---
_id: '3736'
abstract:
- lang: eng
text: In retina and in cortical slice the collective response of spiking neural
populations is well described by "maximum-entropy" models in which only
pairs of neurons interact. We asked, how should such interactions be organized
to maximize the amount of information represented in population responses? To
this end, we extended the linear-nonlinear-Poisson model of single neural response
to include pairwise interactions, yielding a stimulus-dependent, pairwise maximum-entropy
model. We found that as we varied the noise level in single neurons and the distribution
of network inputs, the optimal pairwise interactions smoothly interpolated to
achieve network functions that are usually regarded as discrete–stimulus decorrelation,
error correction, and independent encoding. These functions reflected a trade-off
between efficient consumption of finite neural bandwidth and the use of redundancy
to mitigate noise. Spontaneous activity in the optimal network reflected stimulus-induced
activity patterns, and single-neuron response variability overestimated network
noise. Our analysis suggests that rather than having a single coding principle
hardwired in their architecture, networks in the brain should adapt their function
to changing noise and stimulus correlations.
acknowledgement: R01 EY08124/EY/NEI NIH HHS/United States; T32-07035/PHS HHS/United
States
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Jason
full_name: Prentice, Jason S
last_name: Prentice
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: Tkačik G, Prentice J, Balasubramanian V, Schneidman E. Optimal population coding
by noisy spiking neurons. PNAS. 2010;107(32):14419-14424. doi:10.1073/pnas.1004906107
apa: Tkačik, G., Prentice, J., Balasubramanian, V., & Schneidman, E. (2010).
Optimal population coding by noisy spiking neurons. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1004906107
chicago: Tkačik, Gašper, Jason Prentice, Vijay Balasubramanian, and Elad Schneidman.
“Optimal Population Coding by Noisy Spiking Neurons.” PNAS. National Academy
of Sciences, 2010. https://doi.org/10.1073/pnas.1004906107.
ieee: G. Tkačik, J. Prentice, V. Balasubramanian, and E. Schneidman, “Optimal population
coding by noisy spiking neurons,” PNAS, vol. 107, no. 32. National Academy
of Sciences, pp. 14419–14424, 2010.
ista: Tkačik G, Prentice J, Balasubramanian V, Schneidman E. 2010. Optimal population
coding by noisy spiking neurons. PNAS. 107(32), 14419–14424.
mla: Tkačik, Gašper, et al. “Optimal Population Coding by Noisy Spiking Neurons.”
PNAS, vol. 107, no. 32, National Academy of Sciences, 2010, pp. 14419–24,
doi:10.1073/pnas.1004906107.
short: G. Tkačik, J. Prentice, V. Balasubramanian, E. Schneidman, PNAS 107 (2010)
14419–14424.
date_created: 2018-12-11T12:04:53Z
date_published: 2010-08-10T00:00:00Z
date_updated: 2021-01-12T07:51:50Z
day: '10'
doi: 10.1073/pnas.1004906107
extern: 1
intvolume: ' 107'
issue: '32'
main_file_link:
- open_access: '0'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922524/
month: '08'
page: 14419 - 14424
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2492'
quality_controlled: 0
status: public
title: Optimal population coding by noisy spiking neurons
type: journal_article
volume: 107
year: '2010'
...
---
_id: '3738'
abstract:
- lang: eng
text: Central to the functioning of a living cell is its ability to control the
readout or expression of information encoded in the genome. In many cases, a single
transcription factor protein activates or represses the expression of many genes.
As the concentration of the transcription factor varies, the target genes thus
undergo correlated changes, and this redundancy limits the ability of the cell
to transmit information about input signals. We explore how interactions among
the target genes can reduce this redundancy and optimize information transmission.
Our discussion builds on recent work [Tkacik, Phys. Rev. E 80, 031920 (2009)],
and there are connections to much earlier work on the role of lateral inhibition
in enhancing the efficiency of information transmission in neural circuits; for
simplicity we consider here the case where the interactions have a feed forward
structure, with no loops. Even with this limitation, the networks that optimize
information transmission have a structure reminiscent of the networks found in
real biological systems.
author:
- first_name: Aleksandra
full_name: Walczak, Aleksandra M
last_name: Walczak
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Walczak A, Tkačik G, Bialek W. Optimizing information flow in small genetic
networks. II. Feed-forward interactions. Physical Review E Statistical Nonlinear
and Soft Matter Physics. 2010;81(4). doi:10.1103/PhysRevE.81.041905
apa: Walczak, A., Tkačik, G., & Bialek, W. (2010). Optimizing information flow
in small genetic networks. II. Feed-forward interactions. Physical Review E
Statistical Nonlinear and Soft Matter Physics. American Institute of Physics.
https://doi.org/10.1103/PhysRevE.81.041905
chicago: Walczak, Aleksandra, Gašper Tkačik, and William Bialek. “Optimizing Information
Flow in Small Genetic Networks. II. Feed-Forward Interactions.” Physical Review
E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics,
2010. https://doi.org/10.1103/PhysRevE.81.041905.
ieee: A. Walczak, G. Tkačik, and W. Bialek, “Optimizing information flow in small
genetic networks. II. Feed-forward interactions,” Physical Review E Statistical
Nonlinear and Soft Matter Physics, vol. 81, no. 4. American Institute of Physics,
2010.
ista: Walczak A, Tkačik G, Bialek W. 2010. Optimizing information flow in small
genetic networks. II. Feed-forward interactions. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 81(4).
mla: Walczak, Aleksandra, et al. “Optimizing Information Flow in Small Genetic Networks.
II. Feed-Forward Interactions.” Physical Review E Statistical Nonlinear and
Soft Matter Physics, vol. 81, no. 4, American Institute of Physics, 2010,
doi:10.1103/PhysRevE.81.041905.
short: A. Walczak, G. Tkačik, W. Bialek, Physical Review E Statistical Nonlinear
and Soft Matter Physics 81 (2010).
date_created: 2018-12-11T12:04:54Z
date_published: 2010-04-06T00:00:00Z
date_updated: 2021-01-12T07:51:50Z
day: '06'
doi: 10.1103/PhysRevE.81.041905
extern: 1
intvolume: ' 81'
issue: '4'
main_file_link:
- open_access: '0'
url: http://arxiv.org/abs/0912.5500
month: '04'
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '2494'
quality_controlled: 0
status: public
title: Optimizing information flow in small genetic networks. II. Feed-forward interactions
type: journal_article
volume: 81
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: '3759'
abstract:
- lang: eng
text: We propose a mesh-based surface tracking method for fluid animation that both
preserves fine surface details and robustly adjusts the topology of the surface
in the presence of arbitrarily thin features like sheets and strands. We replace
traditional re-sampling methods with a convex hull method for connecting surface
features during topological changes. This technique permits arbitrarily thin fluid
features with minimal re-sampling errors by reusing points from the original surface.
We further reduce re-sampling artifacts with a subdivision-based mesh-stitching
algorithm, and we use a higher order interpolating subdivision scheme to determine
the location of any newly-created vertices. The resulting algorithm efficiently
produces detailed fluid surfaces with arbitrarily thin features while maintaining
a consistent topology with the underlying fluid simulation.
article_processing_charge: No
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Nils
full_name: Thürey, Nils
last_name: Thürey
- first_name: Markus
full_name: Gross, Markus
last_name: Gross
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: Wojtan C, Thürey N, Gross M, Turk G. Physics-inspired topology changes for
thin fluid features. ACM Transactions on Graphics. 2010;29(4). doi:10.1145/1778765.1778787
apa: Wojtan, C., Thürey, N., Gross, M., & Turk, G. (2010). Physics-inspired
topology changes for thin fluid features. ACM Transactions on Graphics.
ACM. https://doi.org/10.1145/1778765.1778787
chicago: Wojtan, Chris, Nils Thürey, Markus Gross, and Greg Turk. “Physics-Inspired
Topology Changes for Thin Fluid Features.” ACM Transactions on Graphics.
ACM, 2010. https://doi.org/10.1145/1778765.1778787.
ieee: C. Wojtan, N. Thürey, M. Gross, and G. Turk, “Physics-inspired topology changes
for thin fluid features,” ACM Transactions on Graphics, vol. 29, no. 4.
ACM, 2010.
ista: Wojtan C, Thürey N, Gross M, Turk G. 2010. Physics-inspired topology changes
for thin fluid features. ACM Transactions on Graphics. 29(4).
mla: Wojtan, Chris, et al. “Physics-Inspired Topology Changes for Thin Fluid Features.”
ACM Transactions on Graphics, vol. 29, no. 4, ACM, 2010, doi:10.1145/1778765.1778787.
short: C. Wojtan, N. Thürey, M. Gross, G. Turk, ACM Transactions on Graphics 29
(2010).
date_created: 2018-12-11T12:05:00Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2023-02-23T11:41:24Z
day: '01'
doi: 10.1145/1778765.1778787
extern: '1'
intvolume: ' 29'
issue: '4'
language:
- iso: eng
main_file_link:
- url: http://kucg.korea.ac.kr/seminar/2010/src/paper-2010-09-02.pdf
month: '01'
oa_version: None
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '2470'
status: public
title: Physics-inspired topology changes for thin fluid features
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2010'
...
---
_id: '3761'
abstract:
- lang: eng
text: We present an algorithm for creating realistic animations of characters that
are swimming through fluids. Our approach combines dynamic simulation with data-driven
kinematic motions (motion capture data) to produce realistic animation in a fluid.
The interaction of the articulated body with the fluid is performed by incorporating
joint constraints with rigid animation and by extending a solid/fluid coupling
method to handle articulated chains. Our solver takes as input the current state
of the simulation and calculates the angular and linear accelerations of the connected
bodies needed to match a particular motion sequence for the articulated body.
These accelerations are used to estimate the forces and torques that are then
applied to each joint. Based on this approach, we demonstrate simulated swimming
results for a variety of different strokes, including crawl, backstroke, breaststroke,
and butterfly. The ability to have articulated bodies interact with fluids also
allows us to generate simulations of simple water creatures that are driven by
simple controllers.
article_processing_charge: No
author:
- first_name: Nipun
full_name: Kwatra, Nipun
last_name: Kwatra
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Mark
full_name: Carlson, Mark
last_name: Carlson
- first_name: Irfan
full_name: Essa, Irfan
last_name: Essa
- first_name: Peter
full_name: Mucha, Peter
last_name: Mucha
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: Kwatra N, Wojtan C, Carlson M, Essa I, Mucha P, Turk G. Fluid simulation with
articulated bodies. IEEE Transactions on Visualization and Computer Graphics.
2010;16(1):70-80. doi:10.1109/TVCG.2009.66
apa: Kwatra, N., Wojtan, C., Carlson, M., Essa, I., Mucha, P., & Turk, G. (2010).
Fluid simulation with articulated bodies. IEEE Transactions on Visualization
and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2009.66
chicago: Kwatra, Nipun, Chris Wojtan, Mark Carlson, Irfan Essa, Peter Mucha, and
Greg Turk. “Fluid Simulation with Articulated Bodies.” IEEE Transactions on
Visualization and Computer Graphics. IEEE, 2010. https://doi.org/10.1109/TVCG.2009.66.
ieee: N. Kwatra, C. Wojtan, M. Carlson, I. Essa, P. Mucha, and G. Turk, “Fluid simulation
with articulated bodies,” IEEE Transactions on Visualization and Computer Graphics,
vol. 16, no. 1. IEEE, pp. 70–80, 2010.
ista: Kwatra N, Wojtan C, Carlson M, Essa I, Mucha P, Turk G. 2010. Fluid simulation
with articulated bodies. IEEE Transactions on Visualization and Computer Graphics.
16(1), 70–80.
mla: Kwatra, Nipun, et al. “Fluid Simulation with Articulated Bodies.” IEEE Transactions
on Visualization and Computer Graphics, vol. 16, no. 1, IEEE, 2010, pp. 70–80,
doi:10.1109/TVCG.2009.66.
short: N. Kwatra, C. Wojtan, M. Carlson, I. Essa, P. Mucha, G. Turk, IEEE Transactions
on Visualization and Computer Graphics 16 (2010) 70–80.
date_created: 2018-12-11T12:05:01Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2023-02-23T11:41:31Z
day: '01'
doi: 10.1109/TVCG.2009.66
extern: '1'
intvolume: ' 16'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 70 - 80
publication: IEEE Transactions on Visualization and Computer Graphics
publication_status: published
publisher: IEEE
publist_id: '2468'
status: public
title: Fluid simulation with articulated bodies
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2010'
...
---
_id: '3766'
abstract:
- lang: eng
text: 'We present an approach to simulate flows driven by surface tension based
on triangle meshes. Our method consists of two simulation layers: the first layer
is an Eulerian method for simulating surface tension forces that is free from
typical strict time step constraints. The second simulation layer is a Lagrangian
finite element method that simulates sub-grid scale wave details on the fluid
surface. The surface wave simulation employs an unconditionally stable, symplectic
time integration method that allows for a high propagation speed due to strong
surface tension. Our approach can naturally separate the grid-and sub-grid scales
based on a volumepreserving mean curvature flow. As our model for the sub-grid
dynamics enforces a local conservation of mass, it leads to realistic pinch off
and merging effects. In addition to this method for simulating dynamic surface
tension effects, we also present an efficient non-oscillatory approximation for
capturing damped surface tension behavior. These approaches allow us to efficiently
simulate complex phenomena associated with strong surface tension, such as Rayleigh-Plateau
instabilities and crown splashes, in a short amount of time.'
article_processing_charge: No
author:
- first_name: Nils
full_name: Thürey, Nils
last_name: Thürey
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Markus
full_name: Gross, Markus
last_name: Gross
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: Thürey N, Wojtan C, Gross M, Turk G. A multiscale approach to mesh-based surface
tension flows. ACM Transactions on Graphics. 2010;29(4). doi:10.1145/1778765.1778785
apa: Thürey, N., Wojtan, C., Gross, M., & Turk, G. (2010). A multiscale approach
to mesh-based surface tension flows. ACM Transactions on Graphics. ACM.
https://doi.org/10.1145/1778765.1778785
chicago: Thürey, Nils, Chris Wojtan, Markus Gross, and Greg Turk. “A Multiscale
Approach to Mesh-Based Surface Tension Flows.” ACM Transactions on Graphics.
ACM, 2010. https://doi.org/10.1145/1778765.1778785.
ieee: N. Thürey, C. Wojtan, M. Gross, and G. Turk, “A multiscale approach to mesh-based
surface tension flows,” ACM Transactions on Graphics, vol. 29, no. 4. ACM,
2010.
ista: Thürey N, Wojtan C, Gross M, Turk G. 2010. A multiscale approach to mesh-based
surface tension flows. ACM Transactions on Graphics. 29(4).
mla: Thürey, Nils, et al. “A Multiscale Approach to Mesh-Based Surface Tension Flows.”
ACM Transactions on Graphics, vol. 29, no. 4, ACM, 2010, doi:10.1145/1778765.1778785.
short: N. Thürey, C. Wojtan, M. Gross, G. Turk, ACM Transactions on Graphics 29
(2010).
date_created: 2018-12-11T12:05:03Z
date_published: 2010-07-01T00:00:00Z
date_updated: 2023-02-23T11:41:44Z
day: '01'
doi: 10.1145/1778765.1778785
extern: '1'
intvolume: ' 29'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '2463'
status: public
title: A multiscale approach to mesh-based surface tension flows
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2010'
...
---
_id: '3772'
article_number: e1000987
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
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).
corr_author: '1'
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-17T00:00:00Z
date_updated: 2025-09-30T09:45:21Z
day: '17'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pgen.1000987
external_id:
isi:
- '000279805200002'
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'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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"
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
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.
corr_author: '1'
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-12T00:00:00Z
date_updated: 2025-09-30T09:45:54Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0001
external_id:
isi:
- '000277208600009'
pmid:
- '20439284'
intvolume: ' 365'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 365
year: '2010'
...
---
_id: '3774'
abstract:
- lang: eng
text: 1. Hybridisation with an invasive species has the potential to alter the phenotype
and hence the ecology of a native counterpart. 2. Here data from populations of
native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland
is used to assess the extent to which hybridisation between them is causing phenotypic
change. This is done by regression of phenotypic traits against genetic hybrid
scores. 3. Hybridisation is causing increases in the body weight of sika-like
deer and decreases in the body weight of red-like females. Hybridisation is causing
increases in jaw length and increases in incisor arcade breadth in sika-like females.
Hybridisation is also causing decreases in incisor arcade breadth in red-like
females. 4. There is currently no evidence that hybridisation is causing changes
in the kidney fat weight or pregnancy rates of either population. 5. Increased
phenotypic similarity between the two species is likely to lead to further hybridisation.
The ecological consequences of this are difficult to predict.
acknowledgement: "This project was funded through a NERC studentship to HVS which
was CASE partnered by the Macaulay Institute.\r\nWe thank the Forestry Commission
Scotland rangers for all their help with providing the larder data for and samples
from red and sika deer, Stephen Senn and Jarrod Hadfield for statistical advice
and Steve Albon for helpful comments on the manuscript."
article_processing_charge: No
author:
- first_name: Helen
full_name: Senn, Helen
last_name: Senn
- first_name: Graeme
full_name: Swanson, Graeme
last_name: Swanson
- first_name: Simon
full_name: Goodman, Simon
last_name: Goodman
- 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: Josephine
full_name: Pemberton, Josephine
last_name: Pemberton
citation:
ama: Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. Phenotypic correlates
of hybridisation between red and sika deer (genus Cervus). Journal of Animal
Ecology. 2010;79(2):414-425. doi:10.1111/j.1365-2656.2009.01633.x
apa: Senn, H., Swanson, G., Goodman, S., Barton, N. H., & Pemberton, J. (2010).
Phenotypic correlates of hybridisation between red and sika deer (genus Cervus).
Journal of Animal Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2656.2009.01633.x
chicago: Senn, Helen, Graeme Swanson, Simon Goodman, Nicholas H Barton, and Josephine
Pemberton. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus
Cervus).” Journal of Animal Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-2656.2009.01633.x.
ieee: H. Senn, G. Swanson, S. Goodman, N. H. Barton, and J. Pemberton, “Phenotypic
correlates of hybridisation between red and sika deer (genus Cervus),” Journal
of Animal Ecology, vol. 79, no. 2. Wiley-Blackwell, pp. 414–425, 2010.
ista: Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. 2010. Phenotypic correlates
of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology.
79(2), 414–425.
mla: Senn, Helen, et al. “Phenotypic Correlates of Hybridisation between Red and
Sika Deer (Genus Cervus).” Journal of Animal Ecology, vol. 79, no. 2, Wiley-Blackwell,
2010, pp. 414–25, doi:10.1111/j.1365-2656.2009.01633.x.
short: H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal
Ecology 79 (2010) 414–425.
date_created: 2018-12-11T12:05:06Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2025-09-30T09:44:45Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-2656.2009.01633.x
external_id:
isi:
- '000274321200014'
pmid:
- '20002231'
intvolume: ' 79'
isi: 1
issue: '2'
language:
- iso: eng
month: '03'
oa_version: None
page: 414 - 425
pmid: 1
publication: Journal of Animal Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2453'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 79
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."
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
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.
corr_author: '1'
date_created: 2018-12-11T12:05:06Z
date_published: 2010-08-27T00:00:00Z
date_updated: 2025-09-30T09:43:27Z
day: '27'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0106
external_id:
isi:
- '000280097000016'
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'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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.
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
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.
corr_author: '1'
date_created: 2018-12-11T12:05:07Z
date_published: 2010-04-27T00:00:00Z
date_updated: 2025-09-30T09:44:03Z
day: '27'
department:
- _id: NiBa
doi: 10.1098/rstb.2009.0320
external_id:
isi:
- '000275811000015'
pmid:
- '20308104'
intvolume: ' 365'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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
article_processing_charge: No
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: 2025-09-30T09:42:52Z
day: '20'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.1000429
external_id:
isi:
- '000280557100013'
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'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2010'
...
---
_id: '3782'
abstract:
- lang: eng
text: In cortex surface segmentation, the extracted surface is required to have
a particular topology, namely, a two-sphere. We present a new method for removing
topology noise of a curve or surface within the level set framework, and thus
produce a cortical surface with correct topology. We define a new energy term
which quantifies topology noise. We then show how to minimize this term by computing
its functional derivative with respect to the level set function. This method
differs from existing methods in that it is inherently continuous and not digital;
and in the way that our energy directly relates to the topology of the underlying
curve or surface, versus existing knot-based measures which are related in a more
indirect fashion. The proposed flow is validated empirically.
acknowledgement: "Partially supported by the Austri an Science Fund unde r grant P20134-N13.\r\nWe
thank Helena Molina-Abril for very helpful discussion. We thank anonymous reviewers
for helpful comments."
alternative_title:
- LNCS
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
citation:
ama: 'Chen C, Freedman D. Topology noise removal for curve and surface evolution.
In: Conference Proceedings MCV 2010. Vol 6533. Springer; 2010:31-42. doi:10.1007/978-3-642-18421-5_4'
apa: 'Chen, C., & Freedman, D. (2010). Topology noise removal for curve and
surface evolution. In Conference proceedings MCV 2010 (Vol. 6533, pp.
31–42). Beijing, China: Springer. https://doi.org/10.1007/978-3-642-18421-5_4'
chicago: Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve and
Surface Evolution.” In Conference Proceedings MCV 2010, 6533:31–42. Springer,
2010. https://doi.org/10.1007/978-3-642-18421-5_4.
ieee: C. Chen and D. Freedman, “Topology noise removal for curve and surface evolution,”
in Conference proceedings MCV 2010, Beijing, China, 2010, vol. 6533, pp.
31–42.
ista: 'Chen C, Freedman D. 2010. Topology noise removal for curve and surface evolution. Conference
proceedings MCV 2010. MCV: Medical Computer Vision, LNCS, vol. 6533, 31–42.'
mla: Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve and Surface
Evolution.” Conference Proceedings MCV 2010, vol. 6533, Springer, 2010,
pp. 31–42, doi:10.1007/978-3-642-18421-5_4.
short: C. Chen, D. Freedman, in:, Conference Proceedings MCV 2010, Springer, 2010,
pp. 31–42.
conference:
end_date: 2010-09-20
location: Beijing, China
name: 'MCV: Medical Computer Vision'
start_date: 2010-09-20
date_created: 2018-12-11T12:05:08Z
date_published: 2010-12-31T00:00:00Z
date_updated: 2021-01-12T07:52:10Z
day: '31'
department:
- _id: HeEd
doi: 10.1007/978-3-642-18421-5_4
intvolume: ' 6533'
language:
- iso: eng
month: '12'
oa_version: None
page: 31 - 42
publication: ' Conference proceedings MCV 2010'
publication_status: published
publisher: Springer
publist_id: '2445'
quality_controlled: '1'
scopus_import: 1
status: public
title: Topology noise removal for curve and surface evolution
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6533
year: '2010'
...
---
_id: '3783'
abstract:
- lang: eng
text: MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that
facilitates several tasks when scoring microsatellites. It implements new subroutines
in R and PERL and takes advantage of features provided by previously developed
freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification
through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite
markers according to their multiplex group, fluorochrome type, and size range.
After peak selection, binning of alleles can be carried out 1) automatically through
AlleloBin or 2) by manual bin definition through Binator. In both cases, several
features for quality checking and further binning improvement are provided. The
genotype table can then be converted into input files for several population genetics
programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence
intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT
is the only freely available public-domain software that facilitates full multiplex
microsatellite scoring, from electropherogram files to user-defined text files
to be used with population genetics software. MICROSATELIGHT has been created
for the Windows XP operating system and has been successfully tested under Windows
7. It is available at http://sourceforge.net/projects/microsatelight/.
acknowledgement: "Ministerio de Educación y Ciencia (CGL2006-13423, CTM2007-66635).
M.P. and FP are part of the research group 2009SGR-636 of the Generalitat de Catalunya.
F.P. acknowledges an EU-Synthesys grant (GB-TAF-4474).\r\n\r\nThanks to José Gabriel
Segarra-Moragues (Centro de Investigaciones sobre Desertificación) for sending us
pictures with several types of stuttering and Pedro Simões and Gemma Calàbria (Universitat
de Barcelona) for testing this software. Finally, thanks are due to 2 anonymous
referees for their valuable comments. These comments certainly helped to improve
the manuscript."
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Fernando
full_name: González Candelas, Fernando
last_name: González Candelas
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: Palero F, González Candelas F, Pascual M. Microsatelight – Pipeline to expedite
microsatellite analysis. Journal of Heredity. 2010;102(2):247-249. doi:10.1093/jhered/esq111
apa: Palero, F., González Candelas, F., & Pascual, M. (2010). Microsatelight
– Pipeline to expedite microsatellite analysis. Journal of Heredity. Oxford
University Press. https://doi.org/10.1093/jhered/esq111
chicago: Palero, Ferran, Fernando González Candelas, and Marta Pascual. “Microsatelight
– Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity. Oxford
University Press, 2010. https://doi.org/10.1093/jhered/esq111.
ieee: F. Palero, F. González Candelas, and M. Pascual, “Microsatelight – Pipeline
to expedite microsatellite analysis,” Journal of Heredity, vol. 102, no.
2. Oxford University Press, pp. 247–249, 2010.
ista: Palero F, González Candelas F, Pascual M. 2010. Microsatelight – Pipeline
to expedite microsatellite analysis. Journal of Heredity. 102(2), 247–249.
mla: Palero, Ferran, et al. “Microsatelight – Pipeline to Expedite Microsatellite
Analysis.” Journal of Heredity, vol. 102, no. 2, Oxford University Press,
2010, pp. 247–49, doi:10.1093/jhered/esq111.
short: F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010)
247–249.
date_created: 2018-12-11T12:05:09Z
date_published: 2010-12-02T00:00:00Z
date_updated: 2025-09-30T09:42:17Z
day: '02'
department:
- _id: NiBa
doi: 10.1093/jhered/esq111
external_id:
isi:
- '000287496700012'
intvolume: ' 102'
isi: 1
issue: '2'
language:
- iso: eng
month: '12'
oa_version: None
page: 247 - 249
publication: Journal of Heredity
publication_status: published
publisher: Oxford University Press
publist_id: '2444'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microsatelight – Pipeline to expedite microsatellite analysis
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 102
year: '2010'
...
---
_id: '3785'
abstract:
- lang: eng
text: Most fisheries involving spiny lobsters of the genus Palinurus have been over
exploited during the last decades, so there is a raising concern about management
decisions for these valuable resources. A total of 13 microsatellite DNA loci
recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave
amplifications and showed polymorphism in all species, with gene diversity values varying from 0.65060.077 SD (Palinurus
barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth
distribution was taken into account, shallower waters pecies consistently showed
larger historical effective population sizes than their deeper-water counterparts. This
could explain why deeper-water species are more sensitive to overfishing, and
would indicate that overexploitation may have a larger impact on their long-term
genetic diversity.
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: E.
full_name: Macpherson, E.
last_name: Macpherson
- first_name: C.
full_name: Matthee, C.
last_name: Matthee
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: 'Palero F, Abello P, Macpherson E, Matthee C, Pascual M. Genetic diversity
levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata).
Journal of Crustacean Biology. 2010;30(4):658-663. doi:10.1651/09-3192.1'
apa: 'Palero, F., Abello, P., Macpherson, E., Matthee, C., & Pascual, M. (2010).
Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus
(Decapoda: Achelata). Journal of Crustacean Biology. Oxford University
Press. https://doi.org/10.1651/09-3192.1'
chicago: 'Palero, Ferran, Pere Abello, E. Macpherson, C. Matthee, and Marta Pascual.
“Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus
(Decapoda: Achelata).” Journal of Crustacean Biology. Oxford University
Press, 2010. https://doi.org/10.1651/09-3192.1.'
ieee: 'F. Palero, P. Abello, E. Macpherson, C. Matthee, and M. Pascual, “Genetic
diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda:
Achelata),” Journal of Crustacean Biology, vol. 30, no. 4. Oxford University
Press, pp. 658–663, 2010.'
ista: 'Palero F, Abello P, Macpherson E, Matthee C, Pascual M. 2010. Genetic diversity
levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata).
Journal of Crustacean Biology. 30(4), 658–663.'
mla: 'Palero, Ferran, et al. “Genetic Diversity Levels in Fishery-Exploited Spiny
Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean
Biology, vol. 30, no. 4, Oxford University Press, 2010, pp. 658–63, doi:10.1651/09-3192.1.'
short: F. Palero, P. Abello, E. Macpherson, C. Matthee, M. Pascual, Journal of Crustacean
Biology 30 (2010) 658–663.
corr_author: '1'
date_created: 2018-12-11T12:05:09Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2025-09-30T09:41:44Z
day: '01'
department:
- _id: NiBa
doi: 10.1651/09-3192.1
external_id:
isi:
- '000284514100015'
intvolume: ' 30'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa_version: None
page: 658 - 663
publication: Journal of Crustacean Biology
publication_identifier:
eissn:
- 1937-240X
issn:
- 0278-0372
publication_status: published
publisher: Oxford University Press
publist_id: '2442'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genetic diversity levels in fishery-exploited spiny lobsters of the Genus
Palinurus (Decapoda: Achelata)'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 30
year: '2010'
...
---
_id: '3786'
abstract:
- lang: eng
text: Four rare palinurid phyllosoma larvae, one mid-stage and three final stage,
were found among the unclassified collections in the Crustacea Section, Natural
History Museum, London. Detailed morphological analysis of the larvae indicated
that they belong to several Palinustus species given the presence of incipient
blunt-horns, length of antennula, length ratio of segments of antennular peduncle,
distribution of pereiopod spines, and shape of uropods and telson. Moreover, the
size of the final-stage larvae agrees with that expected given the size of the
recently described puerulus stage of Palinustus mossambicus. This constitutes
the first description of a complete phyllosoma assigned to Palinustus species.
The phyllosoma described in the present study include the largest Palinuridae
larva ever found.
article_processing_charge: No
article_type: original
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Guillermo
full_name: Guerao, Guillermo
last_name: Guerao
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
citation:
ama: 'Palero F, Guerao G, Clark P, Abello P. Final-stage phyllosoma of Palinustus
A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first
complete description. Zootaxa. 2010;2403(1):42-58. doi:10.11646/zootaxa.2403.1.4'
apa: 'Palero, F., Guerao, G., Clark, P., & Abello, P. (2010). Final-stage phyllosoma
of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The
first complete description. Zootaxa. Magnolia Press. https://doi.org/10.11646/zootaxa.2403.1.4'
chicago: 'Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Final-Stage
Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata:
Palinuridae)-The First Complete Description.” Zootaxa. Magnolia Press,
2010. https://doi.org/10.11646/zootaxa.2403.1.4.'
ieee: 'F. Palero, G. Guerao, P. Clark, and P. Abello, “Final-stage phyllosoma of
Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The
first complete description,” Zootaxa, vol. 2403, no. 1. Magnolia Press,
pp. 42–58, 2010.'
ista: 'Palero F, Guerao G, Clark P, Abello P. 2010. Final-stage phyllosoma of Palinustus
A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first
complete description. Zootaxa. 2403(1), 42–58.'
mla: 'Palero, Ferran, et al. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards,
1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.”
Zootaxa, vol. 2403, no. 1, Magnolia Press, 2010, pp. 42–58, doi:10.11646/zootaxa.2403.1.4.'
short: F. Palero, G. Guerao, P. Clark, P. Abello, Zootaxa 2403 (2010) 42–58.
date_created: 2018-12-11T12:05:10Z
date_published: 2010-03-19T00:00:00Z
date_updated: 2022-03-21T08:22:58Z
day: '19'
department:
- _id: NiBa
doi: 10.11646/zootaxa.2403.1.4
intvolume: ' 2403'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 42 - 58
publication: Zootaxa
publication_status: published
publisher: Magnolia Press
publist_id: '2441'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda:
Achelata: Palinuridae)-The first complete description'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2403
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"
article_processing_charge: No
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.
corr_author: '1'
date_created: 2018-12-11T12:05:10Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2025-09-30T09:41:18Z
day: '01'
department:
- _id: NiBa
doi: 10.3989/scimar.2010.74n3465
external_id:
isi:
- '000280917100005'
intvolume: ' 74'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 74
year: '2010'
...
---
_id: '3788'
abstract:
- lang: eng
text: Cell sorting is a widespread phenomenon pivotal to the early development of
multicellular organisms. In vitro cell sorting studies have been instrumental
in revealing the cellular properties driving this process. However, these studies
have as yet been limited to two-dimensional analysis of three-dimensional cell
sorting events. Here we describe a method to record the sorting of primary zebrafish
ectoderm and mesoderm germ layer progenitor cells in three dimensions over time,
and quantitatively analyze their sorting behavior using an order parameter related
to heterotypic interface length. We investigate the cell population size dependence
of sorted aggregates and find that the germ layer progenitor cells engulfed in
the final configuration display a relationship between total interfacial length
and system size according to a simple geometrical argument, subject to a finite-size
effect.
article_processing_charge: No
author:
- first_name: Abigail
full_name: Klopper, Abigail
last_name: Klopper
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Stephan
full_name: Grill, Stephan
last_name: Grill
- 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: 'Klopper A, Krens G, Grill S, Heisenberg C-PJ. Finite-size corrections to scaling
behavior in sorted cell aggregates. The European Physical Journal E: Soft Matter
and Biological Physics. 2010;33(2):99-103. doi:10.1140/epje/i2010-10642-y'
apa: 'Klopper, A., Krens, G., Grill, S., & Heisenberg, C.-P. J. (2010). Finite-size
corrections to scaling behavior in sorted cell aggregates. The European Physical
Journal E: Soft Matter and Biological Physics. Springer. https://doi.org/10.1140/epje/i2010-10642-y'
chicago: 'Klopper, Abigail, Gabriel Krens, Stephan Grill, and Carl-Philipp J Heisenberg.
“Finite-Size Corrections to Scaling Behavior in Sorted Cell Aggregates.” The
European Physical Journal E: Soft Matter and Biological Physics. Springer,
2010. https://doi.org/10.1140/epje/i2010-10642-y.'
ieee: 'A. Klopper, G. Krens, S. Grill, and C.-P. J. Heisenberg, “Finite-size corrections
to scaling behavior in sorted cell aggregates,” The European Physical Journal
E: Soft Matter and Biological Physics, vol. 33, no. 2. Springer, pp. 99–103,
2010.'
ista: 'Klopper A, Krens G, Grill S, Heisenberg C-PJ. 2010. Finite-size corrections
to scaling behavior in sorted cell aggregates. The European Physical Journal E:
Soft Matter and Biological Physics. 33(2), 99–103.'
mla: 'Klopper, Abigail, et al. “Finite-Size Corrections to Scaling Behavior in Sorted
Cell Aggregates.” The European Physical Journal E: Soft Matter and Biological
Physics, vol. 33, no. 2, Springer, 2010, pp. 99–103, doi:10.1140/epje/i2010-10642-y.'
short: 'A. Klopper, G. Krens, S. Grill, C.-P.J. Heisenberg, The European Physical
Journal E: Soft Matter and Biological Physics 33 (2010) 99–103.'
corr_author: '1'
date_created: 2018-12-11T12:05:10Z
date_published: 2010-09-18T00:00:00Z
date_updated: 2025-09-30T09:40:53Z
day: '18'
department:
- _id: CaHe
doi: 10.1140/epje/i2010-10642-y
external_id:
isi:
- '000284841700002'
intvolume: ' 33'
isi: 1
issue: '2'
language:
- iso: eng
month: '09'
oa_version: None
page: 99 - 103
publication: 'The European Physical Journal E: Soft Matter and Biological Physics'
publication_status: published
publisher: Springer
publist_id: '2439'
scopus_import: '1'
status: public
title: Finite-size corrections to scaling behavior in sorted cell aggregates
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 33
year: '2010'
...