---
_id: '3122'
abstract:
- lang: eng
text: 'Since Darwin''s pioneering research on plant reproductive biology (e.g. Darwin
1877), understanding the mechanisms maintaining the diverse sexual strategies
of plants has remained an important challenge for evolutionary biologists. In
some species, populations are sexually polymorphic and contain two or more mating
morphs (sex phenotypes). Differences in morphology or phenology among the morphs
influence patterns of non-random mating. In these populations, negative frequency-dependent
selection arising from disassortative (intermorph) mating is usually required
for the evolutionary maintenance of sexual polymorphism, but few studies have
demonstrated the required patterns of non-random mating. In the current issue
of Molecular Ecology, Shang (2012) make an important contribution to our understanding
of how disassortative mating influences sex phenotype ratios in Acer pictum subsp.
mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They
monitored sex expression in 97 adults and used paternity analysis of open-pollinated
seed to examine disassortative mating among three sex phenotypes. Using a deterministic
''pollen transfer'' model, Shang et al. present convincing evidence that differences
in the degree of disassortative mating in progeny arrays of the sex phenotypes
can explain their uneven frequencies in the adult population. This study provides
a useful example of how the deployment of genetic markers, demographic monitoring
and modelling can be integrated to investigate the maintenance of sexual diversity
in plants. '
author:
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Spencer
full_name: Barrett, Spencer
last_name: Barrett
citation:
ama: Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism
in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x
apa: Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance
of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell.
https://doi.org/10.1111/j.1365-294X.2012.05643.x
chicago: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance
of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell,
2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x.
ieee: D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual
polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell,
pp. 3640–3643, 2012.
ista: Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual
polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.
mla: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance
of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no.
15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x.
short: D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643.
date_created: 2018-12-11T12:01:31Z
date_published: 2012-08-01T00:00:00Z
date_updated: 2021-01-12T07:41:13Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2012.05643.x
intvolume: ' 21'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3640 - 3643
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3577'
quality_controlled: '1'
scopus_import: 1
status: public
title: Disassortative mating and the maintenance of sexual polymorphism in painted
maple
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2012'
...
---
_id: '3121'
abstract:
- lang: eng
text: Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger
action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+)
regulates spontaneous transmission is unclear. We found that VACCs are the major
physiological triggers for spontaneous release at mouse neocortical inhibitory
synapses. Moreover, despite the absence of a synchronizing action potential, we
found that spontaneous fusion of a GABA-containing vesicle required the activation
of multiple tightly coupled VACCs of variable type.
acknowledgement: "The work was supported by the US National Institutes of Health (DA027110
and GM097433) and OCTRI. C.W. and N.P.V. were supported by a grant from the National
Heart, Lung, and Blood Institute (T32HL033808).\r\nWe thank M. Andresen and K. Khodakhah
for helpful comments. "
author:
- first_name: Courtney
full_name: Williams, Courtney
last_name: Williams
- first_name: Wenyan
full_name: Chen, Wenyan
last_name: Chen
- first_name: Chia
full_name: Lee, Chia
last_name: Lee
- first_name: Daniel
full_name: Yaeger, Daniel
last_name: Yaeger
- first_name: Nicholas
full_name: Vyleta, Nicholas
id: 36C4978E-F248-11E8-B48F-1D18A9856A87
last_name: Vyleta
- first_name: Stephen
full_name: Smith, Stephen
last_name: Smith
citation:
ama: Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. Coactivation of multiple
tightly coupled calcium channels triggers spontaneous release of GABA. Nature
Neuroscience. 2012;15(9):1195-1197. doi:10.1038/nn.3162
apa: Williams, C., Chen, W., Lee, C., Yaeger, D., Vyleta, N., & Smith, S. (2012).
Coactivation of multiple tightly coupled calcium channels triggers spontaneous
release of GABA. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3162
chicago: Williams, Courtney, Wenyan Chen, Chia Lee, Daniel Yaeger, Nicholas Vyleta,
and Stephen Smith. “Coactivation of Multiple Tightly Coupled Calcium Channels
Triggers Spontaneous Release of GABA.” Nature Neuroscience. Nature Publishing
Group, 2012. https://doi.org/10.1038/nn.3162.
ieee: C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, and S. Smith, “Coactivation
of multiple tightly coupled calcium channels triggers spontaneous release of GABA,”
Nature Neuroscience, vol. 15, no. 9. Nature Publishing Group, pp. 1195–1197,
2012.
ista: Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. 2012. Coactivation
of multiple tightly coupled calcium channels triggers spontaneous release of GABA.
Nature Neuroscience. 15(9), 1195–1197.
mla: Williams, Courtney, et al. “Coactivation of Multiple Tightly Coupled Calcium
Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience, vol.
15, no. 9, Nature Publishing Group, 2012, pp. 1195–97, doi:10.1038/nn.3162.
short: C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, S. Smith, Nature Neuroscience
15 (2012) 1195–1197.
date_created: 2018-12-11T12:01:30Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:12Z
day: '01'
department:
- _id: PeJo
doi: 10.1038/nn.3162
external_id:
pmid:
- '22842148'
intvolume: ' 15'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431448/
month: '09'
oa: 1
oa_version: Submitted Version
page: 1195 - 1197
pmid: 1
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '3578'
quality_controlled: '1'
scopus_import: 1
status: public
title: Coactivation of multiple tightly coupled calcium channels triggers spontaneous
release of GABA
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2012'
...
---
_id: '3120'
abstract:
- lang: eng
text: We introduce a strategy based on Kustin-Miller unprojection that allows us
to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions
(that is, nine equations and sixteen first syzygies). Our two basic games are
called Tom and Jerry; the main application is the biregular construction of most
of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There
are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type
I projection. In every case, at least one Tom and one Jerry construction works,
providing at least two deformation families of quasismooth Fano 3-folds having
the same numerics but different topology. © 2012 Copyright Foundation Compositio
Mathematica.
acknowledgement: This research is supported by the Korean Government WCU Grant R33-2008-000-10101-0.
author:
- first_name: Gavin
full_name: Brown, Gavin
last_name: Brown
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Miles
full_name: Reid, Miles
last_name: Reid
citation:
ama: Brown G, Kerber M, Reid M. Fano 3 folds in codimension 4 Tom and Jerry Part
I. Compositio Mathematica. 2012;148(4):1171-1194. doi:10.1112/S0010437X11007226
apa: Brown, G., Kerber, M., & Reid, M. (2012). Fano 3 folds in codimension 4
Tom and Jerry Part I. Compositio Mathematica. Cambridge University Press.
https://doi.org/10.1112/S0010437X11007226
chicago: Brown, Gavin, Michael Kerber, and Miles Reid. “Fano 3 Folds in Codimension
4 Tom and Jerry Part I.” Compositio Mathematica. Cambridge University Press,
2012. https://doi.org/10.1112/S0010437X11007226.
ieee: G. Brown, M. Kerber, and M. Reid, “Fano 3 folds in codimension 4 Tom and Jerry
Part I,” Compositio Mathematica, vol. 148, no. 4. Cambridge University
Press, pp. 1171–1194, 2012.
ista: Brown G, Kerber M, Reid M. 2012. Fano 3 folds in codimension 4 Tom and Jerry
Part I. Compositio Mathematica. 148(4), 1171–1194.
mla: Brown, Gavin, et al. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.”
Compositio Mathematica, vol. 148, no. 4, Cambridge University Press, 2012,
pp. 1171–94, doi:10.1112/S0010437X11007226.
short: G. Brown, M. Kerber, M. Reid, Compositio Mathematica 148 (2012) 1171–1194.
date_created: 2018-12-11T12:01:30Z
date_published: 2012-07-01T00:00:00Z
date_updated: 2021-01-12T07:41:12Z
day: '01'
department:
- _id: HeEd
doi: 10.1112/S0010437X11007226
intvolume: ' 148'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1009.4313
month: '07'
oa: 1
oa_version: Preprint
page: 1171 - 1194
publication: Compositio Mathematica
publication_status: published
publisher: Cambridge University Press
publist_id: '3579'
quality_controlled: '1'
scopus_import: 1
status: public
title: Fano 3 folds in codimension 4 Tom and Jerry Part I
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 148
year: '2012'
...
---
_id: '3117'
abstract:
- lang: eng
text: We consider the problem of minimizing a function represented as a sum of submodular
terms. We assume each term allows an efficient computation of exchange capacities.
This holds, for example, for terms depending on a small number of variables, or
for certain cardinality-dependent terms. A naive application of submodular minimization
algorithms would not exploit the existence of specialized exchange capacity subroutines
for individual terms. To overcome this, we cast the problem as a submodular flow
(SF) problem in an auxiliary graph in such a way that applying most existing SF
algorithms would rely only on these subroutines. We then explore in more detail
Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular,
we show how to improve its complexity in the case when the function contains cardinality-dependent
terms.
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Kolmogorov V. Minimizing a sum of submodular functions. Discrete Applied
Mathematics. 2012;160(15):2246-2258. doi:10.1016/j.dam.2012.05.025
apa: Kolmogorov, V. (2012). Minimizing a sum of submodular functions. Discrete
Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2012.05.025
chicago: Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete
Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2012.05.025.
ieee: V. Kolmogorov, “Minimizing a sum of submodular functions,” Discrete Applied
Mathematics, vol. 160, no. 15. Elsevier, pp. 2246–2258, 2012.
ista: Kolmogorov V. 2012. Minimizing a sum of submodular functions. Discrete Applied
Mathematics. 160(15), 2246–2258.
mla: Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete
Applied Mathematics, vol. 160, no. 15, Elsevier, 2012, pp. 2246–58, doi:10.1016/j.dam.2012.05.025.
short: V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 2246–2258.
date_created: 2018-12-11T12:01:29Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2021-01-12T07:41:11Z
day: '01'
department:
- _id: VlKo
doi: 10.1016/j.dam.2012.05.025
intvolume: ' 160'
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1006.1990
month: '10'
oa: 1
oa_version: Preprint
page: 2246 - 2258
publication: Discrete Applied Mathematics
publication_status: published
publisher: Elsevier
publist_id: '3582'
quality_controlled: '1'
scopus_import: 1
status: public
title: Minimizing a sum of submodular functions
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 160
year: '2012'
...
---
_id: '3131'
abstract:
- lang: eng
text: 'In large populations, many beneficial mutations may be simultaneously available
and may compete with one another, slowing adaptation. By finding the probability
of fixation of a favorable allele in a simple model of a haploid sexual population,
we find limits to the rate of adaptive substitution, Λ, that depend on simple
parameter combinations. When variance in fitness is low and linkage is loose,
the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the
rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage.
Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under
polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans,
interference is yet stronger. We use a scaling argument to show that the density
of adaptive substitutions depends on s, N, U, and R only through the baseline
density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different
sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference
prevents the rate of adaptive substitution from exceeding one per centimorgan
per 200 generations. Simulations and numerical calculations confirm the scaling
argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R,
the rate of adaptation grows above R/2, but only very slowly. We also consider
the effect of sweeps on neutral diversity and show that, while even occasional
sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become
more common-diversity can be maintained even in populations experiencing very
strong interference. Our results indicate that for some organisms the rate of
adaptive substitution may be primarily recombination-limited, depending only weakly
on the mutation supply and the strength of selection.'
acknowledgement: "The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth,
O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers
for their helpful suggestions."
article_number: e1002740
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- 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: Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual
populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740
apa: Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution
in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740
chicago: Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive
Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science,
2012. https://doi.org/10.1371/journal.pgen.1002740.
ieee: D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution
in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of
Science, 2012.
ista: Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in
sexual populations. PLoS Genetics. 8(6), e1002740.
mla: Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution
in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public
Library of Science, 2012, doi:10.1371/journal.pgen.1002740.
short: D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).
date_created: 2018-12-11T12:01:34Z
date_published: 2012-06-07T00:00:00Z
date_updated: 2021-01-12T07:41:17Z
day: '07'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pgen.1002740
ec_funded: 1
file:
- access_level: open_access
checksum: 729a4becda7d786c4c3db8f9a1f77953
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:00Z
date_updated: 2020-07-14T12:46:01Z
file_id: '4659'
file_name: IST-2013-114-v1+1_WeissmanBarton2012.pdf
file_size: 1284801
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '3566'
pubrep_id: '114'
quality_controlled: '1'
scopus_import: 1
status: public
title: Limits to the rate of adaptive substitution in sexual populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2012'
...
---
_id: '3130'
abstract:
- lang: eng
text: 'Essential genes code for fundamental cellular functions required for the
viability of an organism. For this reason, essential genes are often highly conserved
across organisms. However, this is not always the case: orthologues of genes that
are essential in one organism are sometimes not essential in other organisms or
are absent from their genomes. This suggests that, in the course of evolution,
essential genes can be rendered nonessential. How can a gene become non-essential?
Here we used genetic manipulation to deplete the products of 26 different essential
genes in Escherichia coli. This depletion results in a lethal phenotype, which
could often be rescued by the overexpression of a non-homologous, non-essential
gene, most likely through replacement of the essential function. We also show
that, in a smaller number of cases, the essential genes can be fully deleted from
the genome, suggesting that complete functional replacement is possible. Finally,
we show that essential genes whose function can be replaced in the laboratory
are more likely to be non-essential or not present in other taxa. These results
are consistent with the notion that patterns of evolutionary conservation of essential
genes are influenced by their compensability-that is, by how easily they can be
functionally replaced, for example through increased expression of other genes.'
acknowledgement: We thank Alex Boehm for discussions and comments.
article_number: e1002803
author:
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
- first_name: Olin
full_name: Silander, Olin
last_name: Silander
citation:
ama: Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation
of essential genes correlate with their compensability. PLoS Genetics.
2012;8(6). doi:10.1371/journal.pgen.1002803
apa: Bergmiller, T., Ackermann, M., & Silander, O. (2012). Patterns of evolutionary
conservation of essential genes correlate with their compensability. PLoS Genetics.
Public Library of Science. https://doi.org/10.1371/journal.pgen.1002803
chicago: Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary
Conservation of Essential Genes Correlate with Their Compensability.” PLoS
Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002803.
ieee: T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation
of essential genes correlate with their compensability,” PLoS Genetics,
vol. 8, no. 6. Public Library of Science, 2012.
ista: Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation
of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803.
mla: Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential
Genes Correlate with Their Compensability.” PLoS Genetics, vol. 8, no.
6, e1002803, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002803.
short: T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).
date_created: 2018-12-11T12:01:34Z
date_published: 2012-06-28T00:00:00Z
date_updated: 2021-01-12T07:41:16Z
day: '28'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1002803
file:
- access_level: open_access
checksum: f8506fb579eda6fc5613ba9bf421b86a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:52Z
date_updated: 2020-07-14T12:46:01Z
file_id: '4973'
file_name: IST-2015-386-v1+1_journal.pgen.1002803.pdf
file_size: 2674138
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 8'
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: '3567'
pubrep_id: '386'
quality_controlled: '1'
scopus_import: 1
status: public
title: Patterns of evolutionary conservation of essential genes correlate with their
compensability
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2012'
...
---
_id: '3136'
abstract:
- lang: eng
text: 'Continuous-time Markov chains (CTMC) with their rich theory and efficient
simulation algorithms have been successfully used in modeling stochastic processes
in diverse areas such as computer science, physics, and biology. However, systems
that comprise non-instantaneous events cannot be accurately and efficiently modeled
with CTMCs. In this paper we define delayed CTMCs, an extension of CTMCs that
allows for the specification of a lower bound on the time interval between an
event''s initiation and its completion, and we propose an algorithm for the computation
of their behavior. Our algorithm effectively decomposes the computation into two
stages: a pure CTMC governs event initiations while a deterministic process guarantees
lower bounds on event completion times. Furthermore, from the nature of delayed
CTMCs, we obtain a parallelized version of our algorithm. We use our formalism
to model genetic regulatory circuits (biological systems where delayed events
are common) and report on the results of our numerical algorithm as run on a cluster.
We compare performance and accuracy of our results with results obtained by using
pure CTMCs. © 2012 Springer-Verlag.'
acknowledgement: This work was supported by the ERC Advanced Investigator grant on
Quantitative Reactive Modeling (QUAREM) and by the Swiss National Science Foundation.
alternative_title:
- LNCS
author:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
id: 3B43276C-F248-11E8-B48F-1D18A9856A87
last_name: Mateescu
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: 'Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. Delayed continuous time
Markov chains for genetic regulatory circuits. In: Vol 7358. Springer; 2012:294-309.
doi:10.1007/978-3-642-31424-7_24'
apa: 'Guet, C. C., Gupta, A., Henzinger, T. A., Mateescu, M., & Sezgin, A. (2012).
Delayed continuous time Markov chains for genetic regulatory circuits (Vol. 7358,
pp. 294–309). Presented at the CAV: Computer Aided Verification, Berkeley, CA,
USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_24'
chicago: Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and
Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,”
7358:294–309. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_24.
ieee: 'C. C. Guet, A. Gupta, T. A. Henzinger, M. Mateescu, and A. Sezgin, “Delayed
continuous time Markov chains for genetic regulatory circuits,” presented at the
CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 294–309.'
ista: 'Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. 2012. Delayed continuous
time Markov chains for genetic regulatory circuits. CAV: Computer Aided Verification,
LNCS, vol. 7358, 294–309.'
mla: Guet, Calin C., et al. Delayed Continuous Time Markov Chains for Genetic
Regulatory Circuits. Vol. 7358, Springer, 2012, pp. 294–309, doi:10.1007/978-3-642-31424-7_24.
short: C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer,
2012, pp. 294–309.
conference:
end_date: 2012-07-13
location: Berkeley, CA, USA
name: 'CAV: Computer Aided Verification'
start_date: 2012-07-07
date_created: 2018-12-11T12:01:36Z
date_published: 2012-07-01T00:00:00Z
date_updated: 2021-01-12T07:41:18Z
day: '01'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1007/978-3-642-31424-7_24
ec_funded: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 294 - 309
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '3561'
quality_controlled: '1'
scopus_import: 1
status: public
title: Delayed continuous time Markov chains for genetic regulatory circuits
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: '7358 '
year: '2012'
...
---
_id: '3135'
abstract:
- lang: eng
text: 'We introduce consumption games, a model for discrete interactive system with
multiple resources that are consumed or reloaded independently. More precisely,
a consumption game is a finite-state graph where each transition is labeled by
a vector of resource updates, where every update is a non-positive number or ω.
The ω updates model the reloading of a given resource. Each vertex belongs either
to player □ or player ◇, where the aim of player □ is to play so that the resources
are never exhausted. We consider several natural algorithmic problems about consumption
games, and show that although these problems are computationally hard in general,
they are solvable in polynomial time for every fixed number of resource types
(i.e., the dimension of the update vectors) and bounded resource updates. '
acknowledgement: 'Tomas Brazdil, Antonin Kucera, and Petr Novotny are supported by
the Czech Science Foundation, grant No. P202/10/1469. Krishnendu Chatterjee is supported
by the FWF (Austrian Science Fund) NFN Grant No S11407-N23 (RiSE) and ERC Start
grant (279307: Graph Games).'
alternative_title:
- LNCS
author:
- first_name: Brázdil
full_name: Brázdil, Brázdil
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
citation:
ama: 'Brázdil B, Chatterjee K, Kučera A, Novotný P. Efficient controller synthesis
for consumption games with multiple resource types. In: Vol 7358. Springer; 2012:23-38.
doi:10.1007/978-3-642-31424-7_8'
apa: 'Brázdil, B., Chatterjee, K., Kučera, A., & Novotný, P. (2012). Efficient
controller synthesis for consumption games with multiple resource types (Vol.
7358, pp. 23–38). Presented at the CAV: Computer Aided Verification, Berkeley,
CA, USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_8'
chicago: Brázdil, Brázdil, Krishnendu Chatterjee, Antonín Kučera, and Petr Novotný.
“Efficient Controller Synthesis for Consumption Games with Multiple Resource Types,”
7358:23–38. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_8.
ieee: 'B. Brázdil, K. Chatterjee, A. Kučera, and P. Novotný, “Efficient controller
synthesis for consumption games with multiple resource types,” presented at the
CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 23–38.'
ista: 'Brázdil B, Chatterjee K, Kučera A, Novotný P. 2012. Efficient controller
synthesis for consumption games with multiple resource types. CAV: Computer Aided
Verification, LNCS, vol. 7358, 23–38.'
mla: Brázdil, Brázdil, et al. Efficient Controller Synthesis for Consumption
Games with Multiple Resource Types. Vol. 7358, Springer, 2012, pp. 23–38,
doi:10.1007/978-3-642-31424-7_8.
short: B. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, in:, Springer, 2012, pp.
23–38.
conference:
end_date: 2012-07-13
location: Berkeley, CA, USA
name: 'CAV: Computer Aided Verification'
start_date: 2012-07-07
date_created: 2018-12-11T12:01:35Z
date_published: 2012-07-01T00:00:00Z
date_updated: 2021-01-12T07:41:18Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-31424-7_8
ec_funded: 1
intvolume: ' 7358'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1202.0796
month: '07'
oa: 1
oa_version: Preprint
page: 23 - 38
project:
- _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
publication_status: published
publisher: Springer
publist_id: '3562'
quality_controlled: '1'
scopus_import: 1
status: public
title: Efficient controller synthesis for consumption games with multiple resource
types
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7358
year: '2012'
...
---
_id: '3133'
abstract:
- lang: eng
text: 'This note contributes to the point calculus of persistent homology by extending
Alexander duality from spaces to real-valued functions. Given a perfect Morse
function f: S n+1 →[0, 1 and a decomposition S n+1 = U ∪ V into two (n + 1)-manifolds
with common boundary M, we prove elementary relationships between the persistence
diagrams of f restricted to U, to V, and to M. '
acknowledgement: "his research is partially supported by the National Science Foundation
(NSF) under grant DBI-0820624, the European Science Foundation under the Research
Networking Programme, and the Russian Government Project 11.G34.31.0053.\r\nThe
authors thank an anonymous referee for suggesting the simplified proof of the Contravariant
PE Theorem given in this paper. They also thank Frederick Cohen, Yuriy Mileyko and
Amit Patel for helpful discussions."
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
citation:
ama: 'Edelsbrunner H, Kerber M. Alexander duality for functions: The persistent
behavior of land and water and shore. In: Proceedings of the Twenty-Eighth
Annual Symposium on Computational Geometry . ACM; 2012:249-258. doi:10.1145/2261250.2261287'
apa: 'Edelsbrunner, H., & Kerber, M. (2012). Alexander duality for functions:
The persistent behavior of land and water and shore. In Proceedings of the
twenty-eighth annual symposium on Computational geometry (pp. 249–258). Chapel
Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261287'
chicago: 'Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions:
The Persistent Behavior of Land and Water and Shore.” In Proceedings of the
Twenty-Eighth Annual Symposium on Computational Geometry , 249–58. ACM, 2012.
https://doi.org/10.1145/2261250.2261287.'
ieee: 'H. Edelsbrunner and M. Kerber, “Alexander duality for functions: The persistent
behavior of land and water and shore,” in Proceedings of the twenty-eighth
annual symposium on Computational geometry , Chapel Hill, NC, USA, 2012, pp.
249–258.'
ista: 'Edelsbrunner H, Kerber M. 2012. Alexander duality for functions: The persistent
behavior of land and water and shore. Proceedings of the twenty-eighth annual
symposium on Computational geometry . SCG: Symposium on Computational Geometry,
249–258.'
mla: 'Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions:
The Persistent Behavior of Land and Water and Shore.” Proceedings of the Twenty-Eighth
Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–58, doi:10.1145/2261250.2261287.'
short: H. Edelsbrunner, M. Kerber, in:, Proceedings of the Twenty-Eighth Annual
Symposium on Computational Geometry , ACM, 2012, pp. 249–258.
conference:
end_date: 2012-06-20
location: Chapel Hill, NC, USA
name: 'SCG: Symposium on Computational Geometry'
start_date: 2012-06-17
date_created: 2018-12-11T12:01:35Z
date_published: 2012-06-20T00:00:00Z
date_updated: 2021-01-12T07:41:17Z
day: '20'
department:
- _id: HeEd
doi: 10.1145/2261250.2261287
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1109.5052
month: '06'
oa: 1
oa_version: Preprint
page: 249 - 258
publication: 'Proceedings of the twenty-eighth annual symposium on Computational geometry '
publication_status: published
publisher: ACM
publist_id: '3564'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Alexander duality for functions: The persistent behavior of land and water
and shore'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '3134'
abstract:
- lang: eng
text: 'It has been an open question whether the sum of finitely many isotropic Gaussian
kernels in n ≥ 2 dimensions can have more modes than kernels, until in 2003 Carreira-Perpiñán
and Williams exhibited n +1 isotropic Gaussian kernels in ℝ n with n + 2 modes.
We give a detailed analysis of this example, showing that it has exponentially
many critical points and that the resilience of the extra mode grows like √n.
In addition, we exhibit finite configurations of isotropic Gaussian kernels with
superlinearly many modes. '
acknowledgement: This research is partially supported by the National Science Foun-
dation (NSF) under grant DBI-0820624, by the European Science Foundation under the
Research Networking Programme, and the Russian Government Project 11.G34.31.0053.
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
full_name: Fasy, Brittany
last_name: Fasy
- first_name: Günter
full_name: Rote, Günter
last_name: Rote
citation:
ama: 'Edelsbrunner H, Fasy B, Rote G. Add isotropic Gaussian kernels at own risk:
More and more resilient modes in higher dimensions. In: Proceedings of the
Twenty-Eighth Annual Symposium on Computational Geometry . ACM; 2012:91-100.
doi:10.1145/2261250.2261265'
apa: 'Edelsbrunner, H., Fasy, B., & Rote, G. (2012). Add isotropic Gaussian
kernels at own risk: More and more resilient modes in higher dimensions. In Proceedings
of the twenty-eighth annual symposium on Computational geometry (pp. 91–100).
Chapel Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261265'
chicago: 'Edelsbrunner, Herbert, Brittany Fasy, and Günter Rote. “Add Isotropic
Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.”
In Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry
, 91–100. ACM, 2012. https://doi.org/10.1145/2261250.2261265.'
ieee: 'H. Edelsbrunner, B. Fasy, and G. Rote, “Add isotropic Gaussian kernels at
own risk: More and more resilient modes in higher dimensions,” in Proceedings
of the twenty-eighth annual symposium on Computational geometry , Chapel Hill,
NC, USA, 2012, pp. 91–100.'
ista: 'Edelsbrunner H, Fasy B, Rote G. 2012. Add isotropic Gaussian kernels at own
risk: More and more resilient modes in higher dimensions. Proceedings of the twenty-eighth
annual symposium on Computational geometry . SCG: Symposium on Computational Geometry,
91–100.'
mla: 'Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk:
More and More Resilient Modes in Higher Dimensions.” Proceedings of the Twenty-Eighth
Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100, doi:10.1145/2261250.2261265.'
short: H. Edelsbrunner, B. Fasy, G. Rote, in:, Proceedings of the Twenty-Eighth
Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100.
conference:
end_date: 2012-06-20
location: Chapel Hill, NC, USA
name: 'SCG: Symposium on Computational Geometry'
start_date: 2012-06-17
date_created: 2018-12-11T12:01:35Z
date_published: 2012-06-20T00:00:00Z
date_updated: 2023-02-23T10:59:27Z
day: '20'
department:
- _id: HeEd
doi: 10.1145/2261250.2261265
language:
- iso: eng
month: '06'
oa_version: None
page: 91 - 100
publication: 'Proceedings of the twenty-eighth annual symposium on Computational geometry '
publication_status: published
publisher: ACM
publist_id: '3563'
quality_controlled: '1'
related_material:
record:
- id: '2815'
relation: later_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: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '3132'
abstract:
- lang: eng
text: 'Reproductive division of labour is a characteristic trait of social insects.
The dominant reproductive individual, often the queen, uses chemical communication
and/or behaviour to maintain her social status. Queens of many social insects
communicate their fertility status via cuticle-bound substances. As these substances
usually possess a low volatility, their range in queen–worker communication is
potentially limited. Here, we investigate the range and impact of behavioural
and chemical queen signals on workers of the ant Temnothorax longispinosus. We
compared the behaviour and ovary development of workers subjected to three different
treatments: workers with direct chemical and physical contact to the queen, those
solely under the influence of volatile queen substances and those entirely separated
from the queen. In addition to short-ranged queen signals preventing ovary development
in workers, we discovered a novel secondary pathway influencing worker behaviour.
Workers with no physical contact to the queen, but exposed to volatile substances,
started to develop their ovaries, but did not change their behaviour compared
to workers in direct contact to the queen. In contrast, workers in queen-separated
groups showed both increased ovary development and aggressive dominance interactions.
We conclude that T. longispinosus queens influence worker ovary development and
behaviour via two independent signals, both ensuring social harmony within the
colony.'
acknowledgement: We like to thank the editor and three anonymous reviewers for their
time and constructive criticism and Inon Scharf, Volker Witte and Andreas Modlmeier
for helpful comments on earlier versions of the manuscript. The first and second
authors appear in alphabetical order and contributed equally to this paper.
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Tobias
full_name: Pamminger, Tobias
last_name: Pamminger
- first_name: Susanne
full_name: Foitzik, Susanne
last_name: Foitzik
citation:
ama: Konrad M, Pamminger T, Foitzik S. Two pathways ensuring social harmony. Naturwissenschaften.
2012;99(8):627-636. doi:10.1007/s00114-012-0943-z
apa: Konrad, M., Pamminger, T., & Foitzik, S. (2012). Two pathways ensuring
social harmony. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-012-0943-z
chicago: Konrad, Matthias, Tobias Pamminger, and Susanne Foitzik. “Two Pathways
Ensuring Social Harmony.” Naturwissenschaften. Springer, 2012. https://doi.org/10.1007/s00114-012-0943-z.
ieee: M. Konrad, T. Pamminger, and S. Foitzik, “Two pathways ensuring social harmony,”
Naturwissenschaften, vol. 99, no. 8. Springer, pp. 627–636, 2012.
ista: Konrad M, Pamminger T, Foitzik S. 2012. Two pathways ensuring social harmony.
Naturwissenschaften. 99(8), 627–636.
mla: Konrad, Matthias, et al. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften,
vol. 99, no. 8, Springer, 2012, pp. 627–36, doi:10.1007/s00114-012-0943-z.
short: M. Konrad, T. Pamminger, S. Foitzik, Naturwissenschaften 99 (2012) 627–636.
date_created: 2018-12-11T12:01:34Z
date_published: 2012-08-01T00:00:00Z
date_updated: 2021-01-12T07:41:17Z
day: '01'
department:
- _id: SyCr
doi: 10.1007/s00114-012-0943-z
intvolume: ' 99'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 627 - 636
publication: Naturwissenschaften
publication_status: published
publisher: Springer
publist_id: '3565'
quality_controlled: '1'
scopus_import: 1
status: public
title: Two pathways ensuring social harmony
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2012'
...
---
_id: '3161'
abstract:
- lang: eng
text: 'Some inflammatory stimuli trigger activation of the NLRP3 inflammasome by
inducing efflux of cellular potassium. Loss of cellular potassium is known to
potently suppress protein synthesis, leading us to test whether the inhibition
of protein synthesis itself serves as an activating signal for the NLRP3 inflammasome.
Murine bone marrow-derived macrophages, either primed by LPS or unprimed, were
exposed to a panel of inhibitors of ribosomal function: ricin, cycloheximide,
puromycin, pactamycin, and anisomycin. Macrophages were also exposed to nigericin,
ATP, monosodium urate (MSU), and poly I:C. Synthesis of pro-IL-ß and release of
IL-1ß from cells in response to these agents was detected by immunoblotting and
ELISA. Release of intracellular potassium was measured by mass spectrometry. Inhibition
of translation by each of the tested translation inhibitors led to processing
of IL-1ß, which was released from cells. Processing and release of IL-1ß was reduced
or absent from cells deficient in NLRP3, ASC, or caspase-1, demonstrating the
role of the NLRP3 inflammasome. Despite the inability of these inhibitors to trigger
efflux of intracellular potassium, the addition of high extracellular potassium
suppressed activation of the NLRP3 inflammasome. MSU and double-stranded RNA,
which are known to activate the NLRP3 inflammasome, also substantially inhibited
protein translation, supporting a close association between inhibition of translation
and inflammasome activation. These data demonstrate that translational inhibition
itself constitutes a heretofore-unrecognized mechanism underlying IL-1ß dependent
inflammatory signaling and that other physical, chemical, or pathogen-associated
agents that impair translation may lead to IL-1ß-dependent inflammation through
activation of the NLRP3 inflammasome. For agents that inhibit translation through
decreased cellular potassium, the application of high extracellular potassium
restores protein translation and suppresses activation of the NLRP inflammasome.
For agents that inhibit translation through mechanisms that do not involve loss
of potassium, high extracellular potassium suppresses IL-1ß processing through
a mechanism that remains undefined.'
acknowledgement: "Supported by National Institutes of Health grants GM071338 (ML)
and AI059355 (BM).\r\nWe acknowledge the expertise of Dr. Martina Ralle in Department
of Biochemistry and Molecular Biology at OHSU for measurements of potassium using
inductively coupled plasma mass spectrometry."
article_number: e36044
author:
- first_name: Meghan
full_name: Vyleta, Meghan
id: 418901AA-F248-11E8-B48F-1D18A9856A87
last_name: Vyleta
- first_name: John
full_name: Wong, John
last_name: Wong
- first_name: Bruce
full_name: Magun, Bruce
last_name: Magun
citation:
ama: Vyleta M, Wong J, Magun B. Suppression of ribosomal function triggers innate
immune signaling through activation of the NLRP3 inflammasome. PLoS One.
2012;7(5). doi:10.1371/journal.pone.0036044
apa: Vyleta, M., Wong, J., & Magun, B. (2012). Suppression of ribosomal function
triggers innate immune signaling through activation of the NLRP3 inflammasome.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036044
chicago: Vyleta, Meghan, John Wong, and Bruce Magun. “Suppression of Ribosomal Function
Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.”
PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0036044.
ieee: M. Vyleta, J. Wong, and B. Magun, “Suppression of ribosomal function triggers
innate immune signaling through activation of the NLRP3 inflammasome,” PLoS
One, vol. 7, no. 5. Public Library of Science, 2012.
ista: Vyleta M, Wong J, Magun B. 2012. Suppression of ribosomal function triggers
innate immune signaling through activation of the NLRP3 inflammasome. PLoS One.
7(5), e36044.
mla: Vyleta, Meghan, et al. “Suppression of Ribosomal Function Triggers Innate Immune
Signaling through Activation of the NLRP3 Inflammasome.” PLoS One, vol.
7, no. 5, e36044, Public Library of Science, 2012, doi:10.1371/journal.pone.0036044.
short: M. Vyleta, J. Wong, B. Magun, PLoS One 7 (2012).
date_created: 2018-12-11T12:01:45Z
date_published: 2012-05-14T00:00:00Z
date_updated: 2021-01-12T07:41:29Z
day: '14'
ddc:
- '610'
department:
- _id: SyCr
doi: 10.1371/journal.pone.0036044
file:
- access_level: open_access
checksum: 30cef37e27eaa467f6571b3640282010
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:30Z
date_updated: 2020-07-14T12:46:01Z
file_id: '5082'
file_name: IST-2012-97-v1+1_journal.pone.0036044.pdf
file_size: 2984012
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3526'
pubrep_id: '97'
quality_controlled: '1'
scopus_import: 1
status: public
title: Suppression of ribosomal function triggers innate immune signaling through
activation of the NLRP3 inflammasome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2012'
...
---
_id: '3162'
abstract:
- lang: eng
text: Given a dense-time real-valued signal and a parameterized temporal logic formula
with both magnitude and timing parameters, we compute the subset of the parameter
space that renders the formula satisfied by the trace. We provide two preliminary
implementations, one which follows the exact semantics and attempts to compute
the validity domain by quantifier elimination in linear arithmetics and one which
conducts adaptive search in the parameter space.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Eugene
full_name: Asarin, Eugene
last_name: Asarin
- first_name: Alexandre
full_name: Donzé, Alexandre
last_name: Donzé
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Asarin E, Donzé A, Maler O, Nickovic D. Parametric identification of temporal
properties. In: Vol 7186. Springer; 2012:147-160. doi:10.1007/978-3-642-29860-8_12'
apa: 'Asarin, E., Donzé, A., Maler, O., & Nickovic, D. (2012). Parametric identification
of temporal properties (Vol. 7186, pp. 147–160). Presented at the RV: Runtime
Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-642-29860-8_12'
chicago: Asarin, Eugene, Alexandre Donzé, Oded Maler, and Dejan Nickovic. “Parametric
Identification of Temporal Properties,” 7186:147–60. Springer, 2012. https://doi.org/10.1007/978-3-642-29860-8_12.
ieee: 'E. Asarin, A. Donzé, O. Maler, and D. Nickovic, “Parametric identification
of temporal properties,” presented at the RV: Runtime Verification, San Francisco,
CA, United States, 2012, vol. 7186, pp. 147–160.'
ista: 'Asarin E, Donzé A, Maler O, Nickovic D. 2012. Parametric identification of
temporal properties. RV: Runtime Verification, LNCS, vol. 7186, 147–160.'
mla: Asarin, Eugene, et al. Parametric Identification of Temporal Properties.
Vol. 7186, Springer, 2012, pp. 147–60, doi:10.1007/978-3-642-29860-8_12.
short: E. Asarin, A. Donzé, O. Maler, D. Nickovic, in:, Springer, 2012, pp. 147–160.
conference:
end_date: 2011-09-30
location: San Francisco, CA, United States
name: 'RV: Runtime Verification'
start_date: 2011-09-27
date_created: 2018-12-11T12:01:45Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:29Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-29860-8_12
file:
- access_level: open_access
checksum: ba4a75287008fc64b8fbf78a7476ec32
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T12:50:15Z
date_updated: 2020-07-14T12:46:01Z
file_id: '7862'
file_name: 2012_RV_Asarin.pdf
file_size: 374726
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 7186'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 147 - 160
publication_status: published
publisher: Springer
publist_id: '3525'
quality_controlled: '1'
scopus_import: 1
status: public
title: Parametric identification of temporal properties
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7186
year: '2012'
...
---
_id: '3160'
abstract:
- lang: eng
text: There is a long-running controversy about how early cell fate decisions are
made in the developing mammalian embryo. 1,2 In particular, it is controversial
when the first events that can predict the establishment of the pluripotent and
extra-embryonic lineages in the blastocyst of the pre-implantation embryo occur.
It has long been proposed that the position and polarity of cells at the 16- to
32-cell stage embryo influence their decision to either give rise to the pluripotent
cell lineage that eventually contributes to the inner cell mass (ICM), comprising
the primitive endoderm (PE) and the epiblast (EPI), or the extra-embryonic trophectoderm
(TE) surrounding the blastocoel. The positioning of cells in the embryo at this
developmental stage could largely be the result of random events, making this
a stochastic model of cell lineage allocation. Contrary to such a stochastic model,
some studies have detected putative differences in the lineage potential of individual
blastomeres before compaction, indicating that the first cell fate decisions may
occur as early as at the 4-cell stage. Using a non-invasive, quantitative in vivo
imaging assay to study the kinetic behavior of Oct4 (also known as POU5F1), a
key transcription factor (TF) controlling pre-implantation development in the
mouse embryo, 3-5 a recent study identifies Oct4 kinetics as a predictive measure
of cell lineage patterning in the early mouse embryo. 6 Here, we discuss the implications
of such molecular heterogeneities in early development and offer potential avenues
toward a mechanistic understanding of these observations, contributing to the
resolution of the controversy of developmental cell lineage allocation.
author:
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Pantazis P, Bollenbach MT. Transcription factor kinetics and the emerging asymmetry
in the early mammalian embryo. Cell Cycle. 2012;11(11):2055-2058. doi:10.4161/cc.20118
apa: Pantazis, P., & Bollenbach, M. T. (2012). Transcription factor kinetics
and the emerging asymmetry in the early mammalian embryo. Cell Cycle. Taylor
and Francis. https://doi.org/10.4161/cc.20118
chicago: Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics
and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle.
Taylor and Francis, 2012. https://doi.org/10.4161/cc.20118.
ieee: P. Pantazis and M. T. Bollenbach, “Transcription factor kinetics and the emerging
asymmetry in the early mammalian embryo,” Cell Cycle, vol. 11, no. 11.
Taylor and Francis, pp. 2055–2058, 2012.
ista: Pantazis P, Bollenbach MT. 2012. Transcription factor kinetics and the emerging
asymmetry in the early mammalian embryo. Cell Cycle. 11(11), 2055–2058.
mla: Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics
and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle,
vol. 11, no. 11, Taylor and Francis, 2012, pp. 2055–58, doi:10.4161/cc.20118.
short: P. Pantazis, M.T. Bollenbach, Cell Cycle 11 (2012) 2055–2058.
date_created: 2018-12-11T12:01:44Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:28Z
day: '01'
department:
- _id: ToBo
doi: 10.4161/cc.20118
intvolume: ' 11'
issue: '11'
language:
- iso: eng
month: '06'
oa_version: None
page: 2055 - 2058
publication: Cell Cycle
publication_status: published
publisher: Taylor and Francis
publist_id: '3531'
quality_controlled: '1'
scopus_import: 1
status: public
title: Transcription factor kinetics and the emerging asymmetry in the early mammalian
embryo
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2012'
...
---
_id: '3164'
abstract:
- lang: eng
text: Overview of the Special Issue on structured prediction and inference.
author:
- first_name: Matthew
full_name: Blaschko, Matthew
last_name: Blaschko
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Blaschko M, Lampert C. Guest editorial: Special issue on structured prediction
and inference. International Journal of Computer Vision. 2012;99(3):257-258.
doi:10.1007/s11263-012-0530-y'
apa: 'Blaschko, M., & Lampert, C. (2012). Guest editorial: Special issue on
structured prediction and inference. International Journal of Computer Vision.
Springer. https://doi.org/10.1007/s11263-012-0530-y'
chicago: 'Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue
on Structured Prediction and Inference.” International Journal of Computer
Vision. Springer, 2012. https://doi.org/10.1007/s11263-012-0530-y.'
ieee: 'M. Blaschko and C. Lampert, “Guest editorial: Special issue on structured
prediction and inference,” International Journal of Computer Vision, vol.
99, no. 3. Springer, pp. 257–258, 2012.'
ista: 'Blaschko M, Lampert C. 2012. Guest editorial: Special issue on structured
prediction and inference. International Journal of Computer Vision. 99(3), 257–258.'
mla: 'Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue
on Structured Prediction and Inference.” International Journal of Computer
Vision, vol. 99, no. 3, Springer, 2012, pp. 257–58, doi:10.1007/s11263-012-0530-y.'
short: M. Blaschko, C. Lampert, International Journal of Computer Vision 99 (2012)
257–258.
date_created: 2018-12-11T12:01:46Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:30Z
day: '01'
department:
- _id: ChLa
doi: 10.1007/s11263-012-0530-y
intvolume: ' 99'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 257 - 258
publication: International Journal of Computer Vision
publication_status: published
publisher: Springer
publist_id: '3521'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Guest editorial: Special issue on structured prediction and inference'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2012'
...
---
_id: '3166'
abstract:
- lang: eng
text: 'There is evidence that the genetic code was established prior to the existence
of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms
had to rely on simple anaerobic bioenergetic processes. In this work I propose
that amino acid fermentation powered metabolism in the RNA world, and that this
was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were
used as carbon sources rather than as catalytic or structural elements. In modern
bacteria, amino acid fermentation is known as the Stickland reaction. This pathway
involves two amino acids: the first undergoes oxidative deamination, and the second
acts as an electron acceptor through reductive deamination. This redox reaction
results in two keto acids that are employed to synthesise ATP via substrate-level
phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some
bacteria of the genus Clostridium. Two other facts support Stickland fermentation
in the RNA world. First, several Stickland amino acid pairs are synthesised in
abiotic amino acid synthesis. This suggests that amino acids that could be used
as an energy substrate were freely available. Second, anticodons that have complementary
sequences often correspond to amino acids that form Stickland pairs. The main
hypothesis of this paper is that pairs of complementary proto-adapters were assigned
to Stickland amino acids pairs. There are signatures of this hypothesis in the
genetic code. Furthermore, it is argued that the proto-adapters formed double
strands that brought amino acid pairs into proximity to facilitate their mutual
redox reaction, structurally constraining the anticodon pairs that are assigned
to these amino acid pairs. Significance tests which randomise the code are performed
to study the extent of the variability of the energetic (ATP) yield. Random assignments
can lead to a substantial yield of ATP and maintain enough variability, thus selection
can act and refine the assignments into a proto-code that optimises the energetic
yield. Monte Carlo simulations are performed to evaluate the establishment of
these simple proto-codes, based on amino acid substitutions and codon swapping.
In all cases, donor amino acids are assigned to anticodons composed of U+G, and
have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to
the the remaining codons. These bioenergetic and structural constraints allow
for a metabolic role for amino acids before their co-option as catalyst cofactors.
Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary
(nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)'
acknowledgement: 'The author was supported by the ERC-2009-AdG Grant for project 250152
SELECTIONINFORMATION. '
article_number: '6'
author:
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology
Direct. 2012;7. doi:10.1186/1745-6150-7-6
apa: de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic
code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6
chicago: Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic
Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6.
ieee: H. de Vladar, “Amino acid fermentation at the origin of the genetic code,”
Biology Direct, vol. 7. BioMed Central, 2012.
ista: de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code.
Biology Direct. 7, 6.
mla: de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.”
Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6.
short: H. de Vladar, Biology Direct 7 (2012).
date_created: 2018-12-11T12:01:46Z
date_published: 2012-02-10T00:00:00Z
date_updated: 2021-01-12T07:41:31Z
day: '10'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1186/1745-6150-7-6
ec_funded: 1
file:
- access_level: open_access
checksum: e511e401e239ef608a7fd79b21a06d78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:44Z
date_updated: 2020-07-14T12:46:02Z
file_id: '5166'
file_name: IST-2012-99-v1+1_1745-6150-7-6.pdf
file_size: 4099536
relation: main_file
file_date_updated: 2020-07-14T12:46:02Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '3518'
pubrep_id: '99'
quality_controlled: '1'
status: public
title: Amino acid fermentation at the origin of the genetic code
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2012'
...
---
_id: '3167'
article_type: letter_note
author:
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
citation:
ama: Weber M. NextGen speaks 13 . Science. 2012;336(6077):32-34. doi:10.1126/science.336.6077.32
apa: Weber, M. (2012). NextGen speaks 13 . Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.336.6077.32
chicago: Weber, Michele. “NextGen Speaks 13 .” Science. American Association
for the Advancement of Science, 2012. https://doi.org/10.1126/science.336.6077.32.
ieee: M. Weber, “NextGen speaks 13 ,” Science, vol. 336, no. 6077. American
Association for the Advancement of Science, pp. 32–34, 2012.
ista: Weber M. 2012. NextGen speaks 13 . Science. 336(6077), 32–34.
mla: Weber, Michele. “NextGen Speaks 13 .” Science, vol. 336, no. 6077, American
Association for the Advancement of Science, 2012, pp. 32–34, doi:10.1126/science.336.6077.32.
short: M. Weber, Science 336 (2012) 32–34.
date_created: 2018-12-11T12:01:47Z
date_published: 2012-04-06T00:00:00Z
date_updated: 2021-01-12T07:41:32Z
day: '06'
department:
- _id: MiSi
doi: 10.1126/science.336.6077.32
external_id:
pmid:
- '22491839'
intvolume: ' 336'
issue: '6077'
language:
- iso: eng
month: '04'
oa_version: None
page: 32-34
pmid: 1
popular_science: '1'
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '3516'
status: public
title: 'NextGen speaks 13 '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 336
year: '2012'
...
---
_id: '3241'
abstract:
- lang: eng
text: 'We prove a negative result concerning error reduction by parallel repetition
for computationally sound protocols, e.g., interactive arguments. Our main result
is a complete and computationally sound eight round interactive argument for which
k-fold parallel repetition does not reduce the error below a constant for any
polynomial k. The starting point for our construction is the work of Bellare,
Impagliazzo and Naor (FOCS''97). For any fixed k, they construct a four round
protocol for which k-fold parallel repetition does not lower the soundness error.
The communication complexity of this protocol is linear in k. By using universal
arguments due to Barak and Goldreich (CCC 2002), we turn this protocol into an
eight-round protocol whose complexity is basically independent of k. '
author:
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Douglas
full_name: Wikström, Douglas
last_name: Wikström
citation:
ama: Pietrzak KZ, Wikström D. Parallel repetition of computationally sound protocols
revisited. Journal of Cryptology. 2012;25(1):116-135. doi:10.1007/s00145-010-9090-x
apa: Pietrzak, K. Z., & Wikström, D. (2012). Parallel repetition of computationally
sound protocols revisited. Journal of Cryptology. Springer. https://doi.org/10.1007/s00145-010-9090-x
chicago: Pietrzak, Krzysztof Z, and Douglas Wikström. “Parallel Repetition of Computationally
Sound Protocols Revisited.” Journal of Cryptology. Springer, 2012. https://doi.org/10.1007/s00145-010-9090-x.
ieee: K. Z. Pietrzak and D. Wikström, “Parallel repetition of computationally sound
protocols revisited,” Journal of Cryptology, vol. 25, no. 1. Springer,
pp. 116–135, 2012.
ista: Pietrzak KZ, Wikström D. 2012. Parallel repetition of computationally sound
protocols revisited. Journal of Cryptology. 25(1), 116–135.
mla: Pietrzak, Krzysztof Z., and Douglas Wikström. “Parallel Repetition of Computationally
Sound Protocols Revisited.” Journal of Cryptology, vol. 25, no. 1, Springer,
2012, pp. 116–35, doi:10.1007/s00145-010-9090-x.
short: K.Z. Pietrzak, D. Wikström, Journal of Cryptology 25 (2012) 116–135.
date_created: 2018-12-11T12:02:12Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T07:42:03Z
day: '01'
doi: 10.1007/s00145-010-9090-x
extern: 1
intvolume: ' 25'
issue: '1'
month: '11'
page: 116 - 135
publication: Journal of Cryptology
publication_status: published
publisher: Springer
publist_id: '3439'
quality_controlled: 0
status: public
title: Parallel repetition of computationally sound protocols revisited
type: journal_article
volume: 25
year: '2012'
...
---
_id: '3252'
abstract:
- lang: eng
text: 'We study the automatic synthesis of fair non-repudiation protocols, a class
of fair exchange protocols, used for digital contract signing. First, we show
how to specify the objectives of the participating agents, the trusted third party
(TTP) and the protocols as path formulas in Linear Temporal Logic (LTL) and prove
that the satisfaction of the objectives of the agents and the TTP imply satisfaction
of the protocol objectives. We then show that weak (co-operative) co-synthesis
and classical (strictly competitive) co-synthesis fail in synthesizing these protocols,
whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success
of assume-guarantee synthesis as follows: (a) any solution of assume-guarantee
synthesis is attack-free; no subset of participants can violate the objectives
of the other participants without violating their own objectives; (b) the Asokan-Shoup-Waidner
(ASW) certified mail protocol that has known vulnerabilities is not a solution
of AGS; and (c) the Kremer-Markowitch (KM) non-repudiation protocol is a solution
of AGS. To our knowledge this is the first application of synthesis to fair non-repudiation
protocols, and our results show how synthesis can generate correct protocols and
automatically discover vulnerabilities. The solution to assume-guarantee synthesis
can be computed efficiently as the secure equilibrium solution of three-player
graph games. © 2012 Springer-Verlag.'
acknowledgement: "The research was supported by Austrian Science Fund (FWF) Grant
No P 23499-N23 (Modern Graph Algorithmic Techniques in Formal Verification), FWF
NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft
faculty fellows award.\r\nThe authors would like to thank Avik Chaudhuri for his
invaluable help and feedback."
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vishwanath
full_name: Raman, Vishwanath
last_name: Raman
citation:
ama: 'Chatterjee K, Raman V. Synthesizing protocols for digital contract signing.
In: Vol 7148. Springer; 2012:152-168. doi:10.1007/978-3-642-27940-9_11'
apa: 'Chatterjee, K., & Raman, V. (2012). Synthesizing protocols for digital
contract signing (Vol. 7148, pp. 152–168). Presented at the VMCAI: Verification,
Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_11'
chicago: Chatterjee, Krishnendu, and Vishwanath Raman. “Synthesizing Protocols for
Digital Contract Signing,” 7148:152–68. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_11.
ieee: 'K. Chatterjee and V. Raman, “Synthesizing protocols for digital contract
signing,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation,
Philadelphia, PA, USA, 2012, vol. 7148, pp. 152–168.'
ista: 'Chatterjee K, Raman V. 2012. Synthesizing protocols for digital contract
signing. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS,
vol. 7148, 152–168.'
mla: Chatterjee, Krishnendu, and Vishwanath Raman. Synthesizing Protocols for
Digital Contract Signing. Vol. 7148, Springer, 2012, pp. 152–68, doi:10.1007/978-3-642-27940-9_11.
short: K. Chatterjee, V. Raman, in:, Springer, 2012, pp. 152–168.
conference:
end_date: 2012-01-24
location: Philadelphia, PA, USA
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2012-01-22
date_created: 2018-12-11T12:02:16Z
date_published: 2012-01-20T00:00:00Z
date_updated: 2021-01-12T07:42:08Z
day: '20'
department:
- _id: KrCh
doi: 10.1007/978-3-642-27940-9_11
ec_funded: 1
intvolume: ' 7148'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.2697
month: '01'
oa: 1
oa_version: Preprint
page: 152 - 168
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _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_status: published
publisher: Springer
publist_id: '3405'
quality_controlled: '1'
scopus_import: 1
status: public
title: Synthesizing protocols for digital contract signing
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7148
year: '2012'
...
---
_id: '3255'
abstract:
- lang: eng
text: In this paper we survey results of two-player games on graphs and Markov decision
processes with parity, mean-payoff and energy objectives, and the combination
of mean-payoff and energy objectives with parity objectives. These problems have
applications in verification and synthesis of reactive systems in resource-constrained
environments.
acknowledgement: This work was partially supported by FWF NFN Grant S11407-N23 (RiSE)
and a Microsoft faculty fellowship.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Games and Markov decision processes with mean payoff
parity and energy parity objectives. In: Vol 7119. Springer; 2012:37-46. doi:10.1007/978-3-642-25929-6_3'
apa: 'Chatterjee, K., & Doyen, L. (2012). Games and Markov decision processes
with mean payoff parity and energy parity objectives (Vol. 7119, pp. 37–46). Presented
at the MEMICS: Mathematical and Engineering Methods in Computer Science, Lednice,
Czech Republic: Springer. https://doi.org/10.1007/978-3-642-25929-6_3'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Games and Markov Decision Processes
with Mean Payoff Parity and Energy Parity Objectives,” 7119:37–46. Springer, 2012.
https://doi.org/10.1007/978-3-642-25929-6_3.
ieee: 'K. Chatterjee and L. Doyen, “Games and Markov decision processes with mean
payoff parity and energy parity objectives,” presented at the MEMICS: Mathematical
and Engineering Methods in Computer Science, Lednice, Czech Republic, 2012, vol.
7119, pp. 37–46.'
ista: 'Chatterjee K, Doyen L. 2012. Games and Markov decision processes with mean
payoff parity and energy parity objectives. MEMICS: Mathematical and Engineering
Methods in Computer Science, LNCS, vol. 7119, 37–46.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. Games and Markov Decision Processes
with Mean Payoff Parity and Energy Parity Objectives. Vol. 7119, Springer,
2012, pp. 37–46, doi:10.1007/978-3-642-25929-6_3.
short: K. Chatterjee, L. Doyen, in:, Springer, 2012, pp. 37–46.
conference:
end_date: 2011-10-16
location: Lednice, Czech Republic
name: 'MEMICS: Mathematical and Engineering Methods in Computer Science'
start_date: 2011-10-14
date_created: 2018-12-11T12:02:17Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:10Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-642-25929-6_3
file:
- access_level: open_access
checksum: eed2cc1e76b160418c977e76e8899a60
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T12:53:12Z
date_updated: 2020-07-14T12:46:05Z
file_id: '7863'
file_name: 2012_MEMICS_Chatterjee.pdf
file_size: 114060
relation: main_file
file_date_updated: 2020-07-14T12:46:05Z
has_accepted_license: '1'
intvolume: ' 7119'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 37 - 46
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '3400'
quality_controlled: '1'
scopus_import: 1
status: public
title: Games and Markov decision processes with mean payoff parity and energy parity
objectives
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7119
year: '2012'
...
---
_id: '3250'
abstract:
- lang: eng
text: The Learning Parity with Noise (LPN) problem has recently found many applications
in cryptography as the hardness assumption underlying the constructions of "provably
secure" cryptographic schemes like encryption or authentication protocols.
Being provably secure means that the scheme comes with a proof showing that the
existence of an efficient adversary against the scheme implies that the underlying
hardness assumption is wrong. LPN based schemes are appealing for theoretical
and practical reasons. On the theoretical side, LPN based schemes offer a very
strong security guarantee. The LPN problem is equivalent to the problem of decoding
random linear codes, a problem that has been extensively studied in the last half
century. The fastest known algorithms run in exponential time and unlike most
number-theoretic problems used in cryptography, the LPN problem does not succumb
to known quantum algorithms. On the practical side, LPN based schemes are often
extremely simple and efficient in terms of code-size as well as time and space
requirements. This makes them prime candidates for light-weight devices like RFID
tags, which are too weak to implement standard cryptographic primitives like the
AES block-cipher. This talk will be a gentle introduction to provable security
using simple LPN based schemes as examples. Starting from pseudorandom generators
and symmetric key encryption, over secret-key authentication protocols, and, if
time admits, touching on recent constructions of public-key identification, commitments
and zero-knowledge proofs.
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. Cryptography from learning parity with noise. In: Vol 7147. Springer;
2012:99-114. doi:10.1007/978-3-642-27660-6_9'
apa: 'Pietrzak, K. Z. (2012). Cryptography from learning parity with noise (Vol.
7147, pp. 99–114). Presented at the SOFSEM: Current Trends in Theory and Practice
of Computer Science, Špindlerův Mlýn, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-27660-6_9'
chicago: Pietrzak, Krzysztof Z. “Cryptography from Learning Parity with Noise,”
7147:99–114. Springer, 2012. https://doi.org/10.1007/978-3-642-27660-6_9.
ieee: 'K. Z. Pietrzak, “Cryptography from learning parity with noise,” presented
at the SOFSEM: Current Trends in Theory and Practice of Computer Science, Špindlerův
Mlýn, Czech Republic, 2012, vol. 7147, pp. 99–114.'
ista: 'Pietrzak KZ. 2012. Cryptography from learning parity with noise. SOFSEM:
Current Trends in Theory and Practice of Computer Science, LNCS, vol. 7147, 99–114.'
mla: Pietrzak, Krzysztof Z. Cryptography from Learning Parity with Noise.
Vol. 7147, Springer, 2012, pp. 99–114, doi:10.1007/978-3-642-27660-6_9.
short: K.Z. Pietrzak, in:, Springer, 2012, pp. 99–114.
conference:
end_date: 2012-01-27
location: Špindlerův Mlýn, Czech Republic
name: 'SOFSEM: Current Trends in Theory and Practice of Computer Science'
start_date: 2012-01-21
date_created: 2018-12-11T12:02:15Z
date_published: 2012-02-19T00:00:00Z
date_updated: 2021-01-12T07:42:07Z
day: '19'
department:
- _id: KrPi
doi: 10.1007/978-3-642-27660-6_9
intvolume: ' 7147'
language:
- iso: eng
month: '02'
oa_version: None
page: 99 - 114
publication_status: published
publisher: Springer
publist_id: '3407'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cryptography from learning parity with noise
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7147
year: '2012'
...
---
_id: '3256'
abstract:
- lang: eng
text: We use a distortion to define the dual complex of a cubical subdivision of
ℝ n as an n-dimensional subcomplex of the nerve of the set of n-cubes. Motivated
by the topological analysis of high-dimensional digital image data, we consider
such subdivisions defined by generalizations of quad- and oct-trees to n dimensions.
Assuming the subdivision is balanced, we show that mapping each vertex to the
center of the corresponding n-cube gives a geometric realization of the dual complex
in ℝ n.
acknowledgement: This research is partially supported by the Defense Advanced Research
Projects Agency (DARPA) under grants HR0011-05-1-0057 and HR0011-09-0065 as well
as the National Science Foundation (NSF) under grant DBI-0820624.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
citation:
ama: Edelsbrunner H, Kerber M. Dual complexes of cubical subdivisions of ℝn. Discrete
& Computational Geometry. 2012;47(2):393-414. doi:10.1007/s00454-011-9382-4
apa: Edelsbrunner, H., & Kerber, M. (2012). Dual complexes of cubical subdivisions
of ℝn. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-011-9382-4
chicago: Edelsbrunner, Herbert, and Michael Kerber. “Dual Complexes of Cubical Subdivisions
of ℝn.” Discrete & Computational Geometry. Springer, 2012. https://doi.org/10.1007/s00454-011-9382-4.
ieee: H. Edelsbrunner and M. Kerber, “Dual complexes of cubical subdivisions of
ℝn,” Discrete & Computational Geometry, vol. 47, no. 2. Springer, pp.
393–414, 2012.
ista: Edelsbrunner H, Kerber M. 2012. Dual complexes of cubical subdivisions of
ℝn. Discrete & Computational Geometry. 47(2), 393–414.
mla: Edelsbrunner, Herbert, and Michael Kerber. “Dual Complexes of Cubical Subdivisions
of ℝn.” Discrete & Computational Geometry, vol. 47, no. 2, Springer,
2012, pp. 393–414, doi:10.1007/s00454-011-9382-4.
short: H. Edelsbrunner, M. Kerber, Discrete & Computational Geometry 47 (2012)
393–414.
date_created: 2018-12-11T12:02:17Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2021-01-12T07:42:10Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s00454-011-9382-4
file:
- access_level: open_access
checksum: 76486f3b2c9e7fd81342f3832ca387e7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:15Z
date_updated: 2020-07-14T12:46:05Z
file_id: '4675'
file_name: IST-2016-543-v1+1_2012-J-08-HierarchyCubeComplex.pdf
file_size: 203636
relation: main_file
file_date_updated: 2020-07-14T12:46:05Z
has_accepted_license: '1'
intvolume: ' 47'
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 393 - 414
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '3398'
pubrep_id: '543'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dual complexes of cubical subdivisions of ℝn
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2012'
...
---
_id: '3254'
abstract:
- lang: eng
text: 'The theory of graph games with ω-regular winning conditions is the foundation
for modeling and synthesizing reactive processes. In the case of stochastic reactive
processes, the corresponding stochastic graph games have three players, two of
them (System and Environment) behaving adversarially, and the third (Uncertainty)
behaving probabilistically. We consider two problems for stochastic graph games:
the qualitative problem asks for the set of states from which a player can win
with probability 1 (almost-sure winning); and the quantitative problem asks for
the maximal probability of winning (optimal winning) from each state. We consider
ω-regular winning conditions formalized as Müller winning conditions. We present
optimal memory bounds for pure (deterministic) almost-sure winning and optimal
winning strategies in stochastic graph games with Müller winning conditions. We
also study the complexity of stochastic Müller games and show that both the qualitative
and quantitative analysis problems are PSPACE-complete. Our results are relevant
in synthesis of stochastic reactive processes.'
acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant
No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph
Games), and 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
citation:
ama: Chatterjee K. The complexity of stochastic Müller games. Information and
Computation. 2012;211:29-48. doi:10.1016/j.ic.2011.11.004
apa: Chatterjee, K. (2012). The complexity of stochastic Müller games. Information
and Computation. Elsevier. https://doi.org/10.1016/j.ic.2011.11.004
chicago: Chatterjee, Krishnendu. “The Complexity of Stochastic Müller Games.” Information
and Computation. Elsevier, 2012. https://doi.org/10.1016/j.ic.2011.11.004.
ieee: K. Chatterjee, “The complexity of stochastic Müller games,” Information
and Computation, vol. 211. Elsevier, pp. 29–48, 2012.
ista: Chatterjee K. 2012. The complexity of stochastic Müller games. Information
and Computation. 211, 29–48.
mla: Chatterjee, Krishnendu. “The Complexity of Stochastic Müller Games.” Information
and Computation, vol. 211, Elsevier, 2012, pp. 29–48, doi:10.1016/j.ic.2011.11.004.
short: K. Chatterjee, Information and Computation 211 (2012) 29–48.
date_created: 2018-12-11T12:02:17Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2021-01-12T07:42:09Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.ic.2011.11.004
ec_funded: 1
intvolume: ' 211'
language:
- iso: eng
main_file_link:
- url: http://arise.or.at/pubpdf/The_complexity_of_stochastic_M___u_ller_games.pdf
month: '02'
oa_version: None
page: 29 - 48
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _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: '3403'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of stochastic Müller games
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 211
year: '2012'
...
---
_id: '3253'
abstract:
- lang: eng
text: We describe a framework for reasoning about programs with lists carrying integer
numerical data. We use abstract domains to describe and manipulate complex constraints
on configurations of these programs mixing constraints on the shape of the heap,
sizes of the lists, on the multisets of data stored in these lists, and on the
data at their different positions. Moreover, we provide powerful techniques for
automatic validation of Hoare-triples and invariant checking, as well as for automatic
synthesis of invariants and procedure summaries using modular inter-procedural
analysis. The approach has been implemented in a tool called Celia and experimented
successfully on a large benchmark of programs.
acknowledgement: This work was partly supported by the French National Research Agency
(ANR) project Veridyc (ANR-09-SEGI-016).
alternative_title:
- LNCS
author:
- first_name: Ahmed
full_name: Bouajjani, Ahmed
last_name: Bouajjani
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- first_name: Constantin
full_name: Enea, Constantin
last_name: Enea
- first_name: Mihaela
full_name: Sighireanu, Mihaela
last_name: Sighireanu
citation:
ama: 'Bouajjani A, Dragoi C, Enea C, Sighireanu M. Abstract domains for automated
reasoning about list manipulating programs with infinite data. In: Vol 7148. Springer;
2012:1-22. doi:10.1007/978-3-642-27940-9_1'
apa: 'Bouajjani, A., Dragoi, C., Enea, C., & Sighireanu, M. (2012). Abstract
domains for automated reasoning about list manipulating programs with infinite
data (Vol. 7148, pp. 1–22). Presented at the VMCAI: Verification, Model Checking
and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_1'
chicago: Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu.
“Abstract Domains for Automated Reasoning about List Manipulating Programs with
Infinite Data,” 7148:1–22. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_1.
ieee: 'A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Abstract domains for
automated reasoning about list manipulating programs with infinite data,” presented
at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia,
PA, USA, 2012, vol. 7148, pp. 1–22.'
ista: 'Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Abstract domains for automated
reasoning about list manipulating programs with infinite data. VMCAI: Verification,
Model Checking and Abstract Interpretation, LNCS, vol. 7148, 1–22.'
mla: Bouajjani, Ahmed, et al. Abstract Domains for Automated Reasoning about
List Manipulating Programs with Infinite Data. Vol. 7148, Springer, 2012,
pp. 1–22, doi:10.1007/978-3-642-27940-9_1.
short: A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Springer, 2012, pp.
1–22.
conference:
end_date: 2012-01-24
location: Philadelphia, PA, USA
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2012-01-22
date_created: 2018-12-11T12:02:17Z
date_published: 2012-02-26T00:00:00Z
date_updated: 2021-01-12T07:42:09Z
day: '26'
department:
- _id: ToHe
doi: 10.1007/978-3-642-27940-9_1
intvolume: ' 7148'
language:
- iso: eng
month: '02'
oa_version: None
page: 1 - 22
publication_status: published
publisher: Springer
publist_id: '3404'
quality_controlled: '1'
status: public
title: Abstract domains for automated reasoning about list manipulating programs with
infinite data
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7148
year: '2012'
...
---
_id: '3265'
abstract:
- lang: eng
text: We propose a mid-level statistical model for image segmentation that composes
multiple figure-ground hypotheses (FG) obtained by applying constraints at different
locations and scales, into larger interpretations (tilings) of the entire image.
Inference is cast as optimization over sets of maximal cliques sampled from a
graph connecting all non-overlapping figure-ground segment hypotheses. Potential
functions over cliques combine unary, Gestalt-based figure qualities, and pairwise
compatibilities among spatially neighboring segments, constrained by T-junctions
and the boundary interface statistics of real scenes. Learning the model parameters
is based on maximum likelihood, alternating between sampling image tilings and
optimizing their potential function parameters. State of the art results are reported
on the Berkeley and Stanford segmentation datasets, as well as VOC2009, where
a 28% improvement was achieved.
article_number: '6126486'
author:
- first_name: Adrian
full_name: Ion, Adrian
id: 29F89302-F248-11E8-B48F-1D18A9856A87
last_name: Ion
- first_name: Joao
full_name: Carreira, Joao
last_name: Carreira
- first_name: Cristian
full_name: Sminchisescu, Cristian
last_name: Sminchisescu
citation:
ama: 'Ion A, Carreira J, Sminchisescu C. Image segmentation by figure-ground composition
into maximal cliques. In: IEEE; 2012. doi:10.1109/ICCV.2011.6126486'
apa: 'Ion, A., Carreira, J., & Sminchisescu, C. (2012). Image segmentation by
figure-ground composition into maximal cliques. Presented at the ICCV: International
Conference on Computer Vision, Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126486'
chicago: Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Image Segmentation
by Figure-Ground Composition into Maximal Cliques.” IEEE, 2012. https://doi.org/10.1109/ICCV.2011.6126486.
ieee: 'A. Ion, J. Carreira, and C. Sminchisescu, “Image segmentation by figure-ground
composition into maximal cliques,” presented at the ICCV: International Conference
on Computer Vision, Barcelona, Spain, 2012.'
ista: 'Ion A, Carreira J, Sminchisescu C. 2012. Image segmentation by figure-ground
composition into maximal cliques. ICCV: International Conference on Computer Vision,
6126486.'
mla: Ion, Adrian, et al. Image Segmentation by Figure-Ground Composition into
Maximal Cliques. 6126486, IEEE, 2012, doi:10.1109/ICCV.2011.6126486.
short: A. Ion, J. Carreira, C. Sminchisescu, in:, IEEE, 2012.
conference:
end_date: 2011-11-13
location: Barcelona, Spain
name: 'ICCV: International Conference on Computer Vision'
start_date: 2011-11-06
date_created: 2018-12-11T12:02:21Z
date_published: 2012-01-12T00:00:00Z
date_updated: 2021-01-12T07:42:15Z
day: '12'
department:
- _id: HeEd
doi: 10.1109/ICCV.2011.6126486
language:
- iso: eng
month: '01'
oa_version: None
publication_status: published
publisher: IEEE
publist_id: '3382'
quality_controlled: '1'
status: public
title: Image segmentation by figure-ground composition into maximal cliques
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '3282'
abstract:
- lang: eng
text: 'Traditionally, symmetric-key message authentication codes (MACs) are easily
built from pseudorandom functions (PRFs). In this work we propose a wide variety
of other approaches to building efficient MACs, without going through a PRF first.
In particular, unlike deterministic PRF-based MACs, where each message has a unique
valid tag, we give a number of probabilistic MAC constructions from various other
primitives/assumptions. Our main results are summarized as follows: We show several
new probabilistic MAC constructions from a variety of general assumptions, including
CCA-secure encryption, Hash Proof Systems and key-homomorphic weak PRFs. By instantiating
these frameworks under concrete number theoretic assumptions, we get several schemes
which are more efficient than just using a state-of-the-art PRF instantiation
under the corresponding assumption. For probabilistic MACs, unlike deterministic
ones, unforgeability against a chosen message attack (uf-cma ) alone does not
imply security if the adversary can additionally make verification queries (uf-cmva
). We give an efficient generic transformation from any uf-cma secure MAC which
is "message-hiding" into a uf-cmva secure MAC. This resolves the main
open problem of Kiltz et al. from Eurocrypt''11; By using our transformation on
their constructions, we get the first efficient MACs from the LPN assumption.
While all our new MAC constructions immediately give efficient actively secure,
two-round symmetric-key identification schemes, we also show a very simple, three-round
actively secure identification protocol from any weak PRF. In particular, the
resulting protocol is much more efficient than the trivial approach of building
a regular PRF from a weak PRF. © 2012 International Association for Cryptologic
Research.'
acknowledgement: Supported by the European Research Council under the European Union’s
Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC)
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Eike
full_name: Kiltz, Eike
last_name: Kiltz
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: 'Dodis Y, Pietrzak KZ, Kiltz E, Wichs D. Message authentication, revisited.
In: Vol 7237. Springer; 2012:355-374. doi:10.1007/978-3-642-29011-4_22'
apa: 'Dodis, Y., Pietrzak, K. Z., Kiltz, E., & Wichs, D. (2012). Message authentication,
revisited (Vol. 7237, pp. 355–374). Presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, Cambridge, UK: Springer. https://doi.org/10.1007/978-3-642-29011-4_22'
chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, Eike Kiltz, and Daniel Wichs. “Message
Authentication, Revisited,” 7237:355–74. Springer, 2012. https://doi.org/10.1007/978-3-642-29011-4_22.
ieee: 'Y. Dodis, K. Z. Pietrzak, E. Kiltz, and D. Wichs, “Message authentication,
revisited,” presented at the EUROCRYPT: Theory and Applications of Cryptographic
Techniques, Cambridge, UK, 2012, vol. 7237, pp. 355–374.'
ista: 'Dodis Y, Pietrzak KZ, Kiltz E, Wichs D. 2012. Message authentication, revisited.
EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 7237,
355–374.'
mla: Dodis, Yevgeniy, et al. Message Authentication, Revisited. Vol. 7237,
Springer, 2012, pp. 355–74, doi:10.1007/978-3-642-29011-4_22.
short: Y. Dodis, K.Z. Pietrzak, E. Kiltz, D. Wichs, in:, Springer, 2012, pp. 355–374.
conference:
end_date: 2012-04-19
location: Cambridge, UK
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2012-04-15
date_created: 2018-12-11T12:02:27Z
date_published: 2012-03-10T00:00:00Z
date_updated: 2021-01-12T07:42:22Z
day: '10'
ddc:
- '000'
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-642-29011-4_22
ec_funded: 1
file:
- access_level: open_access
checksum: 8557c17a8c2586d06ebfe62d934f5c5f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:23Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5074'
file_name: IST-2016-686-v1+1_059.pdf
file_size: 372292
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
intvolume: ' 7237'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 355 - 374
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '3364'
pubrep_id: '686'
quality_controlled: '1'
status: public
title: Message authentication, revisited
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: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7237
year: '2012'
...
---
_id: '3280'
abstract:
- lang: eng
text: 'The (decisional) learning with errors problem (LWE) asks to distinguish "noisy"
inner products of a secret vector with random vectors from uniform. The learning
parities with noise problem (LPN) is the special case where the elements of the
vectors are bits. In recent years, the LWE and LPN problems have found many applications
in cryptography. In this paper we introduce a (seemingly) much stronger adaptive
assumption, called "subspace LWE" (SLWE), where the adversary can learn
the inner product of the secret and random vectors after they were projected into
an adaptively and adversarially chosen subspace. We prove that, surprisingly,
the SLWE problem mapping into subspaces of dimension d is almost as hard as LWE
using secrets of length d (the other direction is trivial.) This result immediately
implies that several existing cryptosystems whose security is based on the hardness
of the LWE/LPN problems are provably secure in a much stronger sense than anticipated.
As an illustrative example we show that the standard way of using LPN for symmetric
CPA secure encryption is even secure against a very powerful class of related
key attacks. '
acknowledgement: Supported by the European Research Council under the European Union’s
Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC).
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. Subspace LWE. In: Vol 7194. Springer; 2012:548-563. doi:10.1007/978-3-642-28914-9_31'
apa: 'Pietrzak, K. Z. (2012). Subspace LWE (Vol. 7194, pp. 548–563). Presented at
the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer.
https://doi.org/10.1007/978-3-642-28914-9_31'
chicago: Pietrzak, Krzysztof Z. “Subspace LWE,” 7194:548–63. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_31.
ieee: 'K. Z. Pietrzak, “Subspace LWE,” presented at the TCC: Theory of Cryptography
Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 548–563.'
ista: 'Pietrzak KZ. 2012. Subspace LWE. TCC: Theory of Cryptography Conference,
LNCS, vol. 7194, 548–563.'
mla: Pietrzak, Krzysztof Z. Subspace LWE. Vol. 7194, Springer, 2012, pp.
548–63, doi:10.1007/978-3-642-28914-9_31.
short: K.Z. Pietrzak, in:, Springer, 2012, pp. 548–563.
conference:
end_date: 2012-03-21
location: Taormina, Sicily, Italy
name: 'TCC: Theory of Cryptography Conference'
start_date: 2012-03-19
date_created: 2018-12-11T12:02:26Z
date_published: 2012-05-04T00:00:00Z
date_updated: 2021-01-12T07:42:21Z
day: '04'
department:
- _id: KrPi
doi: 10.1007/978-3-642-28914-9_31
ec_funded: 1
intvolume: ' 7194'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.iacr.org/archive/tcc2012/71940166/71940166.pdf
month: '05'
oa: 1
oa_version: Submitted Version
page: 548 - 563
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '3366'
quality_controlled: '1'
status: public
title: Subspace LWE
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7194
year: '2012'
...
---
_id: '3281'
abstract:
- lang: eng
text: 'We consider the problem of amplifying the "lossiness" of functions.
We say that an oracle circuit C*: {0,1} m → {0,1}* amplifies relative lossiness
from ℓ/n to L/m if for every function f:{0,1} n → {0,1} n it holds that 1 If f
is injective then so is C f. 2 If f has image size of at most 2 n-ℓ, then C f
has image size at most 2 m-L. The question is whether such C* exists for L/m ≫
ℓ/n. This problem arises naturally in the context of cryptographic "lossy
functions," where the relative lossiness is the key parameter. We show that
for every circuit C* that makes at most t queries to f, the relative lossiness
of C f is at most L/m ≤ ℓ/n + O(log t)/n. In particular, no black-box method making
a polynomial t = poly(n) number of queries can amplify relative lossiness by more
than an O(logn)/n additive term. We show that this is tight by giving a simple
construction (cascading with some randomization) that achieves such amplification.'
acknowledgement: "We would like to thank Oded Goldreich and Omer Rein- gold for discussions
at an early stage of this project, and Scott Aaronson for clarifications regarding
the collision problem.\r\n"
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Alon
full_name: Rosen, Alon
last_name: Rosen
- first_name: Gil
full_name: Segev, Gil
last_name: Segev
citation:
ama: 'Pietrzak KZ, Rosen A, Segev G. Lossy functions do not amplify well. In: Vol
7194. Springer; 2012:458-475. doi:10.1007/978-3-642-28914-9_26'
apa: 'Pietrzak, K. Z., Rosen, A., & Segev, G. (2012). Lossy functions do not
amplify well (Vol. 7194, pp. 458–475). Presented at the TCC: Theory of Cryptography
Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_26'
chicago: Pietrzak, Krzysztof Z, Alon Rosen, and Gil Segev. “Lossy Functions Do Not
Amplify Well,” 7194:458–75. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_26.
ieee: 'K. Z. Pietrzak, A. Rosen, and G. Segev, “Lossy functions do not amplify well,”
presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy,
2012, vol. 7194, pp. 458–475.'
ista: 'Pietrzak KZ, Rosen A, Segev G. 2012. Lossy functions do not amplify well.
TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 458–475.'
mla: Pietrzak, Krzysztof Z., et al. Lossy Functions Do Not Amplify Well.
Vol. 7194, Springer, 2012, pp. 458–75, doi:10.1007/978-3-642-28914-9_26.
short: K.Z. Pietrzak, A. Rosen, G. Segev, in:, Springer, 2012, pp. 458–475.
conference:
end_date: 2012-03-21
location: Taormina, Sicily, Italy
name: 'TCC: Theory of Cryptography Conference'
start_date: 2012-03-19
date_created: 2018-12-11T12:02:26Z
date_published: 2012-05-04T00:00:00Z
date_updated: 2021-01-12T07:42:22Z
day: '04'
department:
- _id: KrPi
doi: 10.1007/978-3-642-28914-9_26
intvolume: ' 7194'
language:
- iso: eng
main_file_link:
- url: http://www.iacr.org/archive/tcc2012/tcc2012-index.html
month: '05'
oa_version: None
page: 458 - 475
publication_status: published
publisher: Springer
publist_id: '3365'
quality_controlled: '1'
status: public
title: Lossy functions do not amplify well
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7194
year: '2012'
...
---
_id: '3284'
abstract:
- lang: eng
text: |-
We study the complexity of valued constraint satisfaction problems (VCSP). A problem from VCSP is characterised by a constraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimise the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well-understood, see Raghavendra [FOCS’08]. However, there is no characterisation of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimisation perspective.
We consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0, ∞}-valued cost functions (i.e. relations), such languages have been called conservative and studied by Bulatov [LICS’03] and recently by Barto [LICS’11]. Since we study valued languages, we call a language conservative if it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [AIJ’06] for languages over Boolean domains, by Deineko et al. [JACM’08] for {0,1}-valued languages (a.k.a Max-CSP), and by Takhanov [STACS’10] for {0,∞}-valued languages containing all finite- valued unary cost functions (a.k.a. Min-Cost-Hom).
We prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination of STP and MJN multimorphisms), then any instance can be solved in polynomial time (via a new algorithm developed in this paper), otherwise the language is NP-hard. This is the first complete complexity classification of general-valued constraint languages over non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains is significantly harder than the Boolean case. The polynomial-time algorithm we present for the tractable cases is a generalisation of the submodular minimisation problem and a result of Cohen et al. [TCS’08].
Our results generalise previous results by Takhanov [STACS’10] and (a subset of results) by Cohen et al. [AIJ’06] and Deineko et al. [JACM’08]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [JACM’08], and provide a powerful tool for proving hardness of finite-valued and general-valued languages.
acknowledgement: Vladimir Kolmogorov is supported by the Royal Academy of Eng ineering/EPSRC.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Stanislav
full_name: Živný, Stanislav
last_name: Živný
citation:
ama: 'Kolmogorov V, Živný S. The complexity of conservative valued CSPs. In: SIAM;
2012:750-759.'
apa: 'Kolmogorov, V., & Živný, S. (2012). The complexity of conservative valued
CSPs (pp. 750–759). Presented at the SODA: Symposium on Discrete Algorithms, SIAM.'
chicago: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative
Valued CSPs,” 750–59. SIAM, 2012.
ieee: 'V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,”
presented at the SODA: Symposium on Discrete Algorithms, 2012, pp. 750–759.'
ista: 'Kolmogorov V, Živný S. 2012. The complexity of conservative valued CSPs.
SODA: Symposium on Discrete Algorithms, 750–759.'
mla: Kolmogorov, Vladimir, and Stanislav Živný. The Complexity of Conservative
Valued CSPs. SIAM, 2012, pp. 750–59.
short: V. Kolmogorov, S. Živný, in:, SIAM, 2012, pp. 750–759.
conference:
name: 'SODA: Symposium on Discrete Algorithms'
date_created: 2018-12-11T12:02:27Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:23Z
day: '01'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1008.1555
month: '01'
oa: 1
page: 750 - 759
publication_status: published
publisher: SIAM
publist_id: '3362'
quality_controlled: 0
status: public
title: The complexity of conservative valued CSPs
type: conference
year: '2012'
...
---
_id: '330'
abstract:
- lang: eng
text: 'A procedure for the continuous production of Cu 2ZnSnS 4 (CZTS) nanoparticles
with controlled composition is presented. CZTS nanoparticles were prepared through
the reaction of the metals'' amino complexes with elemental sulfur in a continuous-flow
reactor at moderate temperatures (300-330 °C). High-resolution transmission electron
microscopy and X-ray diffraction analysis showed the nanocrystals to have a crystallographic
structure compatible with that of the kesterite. Chemical characterization of
the materials showed the presence of the four elements in each individual nanocrystal.
Composition control was achieved by adjusting the solution flow rate through the
reactor and the proper choice of the nominal precursor concentration within the
flowing solution. Single-particle analysis revealed a composition distribution
within each sample, which was optimized at the highest synthesis temperatures
used. '
article_processing_charge: No
article_type: original
author:
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Alex
full_name: Carrete, Alex
last_name: Carrete
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. Continuous production of
Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the
American Chemical Society. 2012;134(3):1438-1441. doi:10.1021/ja209688a
apa: Shavel, A., Cadavid, D., Ibáñez, M., Carrete, A., & Cabot, A. (2012). Continuous
production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal
of the American Chemical Society. ACS. https://doi.org/10.1021/ja209688a
chicago: Shavel, Alexey, Doris Cadavid, Maria Ibáñez, Alex Carrete, and Andreu Cabot.
“Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow
Reactor.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja209688a.
ieee: A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, and A. Cabot, “Continuous production
of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor,” Journal of
the American Chemical Society, vol. 134, no. 3. ACS, pp. 1438–1441, 2012.
ista: Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. 2012. Continuous production
of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the
American Chemical Society. 134(3), 1438–1441.
mla: Shavel, Alexey, et al. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf
Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society,
vol. 134, no. 3, ACS, 2012, pp. 1438–41, doi:10.1021/ja209688a.
short: A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, A. Cabot, Journal of the American
Chemical Society 134 (2012) 1438–1441.
date_created: 2018-12-11T11:45:51Z
date_published: 2012-01-02T00:00:00Z
date_updated: 2021-01-12T07:42:29Z
day: '02'
doi: 10.1021/ja209688a
extern: '1'
intvolume: ' 134'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 1438 - 1441
publication: Journal of the American Chemical Society
publication_status: published
publisher: ACS
publist_id: '7531'
quality_controlled: '1'
status: public
title: Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow
reactor
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 134
year: '2012'
...
---
_id: '3317'
abstract:
- lang: eng
text: The physical distance between presynaptic Ca2+ channels and the Ca2+ sensors
that trigger exocytosis of neurotransmitter-containing vesicles is a key determinant
of the signalling properties of synapses in the nervous system. Recent functional
analysis indicates that in some fast central synapses, transmitter release is
triggered by a small number of Ca2+ channels that are coupled to Ca2+ sensors
at the nanometre scale. Molecular analysis suggests that this tight coupling is
generated by protein–protein interactions involving Ca2+ channels, Ca2+ sensors
and various other synaptic proteins. Nanodomain coupling has several functional
advantages, as it increases the efficacy, speed and energy efficiency of synaptic
transmission.
acknowledgement: "Work of the authors was funded by grants of the Deutsche Forschungsgemeinschaft
to P.J. (grants SFB 780/A5, TR 3/B10 and the Leibniz programme), a European Research
Council Advanced grant to P.J. and a Swiss National Foundation fellowship to E.E.\r\nWe
thank D. Tsien and E. Neher for their comments on this Review, J. Guzmán and A.
Pernía-Andrade for reading earlier versions and E. Kramberger for perfect editorial
support. We apologize that owing to space constraints, not all relevant papers could
be cited.\r\n"
author:
- first_name: Emmanuel
full_name: Eggermann, Emmanuel
id: 34DACA34-E9AE-11E9-849C-D35BD8ADC20C
last_name: Eggermann
- first_name: Iancu
full_name: Bucurenciu, Iancu
id: 4BD1D872-E9AE-11E9-9EE9-8BF4597A9E2A
last_name: Bucurenciu
- first_name: Sarit
full_name: Goswami, Sarit
id: 3A578F32-F248-11E8-B48F-1D18A9856A87
last_name: Goswami
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Eggermann E, Bucurenciu I, Goswami S, Jonas PM. Nanodomain coupling between
Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature
Reviews Neuroscience. 2012;13(1):7-21. doi:10.1038/nrn3125
apa: Eggermann, E., Bucurenciu, I., Goswami, S., & Jonas, P. M. (2012). Nanodomain
coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses.
Nature Reviews Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nrn3125
chicago: Eggermann, Emmanuel, Iancu Bucurenciu, Sarit Goswami, and Peter M Jonas.
“Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast
Mammalian Synapses.” Nature Reviews Neuroscience. Nature Publishing Group,
2012. https://doi.org/10.1038/nrn3125.
ieee: E. Eggermann, I. Bucurenciu, S. Goswami, and P. M. Jonas, “Nanodomain coupling
between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses,”
Nature Reviews Neuroscience, vol. 13, no. 1. Nature Publishing Group, pp.
7–21, 2012.
ista: Eggermann E, Bucurenciu I, Goswami S, Jonas PM. 2012. Nanodomain coupling
between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses.
Nature Reviews Neuroscience. 13(1), 7–21.
mla: Eggermann, Emmanuel, et al. “Nanodomain Coupling between Ca(2+) Channels and
Sensors of Exocytosis at Fast Mammalian Synapses.” Nature Reviews Neuroscience,
vol. 13, no. 1, Nature Publishing Group, 2012, pp. 7–21, doi:10.1038/nrn3125.
short: E. Eggermann, I. Bucurenciu, S. Goswami, P.M. Jonas, Nature Reviews Neuroscience
13 (2012) 7–21.
date_created: 2018-12-11T12:02:38Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:36Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/nrn3125
file:
- access_level: open_access
checksum: 4c1c86b2f6e4e1562f5bb800b457ea9f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:13Z
date_updated: 2020-07-14T12:46:07Z
file_id: '4931'
file_name: IST-2017-820-v1+1_17463_3_art_file_109404_ltmxbw.pdf
file_size: 314246
relation: main_file
- access_level: open_access
checksum: bceb2efdd49d115f4dde8486bc1be3f2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:14Z
date_updated: 2020-07-14T12:46:07Z
file_id: '4932'
file_name: IST-2017-820-v1+2_17463_3_figure_109402_ltmwlp.pdf
file_size: 1840216
relation: main_file
file_date_updated: 2020-07-14T12:46:07Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 7 - 21
project:
- _id: 25BC64A8-B435-11E9-9278-68D0E5697425
grant_number: JO_780/A5
name: Synaptic Mechanisms of Neuronal Network Function
- _id: 25BDE9A4-B435-11E9-9278-68D0E5697425
grant_number: SFB-TR3-TP10B
name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen
publication: Nature Reviews Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '3322'
pubrep_id: '820'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast
mammalian synapses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2012'
...
---
_id: '3314'
abstract:
- lang: eng
text: We introduce two-level discounted and mean-payoff games played by two players
on a perfect-information stochastic game graph. The upper level game is a discounted
or mean-payoff game and the lower level game is a (undiscounted) reachability
game. Two-level games model hierarchical and sequential decision making under
uncertainty across different time scales. For both discounted and mean-payoff
two-level games, we show the existence of pure memoryless optimal strategies for
both players and an ordered field property. We show that if there is only one
player (Markov decision processes), then the values can be computed in polynomial
time. It follows that whether the value of a player is equal to a given rational
constant in two-level discounted or mean-payoff games can be decided in NP ∩ coNP.
We also give an alternate strategy improvement algorithm to compute the value.
© 2012 World Scientific Publishing Company.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: Chatterjee K, Majumdar R. Discounting and averaging in games across time scales.
International Journal of Foundations of Computer Science. 2012;23(3):609-625.
doi:10.1142/S0129054112400308
apa: Chatterjee, K., & Majumdar, R. (2012). Discounting and averaging in games
across time scales. International Journal of Foundations of Computer Science.
World Scientific Publishing. https://doi.org/10.1142/S0129054112400308
chicago: Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging
in Games across Time Scales.” International Journal of Foundations of Computer
Science. World Scientific Publishing, 2012. https://doi.org/10.1142/S0129054112400308.
ieee: K. Chatterjee and R. Majumdar, “Discounting and averaging in games across
time scales,” International Journal of Foundations of Computer Science,
vol. 23, no. 3. World Scientific Publishing, pp. 609–625, 2012.
ista: Chatterjee K, Majumdar R. 2012. Discounting and averaging in games across
time scales. International Journal of Foundations of Computer Science. 23(3),
609–625.
mla: Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging in
Games across Time Scales.” International Journal of Foundations of Computer
Science, vol. 23, no. 3, World Scientific Publishing, 2012, pp. 609–25, doi:10.1142/S0129054112400308.
short: K. Chatterjee, R. Majumdar, International Journal of Foundations of Computer
Science 23 (2012) 609–625.
date_created: 2018-12-11T12:02:37Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2021-01-12T07:42:35Z
day: '01'
department:
- _id: KrCh
doi: 10.1142/S0129054112400308
intvolume: ' 23'
issue: '3'
language:
- iso: eng
month: '04'
oa_version: None
page: 609 - 625
project:
- _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: International Journal of Foundations of Computer Science
publication_status: published
publisher: World Scientific Publishing
publist_id: '3326'
quality_controlled: '1'
scopus_import: 1
status: public
title: Discounting and averaging in games across time scales
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2012'
...
---
_id: '3115'
abstract:
- lang: eng
text: 'We consider the offset-deconstruction problem: Given a polygonal shape Q
with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance,
as the Minkowski sum of another polygonal shape P with a disk of fixed radius?
If it does, we also seek a preferably simple-looking solution P; then, P''s offset
constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We
give an O(nlogn)-time exact decision algorithm that handles any polygonal shape,
assuming the real-RAM model of computation. A variant of the algorithm, which
we have implemented using the cgal library, is based on rational arithmetic and
answers the same deconstruction problem up to an uncertainty parameter δ its running
time additionally depends on δ. If the input shape is found to be approximable,
this algorithm also computes an approximate solution for the problem. It also
allows us to solve parameter-optimization problems induced by the offset-deconstruction
problem. For convex shapes, the complexity of the exact decision algorithm drops
to O(n), which is also the time required to compute a solution P with at most
one more vertex than a vertex-minimal one.'
acknowledgement: "We thank Eyal Flato (Plataine Ltd.) for raising the offset-deconstruction
problem in connection with wood cutting. We also thank Tim Bretl (UIUC) for suggesting
the digital-pen offset-deconstruction problem. This work has been supported in part
by the Israel Science Foundation (grant no. 1102/11), by the German–Israeli Foundation
(grant no. 969/07), by the Hermann Minkowski–Minerva Center for Geometry at Tel
Aviv University, and by the EU Project under Contract No. 255827 (CGL—Computational
Geometry Learning).\r\n"
author:
- first_name: Eric
full_name: Berberich, Eric
last_name: Berberich
- first_name: Dan
full_name: Halperin, Dan
last_name: Halperin
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Roza
full_name: Pogalnikova, Roza
last_name: Pogalnikova
citation:
ama: Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate
offsets. Discrete & Computational Geometry. 2012;48(4):964-989. doi:10.1007/s00454-012-9441-5
apa: Berberich, E., Halperin, D., Kerber, M., & Pogalnikova, R. (2012). Deconstructing
approximate offsets. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-012-9441-5
chicago: Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing
Approximate Offsets.” Discrete & Computational Geometry. Springer,
2012. https://doi.org/10.1007/s00454-012-9441-5.
ieee: E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing
approximate offsets,” Discrete & Computational Geometry, vol. 48, no.
4. Springer, pp. 964–989, 2012.
ista: Berberich E, Halperin D, Kerber M, Pogalnikova R. 2012. Deconstructing approximate
offsets. Discrete & Computational Geometry. 48(4), 964–989.
mla: Berberich, Eric, et al. “Deconstructing Approximate Offsets.” Discrete &
Computational Geometry, vol. 48, no. 4, Springer, 2012, pp. 964–89, doi:10.1007/s00454-012-9441-5.
short: E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, Discrete & Computational
Geometry 48 (2012) 964–989.
date_created: 2018-12-11T12:01:28Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2023-02-23T11:22:30Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00454-012-9441-5
external_id:
arxiv:
- '1109.2158'
intvolume: ' 48'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1109.2158
month: '12'
oa: 1
oa_version: Preprint
page: 964 - 989
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '3584'
quality_controlled: '1'
related_material:
record:
- id: '3329'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Deconstructing approximate offsets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2012'
...
---
_id: '3331'
abstract:
- lang: eng
text: Computing the topology of an algebraic plane curve C means computing a combinatorial
graph that is isotopic to C and thus represents its topology in R2. We prove that,
for a polynomial of degree n with integer coefficients bounded by 2ρ, the topology
of the induced curve can be computed with bit operations ( indicates that we
omit logarithmic factors). Our analysis improves the previous best known complexity
bounds by a factor of n2. The improvement is based on new techniques to compute
and refine isolating intervals for the real roots of polynomials, and on the consequent
amortized analysis of the critical fibers of the algebraic curve.
author:
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Michael
full_name: Sagraloff, Michael
last_name: Sagraloff
citation:
ama: Kerber M, Sagraloff M. A worst case bound for topology computation of algebraic
curves. Journal of Symbolic Computation. 2012;47(3):239-258. doi:10.1016/j.jsc.2011.11.001
apa: Kerber, M., & Sagraloff, M. (2012). A worst case bound for topology computation
of algebraic curves. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2011.11.001
chicago: Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology
Computation of Algebraic Curves.” Journal of Symbolic Computation. Elsevier,
2012. https://doi.org/10.1016/j.jsc.2011.11.001.
ieee: M. Kerber and M. Sagraloff, “A worst case bound for topology computation of
algebraic curves,” Journal of Symbolic Computation, vol. 47, no. 3. Elsevier,
pp. 239–258, 2012.
ista: Kerber M, Sagraloff M. 2012. A worst case bound for topology computation of
algebraic curves. Journal of Symbolic Computation. 47(3), 239–258.
mla: Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology Computation
of Algebraic Curves.” Journal of Symbolic Computation, vol. 47, no. 3,
Elsevier, 2012, pp. 239–58, doi:10.1016/j.jsc.2011.11.001.
short: M. Kerber, M. Sagraloff, Journal of Symbolic Computation 47 (2012) 239–258.
date_created: 2018-12-11T12:02:43Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2021-01-12T07:42:43Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.jsc.2011.11.001
intvolume: ' 47'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1104.1510
month: '03'
oa: 1
oa_version: Preprint
page: 239 - 258
publication: ' Journal of Symbolic Computation'
publication_status: published
publisher: Elsevier
publist_id: '3303'
quality_controlled: '1'
scopus_import: 1
status: public
title: A worst case bound for topology computation of algebraic curves
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2012'
...
---
_id: '346'
abstract:
- lang: eng
text: Arrays of vertically aligned ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell
nanowires (NWs) were prepared by means of the combination of two solution-growth
processes. First, single-crystal ZnO NWs with controlled n-type doping were grown
on conducting substrates by a low-cost, high-yield and seed-free electrochemical
route. These NWs were covered by a titanium oxide shell of tunable thickness mediating
successive adsorption-hydrolysis-condensation steps. Using this atomic-layer growth
procedure, titania shells with controlled thickness and the anatase TiO2 phase
were obtained after sintering at 450 °C. Higher sintering temperatures resulted
in the formation of ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs by the interdiffusion
of Zn and Ti ions at the ZnO–TiO2 interface. The performance of ZnO : Cl/TiO2
and ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs towards photoelectrochemical (PEC) water
splitting was investigated as a function of the titania shell thickness. Furthermore,
the performance of such core–shell NWs as photoelectrodes in dye-sensitized solar
cells was also characterized. The TiO2 presence at the ZnO : Cl surface promoted
a two-fold increase on the produced photocurrent densities, probing their potential
for PEC and optoelectronic applications. Electrochemical impedance spectroscopy
was used to corroborate the lower resistance for charge transfer between the NWs
and the electrolyte in the presence of the TiO2 shell.
acknowledgement: The research was supported by the European Regional Development Funds
and the Spanish MICINN projects MAT2010-15138, MAT2010-21510 and CSD2009-00050.
JF and AS thank the FI-DGR and BP grants from the Agència de Gestió d'Ajuts Universitaris
i de Recerca (AGAUR) from the Catalan Government. MI and AC thank the Spanish MICINN
for the PhD grant and the financial support through the Ramóny Cajal program.
article_processing_charge: No
article_type: original
author:
- first_name: Jiandong
full_name: Fan, Jiandong
last_name: Fan
- first_name: Reza
full_name: Zamani, Reza
last_name: Zamani
- first_name: Cristina
full_name: Fábrega, Cristina
last_name: Fábrega
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Cristina
full_name: Flox, Cristina
last_name: Flox
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Teresa
full_name: Andreu, Teresa
last_name: Andreu
- first_name: Amtonio
full_name: López, Amtonio
last_name: López
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Joan
full_name: Morante, Joan
last_name: Morante
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Fan J, Zamani R, Fábrega C, et al. Solution-growth and optoelectronic performance
of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell
thickness. Journal of Physics D: Applied Physics. 2012;45(41). doi:10.1088/0022-3727/45/41/415301'
apa: 'Fan, J., Zamani, R., Fábrega, C., Shavel, A., Flox, C., Ibáñez, M., … Cabot,
A. (2012). Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and
ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness. Journal
of Physics D: Applied Physics. IOP Publishing Ltd. https://doi.org/10.1088/0022-3727/45/41/415301'
chicago: 'Fan, Jiandong, Reza Zamani, Cristina Fábrega, Alexey Shavel, Cristina
Flox, Maria Ibáñez, Teresa Andreu, et al. “Solution-Growth and Optoelectronic
Performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 Core–Shell Nanowires with
Tunable Shell Thickness.” Journal of Physics D: Applied Physics. IOP Publishing
Ltd., 2012. https://doi.org/10.1088/0022-3727/45/41/415301.'
ieee: 'J. Fan et al., “Solution-growth and optoelectronic performance of
ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell
thickness,” Journal of Physics D: Applied Physics, vol. 45, no. 41. IOP
Publishing Ltd., 2012.'
ista: 'Fan J, Zamani R, Fábrega C, Shavel A, Flox C, Ibáñez M, Andreu T, López A,
Arbiol J, Morante J, Cabot A. 2012. Solution-growth and optoelectronic performance
of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell
thickness. Journal of Physics D: Applied Physics. 45(41).'
mla: 'Fan, Jiandong, et al. “Solution-Growth and Optoelectronic Performance of ZnO : Cl/TiO2
and ZnO : Cl/ZnxTiOy/TiO2 Core–Shell Nanowires with Tunable Shell Thickness.”
Journal of Physics D: Applied Physics, vol. 45, no. 41, IOP Publishing
Ltd., 2012, doi:10.1088/0022-3727/45/41/415301.'
short: 'J. Fan, R. Zamani, C. Fábrega, A. Shavel, C. Flox, M. Ibáñez, T. Andreu,
A. López, J. Arbiol, J. Morante, A. Cabot, Journal of Physics D: Applied Physics
45 (2012).'
date_created: 2018-12-11T11:45:56Z
date_published: 2012-10-17T00:00:00Z
date_updated: 2021-01-12T07:43:36Z
day: '17'
doi: 10.1088/0022-3727/45/41/415301
extern: '1'
intvolume: ' 45'
issue: '41'
language:
- iso: eng
month: '10'
oa_version: None
publication: 'Journal of Physics D: Applied Physics'
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '7486'
quality_controlled: '1'
status: public
title: Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2
core–shell nanowires with tunable shell thickness
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2012'
...
---
_id: '3168'
abstract:
- lang: eng
text: The induction of a signaling pathway is characterized by transient complex
formation and mutual posttranslational modification of proteins. To faithfully
capture this combinatorial process in a mathematical model is an important challenge
in systems biology. Exploiting the limited context on which most binding and modification
events are conditioned, attempts have been made to reduce the combinatorial complexity
by quotienting the reachable set of molecular species into species aggregates
while preserving the deterministic semantics of the thermodynamic limit. Recently,
we proposed a quotienting that also preserves the stochastic semantics and that
is complete in the sense that the semantics of individual species can be recovered
from the aggregate semantics. In this paper, we prove that this quotienting yields
a sufficient condition for weak lumpability (that is to say that the quotient
system is still Markovian for a given set of initial distributions) and that it
gives rise to a backward Markov bisimulation between the original and aggregated
transition system (which means that the conditional probability of being in a
given state in the original system knowing that we are in its equivalence class
is an invariant of the system). We illustrate the framework on a case study of
the epidermal growth factor (EGF)/insulin receptor crosstalk.
acknowledgement: "We would like to thank the anonymous reviewers for their comments
on the different versions of the paper. We would also like to thank Ferdinanda Camporesi
for her careful reading and the useful insights that she gave us about the paper.\r\nJérôme
Feret’s contribution was partially supported by the AbstractCell ANR-Chair of Excellence.
Heinz Koeppl’s research is supported by the Swiss National Science Foundation, grant
no. 200020-117975/1. Tatjana Petrov’s research is supported by SystemsX.ch (the
Swiss Initiative in Systems Biology)."
author:
- first_name: Jérôme
full_name: Feret, Jérôme
last_name: Feret
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Heinz
full_name: Koeppl, Heinz
last_name: Koeppl
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule
based systems. Theoretical Computer Science. 2012;431:137-164. doi:10.1016/j.tcs.2011.12.059
apa: Feret, J., Henzinger, T. A., Koeppl, H., & Petrov, T. (2012). Lumpability
abstractions of rule based systems. Theoretical Computer Science. Elsevier.
https://doi.org/10.1016/j.tcs.2011.12.059
chicago: Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability
Abstractions of Rule Based Systems.” Theoretical Computer Science. Elsevier,
2012. https://doi.org/10.1016/j.tcs.2011.12.059.
ieee: J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions
of rule based systems,” Theoretical Computer Science, vol. 431. Elsevier,
pp. 137–164, 2012.
ista: Feret J, Henzinger TA, Koeppl H, Petrov T. 2012. Lumpability abstractions
of rule based systems. Theoretical Computer Science. 431, 137–164.
mla: Feret, Jérôme, et al. “Lumpability Abstractions of Rule Based Systems.” Theoretical
Computer Science, vol. 431, Elsevier, 2012, pp. 137–64, doi:10.1016/j.tcs.2011.12.059.
short: J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, Theoretical Computer Science
431 (2012) 137–164.
date_created: 2018-12-11T12:01:47Z
date_published: 2012-05-04T00:00:00Z
date_updated: 2023-02-23T11:39:40Z
day: '04'
department:
- _id: ToHe
doi: 10.1016/j.tcs.2011.12.059
intvolume: ' 431'
language:
- iso: eng
month: '05'
oa_version: None
page: 137 - 164
publication: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '3515'
pubrep_id: '73'
quality_controlled: '1'
related_material:
record:
- id: '3719'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Lumpability abstractions of rule based systems
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 431
year: '2012'
...
---
_id: '377'
abstract:
- lang: eng
text: The potential to control the composition and crystal phase at the nanometer
scale enable the production of nanocrystalline materials with enhanced functionalities
and new applications. In the present work, we detail a novel colloidal synthesis
route to prepare nanoparticles of the ternary semiconductor Cu2GeSe3 (CGSe) with
nanometer-scale control over their crystal phases. We also demonstrate the structural
effect on the thermoelectric properties of bottom-up-prepared CGSe nanomaterials.
By careful adjustment of the nucleation and growth temperatures, pure orthorhombic
CGSe nanoparticles with cationic order or polytypic CGSe nanoparticles with disordered
cation positions can be produced. In this second type of nanoparticle, a high
density of twins can be created to periodically change the atomic plane stacking,
forming a hexagonal wurtzite CGSe phase. The high yield of the synthetic routes
reported here allows the production of single-phase and multiphase CGSe nanoparticles
in the gram scale, which permits characterization of the thermoelectric properties
of these materials. Reduced thermal conductivities and a related 2.5-fold increase
of the thermoelectric figure of merit for multiphase nanomaterials compared to
pure-phase CGSe are systematically obtained. These results are discussed in terms
of the density and efficiency of phonon scattering centers in both types of materials.
article_processing_charge: No
author:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Reza
full_name: Zamani, Reza
last_name: Zamani
- first_name: Wenhua
full_name: Li, Wenhua
last_name: Li
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Stéphane
full_name: Gorse, Stéphane
last_name: Gorse
- first_name: Nebll
full_name: Katchoi, Nebll
last_name: Katchoi
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Antonioo
full_name: López, Antonioo
last_name: López
- first_name: Joan
full_name: Morante, Joan
last_name: Morante
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Ibáñez M, Zamani R, Li W, et al. Crystallographic control at the nanoscale
to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials.
Chemistry of Materials. 2012;24(23):4615-4622. doi:10.1021/cm303252q'
apa: 'Ibáñez, M., Zamani, R., Li, W., Cadavid, D., Gorse, S., Katchoi, N., … Cabot,
A. (2012). Crystallographic control at the nanoscale to enhance functionality:
Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials. Chemistry of
Materials. American Chemical Society. https://doi.org/10.1021/cm303252q'
chicago: 'Ibáñez, Maria, Reza Zamani, Wenhua Li, Doris Cadavid, Stéphane Gorse,
Nebll Katchoi, Alexey Shavel, et al. “Crystallographic Control at the Nanoscale
to Enhance Functionality: Polytypic Cu2GeSe3 Nanoparticles as Thermoelectric Materials.”
Chemistry of Materials. American Chemical Society, 2012. https://doi.org/10.1021/cm303252q.'
ieee: 'M. Ibáñez et al., “Crystallographic control at the nanoscale to enhance
functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials,”
Chemistry of Materials, vol. 24, no. 23. American Chemical Society, pp.
4615–4622, 2012.'
ista: 'Ibáñez M, Zamani R, Li W, Cadavid D, Gorse S, Katchoi N, Shavel A, López
A, Morante J, Arbiol J, Cabot A. 2012. Crystallographic control at the nanoscale
to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials.
Chemistry of Materials. 24(23), 4615–4622.'
mla: 'Ibáñez, Maria, et al. “Crystallographic Control at the Nanoscale to Enhance
Functionality: Polytypic Cu2GeSe3 Nanoparticles as Thermoelectric Materials.”
Chemistry of Materials, vol. 24, no. 23, American Chemical Society, 2012,
pp. 4615–22, doi:10.1021/cm303252q.'
short: M. Ibáñez, R. Zamani, W. Li, D. Cadavid, S. Gorse, N. Katchoi, A. Shavel,
A. López, J. Morante, J. Arbiol, A. Cabot, Chemistry of Materials 24 (2012) 4615–4622.
date_created: 2018-12-11T11:46:07Z
date_published: 2012-11-14T00:00:00Z
date_updated: 2021-01-12T07:52:04Z
day: '14'
doi: 10.1021/cm303252q
extern: '1'
intvolume: ' 24'
issue: '23'
language:
- iso: eng
month: '11'
oa_version: None
page: 4615 - 4622
publication: Chemistry of Materials
publication_status: published
publisher: American Chemical Society
publist_id: '7452'
status: public
title: 'Crystallographic control at the nanoscale to enhance functionality: Polytypic
Cu2GeSe3 nanoparticles as thermoelectric materials'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2012'
...
---
_id: '3846'
abstract:
- lang: eng
text: We summarize classical and recent results about two-player games played on
graphs with ω-regular objectives. These games have applications in the verification
and synthesis of reactive systems. Important distinctions are whether a graph
game is turn-based or concurrent; deterministic or stochastic; zero-sum or not.
We cluster known results and open problems according to these classifications.
acknowledgement: This research was supported in part by the ONR grant N00014-02-1-0671,
by the AFOSR MURI grant F49620-00-1-0327, and by the NSF grants CCR-9988172, CCR-0085949,
and CCR-0225610.
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Chatterjee K, Henzinger TA. A survey of stochastic ω regular games. Journal
of Computer and System Sciences. 2012;78(2):394-413. doi:10.1016/j.jcss.2011.05.002
apa: Chatterjee, K., & Henzinger, T. A. (2012). A survey of stochastic ω regular
games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2011.05.002
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “A Survey of Stochastic
ω Regular Games.” Journal of Computer and System Sciences. Elsevier, 2012.
https://doi.org/10.1016/j.jcss.2011.05.002.
ieee: K. Chatterjee and T. A. Henzinger, “A survey of stochastic ω regular games,”
Journal of Computer and System Sciences, vol. 78, no. 2. Elsevier, pp.
394–413, 2012.
ista: Chatterjee K, Henzinger TA. 2012. A survey of stochastic ω regular games.
Journal of Computer and System Sciences. 78(2), 394–413.
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. “A Survey of Stochastic ω
Regular Games.” Journal of Computer and System Sciences, vol. 78, no. 2,
Elsevier, 2012, pp. 394–413, doi:10.1016/j.jcss.2011.05.002.
short: K. Chatterjee, T.A. Henzinger, Journal of Computer and System Sciences 78
(2012) 394–413.
date_created: 2018-12-11T12:05:29Z
date_published: 2012-03-02T00:00:00Z
date_updated: 2022-05-24T08:00:54Z
day: '02'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.jcss.2011.05.002
file:
- access_level: open_access
checksum: 241b939deb4517cdd4426d49c67e3fa2
content_type: application/pdf
creator: kschuh
date_created: 2019-01-29T10:54:28Z
date_updated: 2020-07-14T12:46:17Z
file_id: '5897'
file_name: a_survey_of_stochastic_omega-regular_games.pdf
file_size: 336450
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: ' 78'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jcss.2011.05.002
month: '03'
oa: 1
oa_version: Submitted Version
page: 394 - 413
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Elsevier
publist_id: '2341'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A survey of stochastic ω regular games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2012'
...
---
_id: '387'
abstract:
- lang: eng
text: In this Letter we present detailed study of the density of states near defects
in Bi 2Se 3. In particular, we present data on the commonly found triangular defects
in this system. While we do not find any measurable quasiparticle scattering interference
effects, we do find localized resonances, which can be well fitted by theory once
the potential is taken to be extended to properly account for the observed defects.
The data together with the fits confirm that while the local density of states
around the Dirac point of the electronic spectrum at the surface is significantly
disrupted near the impurity by the creation of low-energy resonance state, the
Dirac point is not locally destroyed. We discuss our results in terms of the expected
protected surface state of topological insulators. © 2012 American Physical Society.
author:
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
- first_name: Rudro
full_name: Biswas, Rudro
last_name: Biswas
- first_name: Alexander
full_name: Balatsky, Alexander
last_name: Balatsky
- first_name: James
full_name: Analytis, James
last_name: Analytis
- first_name: Jiunhaw
full_name: Chu, Jiunhaw
last_name: Chu
- first_name: Ian
full_name: Fisher, Ian
last_name: Fisher
- first_name: Aharon
full_name: Kapitulnik, Aharon
last_name: Kapitulnik
citation:
ama: Alpichshev Z, Biswas R, Balatsky A, et al. STM imaging of impurity resonances
on Bi 2Se 3. Physical Review Letters. 2012;108(20). doi:10.1103/PhysRevLett.108.206402
apa: Alpichshev, Z., Biswas, R., Balatsky, A., Analytis, J., Chu, J., Fisher, I.,
& Kapitulnik, A. (2012). STM imaging of impurity resonances on Bi 2Se 3. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.108.206402
chicago: Alpichshev, Zhanybek, Rudro Biswas, Alexander Balatsky, James Analytis,
Jiunhaw Chu, Ian Fisher, and Aharon Kapitulnik. “STM Imaging of Impurity Resonances
on Bi 2Se 3.” Physical Review Letters. American Physical Society, 2012.
https://doi.org/10.1103/PhysRevLett.108.206402.
ieee: Z. Alpichshev et al., “STM imaging of impurity resonances on Bi 2Se
3,” Physical Review Letters, vol. 108, no. 20. American Physical Society,
2012.
ista: Alpichshev Z, Biswas R, Balatsky A, Analytis J, Chu J, Fisher I, Kapitulnik
A. 2012. STM imaging of impurity resonances on Bi 2Se 3. Physical Review Letters.
108(20).
mla: Alpichshev, Zhanybek, et al. “STM Imaging of Impurity Resonances on Bi 2Se
3.” Physical Review Letters, vol. 108, no. 20, American Physical Society,
2012, doi:10.1103/PhysRevLett.108.206402.
short: Z. Alpichshev, R. Biswas, A. Balatsky, J. Analytis, J. Chu, I. Fisher, A.
Kapitulnik, Physical Review Letters 108 (2012).
date_created: 2018-12-11T11:46:11Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:49Z
day: '01'
doi: 10.1103/PhysRevLett.108.206402
extern: '1'
intvolume: ' 108'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1108.0022
month: '01'
oa: 1
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7442'
status: public
title: STM imaging of impurity resonances on Bi 2Se 3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2012'
...
---
_id: '3110'
abstract:
- lang: eng
text: 'The directional transport of the phytohormone auxin depends on the phosphorylation
status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While
PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins,
the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain
elusive. Here, we demonstrate that mutations simultaneously disrupting the function
of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein
phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits
of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN
proteins, correlating with a basal-to-apical shift in subcellular PIN localization.
The changes in PIN polarity result in increased root basipetal auxin transport
and severe defects, including shorter roots, fewer lateral roots, defective columella
cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused
cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic
data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins
(RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3)
physically interact to form a novel PP6-type heterotrimeric holoenzyme complex.
We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins
and that for SAL the strength of the interaction depends on the PIN phosphorylation
status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically
with PID to direct auxin transport polarity and plant development by directly
regulating PIN phosphorylation. '
author:
- first_name: Mingqiu
full_name: Dai, Mingqiu
last_name: Dai
- first_name: Chen
full_name: Zhang, Chen
last_name: Zhang
- first_name: Urszula
full_name: Urszula Kania
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Fang
full_name: Chen, Fang
last_name: Chen
- first_name: Qin
full_name: Xue, Qin
last_name: Xue
- first_name: Tyra
full_name: McCray, Tyra
last_name: Mccray
- first_name: Gang
full_name: Li, Gang
last_name: Li
- first_name: Genji
full_name: Qin, Genji
last_name: Qin
- first_name: Michelle
full_name: Wakeley, Michelle
last_name: Wakeley
- first_name: William
full_name: Terzaghi, William
last_name: Terzaghi
- first_name: Jianmin
full_name: Wan, Jianmin
last_name: Wan
- first_name: Yunde
full_name: Zhao, Yunde
last_name: Zhao
- first_name: Jian
full_name: Xu, Jian
last_name: Xu
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Xing
full_name: Deng, Xing W
last_name: Deng
- first_name: Haiyang
full_name: Wang, Haiyang
last_name: Wang
citation:
ama: Dai M, Zhang C, Kania U, et al. A PP6 type phosphatase holoenzyme directly
regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell.
2012;24(6):2497-2514. doi:10.1105/tpc.112.098905
apa: Dai, M., Zhang, C., Kania, U., Chen, F., Xue, Q., Mccray, T., … Wang, H. (2012).
A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin
efflux in Arabidopsis. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.112.098905
chicago: Dai, Mingqiu, Chen Zhang, Urszula Kania, Fang Chen, Qin Xue, Tyra Mccray,
Gang Li, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation
and Auxin Efflux in Arabidopsis.” Plant Cell. American Society of Plant
Biologists, 2012. https://doi.org/10.1105/tpc.112.098905.
ieee: M. Dai et al., “A PP6 type phosphatase holoenzyme directly regulates
PIN phosphorylation and auxin efflux in Arabidopsis,” Plant Cell, vol.
24, no. 6. American Society of Plant Biologists, pp. 2497–2514, 2012.
ista: Dai M, Zhang C, Kania U, Chen F, Xue Q, Mccray T, Li G, Qin G, Wakeley M,
Terzaghi W, Wan J, Zhao Y, Xu J, Friml J, Deng X, Wang H. 2012. A PP6 type phosphatase
holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis.
Plant Cell. 24(6), 2497–2514.
mla: Dai, Mingqiu, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates
PIN Phosphorylation and Auxin Efflux in Arabidopsis.” Plant Cell, vol.
24, no. 6, American Society of Plant Biologists, 2012, pp. 2497–514, doi:10.1105/tpc.112.098905.
short: M. Dai, C. Zhang, U. Kania, F. Chen, Q. Xue, T. Mccray, G. Li, G. Qin, M.
Wakeley, W. Terzaghi, J. Wan, Y. Zhao, J. Xu, J. Friml, X. Deng, H. Wang, Plant
Cell 24 (2012) 2497–2514.
date_created: 2018-12-11T12:01:27Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:08Z
day: '01'
doi: 10.1105/tpc.112.098905
extern: 1
intvolume: ' 24'
issue: '6'
month: '06'
page: 2497 - 2514
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3589'
quality_controlled: 0
status: public
title: A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and
auxin efflux in Arabidopsis
type: journal_article
volume: 24
year: '2012'
...
---
_id: '3113'
abstract:
- lang: eng
text: A cell membrane can be considered a liquid-phase plane in which lipids and
proteins theoretically are free to diffuse. Numerous reports,however, describe
retarded diffusion ofmembrane proteins in animal cells. This anomalous diffusion
results from a combination of structuring factors including protein-protein interactions,
cytoskeleton corralling, and lipid organization into microdomains. In plant cells,
plasma-membrane (PM) proteins have been described as relatively immobile, but
the control mechanisms that structure the PM have not been studied. Here, we use
fluorescence recovery after photobleaching to estimate mobility of a set of minimal
PM proteins. These proteins consist only of a PM-anchoring domain fused to a fluorescent
protein, but their mobilities remained limited, as is the case for many full-length
proteins. Neither the cytoskeleton nor membrane microdomain structure was involved
in constraining the diffusion of these proteins. The cell wall, however, was shown
to have a crucial role in immobilizing PM proteins. In addition, by single-molecule
fluorescence imaging we confirmed that the pattern of cellulose deposition in
the cell wall affects the trajectory and speed ofPMprotein diffusion. Regulation
ofPMprotein dynamics by the plant cell wall can be interpreted as a mechanism
for regulating protein interactions in processes such as trafficking and signal
transduction.
author:
- first_name: Alexandre
full_name: Martinière, Alexandre
last_name: Martinière
- first_name: Irene
full_name: Lavagi, Irene
last_name: Lavagi
- first_name: Gayathri
full_name: Nageswaran, Gayathri
last_name: Nageswaran
- first_name: Daniel
full_name: Rolfe, Daniel J
last_name: Rolfe
- first_name: Lilly
full_name: Maneta-Peyret, Lilly
last_name: Maneta Peyret
- first_name: Doan
full_name: Luu, Doan-Trung
last_name: Luu
- first_name: Stanley
full_name: Botchway, Stanley W
last_name: Botchway
- first_name: Stephen
full_name: Webb, Stephen E
last_name: Webb
- first_name: Sebastien
full_name: Mongrand, Sebastien
last_name: Mongrand
- first_name: Christophe
full_name: Maurel, Christophe
last_name: Maurel
- first_name: Marisa
full_name: Martin-Fernandez, Marisa L
last_name: Martin Fernandez
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Patrick
full_name: Moreau, Patrick
last_name: Moreau
- first_name: John
full_name: Runions, John
last_name: Runions
citation:
ama: Martinière A, Lavagi I, Nageswaran G, et al. Cell wall constrains lateral diffusion
of plant plasma membrane proteins. PNAS. 2012;109(31):12805-12810. doi:10.1073/pnas.1202040109
apa: Martinière, A., Lavagi, I., Nageswaran, G., Rolfe, D., Maneta Peyret, L., Luu,
D., … Runions, J. (2012). Cell wall constrains lateral diffusion of plant plasma
membrane proteins. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1202040109
chicago: Martinière, Alexandre, Irene Lavagi, Gayathri Nageswaran, Daniel Rolfe,
Lilly Maneta Peyret, Doan Luu, Stanley Botchway, et al. “Cell Wall Constrains
Lateral Diffusion of Plant Plasma Membrane Proteins.” PNAS. National Academy
of Sciences, 2012. https://doi.org/10.1073/pnas.1202040109.
ieee: A. Martinière et al., “Cell wall constrains lateral diffusion of plant
plasma membrane proteins,” PNAS, vol. 109, no. 31. National Academy of
Sciences, pp. 12805–12810, 2012.
ista: Martinière A, Lavagi I, Nageswaran G, Rolfe D, Maneta Peyret L, Luu D, Botchway
S, Webb S, Mongrand S, Maurel C, Martin Fernandez M, Kleine Vehn J, Friml J, Moreau
P, Runions J. 2012. Cell wall constrains lateral diffusion of plant plasma membrane
proteins. PNAS. 109(31), 12805–12810.
mla: Martinière, Alexandre, et al. “Cell Wall Constrains Lateral Diffusion of Plant
Plasma Membrane Proteins.” PNAS, vol. 109, no. 31, National Academy of
Sciences, 2012, pp. 12805–10, doi:10.1073/pnas.1202040109.
short: A. Martinière, I. Lavagi, G. Nageswaran, D. Rolfe, L. Maneta Peyret, D. Luu,
S. Botchway, S. Webb, S. Mongrand, C. Maurel, M. Martin Fernandez, J. Kleine Vehn,
J. Friml, P. Moreau, J. Runions, PNAS 109 (2012) 12805–12810.
date_created: 2018-12-11T12:01:28Z
date_published: 2012-07-31T00:00:00Z
date_updated: 2021-01-12T07:41:09Z
day: '31'
doi: 10.1073/pnas.1202040109
extern: 1
intvolume: ' 109'
issue: '31'
month: '07'
page: 12805 - 12810
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3586'
quality_controlled: 0
status: public
title: Cell wall constrains lateral diffusion of plant plasma membrane proteins
type: journal_article
volume: 109
year: '2012'
...
---
_id: '3114'
abstract:
- lang: eng
text: Auxin is a key coordinative signal required for many aspects of plant development
and its levels are controlled by auxin metabolism and intercellular auxin transport.
Here we find that a member of PIN auxin transporter family, PIN8 is expressed
in male gametophyte of Arabidopsis thaliana and has a crucial role in pollen development
and functionality. Ectopic expression in sporophytic tissues establishes a role
of PIN8 in regulating auxin homoeostasis and metabolism. PIN8 co-localizes with
PIN5 to the endoplasmic reticulum (ER) where it acts as an auxin transporter.
Genetic analyses reveal an antagonistic action of PIN5 and PIN8 in the regulation
of intracellular auxin homoeostasis and gametophyte as well as sporophyte development.
Our results reveal a role of the auxin transport in male gametophyte development
in which the distinct actions of ER-localized PIN transporters regulate cellular
auxin homoeostasis and maintain the auxin levels optimal for pollen development
and pollen tube growth.
author:
- first_name: Zhaojun
full_name: Ding, Zhaojun
last_name: Ding
- first_name: Bangjun
full_name: Wang, Bangjun
last_name: Wang
- first_name: Ignacio
full_name: Moreno, Ignacio
last_name: Moreno
- first_name: Nikoleta
full_name: Dupláková, Nikoleta
last_name: Dupláková
- first_name: Sibu
full_name: Sibu Simon
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Nicola
full_name: Carraro, Nicola
last_name: Carraro
- first_name: Jesica
full_name: Reemmer, Jesica
last_name: Reemmer
- first_name: Aleš
full_name: Pěnčík, Aleš
last_name: Pěnčík
- first_name: Xu
full_name: Xu Chen
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Ricardo
full_name: Tejos, Ricardo I
last_name: Tejos
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Stephan
full_name: Pollmann, Stephan
last_name: Pollmann
- first_name: Jozef
full_name: Mravec, Jozef
last_name: Mravec
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: David
full_name: Honys, David
last_name: Honys
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Angus
full_name: Murphy, Angus S
last_name: Murphy
- first_name: Ariel
full_name: Orellana, Ariel
last_name: Orellana
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Ding Z, Wang B, Moreno I, et al. ER-localized auxin transporter PIN8 regulates
auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications.
2012;3(AN 941). doi:10.1038/ncomms1941
apa: Ding, Z., Wang, B., Moreno, I., Dupláková, N., Simon, S., Carraro, N., … Friml,
J. (2012). ER-localized auxin transporter PIN8 regulates auxin homeostasis and
male gametophyte development in Arabidopsis. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms1941
chicago: Ding, Zhaojun, Bangjun Wang, Ignacio Moreno, Nikoleta Dupláková, Sibu Simon,
Nicola Carraro, Jesica Reemmer, et al. “ER-Localized Auxin Transporter PIN8 Regulates
Auxin Homeostasis and Male Gametophyte Development in Arabidopsis.” Nature
Communications. Nature Publishing Group, 2012. https://doi.org/10.1038/ncomms1941.
ieee: Z. Ding et al., “ER-localized auxin transporter PIN8 regulates auxin
homeostasis and male gametophyte development in Arabidopsis,” Nature Communications,
vol. 3, no. AN 941. Nature Publishing Group, 2012.
ista: Ding Z, Wang B, Moreno I, Dupláková N, Simon S, Carraro N, Reemmer J, Pěnčík
A, Chen X, Tejos R, Skůpa P, Pollmann S, Mravec J, Petrášek J, Zažímalová E, Honys
D, Rolčík J, Murphy A, Orellana A, Geisler M, Friml J. 2012. ER-localized auxin
transporter PIN8 regulates auxin homeostasis and male gametophyte development
in Arabidopsis. Nature Communications. 3(AN 941).
mla: Ding, Zhaojun, et al. “ER-Localized Auxin Transporter PIN8 Regulates Auxin
Homeostasis and Male Gametophyte Development in Arabidopsis.” Nature Communications,
vol. 3, no. AN 941, Nature Publishing Group, 2012, doi:10.1038/ncomms1941.
short: Z. Ding, B. Wang, I. Moreno, N. Dupláková, S. Simon, N. Carraro, J. Reemmer,
A. Pěnčík, X. Chen, R. Tejos, P. Skůpa, S. Pollmann, J. Mravec, J. Petrášek, E.
Zažímalová, D. Honys, J. Rolčík, A. Murphy, A. Orellana, M. Geisler, J. Friml,
Nature Communications 3 (2012).
date_created: 2018-12-11T12:01:28Z
date_published: 2012-07-03T00:00:00Z
date_updated: 2021-01-12T07:41:09Z
day: '03'
doi: 10.1038/ncomms1941
extern: 1
intvolume: ' 3'
issue: AN 941
month: '07'
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '3585'
quality_controlled: 0
status: public
title: ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte
development in Arabidopsis
type: journal_article
volume: 3
year: '2012'
...
---
_id: '3111'
abstract:
- lang: eng
text: PIN-FORMED (PIN) protein-mediated auxin polar transport is critically important
for development, pattern formation, and morphogenesis in plants. Auxin has been
implicated in the regulation of polar auxin transport by inhibiting PIN endocytosis
[1, 2], but how auxin regulates this process is poorly understood. Our genetic
screen identified the Arabidopsis SPIKE1 (SPK1) gene whose loss-of-function mutations
increased lateral root density and retarded gravitropic responses, as do pin2
knockout mutations [3]. SPK1 belongs to the conserved DHR2-Dock family of Rho
guanine nucleotide exchange factors [4-6]. The spk1 mutations induced PIN2 internalization
that was not suppressed by auxin, as did the loss-of-function mutations for Rho-like
GTPase from Plants 6 (ROP6)-GTPase or its effector RIC1. Furthermore, SPK1 was
required for auxin induction of ROP6 activation. Our results have established
a Rho GTPase-based auxin signaling pathway that maintains PIN2 polar distribution
to the plasma membrane via inhibition of its internalization in Arabidopsis roots.
Our findings provide new insights into signaling mechanisms that underlie the
regulation of the dynamic trafficking of PINs required for long-distance auxin
transport and that link auxin signaling to PIN-mediated pattern formation and
morphogenesis.
author:
- first_name: Deshu
full_name: Lin, Deshu
last_name: Lin
- first_name: Shingo
full_name: Nagawa, Shingo
last_name: Nagawa
- first_name: Jisheng
full_name: Chen, Jisheng
last_name: Chen
- first_name: Lingyan
full_name: Cao, Lingyan
last_name: Cao
- first_name: Xu
full_name: Xu Chen
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Hongjiang
full_name: Hongjiang Li
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Chizuko
full_name: Yamamuro, Chizuko
last_name: Yamamuro
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Ying
full_name: Fu, Ying
last_name: Fu
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
citation:
ama: Lin D, Nagawa S, Chen J, et al. A ROP GTPase dependent auxin signaling pathway
regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current
Biology. 2012;22(14):1319-1325. doi:10.1016/j.cub.2012.05.019
apa: Lin, D., Nagawa, S., Chen, J., Cao, L., Chen, X., Xu, T., … Yang, Z. (2012).
A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution
of PIN2 in Arabidopsis roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.05.019
chicago: Lin, Deshu, Shingo Nagawa, Jisheng Chen, Lingyan Cao, Xu Chen, Tongda Xu,
Hongjiang Li, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates
the Subcellular Distribution of PIN2 in Arabidopsis Roots.” Current Biology.
Cell Press, 2012. https://doi.org/10.1016/j.cub.2012.05.019.
ieee: D. Lin et al., “A ROP GTPase dependent auxin signaling pathway regulates
the subcellular distribution of PIN2 in Arabidopsis roots,” Current Biology,
vol. 22, no. 14. Cell Press, pp. 1319–1325, 2012.
ista: Lin D, Nagawa S, Chen J, Cao L, Chen X, Xu T, Li H, Dhonukshe P, Yamamuro
C, Friml J, Scheres B, Fu Y, Yang Z. 2012. A ROP GTPase dependent auxin signaling
pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current
Biology. 22(14), 1319–1325.
mla: Lin, Deshu, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates
the Subcellular Distribution of PIN2 in Arabidopsis Roots.” Current Biology,
vol. 22, no. 14, Cell Press, 2012, pp. 1319–25, doi:10.1016/j.cub.2012.05.019.
short: D. Lin, S. Nagawa, J. Chen, L. Cao, X. Chen, T. Xu, H. Li, P. Dhonukshe,
C. Yamamuro, J. Friml, B. Scheres, Y. Fu, Z. Yang, Current Biology 22 (2012) 1319–1325.
date_created: 2018-12-11T12:01:27Z
date_published: 2012-07-24T00:00:00Z
date_updated: 2021-01-12T07:41:08Z
day: '24'
doi: 10.1016/j.cub.2012.05.019
extern: 1
intvolume: ' 22'
issue: '14'
month: '07'
page: 1319 - 1325
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3588'
quality_controlled: 0
status: public
title: A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution
of PIN2 in Arabidopsis roots
type: journal_article
volume: 22
year: '2012'
...
---
_id: '3112'
abstract:
- lang: eng
text: The dynamic spatial and temporal distribution of the crucial plant signaling
molecule auxin is achieved by feedback coordination of auxin signaling and intercellular
auxin transport pathways [1, 2]. Developmental roles of auxin have been attributed
predominantly to its effect on transcription; however, an alternative pathway
involving AUXIN BINDING PROTEIN1 (ABP1) has been proposed to regulate clathrin-mediated
endocytosis in roots and Rho-like GTPase (ROP)-dependent pavement cell interdigitation
in leaves [3, 4]. In this study, we show that ROP6 and its downstream effector
RIC1 regulate clathrin association with the plasma membrane for clathrin-mediated
endocytosis, as well as for its feedback regulation by auxin. Genetic analysis
revealed that ROP6/RIC1 acts downstream of ABP1 to regulate endocytosis. This
signaling circuit is also involved in the feedback regulation of PIN-FORMED 1
(PIN1) and PIN2 auxin transporters activity (via its constitutive endocytosis)
and corresponding auxin transport-mediated processes, including root gravitropism
and leave vascular tissue patterning. Our findings suggest that the signaling
module auxin-ABP1-ROP6/RIC1-clathrin-PIN1/PIN2 is a shared component of the feedback
regulation of auxin transport during both root and aerial development.
author:
- first_name: Xu
full_name: Xu Chen
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Deshu
full_name: Lin, Deshu
last_name: Lin
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Chen X, Naramoto S, Robert S, et al. ABP1 and ROP6 GTPase signaling regulate
clathrin mediated endocytosis in Arabidopsis roots. Current Biology. 2012;22(14):1326-1332.
doi:10.1016/j.cub.2012.05.020
apa: Chen, X., Naramoto, S., Robert, S., Tejos, R., Löfke, C., Lin, D., … Friml,
J. (2012). ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis
in Arabidopsis roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.05.020
chicago: Chen, Xu, Satoshi Naramoto, Stéphanie Robert, Ricardo Tejos, Christian
Löfke, Deshu Lin, Zhenbiao Yang, and Jiří Friml. “ABP1 and ROP6 GTPase Signaling
Regulate Clathrin Mediated Endocytosis in Arabidopsis Roots.” Current Biology.
Cell Press, 2012. https://doi.org/10.1016/j.cub.2012.05.020.
ieee: X. Chen et al., “ABP1 and ROP6 GTPase signaling regulate clathrin mediated
endocytosis in Arabidopsis roots,” Current Biology, vol. 22, no. 14. Cell
Press, pp. 1326–1332, 2012.
ista: Chen X, Naramoto S, Robert S, Tejos R, Löfke C, Lin D, Yang Z, Friml J. 2012.
ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis
roots. Current Biology. 22(14), 1326–1332.
mla: Chen, Xu, et al. “ABP1 and ROP6 GTPase Signaling Regulate Clathrin Mediated
Endocytosis in Arabidopsis Roots.” Current Biology, vol. 22, no. 14, Cell
Press, 2012, pp. 1326–32, doi:10.1016/j.cub.2012.05.020.
short: X. Chen, S. Naramoto, S. Robert, R. Tejos, C. Löfke, D. Lin, Z. Yang, J.
Friml, Current Biology 22 (2012) 1326–1332.
date_created: 2018-12-11T12:01:27Z
date_published: 2012-07-24T00:00:00Z
date_updated: 2021-01-12T07:41:08Z
day: '24'
doi: 10.1016/j.cub.2012.05.020
extern: 1
intvolume: ' 22'
issue: '14'
month: '07'
page: 1326 - 1332
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3587'
quality_controlled: 0
status: public
title: ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis
roots
type: journal_article
volume: 22
year: '2012'
...
---
_id: '3128'
abstract:
- lang: eng
text: 'We consider two-player zero-sum stochastic games on graphs with ω-regular
winning conditions specified as parity objectives. These games have applications
in the design and control of reactive systems. We survey the complexity results
for the problem of deciding the winner in such games, and in classes of interest
obtained as special cases, based on the information and the power of randomization
available to the players, on the class of objectives and on the winning mode.
On the basis of information, these games can be classified as follows: (a) partial-observation
(both players have partial view of the game); (b) one-sided partial-observation
(one player has partial-observation and the other player has complete-observation);
and (c) complete-observation (both players have complete view of the game). The
one-sided partial-observation games have two important subclasses: the one-player
games, known as partial-observation Markov decision processes (POMDPs), and the
blind one-player games, known as probabilistic automata. On the basis of randomization,
(a) the players may not be allowed to use randomization (pure strategies), or
(b) they may choose a probability distribution over actions but the actual random
choice is external and not visible to the player (actions invisible), or (c) they
may use full randomization. Finally, various classes of games are obtained by
restricting the parity objective to a reachability, safety, Büchi, or coBüchi
condition. We also consider several winning modes, such as sure-winning (i.e.,
all outcomes of a strategy have to satisfy the winning condition), almost-sure
winning (i.e., winning with probability 1), limit-sure winning (i.e., winning
with probability arbitrarily close to 1), and value-threshold winning (i.e., winning
with probability at least ν, where ν is a given rational). '
acknowledgement: 'The research was supported 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), Microsoft
faculty fellows award, ERC Advanced grant QUAREM, and FWF Grant No. S11403-N23 (RiSE).'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Chatterjee K, Doyen L, Henzinger TA. A survey of partial-observation stochastic
parity games. Formal Methods in System Design. 2012;43(2):268-284. doi:10.1007/s10703-012-0164-2
apa: Chatterjee, K., Doyen, L., & Henzinger, T. A. (2012). A survey of partial-observation
stochastic parity games. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-012-0164-2
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey
of Partial-Observation Stochastic Parity Games.” Formal Methods in System Design.
Springer, 2012. https://doi.org/10.1007/s10703-012-0164-2.
ieee: K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of partial-observation
stochastic parity games,” Formal Methods in System Design, vol. 43, no.
2. Springer, pp. 268–284, 2012.
ista: Chatterjee K, Doyen L, Henzinger TA. 2012. A survey of partial-observation
stochastic parity games. Formal Methods in System Design. 43(2), 268–284.
mla: Chatterjee, Krishnendu, et al. “A Survey of Partial-Observation Stochastic
Parity Games.” Formal Methods in System Design, vol. 43, no. 2, Springer,
2012, pp. 268–84, doi:10.1007/s10703-012-0164-2.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, Formal Methods in System Design
43 (2012) 268–284.
date_created: 2018-12-11T12:01:33Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2021-01-12T07:41:15Z
day: '01'
ddc:
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/s10703-012-0164-2
ec_funded: 1
file:
- access_level: open_access
checksum: dd3d590f383bb2ac6cfda1489ac1c42a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:27Z
date_updated: 2020-07-14T12:46:00Z
file_id: '4882'
file_name: IST-2014-303-v1+1_Survey_Partial-Observation_Stochastic_Parity_Games.pdf
file_size: 163983
relation: main_file
file_date_updated: 2020-07-14T12:46:00Z
has_accepted_license: '1'
intvolume: ' 43'
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 268 - 284
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: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '3570'
pubrep_id: '303'
quality_controlled: '1'
scopus_import: 1
status: public
title: A survey of partial-observation stochastic parity games
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2012'
...
---
_id: '3125'
abstract:
- lang: eng
text: We propose a new learning method to infer a mid-level feature representation
that combines the advantage of semantic attribute representations with the higher
expressive power of non-semantic features. The idea lies in augmenting an existing
attribute-based representation with additional dimensions for which an autoencoder
model is coupled with a large-margin principle. This construction allows a smooth
transition between the zero-shot regime with no training example, the unsupervised
regime with training examples but without class labels, and the supervised regime
with training examples and with class labels. The resulting optimization problem
can be solved efficiently, because several of the necessity steps have closed-form
solutions. Through extensive experiments we show that the augmented representation
achieves better results in terms of object categorization accuracy than the semantic
representation alone.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Viktoriia
full_name: Sharmanska, Viktoriia
id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87
last_name: Sharmanska
orcid: 0000-0003-0192-9308
- first_name: Novi
full_name: Quadrianto, Novi
last_name: Quadrianto
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Sharmanska V, Quadrianto N, Lampert C. Augmented attribute representations.
In: Vol 7576. Springer; 2012:242-255. doi:10.1007/978-3-642-33715-4_18'
apa: 'Sharmanska, V., Quadrianto, N., & Lampert, C. (2012). Augmented attribute
representations (Vol. 7576, pp. 242–255). Presented at the ECCV: European Conference
on Computer Vision, Florence, Italy: Springer. https://doi.org/10.1007/978-3-642-33715-4_18'
chicago: Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Augmented
Attribute Representations,” 7576:242–55. Springer, 2012. https://doi.org/10.1007/978-3-642-33715-4_18.
ieee: 'V. Sharmanska, N. Quadrianto, and C. Lampert, “Augmented attribute representations,”
presented at the ECCV: European Conference on Computer Vision, Florence, Italy,
2012, vol. 7576, no. PART 5, pp. 242–255.'
ista: 'Sharmanska V, Quadrianto N, Lampert C. 2012. Augmented attribute representations.
ECCV: European Conference on Computer Vision, LNCS, vol. 7576, 242–255.'
mla: Sharmanska, Viktoriia, et al. Augmented Attribute Representations. Vol.
7576, no. PART 5, Springer, 2012, pp. 242–55, doi:10.1007/978-3-642-33715-4_18.
short: V. Sharmanska, N. Quadrianto, C. Lampert, in:, Springer, 2012, pp. 242–255.
conference:
end_date: 2012-10-13
location: Florence, Italy
name: 'ECCV: European Conference on Computer Vision'
start_date: 2012-10-07
date_created: 2018-12-11T12:01:32Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2023-02-23T11:13:25Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1007/978-3-642-33715-4_18
file:
- access_level: open_access
checksum: bccdbe0663780d25a1e0524002b2d896
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T12:29:04Z
date_updated: 2020-07-14T12:46:00Z
file_id: '7861'
file_name: 2012_ECCV_Sharmanska.pdf
file_size: 6073897
relation: main_file
file_date_updated: 2020-07-14T12:46:00Z
has_accepted_license: '1'
intvolume: ' 7576'
issue: PART 5
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 242 - 255
publication_status: published
publisher: Springer
publist_id: '3574'
quality_controlled: '1'
scopus_import: 1
status: public
title: Augmented attribute representations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7576
year: '2012'
...
---
_id: '3129'
abstract:
- lang: eng
text: "Let K be a simplicial complex and g the rank of its p-th homology group Hp(K)
defined with ℤ2 coefficients. We show that we can compute a basis H of Hp(K) and
annotate each p-simplex of K with a binary vector of length g with the following
property: the annotations, summed over all p-simplices in any p-cycle z, provide
the coordinate vector of the homology class [z] in the basis H. The basis and
the annotations for all simplices can be computed in O(n ω ) time, where n is
the size of K and ω < 2.376 is a quantity so that two n×n matrices can be multiplied
in O(n ω ) time. The precomputed annotations permit answering queries about the
independence or the triviality of p-cycles efficiently.\r\n\r\nUsing annotations
of edges in 2-complexes, we derive better algorithms for computing optimal basis
and optimal homologous cycles in 1 - dimensional homology. Specifically, for computing
an optimal basis of H1(K) , we improve the previously known time complexity from
O(n 4) to O(n ω + n 2 g ω − 1). Here n denotes the size of the 2-skeleton of
K and g the rank of H1(K) . Computing an optimal cycle homologous to a given 1-cycle
is NP-hard even for surfaces and an algorithm taking 2 O(g) nlogn time is known
for surfaces. We extend this algorithm to work with arbitrary 2-complexes in O(n
ω ) + 2 O(g) n 2logn time using annotations.\r\n"
alternative_title:
- LNCS
author:
- first_name: Oleksiy
full_name: Busaryev, Oleksiy
last_name: Busaryev
- first_name: Sergio
full_name: Cabello, Sergio
last_name: Cabello
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Tamal
full_name: Dey, Tamal
last_name: Dey
- first_name: Yusu
full_name: Wang, Yusu
last_name: Wang
citation:
ama: 'Busaryev O, Cabello S, Chen C, Dey T, Wang Y. Annotating simplices with a
homology basis and its applications. In: Vol 7357. Springer; 2012:189-200. doi:10.1007/978-3-642-31155-0_17'
apa: 'Busaryev, O., Cabello, S., Chen, C., Dey, T., & Wang, Y. (2012). Annotating
simplices with a homology basis and its applications (Vol. 7357, pp. 189–200).
Presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki,
Finland: Springer. https://doi.org/10.1007/978-3-642-31155-0_17'
chicago: Busaryev, Oleksiy, Sergio Cabello, Chao Chen, Tamal Dey, and Yusu Wang.
“Annotating Simplices with a Homology Basis and Its Applications,” 7357:189–200.
Springer, 2012. https://doi.org/10.1007/978-3-642-31155-0_17.
ieee: 'O. Busaryev, S. Cabello, C. Chen, T. Dey, and Y. Wang, “Annotating simplices
with a homology basis and its applications,” presented at the SWAT: Symposium
and Workshops on Algorithm Theory, Helsinki, Finland, 2012, vol. 7357, pp. 189–200.'
ista: 'Busaryev O, Cabello S, Chen C, Dey T, Wang Y. 2012. Annotating simplices
with a homology basis and its applications. SWAT: Symposium and Workshops on Algorithm
Theory, LNCS, vol. 7357, 189–200.'
mla: Busaryev, Oleksiy, et al. Annotating Simplices with a Homology Basis and
Its Applications. Vol. 7357, Springer, 2012, pp. 189–200, doi:10.1007/978-3-642-31155-0_17.
short: O. Busaryev, S. Cabello, C. Chen, T. Dey, Y. Wang, in:, Springer, 2012, pp.
189–200.
conference:
end_date: 2012-07-06
location: Helsinki, Finland
name: 'SWAT: Symposium and Workshops on Algorithm Theory'
start_date: 2012-07-04
date_created: 2018-12-11T12:01:33Z
date_published: 2012-06-19T00:00:00Z
date_updated: 2021-01-12T07:41:15Z
day: '19'
department:
- _id: HeEd
doi: 10.1007/978-3-642-31155-0_17
external_id:
arxiv:
- '1107.3793'
intvolume: ' 7357'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1107.3793
month: '06'
oa: 1
oa_version: Preprint
page: 189 - 200
publication_status: published
publisher: Springer
publist_id: '3569'
quality_controlled: '1'
scopus_import: 1
status: public
title: Annotating simplices with a homology basis and its applications
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7357
year: '2012'
...
---
_id: '3126'
abstract:
- lang: eng
text: "In this work we propose a new information-theoretic clustering algorithm
that infers cluster memberships by direct optimization of a non-parametric mutual
information estimate between data distribution and cluster assignment. Although
the optimization objective has a solid theoretical foundation it is hard to optimize.
We propose an approximate optimization formulation that leads to an efficient
algorithm with low runtime complexity. The algorithm has a single free parameter,
the number of clusters to find. We demonstrate superior performance on several
synthetic and real datasets.\r\n"
alternative_title:
- LNCS
author:
- first_name: Andreas
full_name: Müller, Andreas
last_name: Müller
- first_name: Sebastian
full_name: Nowozin, Sebastian
last_name: Nowozin
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Müller A, Nowozin S, Lampert C. Information theoretic clustering using minimal
spanning trees. In: Vol 7476. Springer; 2012:205-215. doi:10.1007/978-3-642-32717-9_21'
apa: 'Müller, A., Nowozin, S., & Lampert, C. (2012). Information theoretic clustering
using minimal spanning trees (Vol. 7476, pp. 205–215). Presented at the DAGM:
German Association For Pattern Recognition, Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_21'
chicago: Müller, Andreas, Sebastian Nowozin, and Christoph Lampert. “Information
Theoretic Clustering Using Minimal Spanning Trees,” 7476:205–15. Springer, 2012.
https://doi.org/10.1007/978-3-642-32717-9_21.
ieee: 'A. Müller, S. Nowozin, and C. Lampert, “Information theoretic clustering
using minimal spanning trees,” presented at the DAGM: German Association For Pattern
Recognition, Graz, Austria, 2012, vol. 7476, pp. 205–215.'
ista: 'Müller A, Nowozin S, Lampert C. 2012. Information theoretic clustering using
minimal spanning trees. DAGM: German Association For Pattern Recognition, LNCS,
vol. 7476, 205–215.'
mla: Müller, Andreas, et al. Information Theoretic Clustering Using Minimal Spanning
Trees. Vol. 7476, Springer, 2012, pp. 205–15, doi:10.1007/978-3-642-32717-9_21.
short: A. Müller, S. Nowozin, C. Lampert, in:, Springer, 2012, pp. 205–215.
conference:
end_date: 2012-08-31
location: Graz, Austria
name: 'DAGM: German Association For Pattern Recognition'
start_date: 2012-08-28
date_created: 2018-12-11T12:01:32Z
date_published: 2012-08-14T00:00:00Z
date_updated: 2021-01-12T07:41:14Z
day: '14'
department:
- _id: ChLa
doi: 10.1007/978-3-642-32717-9_21
intvolume: ' 7476'
language:
- iso: eng
month: '08'
oa_version: None
page: 205 - 215
publication_status: published
publisher: Springer
publist_id: '3573'
quality_controlled: '1'
scopus_import: 1
status: public
title: Information theoretic clustering using minimal spanning trees
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7476
year: '2012'
...
---
_id: '3155'
abstract:
- lang: eng
text: 'We propose synchronous interfaces, a new interface theory for discrete-time
systems. We use an application to time-triggered scheduling to drive the design
choices for our formalism; in particular, additionally to deriving useful mathematical
properties, we focus on providing a syntax which is adapted to natural high-level
system modeling. As a result, we develop an interface model that relies on a guarded-command
based language and is equipped with shared variables and explicit discrete-time
clocks. We define all standard interface operations: compatibility checking, composition,
refinement, and shared refinement. Apart from the synchronous interface model,
the contribution of this paper is the establishment of a formal relation between
interface theories and real-time scheduling, where we demonstrate a fully automatic
framework for the incremental computation of time-triggered schedules.'
acknowledgement: Research partially supported by the Danish-Chinese Center for Cyber
Physical Systems (Grant No.61061130541) and VKR Center of Excellence MT-LAB.
alternative_title:
- LNCS
author:
- first_name: Benoît
full_name: Delahaye, Benoît
last_name: Delahaye
- first_name: Uli
full_name: Fahrenberg, Uli
last_name: Fahrenberg
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Axel
full_name: Legay, Axel
last_name: Legay
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. Synchronous interface
theories and time triggered scheduling. In: Vol 7273. Springer; 2012:203-218.
doi:10.1007/978-3-642-30793-5_13'
apa: 'Delahaye, B., Fahrenberg, U., Henzinger, T. A., Legay, A., & Nickovic,
D. (2012). Synchronous interface theories and time triggered scheduling (Vol.
7273, pp. 203–218). Presented at the FORTE: Formal Techniques for Networked and
Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed
Systems , Stockholm, Sweden: Springer. https://doi.org/10.1007/978-3-642-30793-5_13'
chicago: Delahaye, Benoît, Uli Fahrenberg, Thomas A Henzinger, Axel Legay, and Dejan
Nickovic. “Synchronous Interface Theories and Time Triggered Scheduling,” 7273:203–18.
Springer, 2012. https://doi.org/10.1007/978-3-642-30793-5_13.
ieee: 'B. Delahaye, U. Fahrenberg, T. A. Henzinger, A. Legay, and D. Nickovic, “Synchronous
interface theories and time triggered scheduling,” presented at the FORTE: Formal
Techniques for Networked and Distributed Systems & FMOODS: Formal Methods
for Open Object-Based Distributed Systems , Stockholm, Sweden, 2012, vol. 7273,
pp. 203–218.'
ista: 'Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. 2012. Synchronous
interface theories and time triggered scheduling. FORTE: Formal Techniques for
Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based
Distributed Systems , LNCS, vol. 7273, 203–218.'
mla: Delahaye, Benoît, et al. Synchronous Interface Theories and Time Triggered
Scheduling. Vol. 7273, Springer, 2012, pp. 203–18, doi:10.1007/978-3-642-30793-5_13.
short: B. Delahaye, U. Fahrenberg, T.A. Henzinger, A. Legay, D. Nickovic, in:, Springer,
2012, pp. 203–218.
conference:
end_date: 2012-06-16
location: Stockholm, Sweden
name: 'FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS:
Formal Methods for Open Object-Based Distributed Systems '
start_date: 2012-06-13
date_created: 2018-12-11T12:01:43Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:26Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-642-30793-5_13
file:
- access_level: open_access
checksum: feae2e07f2d9a59843f8ddabf25d179f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:25Z
date_updated: 2020-07-14T12:46:01Z
file_id: '4879'
file_name: IST-2012-88-v1+1_Synchronous_interface_theories_and_time_triggered_scheduling.pdf
file_size: 493198
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 7273'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 203 - 218
publication_status: published
publisher: Springer
publist_id: '3539'
pubrep_id: '88'
quality_controlled: '1'
scopus_import: 1
status: public
title: Synchronous interface theories and time triggered scheduling
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7273
year: '2012'
...
---
_id: '3159'
abstract:
- lang: eng
text: The structure of hierarchical networks in biological and physical systems
has long been characterized using the Horton-Strahler ordering scheme. The scheme
assigns an integer order to each edge in the network based on the topology of
branching such that the order increases from distal parts of the network (e.g.,
mountain streams or capillaries) to the "root" of the network (e.g.,
the river outlet or the aorta). However, Horton-Strahler ordering cannot be applied
to networks with loops because they they create a contradiction in the edge ordering
in terms of which edge precedes another in the hierarchy. Here, we present a generalization
of the Horton-Strahler order to weighted planar reticular networks, where weights
are assumed to correlate with the importance of network edges, e.g., weights estimated
from edge widths may correlate to flow capacity. Our method assigns hierarchical
levels not only to edges of the network, but also to its loops, and classifies
the edges into reticular edges, which are responsible for loop formation, and
tree edges. In addition, we perform a detailed and rigorous theoretical analysis
of the sensitivity of the hierarchical levels to weight perturbations. In doing
so, we show that the ordering of the reticular edges is more robust to noise in
weight estimation than is the ordering of the tree edges. We discuss applications
of this generalized Horton-Strahler ordering to the study of leaf venation and
other biological networks.
acknowledgement: "his work was supported by the National Science Foundation Plant
Genome Research Program (grant 0820624 to H.E. and J.S.W.), the Defense Advanced
Projects Research Agency (grant HR0011-09-1-0055 to H.E. and J.S.W.), and the European
Science Foundation (under the Research Networking Programme on “Applied and Computational
Algebraic Topology” run by H.E.). Joshua S. Weitz, Ph.D., holds a Career Award at
the Scientific Interface from the Burroughs Wellcome Fund.\r\n\r\n\r\n\r\nDuring
preparation of this manuscript the authors became aware of a related work by Katifori
and Magnasco (arXiv:1110.1412v1), concurrently submitted and accepted for publication
in PLoS ONE."
article_number: e36715
author:
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Charles
full_name: Price, Charles
last_name: Price
- first_name: Joshua
full_name: Weitz, Joshua
last_name: Weitz
citation:
ama: Mileyko Y, Edelsbrunner H, Price C, Weitz J. Hierarchical ordering of reticular
networks. PLoS One. 2012;7(6). doi:10.1371/journal.pone.0036715
apa: Mileyko, Y., Edelsbrunner, H., Price, C., & Weitz, J. (2012). Hierarchical
ordering of reticular networks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036715
chicago: Mileyko, Yuriy, Herbert Edelsbrunner, Charles Price, and Joshua Weitz.
“Hierarchical Ordering of Reticular Networks.” PLoS One. Public Library
of Science, 2012. https://doi.org/10.1371/journal.pone.0036715.
ieee: Y. Mileyko, H. Edelsbrunner, C. Price, and J. Weitz, “Hierarchical ordering
of reticular networks,” PLoS One, vol. 7, no. 6. Public Library of Science,
2012.
ista: Mileyko Y, Edelsbrunner H, Price C, Weitz J. 2012. Hierarchical ordering of
reticular networks. PLoS One. 7(6), e36715.
mla: Mileyko, Yuriy, et al. “Hierarchical Ordering of Reticular Networks.” PLoS
One, vol. 7, no. 6, e36715, Public Library of Science, 2012, doi:10.1371/journal.pone.0036715.
short: Y. Mileyko, H. Edelsbrunner, C. Price, J. Weitz, PLoS One 7 (2012).
date_created: 2018-12-11T12:01:44Z
date_published: 2012-06-06T00:00:00Z
date_updated: 2021-01-12T07:41:28Z
day: '06'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1371/journal.pone.0036715
file:
- access_level: open_access
checksum: 515a98ad72e470752f03f13663dcaff8
content_type: application/pdf
creator: kschuh
date_created: 2019-02-05T12:38:43Z
date_updated: 2020-07-14T12:46:01Z
file_id: '5922'
file_name: 2012_PLoS_Mileyko.PDF
file_size: 541583
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3530'
pubrep_id: '385'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hierarchical ordering of reticular networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2012'
...