
increases the proportion of cellular blebs and reduces the directionality of cell
migration. We propose that MCA is a key parameter controlling the relative proportions
of different cell protrusion types in mesendoderm progenitors, and thus is key
in controlling directed migration during gastrulation.
acknowledgement: "We would like to thank A. G. Clark, S. Grill, A. Oates, E. Raz,
L. Rohde, and M. Zerial for reading earlier versions of the manuscript. We are grateful
to W. Zachariae, Y. Arboleda-Estudillo, S. Schneider, P. Stockinger, D. Panhans,
M. Biro, J. C. Olaya, and the BIOTEC/MPI-CBG zebrafish and imaging facilities for
help and advice at various stages of this project and to J. Helenius for help with
programming. This work was supported by grants from the Boehringer Ingelheim Fonds
to MK, the Polish Ministry of Science and Higher Education to E. P., and the Deutsche
Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EP.\r\n"
article_number: e1000544
author:
- first_name: Alba
full_name: Diz Muñoz, Alba
last_name: Diz Muñoz
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Martin
full_name: Bergert, Martin
last_name: Bergert
- first_name: Itziar
full_name: Ibarlucea Benitez, Itziar
last_name: Ibarlucea Benitez
- first_name: Daniel
full_name: Müller, Daniel
last_name: Müller
- first_name: Ewa
full_name: Paluch, Ewa
last_name: Paluch
- 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: Diz Muñoz A, Krieg M, Bergert M, et al. Control of directed cell migration
in vivo by membrane-to-cortex attachment. PLoS Biology. 2010;8(11). doi:10.1371/journal.pbio.1000544
apa: Diz Muñoz, A., Krieg, M., Bergert, M., Ibarlucea Benitez, I., Müller, D., Paluch,
E., & Heisenberg, C.-P. J. (2010). Control of directed cell migration in vivo
by membrane-to-cortex attachment. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.1000544
chicago: Diz Muñoz, Alba, Michael Krieg, Martin Bergert, Itziar Ibarlucea Benitez,
Daniel Müller, Ewa Paluch, and Carl-Philipp J Heisenberg. “Control of Directed
Cell Migration in Vivo by Membrane-to-Cortex Attachment.” PLoS Biology.
Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000544.
ieee: A. Diz Muñoz et al., “Control of directed cell migration in vivo by
membrane-to-cortex attachment,” PLoS Biology, vol. 8, no. 11. Public Library
of Science, 2010.
ista: Diz Muñoz A, Krieg M, Bergert M, Ibarlucea Benitez I, Müller D, Paluch E,
Heisenberg C-PJ. 2010. Control of directed cell migration in vivo by membrane-to-cortex
attachment. PLoS Biology. 8(11), e1000544.
mla: Diz Muñoz, Alba, et al. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex
Attachment.” PLoS Biology, vol. 8, no. 11, e1000544, Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000544.
short: A. Diz Muñoz, M. Krieg, M. Bergert, I. Ibarlucea Benitez, D. Müller, E. Paluch,
C.-P.J. Heisenberg, PLoS Biology 8 (2010).
date_created: 2018-12-11T12:05:11Z
date_published: 2010-11-30T00:00:00Z
date_updated: 2021-01-12T07:52:13Z
day: '30'
ddc:
- '576'
department:
- _id: CaHe
doi: 10.1371/journal.pbio.1000544
file:
- access_level: open_access
checksum: 52d18c90ca6b02234cea5e8b399b7f46
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:24Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4685'
file_name: IST-2015-365-v1+1_journal.pbio.1000544.pdf
file_size: 799506
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '2437'
pubrep_id: '365'
quality_controlled: '1'
scopus_import: 1
status: public
title: Control of directed cell migration in vivo by membrane-to-cortex attachment
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
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2010'
...
---
_id: '3793'
abstract:
- lang: eng
text: "Recent progress in per-pixel object class labeling of natural images can
be attributed to the use of multiple types of image features and sound statistical
learning approaches. Within the latter, Conditional Random Fields (CRF) are prominently
used for their ability to represent interactions between random variables. Despite
their popularity in computer vision, parameter learning for CRFs has remained
difficult, popular approaches being cross-validation and piecewise training.\r\nIn
this work, we propose a simple yet expressive tree-structured CRF based on a recent
hierarchical image segmentation method. Our model combines and weights multiple
image features within a hierarchical representation and allows simple and efficient
globally-optimal learning of ≈ 105 parameters. The tractability of our model allows
us to pose and answer some of the open questions regarding parameter learning
applying to CRF-based approaches. The key findings for learning CRF models are,
from the obvious to the surprising, i) multiple image features always help, ii)
the limiting dimension with respect to current models is the amount of training
data, iii) piecewise training is competitive, iv) current methods for max-margin
training fail for models with many parameters.\r\n"
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Nowozin, Sebastian
last_name: Nowozin
- first_name: Peter
full_name: Gehler, Peter
last_name: Gehler
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Nowozin S, Gehler P, Lampert C. On parameter learning in CRF-based approaches
to object class image segmentation. In: Vol 6316. Springer; 2010:98-111. doi:10.1007/978-3-642-15567-3_8'
apa: 'Nowozin, S., Gehler, P., & Lampert, C. (2010). On parameter learning in
CRF-based approaches to object class image segmentation (Vol. 6316, pp. 98–111).
Presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete,
Greece: Springer. https://doi.org/10.1007/978-3-642-15567-3_8'
chicago: Nowozin, Sebastian, Peter Gehler, and Christoph Lampert. “On Parameter
Learning in CRF-Based Approaches to Object Class Image Segmentation,” 6316:98–111.
Springer, 2010. https://doi.org/10.1007/978-3-642-15567-3_8.
ieee: 'S. Nowozin, P. Gehler, and C. Lampert, “On parameter learning in CRF-based
approaches to object class image segmentation,” presented at the ECCV: European
Conference on Computer Vision, Heraklion, Crete, Greece, 2010, vol. 6316, pp.
98–111.'
ista: 'Nowozin S, Gehler P, Lampert C. 2010. On parameter learning in CRF-based
approaches to object class image segmentation. ECCV: European Conference on Computer
Vision, LNCS, vol. 6316, 98–111.'
mla: Nowozin, Sebastian, et al. On Parameter Learning in CRF-Based Approaches
to Object Class Image Segmentation. Vol. 6316, Springer, 2010, pp. 98–111,
doi:10.1007/978-3-642-15567-3_8.
short: S. Nowozin, P. Gehler, C. Lampert, in:, Springer, 2010, pp. 98–111.
conference:
end_date: 2010-09-11
location: Heraklion, Crete, Greece
name: 'ECCV: European Conference on Computer Vision'
start_date: 2010-09-05
date_created: 2018-12-11T12:05:12Z
date_published: 2010-11-04T00:00:00Z
date_updated: 2021-01-12T07:52:14Z
day: '04'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1007/978-3-642-15567-3_8
file:
- access_level: open_access
checksum: 3716e10e161f7c714fd17ec193a223c3
content_type: application/pdf
creator: dernst
date_created: 2020-05-19T16:27:34Z
date_updated: 2020-07-14T12:46:16Z
file_id: '7871'
file_name: 2010_ECCV_Nowozin.pdf
file_size: 4087332
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 6316'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 98 - 111
publication_status: published
publisher: Springer
publist_id: '2431'
quality_controlled: '1'
scopus_import: 1
status: public
title: On parameter learning in CRF-based approaches to object class image segmentation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6316
year: '2010'
...
---
_id: '3795'
abstract:
- lang: eng
text: 'The (apparent) contour of a smooth mapping from a 2-manifold to the plane,
f: M → R2 , is the set of critical values, that is, the image of the points at
which the gradients of the two component functions are linearly dependent. Assuming
M is compact and orientable and measuring difference with the erosion distance,
we prove that the contour is stable.'
acknowledgement: This research is partially supported by the Defense Advanced Research
Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.
alternative_title:
- Mathematics and Visualization
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: 'Edelsbrunner H, Morozov D, Patel A. The stability of the apparent contour
of an orientable 2-manifold. In: Topological Data Analysis and Visualization:
Theory, Algorithms and Applications. Springer; 2010:27-42. doi:10.1007/978-3-642-15014-2_3'
apa: 'Edelsbrunner, H., Morozov, D., & Patel, A. (2010). The stability of the
apparent contour of an orientable 2-manifold. In Topological Data Analysis
and Visualization: Theory, Algorithms and Applications (pp. 27–42). Springer.
https://doi.org/10.1007/978-3-642-15014-2_3'
chicago: 'Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “The Stability
of the Apparent Contour of an Orientable 2-Manifold.” In Topological Data Analysis
and Visualization: Theory, Algorithms and Applications, 27–42. Springer, 2010.
https://doi.org/10.1007/978-3-642-15014-2_3.'
ieee: 'H. Edelsbrunner, D. Morozov, and A. Patel, “The stability of the apparent
contour of an orientable 2-manifold,” in Topological Data Analysis and Visualization:
Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.'
ista: 'Edelsbrunner H, Morozov D, Patel A. 2010.The stability of the apparent contour
of an orientable 2-manifold. In: Topological Data Analysis and Visualization:
Theory, Algorithms and Applications. Mathematics and Visualization, , 27–42.'
mla: 'Edelsbrunner, Herbert, et al. “The Stability of the Apparent Contour of an
Orientable 2-Manifold.” Topological Data Analysis and Visualization: Theory,
Algorithms and Applications, Springer, 2010, pp. 27–42, doi:10.1007/978-3-642-15014-2_3.'
short: 'H. Edelsbrunner, D. Morozov, A. Patel, in:, Topological Data Analysis and
Visualization: Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.'
date_created: 2018-12-11T12:05:13Z
date_published: 2010-12-22T00:00:00Z
date_updated: 2021-01-12T07:52:15Z
day: '22'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/978-3-642-15014-2_3
file:
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creator: system
date_created: 2018-12-12T10:11:40Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4896'
file_name: IST-2016-538-v1+1_2011-B-02-ApparentContour.pdf
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file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 27 - 42
publication: 'Topological Data Analysis and Visualization: Theory, Algorithms and
Applications'
publication_status: published
publisher: Springer
publist_id: '2428'
pubrep_id: '538'
quality_controlled: '1'
scopus_import: 1
status: public
title: The stability of the apparent contour of an orientable 2-manifold
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3831'
abstract:
- lang: eng
text: Fast-spiking, parvalbumin-expressing basket cells (BCs) play a key role in
feedforward and feedback inhibition in the hippocampus. However, the dendritic
mechanisms underlying rapid interneuron recruitment have remained unclear. To
quantitatively address this question, we developed detailed passive cable models
of BCs in the dentate gyrus based on dual somatic or somatodendritic recordings
and complete morphologic reconstructions. Both specific membrane capacitance and
axial resistivity were comparable to those of pyramidal neurons, but the average
somatodendritic specific membrane resistance (R(m)) was substantially lower in
BCs. Furthermore, R(m) was markedly nonuniform, being lowest in soma and proximal
dendrites, intermediate in distal dendrites, and highest in the axon. Thus, the
somatodendritic gradient of R(m) was the reverse of that in pyramidal neurons.
Further computational analysis revealed that these unique cable properties accelerate
the time course of synaptic potentials at the soma in response to fast inputs,
while boosting the efficacy of slow distal inputs. These properties will facilitate
both rapid phasic and efficient tonic activation of BCs in hippocampal microcircuits.
author:
- first_name: Anja
full_name: Norenberg, Anja
last_name: Norenberg
- first_name: Hua
full_name: Hua Hu
id: 4AC0145C-F248-11E8-B48F-1D18A9856A87
last_name: Hu
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. Distinct nonuniform cable properties
optimize rapid and efficient activation of fast-spiking GABAergic interneurons.
PNAS. 2010;107(2):894-899. doi:10.1073/pnas.0910716107
apa: Norenberg, A., Hu, H., Vida, I., Bartos, M., & Jonas, P. M. (2010). Distinct
nonuniform cable properties optimize rapid and efficient activation of fast-spiking
GABAergic interneurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0910716107
chicago: Norenberg, Anja, Hua Hu, Imre Vida, Marlene Bartos, and Peter M Jonas.
“Distinct Nonuniform Cable Properties Optimize Rapid and Efficient Activation
of Fast-Spiking GABAergic Interneurons.” PNAS. National Academy of Sciences,
2010. https://doi.org/10.1073/pnas.0910716107.
ieee: A. Norenberg, H. Hu, I. Vida, M. Bartos, and P. M. Jonas, “Distinct nonuniform
cable properties optimize rapid and efficient activation of fast-spiking GABAergic
interneurons,” PNAS, vol. 107, no. 2. National Academy of Sciences, pp.
894–9, 2010.
ista: Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. 2010. Distinct nonuniform cable
properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons.
PNAS. 107(2), 894–9.
mla: Norenberg, Anja, et al. “Distinct Nonuniform Cable Properties Optimize Rapid
and Efficient Activation of Fast-Spiking GABAergic Interneurons.” PNAS,
vol. 107, no. 2, National Academy of Sciences, 2010, pp. 894–99, doi:10.1073/pnas.0910716107.
short: A. Norenberg, H. Hu, I. Vida, M. Bartos, P.M. Jonas, PNAS 107 (2010) 894–9.
date_created: 2018-12-11T12:05:24Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:31Z
day: '01'
doi: 10.1073/pnas.0910716107
extern: 1
intvolume: ' 107'
issue: '2'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818894/#!po=4.16667
month: '01'
oa: 1
page: 894 - 9
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2379'
quality_controlled: 0
status: public
title: Distinct nonuniform cable properties optimize rapid and efficient activation
of fast-spiking GABAergic interneurons
type: journal_article
volume: 107
year: '2010'
...