---
_id: '2720'
abstract:
- lang: eng
text: 'Knowledge of the rate and fitness effects of mutations is essential for understanding
the process of evolution. Mutations are inherently difficult to study because
they are rare and are frequently eliminated by natural selection. In the ciliate
Tetrahymena thermophila, mutations can accumulate in the germline genome without
being exposed to selection. We have conducted a mutation accumulation (MA) experiment
in this species. Assuming that all mutations are deleterious and have the same
effect, we estimate that the deleterious mutation rate per haploid germline genome
per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that
germline mutations decrease fitness by s = 11% when expressed in a homozygous
state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially
recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal
mutations is <10% of the deleterious mutation rate. Comparisons between the
observed evolutionary responses in the germline and somatic genomes and the results
from individual-based simulations of MA suggest that the two genomes have similar
mutational parameters. These are the first estimates of the deleterious mutation
rate and fitness effects from the eukaryotic supergroup Chromalveolata and are
within the range of those of other eukaryotes.'
article_processing_charge: No
author:
- first_name: Hongan
full_name: Long, Hongan
last_name: Long
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Ricardo
full_name: Azevedo, Ricardo
last_name: Azevedo
- first_name: Rebecca
full_name: Zufall, Rebecca
last_name: Zufall
citation:
ama: Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations
in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540.
doi:10.1534/genetics.113.153536
apa: Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of
spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.113.153536
chicago: Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation
of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics.
Genetics Society of America, 2013. https://doi.org/10.1534/genetics.113.153536.
ieee: H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous
mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195,
no. 2. Genetics Society of America, pp. 527–540, 2013.
ista: Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations
in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.
mla: Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate
Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of
America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536.
short: H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.
date_created: 2018-12-11T11:59:15Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2021-01-12T06:59:16Z
day: '01'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1534/genetics.113.153536
ec_funded: 1
external_id:
pmid:
- '23934880'
intvolume: ' 195'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/
month: '10'
oa: 1
oa_version: Submitted Version
page: 527-540
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '4172'
quality_controlled: '1'
scopus_import: 1
status: public
title: Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 195
year: '2013'
...
---
_id: '2782'
abstract:
- lang: eng
text: We consider random n×n matrices of the form (XX*+YY*)^{-1/2}YY*(XX*+YY*)^{-1/2},
where X and Y have independent entries with zero mean and variance one. These
matrices are the natural generalization of the Gaussian case, which are known
as MANOVA matrices and which have joint eigenvalue density given by the third
classical ensemble, the Jacobi ensemble. We show that, away from the spectral
edge, the eigenvalue density converges to the limiting density of the Jacobi ensemble
even on the shortest possible scales of order 1/n (up to log n factors). This
result is the analogue of the local Wigner semicircle law and the local Marchenko-Pastur
law for general MANOVA matrices.
arxiv: 1
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Brendan
full_name: Farrell, Brendan
last_name: Farrell
citation:
ama: Erdös L, Farrell B. Local eigenvalue density for general MANOVA matrices. Journal
of Statistical Physics. 2013;152(6):1003-1032. doi:10.1007/s10955-013-0807-8
apa: Erdös, L., & Farrell, B. (2013). Local eigenvalue density for general MANOVA
matrices. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-013-0807-8
chicago: Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General
MANOVA Matrices.” Journal of Statistical Physics. Springer, 2013. https://doi.org/10.1007/s10955-013-0807-8.
ieee: L. Erdös and B. Farrell, “Local eigenvalue density for general MANOVA matrices,”
Journal of Statistical Physics, vol. 152, no. 6. Springer, pp. 1003–1032,
2013.
ista: Erdös L, Farrell B. 2013. Local eigenvalue density for general MANOVA matrices.
Journal of Statistical Physics. 152(6), 1003–1032.
mla: Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA
Matrices.” Journal of Statistical Physics, vol. 152, no. 6, Springer, 2013,
pp. 1003–32, doi:10.1007/s10955-013-0807-8.
short: L. Erdös, B. Farrell, Journal of Statistical Physics 152 (2013) 1003–1032.
date_created: 2018-12-11T11:59:34Z
date_published: 2013-07-18T00:00:00Z
date_updated: 2021-01-12T06:59:41Z
day: '18'
department:
- _id: LaEr
doi: 10.1007/s10955-013-0807-8
external_id:
arxiv:
- '1207.0031'
intvolume: ' 152'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.0031
month: '07'
oa: 1
oa_version: Preprint
page: 1003 - 1032
publication: Journal of Statistical Physics
publication_status: published
publisher: Springer
publist_id: '4107'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local eigenvalue density for general MANOVA matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 152
year: '2013'
...
---
_id: '2806'
abstract:
- lang: eng
text: A novel Taylor-Couette system has been constructed for investigations of transitional
as well as high Reynolds number turbulent flows in very large aspect ratios. The
flexibility of the setup enables studies of a variety of problems regarding hydrodynamic
instabilities and turbulence in rotating flows. The inner and outer cylinders
and the top and bottom endplates can be rotated independently with rotation rates
of up to 30 Hz, thereby covering five orders of magnitude in Reynolds numbers
(Re = 101-106). The radius ratio can be easily changed, the highest realized one
is η = 0.98 corresponding to an aspect ratio of 260 gap width in the vertical
and 300 in the azimuthal direction. For η < 0.98 the aspect ratio can be dynamically
changed during measurements and complete transparency in the radial direction
over the full length of the cylinders is provided by the usage of a precision
glass inner cylinder. The temperatures of both cylinders are controlled independently.
Overall this apparatus combines an unmatched variety in geometry, rotation rates,
and temperatures, which is provided by a sophisticated high-precision bearing
system. Possible applications are accurate studies of the onset of turbulence
and spatio-temporal intermittent flow patterns in very large domains, transport
processes of turbulence at high Re, the stability of Keplerian flows for different
boundary conditions, and studies of baroclinic instabilities.
article_number: '065106'
author:
- first_name: Kerstin
full_name: Avila, Kerstin
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Avila K, Hof B. High-precision Taylor-Couette experiment to study subcritical
transitions and the role of boundary conditions and size effects. Review of
Scientific Instruments. 2013;84(6). doi:10.1063/1.4807704
apa: Avila, K., & Hof, B. (2013). High-precision Taylor-Couette experiment to
study subcritical transitions and the role of boundary conditions and size effects.
Review of Scientific Instruments. American Institute of Physics. https://doi.org/10.1063/1.4807704
chicago: Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment
to Study Subcritical Transitions and the Role of Boundary Conditions and Size
Effects.” Review of Scientific Instruments. American Institute of Physics,
2013. https://doi.org/10.1063/1.4807704.
ieee: K. Avila and B. Hof, “High-precision Taylor-Couette experiment to study subcritical
transitions and the role of boundary conditions and size effects,” Review of
Scientific Instruments, vol. 84, no. 6. American Institute of Physics, 2013.
ista: Avila K, Hof B. 2013. High-precision Taylor-Couette experiment to study subcritical
transitions and the role of boundary conditions and size effects. Review of Scientific
Instruments. 84(6), 065106.
mla: Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to
Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.”
Review of Scientific Instruments, vol. 84, no. 6, 065106, American Institute
of Physics, 2013, doi:10.1063/1.4807704.
short: K. Avila, B. Hof, Review of Scientific Instruments 84 (2013).
date_created: 2018-12-11T11:59:42Z
date_published: 2013-06-06T00:00:00Z
date_updated: 2021-01-12T06:59:50Z
day: '06'
department:
- _id: BjHo
doi: 10.1063/1.4807704
intvolume: ' 84'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
publication: Review of Scientific Instruments
publication_status: published
publisher: American Institute of Physics
publist_id: '4081'
quality_controlled: '1'
scopus_import: 1
status: public
title: High-precision Taylor-Couette experiment to study subcritical transitions and
the role of boundary conditions and size effects
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2013'
...
---
_id: '2807'
abstract:
- lang: eng
text: 'We consider several basic problems of algebraic topology, with connections
to combinatorial and geometric questions, from the point of view of computational
complexity. The extension problem asks, given topological spaces X; Y , a subspace
A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X
→ Y . For computational purposes, we assume that X and Y are represented as finite
simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map.
In this generality the problem is undecidable, as follows from Novikov''s result
from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study
the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected;
informally, this means that Y has \no holes up to dimension k-1" (a basic
example of such a Y is the sphere Sk). We prove that, on the one hand, this problem
is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2,
we obtain an algorithm that solves the extension problem in polynomial time assuming
Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides
a classification of all extensions up to homotopy (continuous deformation). This
relies on results of our SODA 2012 paper, and the main new ingredient is a machinery
of objects with polynomial-time homology, which is a polynomial-time analog of
objects with effective homology developed earlier by Sergeraert et al. We also
consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected
Y . Their computability was established by Brown in 1957; we show that πk(Y )
can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick
proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where
Y is a cell complex with certain rather compact encoding. We strengthen his result
to #P-hardness for Y given as a simplicial complex. '
author:
- first_name: Martin
full_name: Čadek, Martin
last_name: Čadek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Lukáš
full_name: Vokřínek, Lukáš
last_name: Vokřínek
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. Extending continuous maps:
Polynomiality and undecidability. In: 45th Annual ACM Symposium on Theory of
Computing. ACM; 2013:595-604. doi:10.1145/2488608.2488683'
apa: 'Čadek, M., Krcál, M., Matoušek, J., Vokřínek, L., & Wagner, U. (2013).
Extending continuous maps: Polynomiality and undecidability. In 45th Annual
ACM Symposium on theory of computing (pp. 595–604). Palo Alto, CA, United
States: ACM. https://doi.org/10.1145/2488608.2488683'
chicago: 'Čadek, Martin, Marek Krcál, Jiří Matoušek, Lukáš Vokřínek, and Uli Wagner.
“Extending Continuous Maps: Polynomiality and Undecidability.” In 45th Annual
ACM Symposium on Theory of Computing, 595–604. ACM, 2013. https://doi.org/10.1145/2488608.2488683.'
ieee: 'M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, and U. Wagner, “Extending continuous
maps: Polynomiality and undecidability,” in 45th Annual ACM Symposium on theory
of computing, Palo Alto, CA, United States, 2013, pp. 595–604.'
ista: 'Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. 2013. Extending continuous
maps: Polynomiality and undecidability. 45th Annual ACM Symposium on theory of
computing. STOC: Symposium on the Theory of Computing, 595–604.'
mla: 'Čadek, Martin, et al. “Extending Continuous Maps: Polynomiality and Undecidability.”
45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604,
doi:10.1145/2488608.2488683.'
short: M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, U. Wagner, in:, 45th Annual
ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604.
conference:
end_date: 2013-06-04
location: Palo Alto, CA, United States
name: 'STOC: Symposium on the Theory of Computing'
start_date: 2013-06-01
date_created: 2018-12-11T11:59:42Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2021-01-12T06:59:51Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
- _id: HeEd
doi: 10.1145/2488608.2488683
file:
- access_level: open_access
checksum: 06c2ce5c1135fbc1f71ca15eeb242dcf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:29Z
date_updated: 2020-07-14T12:45:48Z
file_id: '5081'
file_name: IST-2016-533-v1+1_Extending_continuous_maps_polynomiality_and_undecidability.pdf
file_size: 447945
relation: main_file
file_date_updated: 2020-07-14T12:45:48Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 595 - 604
publication: 45th Annual ACM Symposium on theory of computing
publication_status: published
publisher: ACM
publist_id: '4078'
pubrep_id: '533'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Extending continuous maps: Polynomiality and undecidability'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2808'
abstract:
- lang: eng
text: In order to establish a reference for analysis of the function of auxin and
the auxin biosynthesis regulators SHORT INTERNODE/ STYLISH (SHI/STY) during Physcomitrella
patens reproductive development, we have described male (antheridial) and female
(archegonial) development in detail, including temporal and positional information
of organ initiation. This has allowed us to define discrete stages of organ morphogenesis
and to show that reproductive organ development in P. patens is highly organized
and that organ phyllotaxis differs between vegetative and reproductive development.
Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3pro:GUS
and PpPINApro:GFP-GUS, and the auxin-conjugating transgene PpSHI2pro:IAAL, we
could show that the PpSHI genes, and by inference also auxin, play important roles
for reproductive organ development in moss. The PpSHI genes are required for the
apical opening of the reproductive organs, the final differentiation of the egg
cell, and the progression of canal cells into a cell death program. The apical
cells of the archegonium, the canal cells, and the egg cell are also sites of
auxin responsiveness and are affected by reduced levels of active auxin, suggesting
that auxin mediates PpSHI function in the reproductive organs.
author:
- first_name: Katarina
full_name: Landberg, Katarina
last_name: Landberg
- first_name: Eric
full_name: Pederson, Eric
last_name: Pederson
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Behruz
full_name: Bozorg, Behruz
last_name: Bozorg
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Henrik
full_name: Jönsson, Henrik
last_name: Jönsson
- first_name: Mattias
full_name: Thelander, Mattias
last_name: Thelander
- first_name: Eva
full_name: Sundberg, Eva
last_name: Sundberg
citation:
ama: Landberg K, Pederson E, Viaene T, et al. The moss physcomitrella patens reproductive
organ development is highly organized, affected by the two SHI/STY genes and by
the level of active auxin in the SHI/STY expression domain. Plant Physiology.
2013;162(3):1406-1419. doi:10.1104/pp.113.214023
apa: Landberg, K., Pederson, E., Viaene, T., Bozorg, B., Friml, J., Jönsson, H.,
… Sundberg, E. (2013). The moss physcomitrella patens reproductive organ development
is highly organized, affected by the two SHI/STY genes and by the level of active
auxin in the SHI/STY expression domain. Plant Physiology. American Society
of Plant Biologists. https://doi.org/10.1104/pp.113.214023
chicago: Landberg, Katarina, Eric Pederson, Tom Viaene, Behruz Bozorg, Jiří Friml,
Henrik Jönsson, Mattias Thelander, and Eva Sundberg. “The Moss Physcomitrella
Patens Reproductive Organ Development Is Highly Organized, Affected by the Two
SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.”
Plant Physiology. American Society of Plant Biologists, 2013. https://doi.org/10.1104/pp.113.214023.
ieee: K. Landberg et al., “The moss physcomitrella patens reproductive organ
development is highly organized, affected by the two SHI/STY genes and by the
level of active auxin in the SHI/STY expression domain,” Plant Physiology,
vol. 162, no. 3. American Society of Plant Biologists, pp. 1406–1419, 2013.
ista: Landberg K, Pederson E, Viaene T, Bozorg B, Friml J, Jönsson H, Thelander
M, Sundberg E. 2013. The moss physcomitrella patens reproductive organ development
is highly organized, affected by the two SHI/STY genes and by the level of active
auxin in the SHI/STY expression domain. Plant Physiology. 162(3), 1406–1419.
mla: Landberg, Katarina, et al. “The Moss Physcomitrella Patens Reproductive Organ
Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the
Level of Active Auxin in the SHI/STY Expression Domain.” Plant Physiology,
vol. 162, no. 3, American Society of Plant Biologists, 2013, pp. 1406–19, doi:10.1104/pp.113.214023.
short: K. Landberg, E. Pederson, T. Viaene, B. Bozorg, J. Friml, H. Jönsson, M.
Thelander, E. Sundberg, Plant Physiology 162 (2013) 1406–1419.
date_created: 2018-12-11T11:59:42Z
date_published: 2013-07-03T00:00:00Z
date_updated: 2021-01-12T06:59:51Z
day: '03'
department:
- _id: JiFr
doi: 10.1104/pp.113.214023
external_id:
pmid:
- '23669745'
intvolume: ' 162'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707547/
month: '07'
oa: 1
oa_version: Submitted Version
page: 1406 - 1419
pmid: 1
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '4079'
quality_controlled: '1'
scopus_import: 1
status: public
title: The moss physcomitrella patens reproductive organ development is highly organized,
affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY
expression domain
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 162
year: '2013'
...
---
_id: '2810'
abstract:
- lang: eng
text: The epistatic interactions that underlie evolutionary constraint have mainly
been studied for constant external conditions. However, environmental changes
may modulate epistasis and hence affect genetic constraints. Here we investigate
genetic constraints in the adaptive evolution of a novel regulatory function in
variable environments, using the lac repressor, LacI, as a model system. We have
systematically reconstructed mutational trajectories from wild type LacI to three
different variants that each exhibit an inverse response to the inducing ligand
IPTG, and analyzed the higher-order interactions between genetic and environmental
changes. We find epistasis to depend strongly on the environment. As a result,
mutational steps essential to inversion but inaccessible by positive selection
in one environment, become accessible in another. We present a graphical method
to analyze the observed complex higher-order interactions between multiple mutations
and environmental change, and show how the interactions can be explained by a
combination of mutational effects on allostery and thermodynamic stability. This
dependency of genetic constraint on the environment should fundamentally affect
evolutionary dynamics and affects the interpretation of phylogenetic data.
article_number: e1003580
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Frank
full_name: Poelwijk, Frank
last_name: Poelwijk
- first_name: Nico
full_name: Battich, Nico
last_name: Battich
- first_name: Joseph
full_name: Ndika, Joseph
last_name: Ndika
- first_name: Sander
full_name: Tans, Sander
last_name: Tans
citation:
ama: de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. Environmental dependence
of genetic constraint. PLoS Genetics. 2013;9(6). doi:10.1371/journal.pgen.1003580
apa: de Vos, M., Poelwijk, F., Battich, N., Ndika, J., & Tans, S. (2013). Environmental
dependence of genetic constraint. PLoS Genetics. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1003580
chicago: Vos, Marjon de, Frank Poelwijk, Nico Battich, Joseph Ndika, and Sander
Tans. “Environmental Dependence of Genetic Constraint.” PLoS Genetics.
Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003580.
ieee: M. de Vos, F. Poelwijk, N. Battich, J. Ndika, and S. Tans, “Environmental
dependence of genetic constraint,” PLoS Genetics, vol. 9, no. 6. Public
Library of Science, 2013.
ista: de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. 2013. Environmental dependence
of genetic constraint. PLoS Genetics. 9(6), e1003580.
mla: de Vos, Marjon, et al. “Environmental Dependence of Genetic Constraint.” PLoS
Genetics, vol. 9, no. 6, e1003580, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003580.
short: M. de Vos, F. Poelwijk, N. Battich, J. Ndika, S. Tans, PLoS Genetics 9 (2013).
date_created: 2018-12-11T11:59:43Z
date_published: 2013-06-27T00:00:00Z
date_updated: 2021-01-12T06:59:52Z
day: '27'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1371/journal.pgen.1003580
file:
- access_level: open_access
checksum: 7a4736dd80496d29ff6908b6f2329b4e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:51Z
date_updated: 2020-07-14T12:45:48Z
file_id: '4713'
file_name: IST-2016-412-v1+1_journal.pgen.1003580.pdf
file_size: 474655
relation: main_file
file_date_updated: 2020-07-14T12:45:48Z
has_accepted_license: '1'
intvolume: ' 9'
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: '4075'
pubrep_id: '412'
quality_controlled: '1'
scopus_import: 1
status: public
title: Environmental dependence of genetic constraint
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '2811'
abstract:
- lang: eng
text: 'In pipe, channel, and boundary layer flows turbulence first occurs intermittently
in space and time: at moderate Reynolds numbers domains of disordered turbulent
motion are separated by quiescent laminar regions. Based on direct numerical simulations
of pipe flow we argue here that the spatial intermittency has its origin in a
nearest neighbor interaction between turbulent regions. We further show that in
this regime turbulent flows are intrinsically intermittent with a well-defined
equilibrium turbulent fraction but without ever assuming a steady pattern. This
transition scenario is analogous to that found in simple models such as coupled
map lattices. The scaling observed implies that laminar intermissions of the turbulent
flow will persist to arbitrarily large Reynolds numbers.'
article_number: '063012'
arxiv: 1
author:
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Avila M, Hof B. Nature of laminar-turbulence intermittency in shear flows.
Physical Review E. 2013;87(6). doi:10.1103/PhysRevE.87.063012
apa: Avila, M., & Hof, B. (2013). Nature of laminar-turbulence intermittency
in shear flows. Physical Review E. American Institute of Physics. https://doi.org/10.1103/PhysRevE.87.063012
chicago: Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency
in Shear Flows.” Physical Review E. American Institute of Physics, 2013.
https://doi.org/10.1103/PhysRevE.87.063012.
ieee: M. Avila and B. Hof, “Nature of laminar-turbulence intermittency in shear
flows,” Physical Review E, vol. 87, no. 6. American Institute of Physics,
2013.
ista: Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear
flows. Physical Review E. 87(6), 063012.
mla: Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in
Shear Flows.” Physical Review E, vol. 87, no. 6, 063012, American Institute
of Physics, 2013, doi:10.1103/PhysRevE.87.063012.
short: M. Avila, B. Hof, Physical Review E 87 (2013).
date_created: 2018-12-11T11:59:43Z
date_published: 2013-06-18T00:00:00Z
date_updated: 2021-01-12T06:59:53Z
day: '18'
department:
- _id: BjHo
doi: 10.1103/PhysRevE.87.063012
ec_funded: 1
external_id:
arxiv:
- '1306.5890'
intvolume: ' 87'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1306.5890
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Physical Review E
publication_status: published
publisher: American Institute of Physics
publist_id: '4074'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nature of laminar-turbulence intermittency in shear flows
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2013'
...
---
_id: '2812'
abstract:
- lang: eng
text: 'We consider the problem of deciding whether the persistent homology group
of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex
X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded
in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel
sets of scalar functions on S3 within a given tolerance constraint. This problem
has relevance to the visualization of medical images by isosurfaces. We also show
an implication to the theory of well groups of scalar functions: not every well
group can be realized by some level set, and deciding whether a well group can
be realized is NP-hard.'
acknowledgement: Some of the authors were partially supported by the GIGA ANR grant
(contract ANR-09-BLAN-0331-01) and the European project CG-Learning (contract 255827).
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Olivier
full_name: Devillers, Olivier
last_name: Devillers
- first_name: Marc
full_name: Glisse, Marc
last_name: Glisse
- first_name: André
full_name: Lieutier, André
last_name: Lieutier
citation:
ama: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction
and simplification in R3. In: Proceedings of the 29th Annual Symposium on Computational
Geometry. ACM; 2013:117-125. doi:10.1145/2462356.2462373'
apa: 'Attali, D., Bauer, U., Devillers, O., Glisse, M., & Lieutier, A. (2013).
Homological reconstruction and simplification in R3. In Proceedings of the
29th annual symposium on Computational Geometry (pp. 117–125). Rio de Janeiro,
Brazil: ACM. https://doi.org/10.1145/2462356.2462373'
chicago: Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André
Lieutier. “Homological Reconstruction and Simplification in R3.” In Proceedings
of the 29th Annual Symposium on Computational Geometry, 117–25. ACM, 2013.
https://doi.org/10.1145/2462356.2462373.
ieee: D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological
reconstruction and simplification in R3,” in Proceedings of the 29th annual
symposium on Computational Geometry, Rio de Janeiro, Brazil, 2013, pp. 117–125.
ista: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2013. Homological reconstruction
and simplification in R3. Proceedings of the 29th annual symposium on Computational
Geometry. SoCG: Symposium on Computational Geometry, 117–125.'
mla: Attali, Dominique, et al. “Homological Reconstruction and Simplification in
R3.” Proceedings of the 29th Annual Symposium on Computational Geometry,
ACM, 2013, pp. 117–25, doi:10.1145/2462356.2462373.
short: D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, in:, Proceedings
of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–125.
conference:
end_date: 2013-06-20
location: Rio de Janeiro, Brazil
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2013-06-17
date_created: 2018-12-11T11:59:44Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2023-02-23T10:15:15Z
day: '01'
department:
- _id: HeEd
doi: 10.1145/2462356.2462373
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://hal.archives-ouvertes.fr/hal-00833791/
month: '06'
oa: 1
oa_version: Submitted Version
page: 117 - 125
publication: Proceedings of the 29th annual symposium on Computational Geometry
publication_status: published
publisher: ACM
publist_id: '4072'
quality_controlled: '1'
related_material:
record:
- id: '1805'
relation: later_version
status: public
scopus_import: 1
status: public
title: Homological reconstruction and simplification in R3
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2813'
abstract:
- lang: eng
text: Turbulence is ubiquitous in nature, yet even for the case of ordinary Newtonian
fluids like water, our understanding of this phenomenon is limited. Many liquids
of practical importance are more complicated (e.g., blood, polymer melts, paints),
however; they exhibit elastic as well as viscous characteristics, and the relation
between stress and strain is nonlinear. We demonstrate here for a model system
of such complex fluids that at high shear rates, turbulence is not simply modified
as previously believed but is suppressed and replaced by a different type of disordered
motion, elasto-inertial turbulence. Elasto-inertial turbulence is found to occur
at much lower Reynolds numbers than Newtonian turbulence, and the dynamical properties
differ significantly. The friction scaling observed coincides with the so-called
"maximum drag reduction" asymptote, which is exhibited by a wide range
of viscoelastic fluids.
author:
- first_name: Devranjan
full_name: Samanta, Devranjan
last_name: Samanta
- first_name: Yves
full_name: Dubief, Yves
last_name: Dubief
- first_name: Markus
full_name: Holzner, Markus
last_name: Holzner
- first_name: Christof
full_name: Schäfer, Christof
last_name: Schäfer
- first_name: Alexander
full_name: Morozov, Alexander
last_name: Morozov
- first_name: Christian
full_name: Wagner, Christian
last_name: Wagner
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Samanta D, Dubief Y, Holzner M, et al. Elasto-inertial turbulence. PNAS.
2013;110(26):10557-10562. doi:10.1073/pnas.1219666110
apa: Samanta, D., Dubief, Y., Holzner, M., Schäfer, C., Morozov, A., Wagner, C.,
& Hof, B. (2013). Elasto-inertial turbulence. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1219666110
chicago: Samanta, Devranjan, Yves Dubief, Markus Holzner, Christof Schäfer, Alexander
Morozov, Christian Wagner, and Björn Hof. “Elasto-Inertial Turbulence.” PNAS.
National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1219666110.
ieee: D. Samanta et al., “Elasto-inertial turbulence,” PNAS, vol.
110, no. 26. National Academy of Sciences, pp. 10557–10562, 2013.
ista: Samanta D, Dubief Y, Holzner M, Schäfer C, Morozov A, Wagner C, Hof B. 2013.
Elasto-inertial turbulence. PNAS. 110(26), 10557–10562.
mla: Samanta, Devranjan, et al. “Elasto-Inertial Turbulence.” PNAS, vol.
110, no. 26, National Academy of Sciences, 2013, pp. 10557–62, doi:10.1073/pnas.1219666110.
short: D. Samanta, Y. Dubief, M. Holzner, C. Schäfer, A. Morozov, C. Wagner, B.
Hof, PNAS 110 (2013) 10557–10562.
date_created: 2018-12-11T11:59:44Z
date_published: 2013-06-25T00:00:00Z
date_updated: 2021-01-12T06:59:54Z
day: '25'
department:
- _id: BjHo
doi: 10.1073/pnas.1219666110
external_id:
pmid:
- '23757498'
intvolume: ' 110'
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696777/
month: '06'
oa: 1
oa_version: Submitted Version
page: 10557 - 10562
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '4073'
quality_controlled: '1'
scopus_import: 1
status: public
title: Elasto-inertial turbulence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2814'
abstract:
- lang: eng
text: We study the problem of generating a test sequence that achieves maximal coverage
for a reactive system under test. We formulate the problem as a repeated game
between the tester and the system, where the system state space is partitioned
according to some coverage criterion and the objective of the tester is to maximize
the set of partitions (or coverage goals) visited during the game. We show the
complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete,
but is NP-complete for deterministic systems. For the special case of non-deterministic
systems with a re-initializing "reset" action, which represent running
a new test input on a re-initialized system, we show that the complexity is coNP-complete.
Our proof technique for reset games uses randomized testing strategies that circumvent
the exponentially large memory requirement of deterministic testing strategies.
We also discuss the memory requirement for deterministic strategies and extensions
of our results to other models, such as pushdown systems and timed systems.
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: Alfaro, Luca
last_name: Alfaro
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: Chatterjee K, Alfaro L, Majumdar R. The complexity of coverage. International
Journal of Foundations of Computer Science. 2013;24(2):165-185. doi:10.1142/S0129054113400066
apa: Chatterjee, K., Alfaro, L., & Majumdar, R. (2013). The complexity of coverage.
International Journal of Foundations of Computer Science. World Scientific
Publishing. https://doi.org/10.1142/S0129054113400066
chicago: Chatterjee, Krishnendu, Luca Alfaro, and Ritankar Majumdar. “The Complexity
of Coverage.” International Journal of Foundations of Computer Science.
World Scientific Publishing, 2013. https://doi.org/10.1142/S0129054113400066.
ieee: K. Chatterjee, L. Alfaro, and R. Majumdar, “The complexity of coverage,” International
Journal of Foundations of Computer Science, vol. 24, no. 2. World Scientific
Publishing, pp. 165–185, 2013.
ista: Chatterjee K, Alfaro L, Majumdar R. 2013. The complexity of coverage. International
Journal of Foundations of Computer Science. 24(2), 165–185.
mla: Chatterjee, Krishnendu, et al. “The Complexity of Coverage.” International
Journal of Foundations of Computer Science, vol. 24, no. 2, World Scientific
Publishing, 2013, pp. 165–85, doi:10.1142/S0129054113400066.
short: K. Chatterjee, L. Alfaro, R. Majumdar, International Journal of Foundations
of Computer Science 24 (2013) 165–185.
date_created: 2018-12-11T11:59:44Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T06:59:54Z
day: '01'
department:
- _id: KrCh
doi: 10.1142/S0129054113400066
ec_funded: 1
external_id:
arxiv:
- '0804.4525'
intvolume: ' 24'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0804.4525
month: '02'
oa: 1
oa_version: Preprint
page: 165 - 185
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: International Journal of Foundations of Computer Science
publication_status: published
publisher: World Scientific Publishing
publist_id: '4070'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of coverage
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2013'
...
---
_id: '2815'
abstract:
- lang: eng
text: The fact that a sum of isotropic Gaussian kernels can have more modes than
kernels is surprising. Extra (ghost) modes do not exist in ℝ1 and are generally
not well studied in higher dimensions. We study a configuration of n+1 Gaussian
kernels for which there are exactly n+2 modes. We show that all modes lie on a
finite set of lines, which we call axes, and study the restriction of the Gaussian
mixture to these axes in order to discover that there are an exponential number
of critical points in this configuration. Although the existence of ghost modes
remained unknown due to the difficulty of finding examples in ℝ2, we show that
the resilience of ghost modes grows like the square root of the dimension. In
addition, we exhibit finite configurations of isotropic Gaussian kernels with
superlinearly many modes.
acknowledgement: This research is partially supported by the National Science Foundation
(NSF) under Grant DBI-0820624, by the European Science Foundation under the Research
Networking Programme, and the Russian Government Project 11.G34.31.0053.
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Brittany Terese
full_name: Fasy, Brittany Terese
id: F65D502E-E68D-11E9-9252-C644099818F6
last_name: Fasy
- first_name: Günter
full_name: Rote, Günter
last_name: Rote
citation:
ama: 'Edelsbrunner H, Fasy BT, Rote G. Add isotropic Gaussian kernels at own risk:
More and more resilient modes in higher dimensions. Discrete & Computational
Geometry. 2013;49(4):797-822. doi:10.1007/s00454-013-9517-x'
apa: 'Edelsbrunner, H., Fasy, B. T., & Rote, G. (2013). Add isotropic Gaussian
kernels at own risk: More and more resilient modes in higher dimensions. Discrete
& Computational Geometry. Springer. https://doi.org/10.1007/s00454-013-9517-x'
chicago: 'Edelsbrunner, Herbert, Brittany Terese Fasy, and Günter Rote. “Add Isotropic
Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.”
Discrete & Computational Geometry. Springer, 2013. https://doi.org/10.1007/s00454-013-9517-x.'
ieee: 'H. Edelsbrunner, B. T. Fasy, and G. Rote, “Add isotropic Gaussian kernels
at own risk: More and more resilient modes in higher dimensions,” Discrete
& Computational Geometry, vol. 49, no. 4. Springer, pp. 797–822, 2013.'
ista: 'Edelsbrunner H, Fasy BT, Rote G. 2013. Add isotropic Gaussian kernels at
own risk: More and more resilient modes in higher dimensions. Discrete & Computational
Geometry. 49(4), 797–822.'
mla: 'Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk:
More and More Resilient Modes in Higher Dimensions.” Discrete & Computational
Geometry, vol. 49, no. 4, Springer, 2013, pp. 797–822, doi:10.1007/s00454-013-9517-x.'
short: H. Edelsbrunner, B.T. Fasy, G. Rote, Discrete & Computational Geometry
49 (2013) 797–822.
date_created: 2018-12-11T11:59:44Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2023-02-23T11:13:49Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00454-013-9517-x
intvolume: ' 49'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00454-013-9517-x
month: '06'
oa: 1
oa_version: Published Version
page: 797 - 822
publication: Discrete & Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer
publist_id: '3991'
quality_controlled: '1'
related_material:
record:
- id: '3134'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Add isotropic Gaussian kernels at own risk: More and more resilient modes
in higher dimensions'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 49
year: '2013'
...
---
_id: '2816'
abstract:
- lang: eng
text: In solid tumors, targeted treatments can lead to dramatic regressions, but
responses are often short-lived because resistant cancer cells arise. The major
strategy proposed for overcoming resistance is combination therapy. We present
a mathematical model describing the evolutionary dynamics of lesions in response
to treatment. We first studied 20 melanoma patients receiving vemurafenib. We
then applied our model to an independent set of pancreatic, colorectal, and melanoma
cancer patients with metastatic disease. We find that dual therapy results in
long-term disease control for most patients, if there are no single mutations
that cause cross-resistance to both drugs; in patients with large disease burden,
triple therapy is needed. We also find that simultaneous therapy with two drugs
is much more effective than sequential therapy. Our results provide realistic
expectations for the efficacy of new drug combinations and inform the design of
trials for new cancer therapeutics.
article_number: e00747
author:
- first_name: Ivana
full_name: Božić, Ivana
last_name: Božić
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Benjamin
full_name: Allen, Benjamin
last_name: Allen
- first_name: Tibor
full_name: Antal, Tibor
last_name: Antal
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Preya
full_name: Shah, Preya
last_name: Shah
- first_name: Yo
full_name: Moon, Yo
last_name: Moon
- first_name: Amin
full_name: Yaqubie, Amin
last_name: Yaqubie
- first_name: Nicole
full_name: Kelly, Nicole
last_name: Kelly
- first_name: Dung
full_name: Le, Dung
last_name: Le
- first_name: Evan
full_name: Lipson, Evan
last_name: Lipson
- first_name: Paul
full_name: Chapman, Paul
last_name: Chapman
- first_name: Luis
full_name: Diaz, Luis
last_name: Diaz
- first_name: Bert
full_name: Vogelstein, Bert
last_name: Vogelstein
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Božić I, Reiter J, Allen B, et al. Evolutionary dynamics of cancer in response
to targeted combination therapy. eLife. 2013;2. doi:10.7554/eLife.00747
apa: Božić, I., Reiter, J., Allen, B., Antal, T., Chatterjee, K., Shah, P., … Nowak,
M. (2013). Evolutionary dynamics of cancer in response to targeted combination
therapy. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.00747
chicago: Božić, Ivana, Johannes Reiter, Benjamin Allen, Tibor Antal, Krishnendu
Chatterjee, Preya Shah, Yo Moon, et al. “Evolutionary Dynamics of Cancer in Response
to Targeted Combination Therapy.” ELife. eLife Sciences Publications, 2013.
https://doi.org/10.7554/eLife.00747.
ieee: I. Božić et al., “Evolutionary dynamics of cancer in response to targeted
combination therapy,” eLife, vol. 2. eLife Sciences Publications, 2013.
ista: Božić I, Reiter J, Allen B, Antal T, Chatterjee K, Shah P, Moon Y, Yaqubie
A, Kelly N, Le D, Lipson E, Chapman P, Diaz L, Vogelstein B, Nowak M. 2013. Evolutionary
dynamics of cancer in response to targeted combination therapy. eLife. 2, e00747.
mla: Božić, Ivana, et al. “Evolutionary Dynamics of Cancer in Response to Targeted
Combination Therapy.” ELife, vol. 2, e00747, eLife Sciences Publications,
2013, doi:10.7554/eLife.00747.
short: I. Božić, J. Reiter, B. Allen, T. Antal, K. Chatterjee, P. Shah, Y. Moon,
A. Yaqubie, N. Kelly, D. Le, E. Lipson, P. Chapman, L. Diaz, B. Vogelstein, M.
Nowak, ELife 2 (2013).
date_created: 2018-12-11T11:59:45Z
date_published: 2013-06-25T00:00:00Z
date_updated: 2023-09-07T11:40:43Z
day: '25'
ddc:
- '570'
- '610'
department:
- _id: KrCh
doi: 10.7554/eLife.00747
file:
- access_level: open_access
checksum: 2c38c47815eacd8fa66cb8b404cf7c61
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:48Z
date_updated: 2020-07-14T12:45:49Z
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file_name: IST-2013-134-v1+1_e00747.full.pdf
file_size: 3358321
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- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '3985'
pubrep_id: '134'
quality_controlled: '1'
related_material:
record:
- id: '1400'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Evolutionary dynamics of cancer in response to targeted combination therapy
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2013'
...
---
_id: '2817'
abstract:
- lang: eng
text: The basic idea of evolutionary game theory is that payoff determines reproductive
rate. Successful individuals have a higher payoff and produce more offspring.
But in evolutionary and ecological situations there is not only reproductive rate
but also carrying capacity. Individuals may differ in their exposure to density
limiting effects. Here we explore an alternative approach to evolutionary game
theory by assuming that the payoff from the game determines the carrying capacity
of individual phenotypes. Successful strategies are less affected by density limitation
(crowding) and reach higher equilibrium abundance. We demonstrate similarities
and differences between our framework and the standard replicator equation. Our
equation is defined on the positive orthant, instead of the simplex, but has the
same equilibrium points as the replicator equation. Linear stability analysis
produces the classical conditions for asymptotic stability of pure strategies,
but the stability properties of internal equilibria can differ in the two frameworks.
For example, in a two-strategy game with an internal equilibrium that is always
stable under the replicator equation, the corresponding equilibrium can be unstable
in the new framework resulting in a limit cycle.
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Novak S, Chatterjee K, Nowak M. Density games. Journal of Theoretical Biology.
2013;334:26-34. doi:10.1016/j.jtbi.2013.05.029
apa: Novak, S., Chatterjee, K., & Nowak, M. (2013). Density games. Journal
of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2013.05.029
chicago: Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.”
Journal of Theoretical Biology. Elsevier, 2013. https://doi.org/10.1016/j.jtbi.2013.05.029.
ieee: S. Novak, K. Chatterjee, and M. Nowak, “Density games,” Journal of Theoretical
Biology, vol. 334. Elsevier, pp. 26–34, 2013.
ista: Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical
Biology. 334, 26–34.
mla: Novak, Sebastian, et al. “Density Games.” Journal of Theoretical Biology,
vol. 334, Elsevier, 2013, pp. 26–34, doi:10.1016/j.jtbi.2013.05.029.
short: S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013)
26–34.
date_created: 2018-12-11T11:59:45Z
date_published: 2013-10-07T00:00:00Z
date_updated: 2025-05-28T11:42:43Z
day: '07'
ddc:
- '000'
department:
- _id: NiBa
- _id: KrCh
doi: 10.1016/j.jtbi.2013.05.029
ec_funded: 1
file:
- access_level: open_access
checksum: 3c29059ab03a4b8f97a07646b817ddbb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:54Z
date_updated: 2020-07-14T12:45:49Z
file_id: '5110'
file_name: IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf
file_size: 834604
relation: main_file
file_date_updated: 2020-07-14T12:45:49Z
has_accepted_license: '1'
intvolume: ' 334'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 26 - 34
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '3984'
pubrep_id: '400'
quality_controlled: '1'
scopus_import: 1
status: public
title: Density games
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 334
year: '2013'
...
---
_id: '2818'
abstract:
- lang: eng
text: Models of neural responses to stimuli with complex spatiotemporal correlation
structure often assume that neurons are selective for only a small number of linear
projections of a potentially high-dimensional input. In this review, we explore
recent modeling approaches where the neural response depends on the quadratic
form of the input rather than on its linear projection, that is, the neuron is
sensitive to the local covariance structure of the signal preceding the spike.
To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic)
stimulus distribution, we review several inference methods, focusing in particular
on two information theory–based approaches (maximization of stimulus energy and
of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered
covariance and extensions of generalized linear models). We analyze the formal
relationship between the likelihood-based and information-based approaches to
demonstrate how they lead to consistent inference. We demonstrate the practical
feasibility of these procedures by using model neurons responding to a flickering
variance stimulus.
arxiv: 1
author:
- first_name: Kanaka
full_name: Rajan, Kanaka
last_name: Rajan
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural
responses to natural stimuli. Neural Computation. 2013;25(7):1661-1692.
doi:10.1162/NECO_a_00463
apa: Rajan, K., Marre, O., & Tkačik, G. (2013). Learning quadratic receptive
fields from neural responses to natural stimuli. Neural Computation. MIT
Press . https://doi.org/10.1162/NECO_a_00463
chicago: Rajan, Kanaka, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive
Fields from Neural Responses to Natural Stimuli.” Neural Computation. MIT
Press , 2013. https://doi.org/10.1162/NECO_a_00463.
ieee: K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from
neural responses to natural stimuli,” Neural Computation, vol. 25, no.
7. MIT Press , pp. 1661–1692, 2013.
ista: Rajan K, Marre O, Tkačik G. 2013. Learning quadratic receptive fields from
neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692.
mla: Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses
to Natural Stimuli.” Neural Computation, vol. 25, no. 7, MIT Press , 2013,
pp. 1661–92, doi:10.1162/NECO_a_00463.
short: K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.
date_created: 2018-12-11T11:59:45Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T06:59:56Z
day: '01'
department:
- _id: GaTk
doi: 10.1162/NECO_a_00463
external_id:
arxiv:
- '1209.0121'
intvolume: ' 25'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1209.0121
month: '07'
oa: 1
oa_version: Preprint
page: 1661 - 1692
publication: Neural Computation
publication_status: published
publisher: 'MIT Press '
publist_id: '3983'
quality_controlled: '1'
scopus_import: 1
status: public
title: Learning quadratic receptive fields from neural responses to natural stimuli
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '2819'
abstract:
- lang: eng
text: 'We introduce quantatitive timed refinement metrics and quantitative timed
simulation functions, incorporating zenoness checks, for timed systems. These
functions assign positive real numbers between zero and infinity which quantify
the timing mismatches between two timed systems, amongst non-zeno runs. We quantify
timing mismatches in three ways: (1) the maximum timing mismatch that can arise,
(2) the "steady-state" maximum timing mismatches, where initial transient
timing mismatches are ignored; and (3) the (long-run) average timing mismatches
amongst two systems. These three kinds of mismatches constitute three important
types of timing differences. Our event times are the global times, measured from
the start of the system execution, not just the time durations of individual steps.
We present algorithms over timed automata for computing the three quantitative
simulation functions to within any desired degree of accuracy. In order to compute
the values of the quantitative simulation functions, we use a game theoretic formulation.
We introduce two new kinds of objectives for two player games on finite state
game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum
level objectives. We present algorithms for computing the optimal values for these
objectives for player 1, and then use these algorithms to compute the values of
the quantitative timed simulation functions. '
acknowledgement: 'This work has been financially supported in part by the European
Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract
# 270180 (NOP-TILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008
(Modeling and control of Networked vehicle systems in persistent autonomous operations);
by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic
Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start
grant (279307: Graph Games); and the Microsoft faculty fellows award'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vinayak
full_name: Prabhu, Vinayak
last_name: Prabhu
citation:
ama: 'Chatterjee K, Prabhu V. Quantitative timed simulation functions and refinement
metrics for real-time systems. In: Proceedings of the 16th International Conference
on Hybrid Systems: Computation and Control. Vol 1. Springer; 2013:273-282.
doi:10.1145/2461328.2461370'
apa: 'Chatterjee, K., & Prabhu, V. (2013). Quantitative timed simulation functions
and refinement metrics for real-time systems. In Proceedings of the 16th International
Conference on Hybrid Systems: Computation and Control (Vol. 1, pp. 273–282).
Philadelphia, PA USA: Springer. https://doi.org/10.1145/2461328.2461370'
chicago: 'Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation
Functions and Refinement Metrics for Real-Time Systems.” In Proceedings of
the 16th International Conference on Hybrid Systems: Computation and Control,
1:273–82. Springer, 2013. https://doi.org/10.1145/2461328.2461370.'
ieee: 'K. Chatterjee and V. Prabhu, “Quantitative timed simulation functions and
refinement metrics for real-time systems,” in Proceedings of the 16th International
Conference on Hybrid Systems: Computation and Control, Philadelphia, PA USA,
2013, vol. 1, pp. 273–282.'
ista: 'Chatterjee K, Prabhu V. 2013. Quantitative timed simulation functions and
refinement metrics for real-time systems. Proceedings of the 16th International
Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems -
Computation and Control vol. 1, 273–282.'
mla: 'Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation
Functions and Refinement Metrics for Real-Time Systems.” Proceedings of the
16th International Conference on Hybrid Systems: Computation and Control,
vol. 1, Springer, 2013, pp. 273–82, doi:10.1145/2461328.2461370.'
short: 'K. Chatterjee, V. Prabhu, in:, Proceedings of the 16th International Conference
on Hybrid Systems: Computation and Control, Springer, 2013, pp. 273–282.'
conference:
end_date: 2013-04-11
location: Philadelphia, PA USA
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2013-04-08
date_created: 2018-12-11T11:59:46Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2021-01-12T06:59:56Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2461328.2461370
ec_funded: 1
intvolume: ' 1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1212.6556
month: '04'
oa: 1
oa_version: Preprint
page: 273 - 282
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 'Proceedings of the 16th International Conference on Hybrid Systems:
Computation and Control'
publication_status: published
publisher: Springer
publist_id: '3982'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantitative timed simulation functions and refinement metrics for real-time
systems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2013'
...
---
_id: '2820'
abstract:
- lang: eng
text: 'In this paper, we introduce the powerful framework of graph games for the
analysis of real-time scheduling with firm deadlines. We introduce a novel instance
of a partial-observation game that is suitable for this purpose, and prove decidability
of all the involved decision problems. We derive a graph game that allows the
automated computation of the competitive ratio (along with an optimal witness
algorithm for the competitive ratio) and establish an NP-completeness proof for
the graph game problem. For a given on-line algorithm, we present polynomial time
solution for computing (i) the worst-case utility; (ii) the worst-case utility
ratio w.r.t. a clairvoyant off-line algorithm; and (iii) the competitive ratio.
A major strength of the proposed approach lies in its flexibility w.r.t. incorporating
additional constraints on the adversary and/or the algorithm, including limited
maximum or average load, finiteness of periods of overload, etc., which are easily
added by means of additional instances of standard objective functions for graph
games. '
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Alexander
full_name: Kößler, Alexander
last_name: Kößler
- first_name: Ulrich
full_name: Schmid, Ulrich
last_name: Schmid
citation:
ama: 'Chatterjee K, Kößler A, Schmid U. Automated analysis of real-time scheduling
using graph games. In: Proceedings of the 16th International Conference on
Hybrid Systems: Computation and Control. ACM; 2013:163-172. doi:10.1145/2461328.2461356'
apa: 'Chatterjee, K., Kößler, A., & Schmid, U. (2013). Automated analysis of
real-time scheduling using graph games. In Proceedings of the 16th International
conference on Hybrid systems: Computation and control (pp. 163–172). Philadelphia,
PA, United States: ACM. https://doi.org/10.1145/2461328.2461356'
chicago: 'Chatterjee, Krishnendu, Alexander Kößler, and Ulrich Schmid. “Automated
Analysis of Real-Time Scheduling Using Graph Games.” In Proceedings of the
16th International Conference on Hybrid Systems: Computation and Control,
163–72. ACM, 2013. https://doi.org/10.1145/2461328.2461356.'
ieee: 'K. Chatterjee, A. Kößler, and U. Schmid, “Automated analysis of real-time
scheduling using graph games,” in Proceedings of the 16th International conference
on Hybrid systems: Computation and control, Philadelphia, PA, United States,
2013, pp. 163–172.'
ista: 'Chatterjee K, Kößler A, Schmid U. 2013. Automated analysis of real-time scheduling
using graph games. Proceedings of the 16th International conference on Hybrid
systems: Computation and control. HSCC: Hybrid Systems - Computation and Control,
163–172.'
mla: 'Chatterjee, Krishnendu, et al. “Automated Analysis of Real-Time Scheduling
Using Graph Games.” Proceedings of the 16th International Conference on Hybrid
Systems: Computation and Control, ACM, 2013, pp. 163–72, doi:10.1145/2461328.2461356.'
short: 'K. Chatterjee, A. Kößler, U. Schmid, in:, Proceedings of the 16th International
Conference on Hybrid Systems: Computation and Control, ACM, 2013, pp. 163–172.'
conference:
end_date: 2013-04-11
location: Philadelphia, PA, United States
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2013-04-08
date_created: 2018-12-11T11:59:46Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2023-09-27T12:52:38Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2461328.2461356
ec_funded: 1
language:
- iso: eng
month: '04'
oa_version: None
page: 163 - 172
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 'Proceedings of the 16th International conference on Hybrid systems:
Computation and control'
publication_identifier:
isbn:
- '978-1-4503-1567-8 '
publication_status: published
publisher: ACM
publist_id: '3981'
quality_controlled: '1'
related_material:
record:
- id: '738'
relation: later_version
status: public
scopus_import: 1
status: public
title: Automated analysis of real-time scheduling using graph games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2821'
abstract:
- lang: eng
text: Many key aspects of plant development are regulated by the polarized transport
of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this
process, has been shown to rely on the coordinated action of PIN-formed (PIN)
and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin
transport in the Arabidopsis thaliana root also requires the action of a Major
Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1).
Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate
that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3,
localize to the tonoplast of root cells and the plasma membrane of leaf stomatal
guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter
regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates
drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization
assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during
shootward auxin transport at the root tip, likely by regulating plasma membrane
PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1
and ZIFL1.3 share H+-coupled K+ transport activity. Thus, by determining the subcellular
and tissue distribution of two isoforms, alternative splicing dictates a dual
function for the ZIFL1 transporter. We propose that this MFS carrier regulates
stomatal movements and polar auxin transport by modulating potassium and proton
fluxes in Arabidopsis cells.
author:
- first_name: Estelle
full_name: Remy, Estelle
last_name: Remy
- first_name: Tânia
full_name: Cabrito, Tânia
last_name: Cabrito
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Rita
full_name: Batista, Rita
last_name: Batista
- first_name: Miguel
full_name: Teixeira, Miguel
last_name: Teixeira
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Isabel
full_name: Sá Correia, Isabel
last_name: Sá Correia
- first_name: Paula
full_name: Duque, Paula
last_name: Duque
citation:
ama: Remy E, Cabrito T, Baster P, et al. A major facilitator superfamily transporter
plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis.
Plant Cell. 2013;25(3):901-926. doi:10.1105/tpc.113.110353
apa: Remy, E., Cabrito, T., Baster, P., Batista, R., Teixeira, M., Friml, J., …
Duque, P. (2013). A major facilitator superfamily transporter plays a dual role
in polar auxin transport and drought stress tolerance in Arabidopsis. Plant
Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.110353
chicago: Remy, Estelle, Tânia Cabrito, Pawel Baster, Rita Batista, Miguel Teixeira,
Jiří Friml, Isabel Sá Correia, and Paula Duque. “A Major Facilitator Superfamily
Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance
in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013.
https://doi.org/10.1105/tpc.113.110353.
ieee: E. Remy et al., “A major facilitator superfamily transporter plays
a dual role in polar auxin transport and drought stress tolerance in Arabidopsis,”
Plant Cell, vol. 25, no. 3. American Society of Plant Biologists, pp. 901–926,
2013.
ista: Remy E, Cabrito T, Baster P, Batista R, Teixeira M, Friml J, Sá Correia I,
Duque P. 2013. A major facilitator superfamily transporter plays a dual role in
polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell.
25(3), 901–926.
mla: Remy, Estelle, et al. “A Major Facilitator Superfamily Transporter Plays a
Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.”
Plant Cell, vol. 25, no. 3, American Society of Plant Biologists, 2013,
pp. 901–26, doi:10.1105/tpc.113.110353.
short: E. Remy, T. Cabrito, P. Baster, R. Batista, M. Teixeira, J. Friml, I. Sá
Correia, P. Duque, Plant Cell 25 (2013) 901–926.
date_created: 2018-12-11T11:59:46Z
date_published: 2013-04-24T00:00:00Z
date_updated: 2021-01-12T06:59:57Z
day: '24'
department:
- _id: JiFr
doi: 10.1105/tpc.113.110353
external_id:
pmid:
- '23524662'
intvolume: ' 25'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634696/
month: '04'
oa: 1
oa_version: Submitted Version
page: 901 - 926
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3980'
quality_controlled: '1'
scopus_import: 1
status: public
title: A major facilitator superfamily transporter plays a dual role in polar auxin
transport and drought stress tolerance in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '2822'
abstract:
- lang: eng
text: Identification of genes that control root system architecture in crop plants
requires innovations that enable high-throughput and accurate measurements of
root system architecture through time. We demonstrate the ability of a semiautomated
3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative
genetic basis of root system growth in a rice biparental mapping population, Bala
x Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for
a suite of 25 traits that quantified the distribution, shape, extent of exploration,
and the intrinsic size of root networks at days 12, 14, and 16 of growth in a
gellan gum medium. From these data we identified 89 quantitative trait loci, some
of which correspond to those found previously in soil-grown plants, and provide
evidence for genetic tradeoffs in root growth allocations, such as between the
extent and thoroughness of exploration. We also developed a multivariate method
for generating and mapping central root architecture phenotypes and used it to
identify five major quantitative trait loci (r2 = 24-37%), two of which were not
identified by our univariate analysis. Our imaging and analytical platform provides
a means to identify genes with high potential for improving root traits and agronomic
qualities of crops.
author:
- first_name: Christopher
full_name: Topp, Christopher
last_name: Topp
- first_name: Anjali
full_name: Iyer Pascuzzi, Anjali
last_name: Iyer Pascuzzi
- first_name: Jill
full_name: Anderson, Jill
last_name: Anderson
- first_name: Cheng
full_name: Lee, Cheng
last_name: Lee
- first_name: Paul
full_name: Zurek, Paul
last_name: Zurek
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
- first_name: Ying
full_name: Zheng, Ying
last_name: Zheng
- first_name: Alexander
full_name: Bucksch, Alexander
last_name: Bucksch
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
- first_name: Taras
full_name: Galkovskyi, Taras
last_name: Galkovskyi
- first_name: Brad
full_name: Moore, Brad
last_name: Moore
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Thomas
full_name: Mitchell Olds, Thomas
last_name: Mitchell Olds
- first_name: Joshua
full_name: Weitz, Joshua
last_name: Weitz
- first_name: Philip
full_name: Benfey, Philip
last_name: Benfey
citation:
ama: Topp C, Iyer Pascuzzi A, Anderson J, et al. 3D phenotyping and quantitative
trait locus mapping identify core regions of the rice genome controlling root
architecture. PNAS. 2013;110(18):E1695-E1704. doi:10.1073/pnas.1304354110
apa: Topp, C., Iyer Pascuzzi, A., Anderson, J., Lee, C., Zurek, P., Symonova, O.,
… Benfey, P. (2013). 3D phenotyping and quantitative trait locus mapping identify
core regions of the rice genome controlling root architecture. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1304354110
chicago: Topp, Christopher, Anjali Iyer Pascuzzi, Jill Anderson, Cheng Lee, Paul
Zurek, Olga Symonova, Ying Zheng, et al. “3D Phenotyping and Quantitative Trait
Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.”
PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1304354110.
ieee: C. Topp et al., “3D phenotyping and quantitative trait locus mapping
identify core regions of the rice genome controlling root architecture,” PNAS,
vol. 110, no. 18. National Academy of Sciences, pp. E1695–E1704, 2013.
ista: Topp C, Iyer Pascuzzi A, Anderson J, Lee C, Zurek P, Symonova O, Zheng Y,
Bucksch A, Mileyko Y, Galkovskyi T, Moore B, Harer J, Edelsbrunner H, Mitchell
Olds T, Weitz J, Benfey P. 2013. 3D phenotyping and quantitative trait locus mapping
identify core regions of the rice genome controlling root architecture. PNAS.
110(18), E1695–E1704.
mla: Topp, Christopher, et al. “3D Phenotyping and Quantitative Trait Locus Mapping
Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS,
vol. 110, no. 18, National Academy of Sciences, 2013, pp. E1695–704, doi:10.1073/pnas.1304354110.
short: C. Topp, A. Iyer Pascuzzi, J. Anderson, C. Lee, P. Zurek, O. Symonova, Y.
Zheng, A. Bucksch, Y. Mileyko, T. Galkovskyi, B. Moore, J. Harer, H. Edelsbrunner,
T. Mitchell Olds, J. Weitz, P. Benfey, PNAS 110 (2013) E1695–E1704.
date_created: 2018-12-11T11:59:47Z
date_published: 2013-04-30T00:00:00Z
date_updated: 2021-01-12T06:59:58Z
day: '30'
department:
- _id: MaJö
- _id: HeEd
doi: 10.1073/pnas.1304354110
external_id:
pmid:
- '25673779'
intvolume: ' 110'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378147/
month: '04'
oa: 1
oa_version: Submitted Version
page: E1695 - E1704
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3979'
quality_controlled: '1'
scopus_import: 1
status: public
title: 3D phenotyping and quantitative trait locus mapping identify core regions of
the rice genome controlling root architecture
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2823'
abstract:
- lang: eng
text: The primary goal of restoration is to create self-sustaining ecological communities
that are resilient to periodic disturbance. Currently, little is known about how
restored communities respond to disturbance events such as fire and how this response
compares to remnant vegetation. Following the 2003 fires in south-eastern Australia
we examined the post-fire response of revegetation plantings and compared this
to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed
for each of three types of vegetation (direct seeding revegetation, revegetation
using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites
were surveyed 6months after fire to quantify the initial survival of mid- and
overstorey plant species in each type of vegetation. Three and 5years after fire
all sites were resurveyed to assess vegetation structure, species diversity and
vigour, as well as indicators of soil function. Overall, revegetation showed high
(>60%) post-fire survival, but this varied among species depending on regeneration
strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey
in both types of plantings showed rapid recovery of vegetation structure and cover
within 3years of fire. This recovery was similar to the burnt remnant woodlands.
Non-native (exotic) ground cover initially increased after fire, but was no different
in burnt and unburnt sites 5years after fire. Fire had no effect on species richness,
but burnt direct seeding sites had reduced species diversity (Simpson's Diversity
Index) while diversity was higher in burnt remnant woodlands. Indices of soil
function in all types of vegetation had recovered to levels found in unburnt sites
5years after fire. These results indicate that even young revegetation (stands
<10years old) showed substantial recovery from disturbance by fire. This suggests
that revegetation can provide an important basis for restoring woodland communities
in the fire-prone Australian environment.
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Susie
full_name: Wilson, Susie
last_name: Wilson
- first_name: David
full_name: Freudenberger, David
last_name: Freudenberger
- first_name: Nick
full_name: Nicholls, Nick
last_name: Nicholls
- first_name: Lori
full_name: Gould, Lori
last_name: Gould
- first_name: Sarah
full_name: Hnatiuk, Sarah
last_name: Hnatiuk
- first_name: Jeni
full_name: Delandre, Jeni
last_name: Delandre
citation:
ama: Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated
woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312.
doi:10.1111/j.1442-9993.2012.02404.x
apa: Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk,
S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities
in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x
chicago: Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori
Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland
Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell,
2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x.
ieee: M. Pickup et al., “Post-fire recovery of revegetated woodland communities
in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell,
pp. 300–312, 2013.
ista: Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre
J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern
Australia. Austral Ecology. 38(3), 300–312.
mla: Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities
in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell,
2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x.
short: M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk,
J. Delandre, Austral Ecology 38 (2013) 300–312.
date_created: 2018-12-11T11:59:47Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2021-01-12T06:59:58Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1442-9993.2012.02404.x
intvolume: ' 38'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
page: 300 - 312
publication: Austral Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3978'
quality_controlled: '1'
scopus_import: 1
status: public
title: Post-fire recovery of revegetated woodland communities in south-eastern Australia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2013'
...
---
_id: '2824'
abstract:
- lang: eng
text: We study synthesis of controllers for real-time systems, where the objective
is to stay in a given safe set. The problem is solved by obtaining winning strategies
in the setting of concurrent two player timed automaton games with safety objectives.
To prevent a player from winning by blocking time, we restrict each player to
strategies that ensure that the player cannot be responsible for causing a Zeno
run. We construct winning strategies for the controller which require access only
to (1) the system clocks (thus, controllers which require their own internal infinitely
precise clocks are not necessary), and (2) a logarithmic (in the number of clocks)
number of memory bits (i.e. a linear number of memory states). Precisely, we show
that for safety objectives, a memory of size (3 + lg (| C | + 1)) bits suffices
for winning controller strategies, where C is the set of clocks of the timed automaton
game, significantly improving the previous known exponential memory states bound.
We also settle the open question of whether winning region-based strategies require
memory for safety objectives by showing with an example the necessity of memory
for such strategies to win for safety objectives. Finally, we show that the decision
problem of determining if there exists a receptive player-1 winning strategy for
safety objectives is EXPTIME-complete over timed automaton games.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vinayak
full_name: Prabhu, Vinayak
last_name: Prabhu
citation:
ama: Chatterjee K, Prabhu V. Synthesis of memory-efficient, clock-memory free, and
non-Zeno safety controllers for timed systems. Information and Computation.
2013;228-229:83-119. doi:10.1016/j.ic.2013.04.003
apa: Chatterjee, K., & Prabhu, V. (2013). Synthesis of memory-efficient, clock-memory
free, and non-Zeno safety controllers for timed systems. Information and Computation.
Elsevier. https://doi.org/10.1016/j.ic.2013.04.003
chicago: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient,
Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information
and Computation. Elsevier, 2013. https://doi.org/10.1016/j.ic.2013.04.003.
ieee: K. Chatterjee and V. Prabhu, “Synthesis of memory-efficient, clock-memory
free, and non-Zeno safety controllers for timed systems,” Information and Computation,
vol. 228–229. Elsevier, pp. 83–119, 2013.
ista: Chatterjee K, Prabhu V. 2013. Synthesis of memory-efficient, clock-memory
free, and non-Zeno safety controllers for timed systems. Information and Computation.
228–229, 83–119.
mla: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient,
Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information
and Computation, vol. 228–229, Elsevier, 2013, pp. 83–119, doi:10.1016/j.ic.2013.04.003.
short: K. Chatterjee, V. Prabhu, Information and Computation 228–229 (2013) 83–119.
date_created: 2018-12-11T11:59:47Z
date_published: 2013-04-24T00:00:00Z
date_updated: 2021-01-12T06:59:58Z
day: '24'
department:
- _id: KrCh
doi: 10.1016/j.ic.2013.04.003
ec_funded: 1
language:
- iso: eng
month: '04'
oa_version: None
page: 83-119
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '3977'
quality_controlled: '1'
scopus_import: 1
status: public
title: Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers
for timed systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 228-229
year: '2013'
...