---
_id: '2952'
abstract:
- lang: eng
text: Body axis elongation represents a common and fundamental morphogenetic process
in development. A key mechanism triggering body axis elongation without additional
growth is convergent extension (CE), whereby a tissue undergoes simultaneous narrowing
and extension. Both collective cell migration and cell intercalation are thought
to drive CE and are used to different degrees in various species as they elongate
their body axis. Here, we provide an overview of CE as a general strategy for
body axis elongation and discuss conserved and divergent mechanisms underlying
CE among different species.
acknowledgement: 'M.T. is supported by the UK Medical Research Council (MRC) and Royal
Society and C.-P.H. by the Fonds zur Förderung der wissenschaftlichen Forschung
(FWF), Deutsche Forschungsgemeinschaft (DFG) and Institute of Science and Technology
Austria. '
author:
- first_name: Masazumi
full_name: Tada, Masazumi
last_name: Tada
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Tada M, Heisenberg C-PJ. Convergent extension Using collective cell migration
and cell intercalation to shape embryos. Development. 2012;139(21):3897-3904.
doi:10.1242/dev.073007
apa: Tada, M., & Heisenberg, C.-P. J. (2012). Convergent extension Using collective
cell migration and cell intercalation to shape embryos. Development. Company
of Biologists. https://doi.org/10.1242/dev.073007
chicago: Tada, Masazumi, and Carl-Philipp J Heisenberg. “Convergent Extension Using
Collective Cell Migration and Cell Intercalation to Shape Embryos.” Development.
Company of Biologists, 2012. https://doi.org/10.1242/dev.073007.
ieee: M. Tada and C.-P. J. Heisenberg, “Convergent extension Using collective cell
migration and cell intercalation to shape embryos,” Development, vol. 139,
no. 21. Company of Biologists, pp. 3897–3904, 2012.
ista: Tada M, Heisenberg C-PJ. 2012. Convergent extension Using collective cell
migration and cell intercalation to shape embryos. Development. 139(21), 3897–3904.
mla: Tada, Masazumi, and Carl-Philipp J. Heisenberg. “Convergent Extension Using
Collective Cell Migration and Cell Intercalation to Shape Embryos.” Development,
vol. 139, no. 21, Company of Biologists, 2012, pp. 3897–904, doi:10.1242/dev.073007.
short: M. Tada, C.-P.J. Heisenberg, Development 139 (2012) 3897–3904.
date_created: 2018-12-11T12:00:31Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T07:40:00Z
day: '01'
department:
- _id: CaHe
doi: 10.1242/dev.073007
intvolume: ' 139'
issue: '21'
language:
- iso: eng
month: '11'
oa_version: None
page: 3897 - 3904
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3776'
quality_controlled: '1'
scopus_import: 1
status: public
title: Convergent extension Using collective cell migration and cell intercalation
to shape embryos
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 139
year: '2012'
...
---
_id: '2953'
author:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
citation:
ama: Heisenberg C-PJ, Fässler R. Cell-cell adhesion and extracellular matrix diversity
counts. Current Opinion in Cell Biology. 2012;24(5):559-561. doi:10.1016/j.ceb.2012.09.002
apa: Heisenberg, C.-P. J., & Fässler, R. (2012). Cell-cell adhesion and extracellular
matrix diversity counts. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2012.09.002
chicago: Heisenberg, Carl-Philipp J, and Reinhard Fässler. “Cell-Cell Adhesion and
Extracellular Matrix Diversity Counts.” Current Opinion in Cell Biology.
Elsevier, 2012. https://doi.org/10.1016/j.ceb.2012.09.002.
ieee: C.-P. J. Heisenberg and R. Fässler, “Cell-cell adhesion and extracellular
matrix diversity counts,” Current Opinion in Cell Biology, vol. 24, no.
5. Elsevier, pp. 559–561, 2012.
ista: Heisenberg C-PJ, Fässler R. 2012. Cell-cell adhesion and extracellular matrix
diversity counts. Current Opinion in Cell Biology. 24(5), 559–561.
mla: Heisenberg, Carl-Philipp J., and Reinhard Fässler. “Cell-Cell Adhesion and
Extracellular Matrix Diversity Counts.” Current Opinion in Cell Biology,
vol. 24, no. 5, Elsevier, 2012, pp. 559–61, doi:10.1016/j.ceb.2012.09.002.
short: C.-P.J. Heisenberg, R. Fässler, Current Opinion in Cell Biology 24 (2012)
559–561.
date_created: 2018-12-11T12:00:31Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2021-01-12T07:40:01Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.ceb.2012.09.002
intvolume: ' 24'
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 559 - 561
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '3773'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cell-cell adhesion and extracellular matrix diversity counts
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2012'
...
---
_id: '2958'
abstract:
- lang: eng
text: 'The activity of hippocampal pyramidal cells reflects both the current position
of the animal and information related to its current behavior. Here we investigated
whether single hippocampal neurons can encode several independent features defining
trials during a memory task. We also tested whether task-related information is
represented by partial remapping of the place cell population or, instead, via
firing rate modulation of spatially stable place cells. To address these two questions,
the activity of hippocampal neurons was recorded in rats performing a conditional
discrimination task on a modified T-maze in which the identity of a food reward
guided behavior. When the rat was on the central arm of the maze, the firing rate
of pyramidal cells changed depending on two independent factors: (1) the identity
of the food reward given to the animal and (2) the previous location of the animal
on the maze. Importantly, some pyramidal cells encoded information relative to
both factors. This trial-type specific and retrospective coding did not interfere
with the spatial representation of the maze: hippocampal cells had stable place
fields and their theta-phase precession profiles were unaltered during the task,
indicating that trial-related information was encoded via rate remapping. During
error trials, encoding of both trial-related information and spatial location
was impaired. Finally, we found that pyramidal cells also encode trial-related
information via rate remapping during the continuous version of the rewarded alternation
task without delays. These results suggest that hippocampal neurons can encode
several task-related cognitive aspects via rate remapping.'
acknowledgement: J.C. was supported by a MRC Intramural Programme Grant (U138197111)
and a European Research Council Starter Grant (281511). K.A. held a Wellcome Trust
PhD studentship and a Humboldt Research Fellowship for Postdoctoral Researchers.
D.M.B. was supported by Wellcome Trust Senior Fellowships (074385 and 087736).
author:
- first_name: Kevin
full_name: Allen, Kevin
last_name: Allen
- first_name: J Nick
full_name: Rawlins, J Nick
last_name: Rawlins
- first_name: David
full_name: Bannerman, David
last_name: Bannerman
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Allen K, Rawlins JN, Bannerman D, Csicsvari JL. Hippocampal place cells can
encode multiple trial-dependent features through rate remapping. Journal of
Neuroscience. 2012;32(42):14752-14766. doi:10.1523/JNEUROSCI.6175-11.2012
apa: Allen, K., Rawlins, J. N., Bannerman, D., & Csicsvari, J. L. (2012). Hippocampal
place cells can encode multiple trial-dependent features through rate remapping.
Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.6175-11.2012
chicago: Allen, Kevin, J Nick Rawlins, David Bannerman, and Jozsef L Csicsvari.
“Hippocampal Place Cells Can Encode Multiple Trial-Dependent Features through
Rate Remapping.” Journal of Neuroscience. Society for Neuroscience, 2012.
https://doi.org/10.1523/JNEUROSCI.6175-11.2012.
ieee: K. Allen, J. N. Rawlins, D. Bannerman, and J. L. Csicsvari, “Hippocampal place
cells can encode multiple trial-dependent features through rate remapping,” Journal
of Neuroscience, vol. 32, no. 42. Society for Neuroscience, pp. 14752–14766,
2012.
ista: Allen K, Rawlins JN, Bannerman D, Csicsvari JL. 2012. Hippocampal place cells
can encode multiple trial-dependent features through rate remapping. Journal of
Neuroscience. 32(42), 14752–14766.
mla: Allen, Kevin, et al. “Hippocampal Place Cells Can Encode Multiple Trial-Dependent
Features through Rate Remapping.” Journal of Neuroscience, vol. 32, no.
42, Society for Neuroscience, 2012, pp. 14752–66, doi:10.1523/JNEUROSCI.6175-11.2012.
short: K. Allen, J.N. Rawlins, D. Bannerman, J.L. Csicsvari, Journal of Neuroscience
32 (2012) 14752–14766.
date_created: 2018-12-11T12:00:33Z
date_published: 2012-10-17T00:00:00Z
date_updated: 2021-01-12T07:40:03Z
day: '17'
department:
- _id: JoCs
doi: 10.1523/JNEUROSCI.6175-11.2012
ec_funded: 1
external_id:
pmid:
- '23077060'
intvolume: ' 32'
issue: '42'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531717/
month: '10'
oa: 1
oa_version: Submitted Version
page: 14752 - 14766
pmid: 1
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '3768'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hippocampal place cells can encode multiple trial-dependent features through
rate remapping
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2012'
...
---
_id: '2959'
abstract:
- lang: eng
text: We study maximum likelihood estimation in Gaussian graphical models from a
geometric point of view. An algebraic elimination criterion allows us to find
exact lower bounds on the number of observations needed to ensure that the maximum
likelihood estimator (MLE) exists with probability one. This is applied to bipartite
graphs, grids and colored graphs. We also study the ML degree, and we present
the first instance of a graph for which the MLE exists with probability one, even
when the number of observations equals the treewidth.
acknowledgement: "I wish to thank Bernd Sturmfels for many helpful discus- sions and
Steffen Lauritzen for introducing me to the problem of the existence of the MLE
in Gaussian graphical models. I would also like to thank two referees who provided
helpful comments on the original version of this paper.\r\n"
author:
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Uhler C. Geometry of maximum likelihood estimation in Gaussian graphical models.
Annals of Statistics. 2012;40(1):238-261. doi:10.1214/11-AOS957
apa: Uhler, C. (2012). Geometry of maximum likelihood estimation in Gaussian graphical
models. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/11-AOS957
chicago: Uhler, Caroline. “Geometry of Maximum Likelihood Estimation in Gaussian
Graphical Models.” Annals of Statistics. Institute of Mathematical Statistics,
2012. https://doi.org/10.1214/11-AOS957.
ieee: C. Uhler, “Geometry of maximum likelihood estimation in Gaussian graphical
models,” Annals of Statistics, vol. 40, no. 1. Institute of Mathematical
Statistics, pp. 238–261, 2012.
ista: Uhler C. 2012. Geometry of maximum likelihood estimation in Gaussian graphical
models. Annals of Statistics. 40(1), 238–261.
mla: Uhler, Caroline. “Geometry of Maximum Likelihood Estimation in Gaussian Graphical
Models.” Annals of Statistics, vol. 40, no. 1, Institute of Mathematical
Statistics, 2012, pp. 238–61, doi:10.1214/11-AOS957.
short: C. Uhler, Annals of Statistics 40 (2012) 238–261.
date_created: 2018-12-11T12:00:33Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2021-01-12T07:40:04Z
day: '01'
department:
- _id: CaUh
doi: 10.1214/11-AOS957
intvolume: ' 40'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1012.2643
month: '02'
oa: 1
oa_version: Preprint
page: 238 - 261
publication: Annals of Statistics
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '3767'
quality_controlled: '1'
scopus_import: 1
status: public
title: Geometry of maximum likelihood estimation in Gaussian graphical models
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2012'
...
---
_id: '2966'
abstract:
- lang: eng
text: 'Background: The outcome of male-male competition can be predicted from the
relative fighting qualities of the opponents, which often depend on their age.
In insects, freshly emerged and still sexually inactive males are morphologically
indistinct from older, sexually active males. These young inactive males may thus
be easy targets for older males if they cannot conceal themselves from their attacks.
The ant Cardiocondyla obscurior is characterised by lethal fighting between wingless
(" ergatoid" ) males. Here, we analyse for how long young males are
defenceless after eclosion, and how early adult males can detect the presence
of rival males.Results: We found that old ergatoid males consistently won fights
against ergatoid males younger than two days. Old males did not differentiate
between different types of unpigmented pupae several days before emergence, but
had more frequent contact to ready-to-eclose pupae of female sexuals and winged
males than of workers and ergatoid males. In rare cases, old ergatoid males displayed
alleviated biting of pigmented ergatoid male pupae shortly before adult eclosion,
as well as copulation attempts to dark pupae of female sexuals and winged males.
Ergatoid male behaviour may be promoted by a closer similarity of the chemical
profile of ready-to-eclose pupae to the profile of adults than that of young pupae
several days prior to emergence.Conclusion: Young ergatoid males of C. obscurior
would benefit greatly by hiding their identity from older, resident males, as
they are highly vulnerable during the first two days of their adult lives. In
contrast to the winged males of the same species, which are able to prevent ergatoid
male attacks by chemical female mimicry, young ergatoids do not seem to be able
to produce a protective chemical profile. Conflicts in male-male competition between
ergatoid males of different age thus seem to be resolved in favour of the older
males. This might represent selection at the colony level rather than the individual
level. © 2012 Cremer et al.; licensee BioMed Central Ltd.'
article_number: '7'
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Masaki
full_name: Suefuji, Masaki
last_name: Suefuji
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Cremer S, Suefuji M, Schrempf A, Heinze J. The dynamics of male-male competition
in Cardiocondyla obscurior ants. BMC Ecology. 2012;12. doi:10.1186/1472-6785-12-7
apa: Cremer, S., Suefuji, M., Schrempf, A., & Heinze, J. (2012). The dynamics
of male-male competition in Cardiocondyla obscurior ants. BMC Ecology.
BioMed Central. https://doi.org/10.1186/1472-6785-12-7
chicago: Cremer, Sylvia, Masaki Suefuji, Alexandra Schrempf, and Jürgen Heinze.
“The Dynamics of Male-Male Competition in Cardiocondyla Obscurior Ants.” BMC
Ecology. BioMed Central, 2012. https://doi.org/10.1186/1472-6785-12-7.
ieee: S. Cremer, M. Suefuji, A. Schrempf, and J. Heinze, “The dynamics of male-male
competition in Cardiocondyla obscurior ants,” BMC Ecology, vol. 12. BioMed
Central, 2012.
ista: Cremer S, Suefuji M, Schrempf A, Heinze J. 2012. The dynamics of male-male
competition in Cardiocondyla obscurior ants. BMC Ecology. 12, 7.
mla: Cremer, Sylvia, et al. “The Dynamics of Male-Male Competition in Cardiocondyla
Obscurior Ants.” BMC Ecology, vol. 12, 7, BioMed Central, 2012, doi:10.1186/1472-6785-12-7.
short: S. Cremer, M. Suefuji, A. Schrempf, J. Heinze, BMC Ecology 12 (2012).
date_created: 2018-12-11T12:00:35Z
date_published: 2012-06-15T00:00:00Z
date_updated: 2021-01-12T07:40:07Z
day: '15'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1186/1472-6785-12-7
file:
- access_level: open_access
checksum: 03d004bdff3724fb1627e3f5004bad80
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:44Z
date_updated: 2020-07-14T12:45:57Z
file_id: '4706'
file_name: IST-2012-94-v1+1_1472-6785-12-7.pdf
file_size: 489994
relation: main_file
file_date_updated: 2020-07-14T12:45:57Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
publication: BMC Ecology
publication_status: published
publisher: BioMed Central
publist_id: '3753'
pubrep_id: '94'
quality_controlled: '1'
scopus_import: 1
status: public
title: The dynamics of male-male competition in Cardiocondyla obscurior ants
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2012'
...
---
_id: '2962'
abstract:
- lang: eng
text: The choice of summary statistics is a crucial step in approximate Bayesian
computation (ABC). Since statistics are often not sufficient, this choice involves
a trade-off between loss of information and reduction of dimensionality. The latter
may increase the efficiency of ABC. Here, we propose an approach for choosing
summary statistics based on boosting, a technique from the machine learning literature.
We consider different types of boosting and compare them to partial least squares
regression as an alternative. To mitigate the lack of sufficiency, we also propose
an approach for choosing summary statistics locally, in the putative neighborhood
of the true parameter value. We study a demographic model motivated by the re-introduction
of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are
the mean and standard deviation across microsatellites of the scaled ancestral
mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to
matings per breeding season (ω). By simulation, we assess the properties of the
posterior distribution obtained with the various methods. According to our criteria,
ABC with summary statistics chosen locally via boosting with the L2-loss performs
best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find
that most of the variation across loci of the ancestral mutation rate u is between
7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access
to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent
estimates.
acknowledged_ssus:
- _id: ScienComp
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
citation:
ama: Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary
statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047.
doi:10.1534/genetics.112.143164
apa: Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach
for choosing summary statistics in approximate Bayesian computation. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.112.143164
chicago: Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach
for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics.
Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164.
ieee: S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing
summary statistics in approximate Bayesian computation,” Genetics, vol.
192, no. 3. Genetics Society of America, pp. 1027–1047, 2012.
ista: Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing
summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047.
mla: Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics
in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics
Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164.
short: S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047.
date_created: 2018-12-11T12:00:34Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T07:40:05Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.112.143164
external_id:
pmid:
- '22960215'
intvolume: ' 192'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/
month: '11'
oa: 1
oa_version: Submitted Version
page: 1027 - 1047
pmid: 1
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3763'
quality_controlled: '1'
scopus_import: 1
status: public
title: A novel approach for choosing summary statistics in approximate Bayesian computation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 192
year: '2012'
...
---
_id: '2965'
abstract:
- lang: eng
text: Dieser Artikel soll die sechs verschiedenen Creative Commons Lizenzen erläutern
und ihre Bedeutung im Rahmen des wissenschaftlichen Publizierens und des Open
Access erklären (CC-BY, CC-BY-SA, CC-BY-NC, CC-BY-ND, CC-BYNC-SA, CC-BY-NC-ND).
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: 'Danowski P. Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen & Bibliothekare. 2012;65(2):200-212.'
apa: 'Danowski, P. (2012). Kontext Open Access: Creative Commons. Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB.'
chicago: 'Danowski, Patrick. “Kontext Open Access: Creative Commons.” Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB,
2012.'
ieee: 'P. Danowski, “Kontext Open Access: Creative Commons,” Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 65,
no. 2. VÖB, pp. 200–212, 2012.'
ista: 'Danowski P. 2012. Kontext Open Access: Creative Commons. Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 65(2), 200–212.'
mla: 'Danowski, Patrick. “Kontext Open Access: Creative Commons.” Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol.
65, no. 2, VÖB, 2012, pp. 200–12.'
short: P. Danowski, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen
& Bibliothekare 65 (2012) 200–212.
date_created: 2018-12-11T12:00:35Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2021-01-12T07:40:07Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
file:
- access_level: open_access
checksum: 162eea47d9d840c26b496ba6ae4d1c09
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:42Z
date_updated: 2020-07-14T12:45:57Z
file_id: '4703'
file_name: IST-2012-95-v1+1_sp-beitrag_danowski_kontext_open_access_creative_commons.pdf
file_size: 503345
relation: main_file
file_date_updated: 2020-07-14T12:45:57Z
has_accepted_license: '1'
intvolume: ' 65'
issue: '2'
language:
- iso: ger
main_file_link:
- open_access: '1'
url: ' http://hdl.handle.net/10760/17625'
month: '09'
oa: 1
oa_version: Published Version
page: 200 - 212
popular_science: '1'
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare
publication_status: published
publisher: VÖB
publist_id: '3754'
pubrep_id: '95'
scopus_import: 1
status: public
title: 'Kontext Open Access: Creative Commons'
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: 65
year: '2012'
...
---
_id: '2963'
abstract:
- lang: eng
text: 'Zebra finches are an ubiquitous model system for the study of vocal learning
in animal communication. Their song has been well described, but its possible
function(s) in social communication are only partly understood. The so-called
‘directed song’ is a high-intensity, high-performance song given during courtship
in close proximity to the female, which is known to mediate mate choice and mating.
However, this singing mode constitutes only a fraction of zebra finch males’ prolific
song output. Potential communicative functions of their second, ‘undirected’ singing
mode remain unresolved in the face of contradicting reports of both facilitating
and inhibiting effects of social company on singing. We addressed this issue by
experimentally manipulating social contexts in a within-subject design, comparing
a solo versus male or female only company condition, each lasting for 24 hours.
Males’ total song output was significantly higher when a conspecific was in audible
and visible distance than when they were alone. Male and female company had an
equally facilitating effect on song output. Our findings thus indicate that singing
motivation is facilitated rather than inhibited by social company, suggesting
that singing in zebra finches might function both in inter- and intrasexual communication. '
author:
- first_name: Fabienne
full_name: Jesse, Fabienne
id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87
last_name: Jesse
- first_name: Katharina
full_name: Riebel, Katharina
last_name: Riebel
citation:
ama: Jesse F, Riebel K. Social facilitation of male song by male and female conspecifics
in the zebra finch, Taeniopygia guttata. Behavioural Processes. 2012;91(3):262-266.
doi:10.1016/j.beproc.2012.09.006
apa: Jesse, F., & Riebel, K. (2012). Social facilitation of male song by male
and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural
Processes. Elsevier. https://doi.org/10.1016/j.beproc.2012.09.006
chicago: Jesse, Fabienne, and Katharina Riebel. “Social Facilitation of Male Song
by Male and Female Conspecifics in the Zebra Finch, Taeniopygia Guttata.” Behavioural
Processes. Elsevier, 2012. https://doi.org/10.1016/j.beproc.2012.09.006.
ieee: F. Jesse and K. Riebel, “Social facilitation of male song by male and female
conspecifics in the zebra finch, Taeniopygia guttata,” Behavioural Processes,
vol. 91, no. 3. Elsevier, pp. 262–266, 2012.
ista: Jesse F, Riebel K. 2012. Social facilitation of male song by male and female
conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. 91(3),
262–266.
mla: Jesse, Fabienne, and Katharina Riebel. “Social Facilitation of Male Song by
Male and Female Conspecifics in the Zebra Finch, Taeniopygia Guttata.” Behavioural
Processes, vol. 91, no. 3, Elsevier, 2012, pp. 262–66, doi:10.1016/j.beproc.2012.09.006.
short: F. Jesse, K. Riebel, Behavioural Processes 91 (2012) 262–266.
date_created: 2018-12-11T12:00:35Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T07:40:06Z
day: '01'
department:
- _id: JoBo
doi: 10.1016/j.beproc.2012.09.006
intvolume: ' 91'
issue: '3'
language:
- iso: eng
month: '11'
oa_version: None
page: 262 - 266
publication: Behavioural Processes
publication_status: published
publisher: Elsevier
publist_id: '3756'
quality_controlled: '1'
status: public
title: Social facilitation of male song by male and female conspecifics in the zebra
finch, Taeniopygia guttata
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2012'
...
---
_id: '2974'
abstract:
- lang: eng
text: "We construct a perfectly binding string commitment scheme whose security
is based on the learning parity with noise (LPN) assumption, or equivalently,
the hardness of decoding random linear codes. Our scheme not only allows for a
simple and efficient zero-knowledge proof of knowledge for committed values (essentially
a Σ-protocol), but also for such proofs showing any kind of relation amongst committed
values, i.e. proving that messages m_0,...,m_u, are such that m_0=C(m_1,...,m_u)
for any circuit C.\r\n\r\nTo get soundness which is exponentially small in a security
parameter t, and when the zero-knowledge property relies on the LPN problem with
secrets of length l, our 3 round protocol has communication complexity O(t|C|l
log(l)) and computational complexity of O(t|C|l) bit operations. The hidden constants
are small, and the computation consists mostly of computing inner products of
bit-vectors."
acknowledgement: "We are grateful to Petros Mol for helpful discussions on the reduction
for the hardness of the xLPN problem.\r\n"
alternative_title:
- LNCS
author:
- first_name: Abhishek
full_name: Jain, Abhishek
last_name: Jain
- first_name: Stephan
full_name: Krenn, Stephan
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- 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: Aris
full_name: Tentes, Aris
last_name: Tentes
citation:
ama: 'Jain A, Krenn S, Pietrzak KZ, Tentes A. Commitments and efficient zero knowledge
proofs from learning parity with noise. In: Wang X, Sako K, eds. Vol 7658. Springer;
2012:663-680. doi:10.1007/978-3-642-34961-4_40'
apa: 'Jain, A., Krenn, S., Pietrzak, K. Z., & Tentes, A. (2012). Commitments
and efficient zero knowledge proofs from learning parity with noise. In X. Wang
& K. Sako (Eds.) (Vol. 7658, pp. 663–680). Presented at the ASIACRYPT: Theory
and Application of Cryptology and Information Security, Beijing, China: Springer.
https://doi.org/10.1007/978-3-642-34961-4_40'
chicago: Jain, Abhishek, Stephan Krenn, Krzysztof Z Pietrzak, and Aris Tentes. “Commitments
and Efficient Zero Knowledge Proofs from Learning Parity with Noise.” edited by
Xiaoyun Wang and Kazue Sako, 7658:663–80. Springer, 2012. https://doi.org/10.1007/978-3-642-34961-4_40.
ieee: 'A. Jain, S. Krenn, K. Z. Pietrzak, and A. Tentes, “Commitments and efficient
zero knowledge proofs from learning parity with noise,” presented at the ASIACRYPT:
Theory and Application of Cryptology and Information Security, Beijing, China,
2012, vol. 7658, pp. 663–680.'
ista: 'Jain A, Krenn S, Pietrzak KZ, Tentes A. 2012. Commitments and efficient zero
knowledge proofs from learning parity with noise. ASIACRYPT: Theory and Application
of Cryptology and Information Security, LNCS, vol. 7658, 663–680.'
mla: Jain, Abhishek, et al. Commitments and Efficient Zero Knowledge Proofs from
Learning Parity with Noise. Edited by Xiaoyun Wang and Kazue Sako, vol. 7658,
Springer, 2012, pp. 663–80, doi:10.1007/978-3-642-34961-4_40.
short: A. Jain, S. Krenn, K.Z. Pietrzak, A. Tentes, in:, X. Wang, K. Sako (Eds.),
Springer, 2012, pp. 663–680.
conference:
end_date: 2012-12-06
location: Beijing, China
name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security'
start_date: 2012-12-02
date_created: 2018-12-11T12:00:38Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:11Z
day: '01'
ddc:
- '004'
- '005'
department:
- _id: KrPi
doi: 10.1007/978-3-642-34961-4_40
ec_funded: 1
editor:
- first_name: Xiaoyun
full_name: Wang, Xiaoyun
last_name: Wang
- first_name: Kazue
full_name: Sako, Kazue
last_name: Sako
file:
- access_level: open_access
checksum: ab879537385efc4cb4203e7ef0fea17b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:00Z
date_updated: 2020-07-14T12:45:58Z
file_id: '5048'
file_name: IST-2016-721-v1+1_513.pdf
file_size: 482570
relation: main_file
file_date_updated: 2020-07-14T12:45:58Z
has_accepted_license: '1'
intvolume: ' 7658'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 663 - 680
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: '3730'
pubrep_id: '721'
scopus_import: 1
status: public
title: Commitments and efficient zero knowledge proofs from learning parity with noise
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: 7658
year: '2012'
...
---
_id: '2969'
abstract:
- lang: eng
text: "The coupling between presynaptic Ca^(2+) channels and Ca^(2+) sensors of
exocytosis is a key determinant of synaptic transmission. Evoked release from
parvalbumin (PV)-expressing interneurons is triggered by nanodomain coupling of
P/Q-type Ca^(2+) channels, whereas release from cholecystokinin (CCK)-containing
interneurons is generated by microdomain coupling of N-type channels. Nanodomain
coupling has several functional advantages, including speed and efficacy of transmission.
One potential disadvantage is that stochastic\r\nopening of presynaptic Ca^(2+)
channels may trigger spontaneous transmitter release. We addressed this possibility
in rat hippocampal\r\ngranule cells, which receive converging inputs from different
inhibitory sources. Both reduction of extracellular Ca^(2+) concentration and
the unselective Ca^(2+) channel blocker Cd^(2+) reduced the frequency of miniature
IPSCs (mIPSCs) in granule cells by ~50%, suggesting that the opening of presynaptic
Ca^(2+) channels contributes to spontaneous release. Application of the selective
P/Q-type Ca^(2+) channel blocker\r\nω-agatoxin IVa had no detectable effects,
whereas both the N-type blocker ω-conotoxin GVIa and the L-type blocker nimodipine
reduced\r\nmIPSC frequency. Furthermore, both the fast Ca^(2+) chelator BAPTA-AM
and the slow chelator EGTA-AM reduced the mIPSC frequency,\r\nsuggesting that
Ca^(2+)-dependent spontaneous release is triggered by microdomain rather than
nanodomain coupling. The CB_(1) receptor\r\nagonist WIN 55212-2 also decreased
spontaneous release; this effect was occluded by prior application of ω-conotoxin
GVIa, suggesting that a major fraction of Ca^(2+)-dependent spontaneous release
was generated at the terminals of CCK-expressing interneurons. Tonic inhibition
generated by spontaneous opening of presynaptic N- and L-type Ca^(2+) channels
may be important for hippocampal information processing.\r\n"
acknowledgement: This work was supported by grants from the Deutsche Forschungsgemeinschaft
(TR 3/B10, Leibniz program, GSC-4 Spemann Graduate School) and the European Union
(European Research Council Advanced Grant).
author:
- first_name: Sarit
full_name: Goswami, Sarit
id: 3A578F32-F248-11E8-B48F-1D18A9856A87
last_name: Goswami
- first_name: Iancu
full_name: Bucurenciu, Iancu
last_name: Bucurenciu
- 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: Goswami S, Bucurenciu I, Jonas PM. Miniature IPSCs in hippocampal granule cells
are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal
of Neuroscience. 2012;32(41):14294-14304. doi:10.1523/JNEUROSCI.6104-11.2012
apa: Goswami, S., Bucurenciu, I., & Jonas, P. M. (2012). Miniature IPSCs in
hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via
microdomain coupling. Journal of Neuroscience. Society for Neuroscience.
https://doi.org/10.1523/JNEUROSCI.6104-11.2012
chicago: Goswami, Sarit, Iancu Bucurenciu, and Peter M Jonas. “Miniature IPSCs in
Hippocampal Granule Cells Are Triggered by Voltage-Gated Ca^(2+) Channels via
Microdomain Coupling.” Journal of Neuroscience. Society for Neuroscience,
2012. https://doi.org/10.1523/JNEUROSCI.6104-11.2012.
ieee: S. Goswami, I. Bucurenciu, and P. M. Jonas, “Miniature IPSCs in hippocampal
granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain
coupling,” Journal of Neuroscience, vol. 32, no. 41. Society for Neuroscience,
pp. 14294–14304, 2012.
ista: Goswami S, Bucurenciu I, Jonas PM. 2012. Miniature IPSCs in hippocampal granule
cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling.
Journal of Neuroscience. 32(41), 14294–14304.
mla: Goswami, Sarit, et al. “Miniature IPSCs in Hippocampal Granule Cells Are Triggered
by Voltage-Gated Ca^(2+) Channels via Microdomain Coupling.” Journal of Neuroscience,
vol. 32, no. 41, Society for Neuroscience, 2012, pp. 14294–304, doi:10.1523/JNEUROSCI.6104-11.2012.
short: S. Goswami, I. Bucurenciu, P.M. Jonas, Journal of Neuroscience 32 (2012)
14294–14304.
date_created: 2018-12-11T12:00:36Z
date_published: 2012-10-10T00:00:00Z
date_updated: 2021-01-12T07:40:08Z
day: '10'
department:
- _id: PeJo
doi: 10.1523/JNEUROSCI.6104-11.2012
external_id:
pmid:
- '23055500'
intvolume: ' 32'
issue: '41'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632771/
month: '10'
oa: 1
oa_version: Submitted Version
page: 14294 - 14304
pmid: 1
project:
- _id: 25BDE9A4-B435-11E9-9278-68D0E5697425
grant_number: SFB-TR3-TP10B
name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '3744'
quality_controlled: '1'
scopus_import: 1
status: public
title: Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated
Ca^(2+) channels via microdomain coupling
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2012'
...
---
_id: '2970'
abstract:
- lang: eng
text: Morphogen gradients regulate the patterning and growth of many tissues, hence
a key question is how they are established and maintained during development.
Theoretical descriptions have helped to explain how gradient shape is controlled
by the rates of morphogen production, spreading and degradation. These effective
rates have been measured using fluorescence recovery after photobleaching (FRAP)
and photoactivation. To unravel which molecular events determine the effective
rates, such tissue-level assays have been combined with genetic analysis, high-resolution
assays, and models that take into account interactions with receptors, extracellular
components and trafficking. Nevertheless, because of the natural and experimental
data variability, and the underlying assumptions of transport models, it remains
challenging to conclusively distinguish between cellular mechanisms.
acknowledgement: AK is currently supported by an MRC CDF. MGG and OW were supported
by the Swiss National Science Foundation, grants from the Swiss SystemsX.ch initiative,
LipidX-2008/011, an ERC advanced investigator grant and the Polish-Swiss research
program.
author:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Ortrud
full_name: Wartlick, Ortrud
last_name: Wartlick
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Marcos
full_name: Gonzalez Gaitan, Marcos
last_name: Gonzalez Gaitan
citation:
ama: 'Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. Investigating
the principles of morphogen gradient formation: from tissues to cells. Current
Opinion in Genetics & Development. 2012;22(6):527-532. doi:10.1016/j.gde.2012.08.004'
apa: 'Kicheva, A., Bollenbach, M. T., Wartlick, O., Julicher, F., & Gonzalez
Gaitan, M. (2012). Investigating the principles of morphogen gradient formation:
from tissues to cells. Current Opinion in Genetics & Development. Elsevier.
https://doi.org/10.1016/j.gde.2012.08.004'
chicago: 'Kicheva, Anna, Mark Tobias Bollenbach, Ortrud Wartlick, Frank Julicher,
and Marcos Gonzalez Gaitan. “Investigating the Principles of Morphogen Gradient
Formation: From Tissues to Cells.” Current Opinion in Genetics & Development.
Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.08.004.'
ieee: 'A. Kicheva, M. T. Bollenbach, O. Wartlick, F. Julicher, and M. Gonzalez Gaitan,
“Investigating the principles of morphogen gradient formation: from tissues to
cells,” Current Opinion in Genetics & Development, vol. 22, no. 6.
Elsevier, pp. 527–532, 2012.'
ista: 'Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. 2012.
Investigating the principles of morphogen gradient formation: from tissues to
cells. Current Opinion in Genetics & Development. 22(6), 527–532.'
mla: 'Kicheva, Anna, et al. “Investigating the Principles of Morphogen Gradient
Formation: From Tissues to Cells.” Current Opinion in Genetics & Development,
vol. 22, no. 6, Elsevier, 2012, pp. 527–32, doi:10.1016/j.gde.2012.08.004.'
short: A. Kicheva, M.T. Bollenbach, O. Wartlick, F. Julicher, M. Gonzalez Gaitan,
Current Opinion in Genetics & Development 22 (2012) 527–532.
date_created: 2018-12-11T12:00:37Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:09Z
day: '01'
department:
- _id: ToBo
doi: 10.1016/j.gde.2012.08.004
intvolume: ' 22'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 527 - 532
publication: Current Opinion in Genetics & Development
publication_status: published
publisher: Elsevier
publist_id: '3739'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Investigating the principles of morphogen gradient formation: from tissues
to cells'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2012'
...
---
_id: '2971'
abstract:
- lang: eng
text: 'We study the task of interactive semantic labeling of a segmentation hierarchy.
To this end we propose a framework interleaving two components: an automatic labeling
step, based on a Conditional Random Field whose dependencies are defined by the
inclusion tree of the segmentation hierarchy, and an interaction step that integrates
incremental input from a human user. Evaluated on two distinct datasets, the proposed
interactive approach efficiently integrates human interventions and illustrates
the advantages of structured prediction in an interactive framework. '
author:
- first_name: Georg
full_name: Zankl, Georg
last_name: Zankl
- first_name: Yll
full_name: Haxhimusa, Yll
last_name: Haxhimusa
- first_name: Adrian
full_name: Ion, Adrian
id: 29F89302-F248-11E8-B48F-1D18A9856A87
last_name: Ion
citation:
ama: 'Zankl G, Haxhimusa Y, Ion A. Interactive labeling of image segmentation hierarchies.
In: Vol 7476. Springer; 2012:11-20. doi:10.1007/978-3-642-32717-9_2'
apa: 'Zankl, G., Haxhimusa, Y., & Ion, A. (2012). Interactive labeling of image
segmentation hierarchies (Vol. 7476, pp. 11–20). Presented at the Pattern Recognition,
Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_2'
chicago: Zankl, Georg, Yll Haxhimusa, and Adrian Ion. “Interactive Labeling of Image
Segmentation Hierarchies,” 7476:11–20. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_2.
ieee: G. Zankl, Y. Haxhimusa, and A. Ion, “Interactive labeling of image segmentation
hierarchies,” presented at the Pattern Recognition, Graz, Austria, 2012, vol.
7476, pp. 11–20.
ista: Zankl G, Haxhimusa Y, Ion A. 2012. Interactive labeling of image segmentation
hierarchies. Pattern Recognition vol. 7476, 11–20.
mla: Zankl, Georg, et al. Interactive Labeling of Image Segmentation Hierarchies.
Vol. 7476, Springer, 2012, pp. 11–20, doi:10.1007/978-3-642-32717-9_2.
short: G. Zankl, Y. Haxhimusa, A. Ion, in:, Springer, 2012, pp. 11–20.
conference:
end_date: 2012-08-31
location: Graz, Austria
name: Pattern Recognition
start_date: 2012-08-28
date_created: 2018-12-11T12:00:37Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:10Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-642-32717-9_2
intvolume: ' 7476'
language:
- iso: eng
month: '01'
oa_version: None
page: 11 - 20
publication_status: published
publisher: Springer
publist_id: '3737'
quality_controlled: '1'
scopus_import: 1
status: public
title: Interactive labeling of image segmentation hierarchies
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7476
year: '2012'
...
---
_id: '3105'
abstract:
- lang: eng
text: Growth and development are coordinated by an array of intercellular communications.
Known plant signaling molecules include phytohormones and hormone peptides. Although
both classes can be implicated in the same developmental processes, little is
known about the interplay between phytohormone action and peptide signaling within
the cellular microenvironment. We show that genes coding for small secretory peptides,
designated GOLVEN (GLV), modulate the distribution of the phytohormone auxin.
The deregulation of the GLV function impairs the formation of auxin gradients
and alters the reorientation of shoots and roots after a gravity stimulus. Specifically,
the GLV signal modulates the trafficking dynamics of the auxin efflux carrier
PIN-FORMED2 involved in root tropic responses and meristem organization. Our work
links the local action of secretory peptides with phytohormone transport. Root
growth factor (RGF) or GOLVEN (GLV) secreted peptides have previously been implicated
in meristem regulation. Whitford et al. now show that RGF/GLV peptides induce
rapid relocalization of the auxin efflux regulator PIN2, regulate auxin gradients,
and modulate auxin-dependent root responses to specific stimuli.
author:
- first_name: Ryan
full_name: Whitford, Ryan
last_name: Whitford
- first_name: Ana
full_name: Fernandez, Ana
last_name: Fernandez
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Amparo
full_name: Pérez, Amparo Cuéllar
last_name: Pérez
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Andrzej
full_name: Drozdzecki, Andrzej
last_name: Drozdzecki
- first_name: Johannes
full_name: Leitner, Johannes
last_name: Leitner
- first_name: Lindy
full_name: Abas, Lindy
last_name: Abas
- first_name: Maarten
full_name: Aerts, Maarten
last_name: Aerts
- first_name: Kurt
full_name: Hoogewijs, Kurt
last_name: Hoogewijs
- first_name: Pawel
full_name: Pawel Baster
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Ruth
full_name: De Groodt, Ruth
last_name: De Groodt
- first_name: Yao
full_name: Lin, Yao-Cheng
last_name: Lin
- first_name: Véronique
full_name: Storme, Véronique
last_name: Storme
- first_name: Yves
full_name: Van de Peer, Yves
last_name: Van De Peer
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Annemieke
full_name: Madder, Annemieke
last_name: Madder
- first_name: Bart
full_name: Devreese, Bart
last_name: Devreese
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Pierre
full_name: Hilson, Pierre
last_name: Hilson
citation:
ama: Whitford R, Fernandez A, Tejos R, et al. GOLVEN secretory peptides regulate
auxin carrier turnover during plant gravitropic responses. Developmental Cell.
2012;22(3):678-685. doi:10.1016/j.devcel.2012.02.002
apa: Whitford, R., Fernandez, A., Tejos, R., Pérez, A., Kleine Vehn, J., Vanneste,
S., … Hilson, P. (2012). GOLVEN secretory peptides regulate auxin carrier turnover
during plant gravitropic responses. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2012.02.002
chicago: Whitford, Ryan, Ana Fernandez, Ricardo Tejos, Amparo Pérez, Jürgen Kleine
Vehn, Steffen Vanneste, Andrzej Drozdzecki, et al. “GOLVEN Secretory Peptides
Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental
Cell. Cell Press, 2012. https://doi.org/10.1016/j.devcel.2012.02.002.
ieee: R. Whitford et al., “GOLVEN secretory peptides regulate auxin carrier
turnover during plant gravitropic responses,” Developmental Cell, vol.
22, no. 3. Cell Press, pp. 678–685, 2012.
ista: Whitford R, Fernandez A, Tejos R, Pérez A, Kleine Vehn J, Vanneste S, Drozdzecki
A, Leitner J, Abas L, Aerts M, Hoogewijs K, Baster P, De Groodt R, Lin Y, Storme
V, Van De Peer Y, Beeckman T, Madder A, Devreese B, Luschnig C, Friml J, Hilson
P. 2012. GOLVEN secretory peptides regulate auxin carrier turnover during plant
gravitropic responses. Developmental Cell. 22(3), 678–685.
mla: Whitford, Ryan, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover
during Plant Gravitropic Responses.” Developmental Cell, vol. 22, no. 3,
Cell Press, 2012, pp. 678–85, doi:10.1016/j.devcel.2012.02.002.
short: R. Whitford, A. Fernandez, R. Tejos, A. Pérez, J. Kleine Vehn, S. Vanneste,
A. Drozdzecki, J. Leitner, L. Abas, M. Aerts, K. Hoogewijs, P. Baster, R. De Groodt,
Y. Lin, V. Storme, Y. Van De Peer, T. Beeckman, A. Madder, B. Devreese, C. Luschnig,
J. Friml, P. Hilson, Developmental Cell 22 (2012) 678–685.
date_created: 2018-12-11T12:01:25Z
date_published: 2012-03-13T00:00:00Z
date_updated: 2021-01-12T07:41:06Z
day: '13'
doi: 10.1016/j.devcel.2012.02.002
extern: 1
intvolume: ' 22'
issue: '3'
month: '03'
page: 678 - 685
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3594'
quality_controlled: 0
status: public
title: GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic
responses
type: journal_article
volume: 22
year: '2012'
...
---
_id: '3109'
abstract:
- lang: eng
text: Receptor-mediated endocytosis is an integral part of signal transduction as
it mediates signal attenuation and provides spatial and temporal dimensions to
signaling events. One of the best-studied leucine-rich repeat receptor-like kinases
in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brassinosteroid
(BR) hormone, at the cell surface and is constitutively endocytosed. However,
the importance of endocytosis for BR signaling remains unclear. Here we developed
a bioactive, fluorescent BR analog, Alexa Fluor 647-castasterone (AFCS), and visualized
the endocytosis of BRI1-AFCS complexes in living Arabidopsis thaliana cells. Impairment
of endocytosis dependent on clathrin and the guanine nucleotide exchange factor
for ARF GTPases (ARF-GEF) GNOM enhanced BR signaling by retaining active BRI1-ligand
complexes at the plasma membrane. Increasing the trans-Golgi network/early endosome
pool of BRI1-BR complexes did not affect BR signaling. Our findings provide what
is to our knowledge the first visualization of receptor-ligand complexes in plants
and reveal clathrin-and ARF-GEF-dependent endocytic regulation of BR signaling
from the plasma membrane.
author:
- first_name: Niloufer
full_name: Irani, Niloufer G
last_name: Irani
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Evelien
full_name: Mylle, Evelien
last_name: Mylle
- first_name: Jos
full_name: Van Den Begin, Jos
last_name: Van Den Begin
- first_name: Joanna
full_name: Schneider-Pizoń, Joanna
last_name: Schneider Pizoń
- first_name: Jaroslava
full_name: Hniliková, Jaroslava
last_name: Hniliková
- first_name: Miroslav
full_name: Šíša, Miroslav
last_name: Šíša
- first_name: Dieter
full_name: Buyst, Dieter
last_name: Buyst
- first_name: Josep
full_name: Vilarrasa-Blasi, Josep
last_name: Vilarrasa Blasi
- first_name: Anna
full_name: Szatmári, Anna-Maria
last_name: Szatmári
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Kiril
full_name: Mishev, Kiril
last_name: Mishev
- first_name: Mirela
full_name: Codreanu, Mirela-Corina
last_name: Codreanu
- first_name: Ladislav
full_name: Kohout, Ladislav
last_name: Kohout
- first_name: Miroslav
full_name: Strnad, Miroslav
last_name: Strnad
- first_name: Ana
full_name: Caño-Delgado, Ana I
last_name: Caño Delgado
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Annemieke
full_name: Madder, Annemieke
last_name: Madder
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Irani N, Di Rubbo S, Mylle E, et al. Fluorescent castasterone reveals BRI1
signaling from the plasma membrane. Nature Chemical Biology. 2012;8(6):583-589.
doi:10.1038/nchembio.958
apa: Irani, N., Di Rubbo, S., Mylle, E., Van Den Begin, J., Schneider Pizoń, J.,
Hniliková, J., … Russinova, E. (2012). Fluorescent castasterone reveals BRI1 signaling
from the plasma membrane. Nature Chemical Biology. Nature Publishing Group.
https://doi.org/10.1038/nchembio.958
chicago: Irani, Niloufer, Simone Di Rubbo, Evelien Mylle, Jos Van Den Begin, Joanna
Schneider Pizoń, Jaroslava Hniliková, Miroslav Šíša, et al. “Fluorescent Castasterone
Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology.
Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.958.
ieee: N. Irani et al., “Fluorescent castasterone reveals BRI1 signaling from
the plasma membrane,” Nature Chemical Biology, vol. 8, no. 6. Nature Publishing
Group, pp. 583–589, 2012.
ista: Irani N, Di Rubbo S, Mylle E, Van Den Begin J, Schneider Pizoń J, Hniliková
J, Šíša M, Buyst D, Vilarrasa Blasi J, Szatmári A, Van Damme D, Mishev K, Codreanu
M, Kohout L, Strnad M, Caño Delgado A, Friml J, Madder A, Russinova E. 2012. Fluorescent
castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical
Biology. 8(6), 583–589.
mla: Irani, Niloufer, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from
the Plasma Membrane.” Nature Chemical Biology, vol. 8, no. 6, Nature Publishing
Group, 2012, pp. 583–89, doi:10.1038/nchembio.958.
short: N. Irani, S. Di Rubbo, E. Mylle, J. Van Den Begin, J. Schneider Pizoń, J.
Hniliková, M. Šíša, D. Buyst, J. Vilarrasa Blasi, A. Szatmári, D. Van Damme, K.
Mishev, M. Codreanu, L. Kohout, M. Strnad, A. Caño Delgado, J. Friml, A. Madder,
E. Russinova, Nature Chemical Biology 8 (2012) 583–589.
date_created: 2018-12-11T12:01:26Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:07Z
day: '01'
doi: 10.1038/nchembio.958
extern: 1
intvolume: ' 8'
issue: '6'
month: '06'
page: 583 - 589
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3590'
quality_controlled: 0
status: public
title: Fluorescent castasterone reveals BRI1 signaling from the plasma membrane
type: journal_article
volume: 8
year: '2012'
...
---
_id: '3104'
abstract:
- lang: eng
text: |2-
Gradients of the plant hormone auxin, which depend on its active intercellular transport, are crucial for the maintenance of root meristematic activity. This directional transport is largely orchestrated by a complex interaction of specific influx and efflux carriers that mediate the auxin flow into and out of cells, respectively. Besides these transport proteins, plant-specific polyphenolic compounds knownasflavonols have beenshownto act as endogenous regulators of auxin transport. However, only limited information is available on how flavonol synthesis is developmentally regulated. Using reduction-of-function and overexpression approaches in parallel, we demonstrate that the WRKY23 transcription factor is needed for proper root growth and development by stimulating the local biosynthesis of flavonols. The expression of WRKY23 itself is controlled by auxin through the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 transcriptional response pathway. Our results suggest a model in which WRKY23 is part of a transcriptional feedback loop of auxin on its own transport through local regulation of flavonol biosynthesis.
author:
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Ive
full_name: De Smet, Ive
last_name: De Smet
- first_name: Daniel
full_name: Lewis, Daniel R
last_name: Lewis
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Leentje
full_name: Jansen, Leentje
last_name: Jansen
- first_name: Geert
full_name: Goeminne, Geert
last_name: Goeminne
- first_name: Robin
full_name: Vanden Bossche, Robin
last_name: Vanden Bossche
- first_name: Mansour
full_name: Karimi, Mansour
last_name: Karimi
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Bartel
full_name: Vanholme, Bartel
last_name: Vanholme
- first_name: Thomas
full_name: Teichmann, Thomas
last_name: Teichmann
- first_name: Wout
full_name: Boerjan, Wout
last_name: Boerjan
- first_name: Marc
full_name: Van Montagu, Marc C
last_name: Van Montagu
- first_name: Godelieve
full_name: Gheysen, Godelieve
last_name: Gheysen
- first_name: Gloria
full_name: Muday, Gloria K
last_name: Muday
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
citation:
ama: Grunewald W, De Smet I, Lewis D, et al. Transcription factor WRKY23 assists
auxin distribution patterns during Arabidopsis root development through local
control on flavonol biosynthesis. PNAS. 2012;109(5):1554-1559. doi:10.1073/pnas.1121134109
apa: Grunewald, W., De Smet, I., Lewis, D., Löfke, C., Jansen, L., Goeminne, G.,
… Beeckman, T. (2012). Transcription factor WRKY23 assists auxin distribution
patterns during Arabidopsis root development through local control on flavonol
biosynthesis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1121134109
chicago: Grunewald, Wim, Ive De Smet, Daniel Lewis, Christian Löfke, Leentje Jansen,
Geert Goeminne, Robin Vanden Bossche, et al. “Transcription Factor WRKY23 Assists
Auxin Distribution Patterns during Arabidopsis Root Development through Local
Control on Flavonol Biosynthesis.” PNAS. National Academy of Sciences,
2012. https://doi.org/10.1073/pnas.1121134109.
ieee: W. Grunewald et al., “Transcription factor WRKY23 assists auxin distribution
patterns during Arabidopsis root development through local control on flavonol
biosynthesis,” PNAS, vol. 109, no. 5. National Academy of Sciences, pp.
1554–1559, 2012.
ista: Grunewald W, De Smet I, Lewis D, Löfke C, Jansen L, Goeminne G, Vanden Bossche
R, Karimi M, De Rybel B, Vanholme B, Teichmann T, Boerjan W, Van Montagu M, Gheysen
G, Muday G, Friml J, Beeckman T. 2012. Transcription factor WRKY23 assists auxin
distribution patterns during Arabidopsis root development through local control
on flavonol biosynthesis. PNAS. 109(5), 1554–1559.
mla: Grunewald, Wim, et al. “Transcription Factor WRKY23 Assists Auxin Distribution
Patterns during Arabidopsis Root Development through Local Control on Flavonol
Biosynthesis.” PNAS, vol. 109, no. 5, National Academy of Sciences, 2012,
pp. 1554–59, doi:10.1073/pnas.1121134109.
short: W. Grunewald, I. De Smet, D. Lewis, C. Löfke, L. Jansen, G. Goeminne, R.
Vanden Bossche, M. Karimi, B. De Rybel, B. Vanholme, T. Teichmann, W. Boerjan,
M. Van Montagu, G. Gheysen, G. Muday, J. Friml, T. Beeckman, PNAS 109 (2012) 1554–1559.
date_created: 2018-12-11T12:01:24Z
date_published: 2012-01-31T00:00:00Z
date_updated: 2021-01-12T07:41:05Z
day: '31'
doi: 10.1073/pnas.1121134109
extern: 1
intvolume: ' 109'
issue: '5'
month: '01'
page: 1554 - 1559
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3595'
quality_controlled: 0
status: public
title: Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis
root development through local control on flavonol biosynthesis
type: journal_article
volume: 109
year: '2012'
...
---
_id: '3108'
abstract:
- lang: eng
text: The phytohormone auxin acts as a prominent signal, providing, by its local
accumulation or depletion in selected cells, a spatial and temporal reference
for changes in the developmental program. The distribution of auxin depends on
both auxin metabolism (biosynthesis, conjugation and degradation) and cellular
auxin transport. We identified in silico a novel putative auxin transport facilitator
family, called PIN-LIKES (PILS). Here we illustrate that PILS proteins are required
for auxin-dependent regulation of plant growth by determining the cellular sensitivity
to auxin. PILS proteins regulate intracellular auxin accumulation at the endoplasmic
reticulum and thus auxin availability for nuclear auxin signalling. PILS activity
affects the level of endogenous auxin indole-3-acetic acid (IAA), presumably via
intracellular accumulation and metabolism. Our findings reveal that the transport
machinery to compartmentalize auxin within the cell is of an unexpected molecular
complexity and demonstrate this compartmentalization to be functionally important
for a number of developmental processes.
author:
- first_name: Elke
full_name: Barbez, Elke
last_name: Barbez
- first_name: Martin
full_name: Kubeš, Martin
last_name: Kubeš
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Chloe
full_name: Béziat, Chloe
last_name: Béziat
- first_name: Aleš
full_name: Pěnčík, Aleš
last_name: Pěnčík
- first_name: Bangjun
full_name: Wang, Bangjun
last_name: Wang
- first_name: Michel
full_name: Rosquete, Michel Ruiz
last_name: Rosquete
- first_name: Jinsheng
full_name: Zhu, Jinsheng
last_name: Zhu
- first_name: Petre
full_name: Dobrev, Petre I
last_name: Dobrev
- first_name: Yuree
full_name: Lee, Yuree
last_name: Lee
- first_name: Eva
full_name: Zašímalová, Eva
last_name: Zašímalová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- 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
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
citation:
ama: Barbez E, Kubeš M, Rolčík J, et al. A novel putative auxin carrier family regulates
intracellular auxin homeostasis in plants. Nature. 2012;485(7396):119-122.
doi:10.1038/nature11001
apa: Barbez, E., Kubeš, M., Rolčík, J., Béziat, C., Pěnčík, A., Wang, B., … Kleine
Vehn, J. (2012). A novel putative auxin carrier family regulates intracellular
auxin homeostasis in plants. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11001
chicago: Barbez, Elke, Martin Kubeš, Jakub Rolčík, Chloe Béziat, Aleš Pěnčík, Bangjun
Wang, Michel Rosquete, et al. “A Novel Putative Auxin Carrier Family Regulates
Intracellular Auxin Homeostasis in Plants.” Nature. Nature Publishing Group,
2012. https://doi.org/10.1038/nature11001.
ieee: E. Barbez et al., “A novel putative auxin carrier family regulates
intracellular auxin homeostasis in plants,” Nature, vol. 485, no. 7396.
Nature Publishing Group, pp. 119–122, 2012.
ista: Barbez E, Kubeš M, Rolčík J, Béziat C, Pěnčík A, Wang B, Rosquete M, Zhu J,
Dobrev P, Lee Y, Zašímalová E, Petrášek J, Geisler M, Friml J, Kleine Vehn J.
2012. A novel putative auxin carrier family regulates intracellular auxin homeostasis
in plants. Nature. 485(7396), 119–122.
mla: Barbez, Elke, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular
Auxin Homeostasis in Plants.” Nature, vol. 485, no. 7396, Nature Publishing
Group, 2012, pp. 119–22, doi:10.1038/nature11001.
short: E. Barbez, M. Kubeš, J. Rolčík, C. Béziat, A. Pěnčík, B. Wang, M. Rosquete,
J. Zhu, P. Dobrev, Y. Lee, E. Zašímalová, J. Petrášek, M. Geisler, J. Friml, J.
Kleine Vehn, Nature 485 (2012) 119–122.
date_created: 2018-12-11T12:01:26Z
date_published: 2012-05-03T00:00:00Z
date_updated: 2021-01-12T07:41:07Z
day: '03'
doi: 10.1038/nature11001
extern: 1
intvolume: ' 485'
issue: '7396'
month: '05'
page: 119 - 122
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3591'
quality_controlled: 0
status: public
title: A novel putative auxin carrier family regulates intracellular auxin homeostasis
in plants
type: journal_article
volume: 485
year: '2012'
...
---
_id: '3106'
abstract:
- lang: eng
text: Cell polarization via asymmetrical distribution of structures or molecules
is essential for diverse cellular functions and development of organisms, but
how polarity is developmentally controlled has been poorly understood. In plants,
the asymmetrical distribution of the PIN-FORMED (PIN) proteins involved in the
cellular efflux of the quintessential phytohormone auxin plays a central role
in developmental patterning, morphogenesis, and differential growth. Recently
we showed that auxin promotes cell interdigitation by activating the Rho family
ROP GTPases in leaf epidermal pavement cells. Here we found that auxin activation
of the ROP2 signaling pathway regulates the asymmetric distribution of PIN1 by
inhibiting its endocytosis. ROP2 inhibits PIN1 endocytosis via the accumulation
of cortical actin microfilaments induced by the ROP2 effector protein RIC4. Our
findings suggest a link between the developmental auxin signal and polar PIN1
distribution via Rho-dependent cytoskeletal reorganization and reveal the conservation
of a design principle for cell polarization that is based on Rho GTPase-mediated
inhibition of endocytosis.
author:
- first_name: Shingo
full_name: Nagawa, Shingo
last_name: Nagawa
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Deshu
full_name: Lin, Deshu
last_name: Lin
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Xingxing
full_name: Zhang, Xingxing
last_name: Zhang
- 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: Nagawa S, Xu T, Lin D, et al. ROP GTPase-dependent actin microfilaments promote
PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS
Biology. 2012;10(4). doi:10.1371/journal.pbio.1001299
apa: Nagawa, S., Xu, T., Lin, D., Dhonukshe, P., Zhang, X., Friml, J., … Yang, Z.
(2012). ROP GTPase-dependent actin microfilaments promote PIN1 polarization by
localized inhibition of clathrin-dependent endocytosis. PLoS Biology. Public
Library of Science. https://doi.org/10.1371/journal.pbio.1001299
chicago: Nagawa, Shingo, Tongda Xu, Deshu Lin, Pankaj Dhonukshe, Xingxing Zhang,
Jiří Friml, Ben Scheres, Ying Fu, and Zhenbiao Yang. “ROP GTPase-Dependent Actin
Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent
Endocytosis.” PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001299.
ieee: S. Nagawa et al., “ROP GTPase-dependent actin microfilaments promote
PIN1 polarization by localized inhibition of clathrin-dependent endocytosis,”
PLoS Biology, vol. 10, no. 4. Public Library of Science, 2012.
ista: Nagawa S, Xu T, Lin D, Dhonukshe P, Zhang X, Friml J, Scheres B, Fu Y, Yang
Z. 2012. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by
localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 10(4).
mla: Nagawa, Shingo, et al. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1
Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS
Biology, vol. 10, no. 4, Public Library of Science, 2012, doi:10.1371/journal.pbio.1001299.
short: S. Nagawa, T. Xu, D. Lin, P. Dhonukshe, X. Zhang, J. Friml, B. Scheres, Y.
Fu, Z. Yang, PLoS Biology 10 (2012).
date_created: 2018-12-11T12:01:25Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2021-01-12T07:41:06Z
day: '01'
doi: 10.1371/journal.pbio.1001299
extern: 1
intvolume: ' 10'
issue: '4'
month: '04'
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3593'
quality_controlled: 0
status: public
title: ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized
inhibition of clathrin-dependent endocytosis
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
volume: 10
year: '2012'
...
---
_id: '3107'
author:
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Vanneste S, Friml J. Plant Signaling: Deconstructing Auxin Sensing.
Vol 8. Nature Publishing Group; 2012:415-416. doi:10.1038/nchembio.943'
apa: 'Vanneste, S., & Friml, J. (2012). Plant signaling: Deconstructing auxin
sensing. Nature Chemical Biology (Vol. 8, pp. 415–416). Nature Publishing
Group. https://doi.org/10.1038/nchembio.943'
chicago: 'Vanneste, Steffen, and Jiří Friml. Plant Signaling: Deconstructing
Auxin Sensing. Nature Chemical Biology. Vol. 8. Nature Publishing Group,
2012. https://doi.org/10.1038/nchembio.943.'
ieee: 'S. Vanneste and J. Friml, Plant signaling: Deconstructing auxin sensing,
vol. 8, no. 5. Nature Publishing Group, 2012, pp. 415–416.'
ista: 'Vanneste S, Friml J. 2012. Plant signaling: Deconstructing auxin sensing,
Nature Publishing Group,p.'
mla: 'Vanneste, Steffen, and Jiří Friml. “Plant Signaling: Deconstructing Auxin
Sensing.” Nature Chemical Biology, vol. 8, no. 5, Nature Publishing Group,
2012, pp. 415–16, doi:10.1038/nchembio.943.'
short: 'S. Vanneste, J. Friml, Plant Signaling: Deconstructing Auxin Sensing, Nature
Publishing Group, 2012.'
date_created: 2018-12-11T12:01:26Z
date_published: 2012-05-01T00:00:00Z
date_updated: 2021-01-12T07:41:06Z
day: '01'
doi: 10.1038/nchembio.943
extern: '1'
intvolume: ' 8'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 415 - 416
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3592'
quality_controlled: '1'
status: public
title: 'Plant signaling: Deconstructing auxin sensing'
type: other_academic_publication
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2012'
...
---
_id: '3119'
abstract:
- lang: eng
text: "We present an approach for artist-directed animation of liquids using multiple
levels of control over the simulation, ranging from the overall tracking of desired
shapes to highly detailed secondary effects such as dripping streams, separating
sheets of fluid, surface waves and ripples. The first portion of our technique
is a volume preserving morph that allows the animator to produce a plausible fluid-like
motion from a sparse set of control meshes. By rasterizing the resulting control
meshes onto the simulation grid, the mesh velocities act as boundary conditions
during the projection step of the fluid simulation. We can then blend this motion
together with uncontrolled fluid velocities to achieve a more relaxed control
over the fluid that captures natural inertial effects. Our method can produce
highly detailed liquid surfaces with control over sub-grid details by using a
mesh-based surface tracker on top of a coarse grid-based fluid simulation. We
can create ripples and waves on the fluid surface attracting the surface mesh
to the control mesh with spring-like forces and also by running a wave simulation
over the surface mesh. Our video results demonstrate how our control scheme can
be used to create animated characters and shapes that are made of water.\r\n"
acknowledgement: This work was partially funded by NSF grants CCF-0811485 and IIS-1130934.
We would like to thank Scanline VFX for additional funding. We would like to thank
Jie Tan as well as our anonymous reviewers for their useful suggestions and feedback.
author:
- first_name: Karthik
full_name: Raveendran, Karthik
last_name: Raveendran
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: 'Raveendran K, Thuerey N, Wojtan C, Turk G. Controlling liquids using meshes.
In: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation.
ACM; 2012:255-264.'
apa: 'Raveendran, K., Thuerey, N., Wojtan, C., & Turk, G. (2012). Controlling
liquids using meshes. In Proceedings of the ACM SIGGRAPH/Eurographics Symposium
on Computer Animation (pp. 255–264). Aire-la-Ville, Switzerland: ACM.'
chicago: Raveendran, Karthik, Nils Thuerey, Chris Wojtan, and Greg Turk. “Controlling
Liquids Using Meshes.” In Proceedings of the ACM SIGGRAPH/Eurographics Symposium
on Computer Animation, 255–64. ACM, 2012.
ieee: K. Raveendran, N. Thuerey, C. Wojtan, and G. Turk, “Controlling liquids using
meshes,” in Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer
Animation, Aire-la-Ville, Switzerland, 2012, pp. 255–264.
ista: 'Raveendran K, Thuerey N, Wojtan C, Turk G. 2012. Controlling liquids using
meshes. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation.
SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 255–264.'
mla: Raveendran, Karthik, et al. “Controlling Liquids Using Meshes.” Proceedings
of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012,
pp. 255–64.
short: K. Raveendran, N. Thuerey, C. Wojtan, G. Turk, in:, Proceedings of the ACM
SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–264.
conference:
end_date: 2012-07-31
location: Aire-la-Ville, Switzerland
name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation'
start_date: 2012-07-29
date_created: 2018-12-11T12:01:30Z
date_published: 2012-07-29T00:00:00Z
date_updated: 2023-02-23T11:13:07Z
day: '29'
ddc:
- '000'
department:
- _id: ChWo
file:
- access_level: open_access
checksum: babda64c24cf90a4d05ae86d712bed08
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:23Z
date_updated: 2020-07-14T12:46:00Z
file_id: '4877'
file_name: IST-2016-600-v1+1_ControllingLiquids_Preprint.pdf
file_size: 4939370
relation: main_file
file_date_updated: 2020-07-14T12:46:00Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 255 - 264
publication: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation
publication_status: published
publisher: ACM
publist_id: '3580'
pubrep_id: '600'
quality_controlled: '1'
related_material:
link:
- relation: table_of_contents
url: http://dl.acm.org/citation.cfm?id=2422393
scopus_import: 1
status: public
title: Controlling liquids using meshes
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '3118'
abstract:
- lang: eng
text: We present a method for recovering a temporally coherent, deforming triangle
mesh with arbitrarily changing topology from an incoherent sequence of static
closed surfaces. We solve this problem using the surface geometry alone, without
any prior information like surface templates or velocity fields. Our system combines
a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid
registration routine, and a reliable technique for changing surface mesh topology.
We also introduce a novel topological constraint enforcement algorithm to ensure
that the output and input always have similar topology. We apply our technique
to a series of diverse input data from video reconstructions, physics simulations,
and artistic morphs. The structured output of our algorithm allows us to efficiently
track information like colors and displacement maps, recover velocity information,
and solve PDEs on the mesh as a post process.
acknowledgement: "This work is supported by the SNF fellowship PBEZP2-134464.\r\nWe
would like to thank Xiaochen Hu for implementing mesh con- version tools, Duygu
Ceylan for helping with the rendering, and Art Tevs for the human performance data
comparison. We also thank Nils Thuerey and Christopher Batty for helpful discussions. "
alternative_title:
- SIGGRAPH
article_number: '53'
article_processing_charge: No
article_type: original
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
- first_name: Hao
full_name: Li, Hao
last_name: Li
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Bojsen-Hansen M, Li H, Wojtan C. Tracking surfaces with evolving topology.
ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185549
apa: Bojsen-Hansen, M., Li, H., & Wojtan, C. (2012). Tracking surfaces with
evolving topology. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185549
chicago: Bojsen-Hansen, Morten, Hao Li, and Chris Wojtan. “Tracking Surfaces with
Evolving Topology.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185549.
ieee: M. Bojsen-Hansen, H. Li, and C. Wojtan, “Tracking surfaces with evolving topology,”
ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012.
ista: Bojsen-Hansen M, Li H, Wojtan C. 2012. Tracking surfaces with evolving topology.
ACM Transactions on Graphics. 31(4), 53.
mla: Bojsen-Hansen, Morten, et al. “Tracking Surfaces with Evolving Topology.” ACM
Transactions on Graphics, vol. 31, no. 4, 53, ACM, 2012, doi:10.1145/2185520.2185549.
short: M. Bojsen-Hansen, H. Li, C. Wojtan, ACM Transactions on Graphics 31 (2012).
date_created: 2018-12-11T12:01:29Z
date_published: 2012-07-01T00:00:00Z
date_updated: 2022-05-24T08:21:11Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2185520.2185549
file:
- access_level: open_access
checksum: 1e219c5bf4e5552c1290c62eefa5cd60
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:37Z
date_updated: 2020-07-14T12:46:00Z
file_id: '5359'
file_name: IST-2016-602-v1+1_topoReg.pdf
file_size: 44538518
relation: main_file
file_date_updated: 2020-07-14T12:46:00Z
has_accepted_license: '1'
intvolume: ' 31'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '3581'
pubrep_id: '602'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tracking surfaces with evolving topology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2012'
...
---
_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'
...
---
_id: '3156'
abstract:
- lang: eng
text: Dispersal is crucial for gene flow and often determines the long-term stability
of meta-populations, particularly in rare species with specialized life cycles.
Such species are often foci of conservation efforts because they suffer disproportionally
from degradation and fragmentation of their habitat. However, detailed knowledge
of effective gene flow through dispersal is often missing, so that conservation
strategies have to be based on mark-recapture observations that are suspected
to be poor predictors of long-distance dispersal. These constraints have been
especially severe in the study of butterfly populations, where microsatellite
markers have been difficult to develop. We used eight microsatellite markers to
analyse genetic population structure of the Large Blue butterfly Maculinea arion
in Sweden. During recent decades, this species has become an icon of insect conservation
after massive decline throughout Europe and extinction in Britain followed by
reintroduction of a seed population from the Swedish island of Öland. We find
that populations are highly structured genetically, but that gene flow occurs
over distances 15 times longer than the maximum distance recorded from mark-recapture
studies, which can only be explained by maximum dispersal distances at least twice
as large as previously accepted. However, we also find evidence that gaps between
sites with suitable habitat exceeding ∼ 20 km induce genetic erosion that can
be detected from bottleneck analyses. Although further work is needed, our results
suggest that M. arion can maintain fully functional metapopulations when they
consist of optimal habitat patches that are no further apart than ∼10 km.
acknowledgement: "The work was financed by the Danish National Science Research Foundation
via a grant to the Centre for Social Evolution.\r\nWe thank four anonymous reviewers
for useful comments on the manuscript, J. Bergsten, P. Bina, B. Carlsson, M. Johannesson
and A.E. Lomborg for providing additional wingtip samples, A. Illum for assistance
in the field, and in particular P.S. Nielsen for mediating the contact to the collectors
and the Swedish authorities. Collection was made possible through a permit by the
Åtgärdsprogrammet, supported by the Swedish Environmental Protection Agency."
author:
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Anne
full_name: Andersen, Anne
last_name: Andersen
- first_name: Jacobus
full_name: Boomsma, Jacobus
last_name: Boomsma
- first_name: David
full_name: Nash, David
last_name: Nash
citation:
ama: Ugelvig LV, Andersen A, Boomsma J, Nash D. Dispersal and gene flow in the rare
parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 2012;21(13):3224-3236.
doi:10.1111/j.1365-294X.2012.05592.x
apa: Ugelvig, L. V., Andersen, A., Boomsma, J., & Nash, D. (2012). Dispersal
and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular
Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05592.x
chicago: Ugelvig, Line V, Anne Andersen, Jacobus Boomsma, and David Nash. “Dispersal
and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” Molecular
Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05592.x.
ieee: L. V. Ugelvig, A. Andersen, J. Boomsma, and D. Nash, “Dispersal and gene flow
in the rare parasitic Large Blue butterfly Maculinea arion,” Molecular Ecology,
vol. 21, no. 13. Wiley-Blackwell, pp. 3224–3236, 2012.
ista: Ugelvig LV, Andersen A, Boomsma J, Nash D. 2012. Dispersal and gene flow in
the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 21(13),
3224–3236.
mla: Ugelvig, Line V., et al. “Dispersal and Gene Flow in the Rare Parasitic Large
Blue Butterfly Maculinea Arion.” Molecular Ecology, vol. 21, no. 13, Wiley-Blackwell,
2012, pp. 3224–36, doi:10.1111/j.1365-294X.2012.05592.x.
short: L.V. Ugelvig, A. Andersen, J. Boomsma, D. Nash, Molecular Ecology 21 (2012)
3224–3236.
date_created: 2018-12-11T12:01:43Z
date_published: 2012-07-01T00:00:00Z
date_updated: 2021-01-12T07:41:27Z
day: '01'
department:
- _id: SyCr
doi: 10.1111/j.1365-294X.2012.05592.x
intvolume: ' 21'
issue: '13'
language:
- iso: eng
month: '07'
oa_version: None
page: 3224 - 3236
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3538'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea
arion
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2012'
...
---
_id: '3158'
abstract:
- lang: eng
text: We describe here the development and characterization of a conditionally inducible
mouse model expressing Lifeact-GFP, a peptide that reports the dynamics of filamentous
actin. We have used this model to study platelets, megakaryocytes and melanoblasts
and we provide evidence that Lifeact-GFP is a useful reporter in these cell types
ex vivo. In the case of platelets and megakaryocytes, these cells are not transfectable
by traditional methods, so conditional activation of Lifeact allows the study
of actin dynamics in these cells live. We studied melanoblasts in native skin
explants from embryos, allowing the visualization of live actin dynamics during
cytokinesis and migration. Our study revealed that melanoblasts lacking the small
GTPase Rac1 show a delay in the formation of new pseudopodia following cytokinesis
that accounts for the previously reported cytokinesis delay in these cells. Thus,
through use of this mouse model, we were able to gain insights into the actin
dynamics of cells that could only previously be studied using fixed specimens
or following isolation from their native tissue environment.
author:
- first_name: Hannah
full_name: Schachtner, Hannah
last_name: Schachtner
- first_name: Ang
full_name: Li, Ang
last_name: Li
- first_name: David
full_name: Stevenson, David
last_name: Stevenson
- first_name: Simon
full_name: Calaminus, Simon
last_name: Calaminus
- first_name: Steven
full_name: Thomas, Steven
last_name: Thomas
- first_name: Steve
full_name: Watson, Steve
last_name: Watson
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Roland
full_name: Wedlich Söldner, Roland
last_name: Wedlich Söldner
- first_name: Douglas
full_name: Strathdee, Douglas
last_name: Strathdee
- first_name: Laura
full_name: Machesky, Laura
last_name: Machesky
citation:
ama: Schachtner H, Li A, Stevenson D, et al. Tissue inducible Lifeact expression
allows visualization of actin dynamics in vivo and ex vivo. European Journal
of Cell Biology. 2012;91(11-12):923-929. doi:10.1016/j.ejcb.2012.04.002
apa: Schachtner, H., Li, A., Stevenson, D., Calaminus, S., Thomas, S., Watson, S.,
… Machesky, L. (2012). Tissue inducible Lifeact expression allows visualization
of actin dynamics in vivo and ex vivo. European Journal of Cell Biology.
Elsevier. https://doi.org/10.1016/j.ejcb.2012.04.002
chicago: Schachtner, Hannah, Ang Li, David Stevenson, Simon Calaminus, Steven Thomas,
Steve Watson, Michael K Sixt, Roland Wedlich Söldner, Douglas Strathdee, and Laura
Machesky. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics
in Vivo and Ex Vivo.” European Journal of Cell Biology. Elsevier, 2012.
https://doi.org/10.1016/j.ejcb.2012.04.002.
ieee: H. Schachtner et al., “Tissue inducible Lifeact expression allows visualization
of actin dynamics in vivo and ex vivo,” European Journal of Cell Biology,
vol. 91, no. 11–12. Elsevier, pp. 923–929, 2012.
ista: Schachtner H, Li A, Stevenson D, Calaminus S, Thomas S, Watson S, Sixt MK,
Wedlich Söldner R, Strathdee D, Machesky L. 2012. Tissue inducible Lifeact expression
allows visualization of actin dynamics in vivo and ex vivo. European Journal of
Cell Biology. 91(11–12), 923–929.
mla: Schachtner, Hannah, et al. “Tissue Inducible Lifeact Expression Allows Visualization
of Actin Dynamics in Vivo and Ex Vivo.” European Journal of Cell Biology,
vol. 91, no. 11–12, Elsevier, 2012, pp. 923–29, doi:10.1016/j.ejcb.2012.04.002.
short: H. Schachtner, A. Li, D. Stevenson, S. Calaminus, S. Thomas, S. Watson, M.K.
Sixt, R. Wedlich Söldner, D. Strathdee, L. Machesky, European Journal of Cell
Biology 91 (2012) 923–929.
date_created: 2018-12-11T12:01:44Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T07:41:27Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/j.ejcb.2012.04.002
external_id:
pmid:
- '22658956'
intvolume: ' 91'
issue: 11-12
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930012/
month: '11'
oa: 1
oa_version: Submitted Version
page: 923 - 929
pmid: 1
publication: European Journal of Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '3534'
quality_controlled: '1'
scopus_import: 1
status: public
title: Tissue inducible Lifeact expression allows visualization of actin dynamics
in vivo and ex vivo
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2012'
...
---
_id: '3248'
abstract:
- lang: eng
text: We describe RTblob, a high speed vision system that detects objects in cluttered
scenes based on their color and shape at a speed of over 800 frames/s. Because
the system is available as open-source software and relies only on off-the-shelf
PC hardware components, it can provide the basis for multiple application scenarios.
As an illustrative example, we show how RTblob can be used in a robotic table
tennis scenario to estimate ball trajectories through 3D space simultaneously
from four cameras images at a speed of 200 Hz.
article_processing_charge: No
article_type: original
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Jan
full_name: Peters, Jan
last_name: Peters
citation:
ama: Lampert C, Peters J. Real-time detection of colored objects in multiple camera
streams with off-the-shelf hardware components. Journal of Real-Time Image
Processing. 2012;7(1):31-41. doi:10.1007/s11554-010-0168-3
apa: Lampert, C., & Peters, J. (2012). Real-time detection of colored objects
in multiple camera streams with off-the-shelf hardware components. Journal
of Real-Time Image Processing. Springer. https://doi.org/10.1007/s11554-010-0168-3
chicago: Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects
in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal
of Real-Time Image Processing. Springer, 2012. https://doi.org/10.1007/s11554-010-0168-3.
ieee: C. Lampert and J. Peters, “Real-time detection of colored objects in multiple
camera streams with off-the-shelf hardware components,” Journal of Real-Time
Image Processing, vol. 7, no. 1. Springer, pp. 31–41, 2012.
ista: Lampert C, Peters J. 2012. Real-time detection of colored objects in multiple
camera streams with off-the-shelf hardware components. Journal of Real-Time Image
Processing. 7(1), 31–41.
mla: Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects
in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal
of Real-Time Image Processing, vol. 7, no. 1, Springer, 2012, pp. 31–41, doi:10.1007/s11554-010-0168-3.
short: C. Lampert, J. Peters, Journal of Real-Time Image Processing 7 (2012) 31–41.
date_created: 2018-12-11T12:02:15Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2022-05-24T08:05:40Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1007/s11554-010-0168-3
file:
- access_level: open_access
checksum: 241be47ea50e81a283bcf4c45b07e8cc
content_type: application/pdf
creator: kschuh
date_created: 2019-02-12T10:52:25Z
date_updated: 2020-07-14T12:46:04Z
file_id: '5958'
file_name: 2012_Springer_Lampert.pdf
file_size: 2933187
relation: main_file
file_date_updated: 2020-07-14T12:46:04Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 31 - 41
publication: Journal of Real-Time Image Processing
publication_identifier:
eissn:
- 1861-8219
issn:
- 1861-8200
publication_status: published
publisher: Springer
publist_id: '3417'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Real-time detection of colored objects in multiple camera streams with off-the-shelf
hardware components
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2012'
...
---
_id: '3247'
abstract:
- lang: eng
text: The Brazilian Merganser is a very rare and threatened species that nowadays
inhabits only a few protected areas and their surroundings in the Brazilian territory.
In order to estimate the remaining genetic diversity and population structure
in this species, two mitochondrial genes were sequenced in 39 individuals belonging
to two populations and in one individual collected in Argentina in 1950. We found
a highly significant divergence between two major remaining populations of Mergus
octosetaceus, which suggests a historical population structure in this species.
Furthermore, two deeply divergent lineages were found in a single location, which
could due to current or historical secondary contact. Based on the available genetic
data, we point out future directions which would contribute to design strategies
for conservation and management of this threatened species.
acknowledgement: "The present study received grants from FAPEMIG, CNPq, Petrobras
Ambiental and Fundação O Boticário de Conservação da Natureza, and followed all
ethical guidelines and legal requirements of Brazil for sampling and studying an
endangered species.\r\nWe thank the Specialist Work Group for the Conservation of
Brazilian Merganser for valuable discussions and opinions on this manuscript. We
also thank all the staff from Instituto Terra Brasilis and Funatura (Vivian S. Braz
and Gislaine Disconzi) for collecting the samples at Serra da Canastra and Chapada
dos Veadeiros, respectively; Dario A. Lijtmaerand and Pablo Tubaro for providing
the samples from Argentina, Bradley C. Livezey for sending copies of his papers,
and Geoff M. Hilton and Paulo de Tarso Z. Antas for useful suggestions that greatly
improved this manuscript."
author:
- first_name: Sibelle
full_name: Vilaça, Sibelle
last_name: Vilaça
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Lívia
full_name: Lins, Lívia
last_name: Lins
- first_name: Fabrício
full_name: Santos, Fabrício
last_name: Santos
citation:
ama: Vilaça S, Fernandes Redondo RA, Lins L, Santos F. Remaining genetic diversity
in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 2012;13(1):293-298.
doi:10.1007/s10592-011-0262-5
apa: Vilaça, S., Fernandes Redondo, R. A., Lins, L., & Santos, F. (2012). Remaining
genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation
Genetics. Springer. https://doi.org/10.1007/s10592-011-0262-5
chicago: Vilaça, Sibelle, Rodrigo A Fernandes Redondo, Lívia Lins, and Fabrício
Santos. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).”
Conservation Genetics. Springer, 2012. https://doi.org/10.1007/s10592-011-0262-5.
ieee: S. Vilaça, R. A. Fernandes Redondo, L. Lins, and F. Santos, “Remaining genetic
diversity in Brazilian Merganser (Mergus octosetaceus),” Conservation Genetics,
vol. 13, no. 1. Springer, pp. 293–298, 2012.
ista: Vilaça S, Fernandes Redondo RA, Lins L, Santos F. 2012. Remaining genetic
diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics.
13(1), 293–298.
mla: Vilaça, Sibelle, et al. “Remaining Genetic Diversity in Brazilian Merganser
(Mergus Octosetaceus).” Conservation Genetics, vol. 13, no. 1, Springer,
2012, pp. 293–98, doi:10.1007/s10592-011-0262-5.
short: S. Vilaça, R.A. Fernandes Redondo, L. Lins, F. Santos, Conservation Genetics
13 (2012) 293–298.
date_created: 2018-12-11T12:02:15Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2021-01-12T07:42:05Z
day: '01'
department:
- _id: JoBo
doi: 10.1007/s10592-011-0262-5
intvolume: ' 13'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 293 - 298
publication: Conservation Genetics
publication_status: published
publisher: Springer
publist_id: '3420'
quality_controlled: '1'
scopus_import: 1
status: public
title: Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2012'
...
---
_id: '3245'
abstract:
- lang: eng
text: How cells orchestrate their behavior during collective migration is a long-standing
question. Using magnetic tweezers to apply mechanical stimuli to Xenopus mesendoderm
cells, Weber etal. (2012) now reveal, in this issue of Developmental Cell, a cadherin-mediated
mechanosensitive response that promotes cell polarization and movement persistence
during the collective mesendoderm migration in gastrulation.
author:
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Behrndt M, Heisenberg C-PJ. Spurred by resistance mechanosensation in collective
migration. Developmental Cell. 2012;22(1):3-4. doi:10.1016/j.devcel.2011.12.018
apa: Behrndt, M., & Heisenberg, C.-P. J. (2012). Spurred by resistance mechanosensation
in collective migration. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.12.018
chicago: Behrndt, Martin, and Carl-Philipp J Heisenberg. “Spurred by Resistance
Mechanosensation in Collective Migration.” Developmental Cell. Cell Press,
2012. https://doi.org/10.1016/j.devcel.2011.12.018.
ieee: M. Behrndt and C.-P. J. Heisenberg, “Spurred by resistance mechanosensation
in collective migration,” Developmental Cell, vol. 22, no. 1. Cell Press,
pp. 3–4, 2012.
ista: Behrndt M, Heisenberg C-PJ. 2012. Spurred by resistance mechanosensation in
collective migration. Developmental Cell. 22(1), 3–4.
mla: Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Spurred by Resistance Mechanosensation
in Collective Migration.” Developmental Cell, vol. 22, no. 1, Cell Press,
2012, pp. 3–4, doi:10.1016/j.devcel.2011.12.018.
short: M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 22 (2012) 3–4.
date_created: 2018-12-11T12:02:14Z
date_published: 2012-01-17T00:00:00Z
date_updated: 2021-01-12T07:42:05Z
day: '17'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2011.12.018
intvolume: ' 22'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 3 - 4
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3426'
quality_controlled: '1'
scopus_import: 1
status: public
title: Spurred by resistance mechanosensation in collective migration
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2012'
...
---
_id: '3262'
abstract:
- lang: eng
text: Living cells must control the reading out or "expression" of information
encoded in their genomes, and this regulation often is mediated by transcription
factors--proteins that bind to DNA and either enhance or repress the expression
of nearby genes. But the expression of transcription factor proteins is itself
regulated, and many transcription factors regulate their own expression in addition
to responding to other input signals. Here we analyze the simplest of such self-regulatory
circuits, asking how parameters can be chosen to optimize information transmission
from inputs to outputs in the steady state. Some nonzero level of self-regulation
is almost always optimal, with self-activation dominant when transcription factor
concentrations are low and self-repression dominant when concentrations are high.
In steady state the optimal self-activation is never strong enough to induce bistability,
although there is a limit in which the optimal parameters are very close to the
critical point.
acknowledgement: "We thank T. Gregor, E. F. Wieschaus, and, especially, C. G. Callan
for helpful discussions.\r\nWork at Princeton was supported in part by NSF Grants
No. PHY–0957573 and No. CCF–0939370, by NIH Grant No. R01 GM077599, and by the W.
M. Keck Foundation. For part of this work, G.T. was supported in part by NSF Grant
No. EF–0928048 and by the Vice Provost for Research at the University of Pennsylvania."
article_number: '041903'
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Aleksandra
full_name: Walczak, Aleksandra
last_name: Walczak
- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic
networks. III. A self-interacting gene. Physical Review E statistical nonlinear
and soft matter physics . 2012;85(4). doi:10.1103/PhysRevE.85.041903
apa: Tkačik, G., Walczak, A., & Bialek, W. (2012). Optimizing information flow
in small genetic networks. III. A self-interacting gene. Physical Review E
Statistical Nonlinear and Soft Matter Physics . American Institute of Physics.
https://doi.org/10.1103/PhysRevE.85.041903
chicago: Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information
Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review
E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics,
2012. https://doi.org/10.1103/PhysRevE.85.041903.
ieee: G. Tkačik, A. Walczak, and W. Bialek, “Optimizing information flow in small
genetic networks. III. A self-interacting gene,” Physical Review E statistical
nonlinear and soft matter physics , vol. 85, no. 4. American Institute of
Physics, 2012.
ista: Tkačik G, Walczak A, Bialek W. 2012. Optimizing information flow in small
genetic networks. III. A self-interacting gene. Physical Review E statistical
nonlinear and soft matter physics . 85(4), 041903.
mla: Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks.
III. A Self-Interacting Gene.” Physical Review E Statistical Nonlinear and
Soft Matter Physics , vol. 85, no. 4, 041903, American Institute of Physics,
2012, doi:10.1103/PhysRevE.85.041903.
short: G. Tkačik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear
and Soft Matter Physics 85 (2012).
date_created: 2018-12-11T12:02:20Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2021-01-12T07:42:14Z
day: '01'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.85.041903
intvolume: ' 85'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1112.5026
month: '04'
oa: 1
oa_version: Preprint
publication: ' Physical Review E statistical nonlinear and soft matter physics '
publication_status: published
publisher: American Institute of Physics
publist_id: '3386'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimizing information flow in small genetic networks. III. A self-interacting
gene
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 85
year: '2012'
...
---
_id: '3257'
abstract:
- lang: eng
text: Consider a convex relaxation f̂ of a pseudo-Boolean function f. We say that
the relaxation is totally half-integral if f̂(x) is a polyhedral function with
half-integral extreme points x, and this property is preserved after adding an
arbitrary combination of constraints of the form x i=x j, x i=1-x j, and x i=γ
where γ∈{0,1,1/2} is a constant. A well-known example is the roof duality relaxation
for quadratic pseudo-Boolean functions f. We argue that total half-integrality
is a natural requirement for generalizations of roof duality to arbitrary pseudo-Boolean
functions. Our contributions are as follows. First, we provide a complete characterization
of totally half-integral relaxations f̂ by establishing a one-to-one correspondence
with bisubmodular functions. Second, we give a new characterization of bisubmodular
functions. Finally, we show some relationships between general totally half-integral
relaxations and relaxations based on the roof duality. On the conceptual level,
our results show that bisubmodular functions provide a natural generalization
of the roof duality approach to higher-order terms. This can be viewed as a non-submodular
analogue of the fact that submodular functions generalize the s-t minimum cut
problem with non-negative weights to higher-order terms.
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Kolmogorov V. Generalized roof duality and bisubmodular functions. Discrete
Applied Mathematics. 2012;160(4-5):416-426. doi:10.1016/j.dam.2011.10.026
apa: Kolmogorov, V. (2012). Generalized roof duality and bisubmodular functions.
Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2011.10.026
chicago: Kolmogorov, Vladimir. “Generalized Roof Duality and Bisubmodular Functions.”
Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2011.10.026.
ieee: V. Kolmogorov, “Generalized roof duality and bisubmodular functions,” Discrete
Applied Mathematics, vol. 160, no. 4–5. Elsevier, pp. 416–426, 2012.
ista: Kolmogorov V. 2012. Generalized roof duality and bisubmodular functions. Discrete
Applied Mathematics. 160(4–5), 416–426.
mla: Kolmogorov, Vladimir. “Generalized Roof Duality and Bisubmodular Functions.”
Discrete Applied Mathematics, vol. 160, no. 4–5, Elsevier, 2012, pp. 416–26,
doi:10.1016/j.dam.2011.10.026.
short: V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 416–426.
date_created: 2018-12-11T12:02:18Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2023-02-23T11:04:49Z
day: '01'
department:
- _id: VlKo
doi: 10.1016/j.dam.2011.10.026
external_id:
arxiv:
- '1005.2305'
intvolume: ' 160'
issue: 4-5
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1005.2305
month: '03'
oa: 1
oa_version: Preprint
page: 416 - 426
publication: Discrete Applied Mathematics
publication_status: published
publisher: Elsevier
publist_id: '3397'
quality_controlled: '1'
related_material:
record:
- id: '2934'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Generalized roof duality and bisubmodular functions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 160
year: '2012'
...
---
_id: '3277'
abstract:
- lang: eng
text: The problem of the origin of metazoa is becoming more urgent in the context
of astrobiology. By now it is clear that clues to the understanding of this crucial
transition in the evolution of life can arise in a fourth pathway besides the
three possibilities in the quest for simplicity outlined by Bonner in his classical
book. In other words, solar system exploration seems to be one way in the long-term
to elucidate the simplicity of evolutionary development. We place these ideas
in the context of different inheritance systems, namely the genotypic and phenotypic
replicators with limited or unlimited heredity, and ask which of these can support
multicellular development, and to which degree of complexity. However, the quest
for evidence on the evolution of biotas from planets around other stars does not
seem to be feasible with present technology with direct visualization of living
organisms on exoplanets. But this may be attempted on the Galilean moons of Jupiter
where there is a possibility of detecting reliable biomarkers in the next decade
with the Europa Jupiter System Mission, in view of recent progress by landing
micropenetrators on planetary, or satellite surfaces. Mars is a second possibility
in the inner Solar System, in spite of the multiple difficulties faced by the
fleet of past, present and future missions. We discuss a series of preliminary
ideas for elucidating the origin of metazoan analogues with available instrumentation
in potential payloads of feasible space missions to the Galilean moons.
alternative_title:
- Cellular Origin, Life in Extreme Habitats and Astrobiology
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Julian
full_name: Chela Flores, Julian
last_name: Chela Flores
citation:
ama: 'de Vladar H, Chela Flores J. Can the evolution of multicellularity be anticipated
in the exploration of the solar system? In: Life on Earth and Other Planetary
Bodies. Vol 24. Springer; 2012:387-405. doi:10.1007/978-94-007-4966-5_22'
apa: de Vladar, H., & Chela Flores, J. (2012). Can the evolution of multicellularity
be anticipated in the exploration of the solar system? In Life on Earth and
other planetary bodies (Vol. 24, pp. 387–405). Springer. https://doi.org/10.1007/978-94-007-4966-5_22
chicago: Vladar, Harold de, and Julian Chela Flores. “Can the Evolution of Multicellularity
Be Anticipated in the Exploration of the Solar System?” In Life on Earth and
Other Planetary Bodies, 24:387–405. Springer, 2012. https://doi.org/10.1007/978-94-007-4966-5_22.
ieee: H. de Vladar and J. Chela Flores, “Can the evolution of multicellularity be
anticipated in the exploration of the solar system?,” in Life on Earth and
other planetary bodies, vol. 24, Springer, 2012, pp. 387–405.
ista: 'de Vladar H, Chela Flores J. 2012.Can the evolution of multicellularity be
anticipated in the exploration of the solar system? In: Life on Earth and other
planetary bodies. Cellular Origin, Life in Extreme Habitats and Astrobiology,
vol. 24, 387–405.'
mla: de Vladar, Harold, and Julian Chela Flores. “Can the Evolution of Multicellularity
Be Anticipated in the Exploration of the Solar System?” Life on Earth and Other
Planetary Bodies, vol. 24, Springer, 2012, pp. 387–405, doi:10.1007/978-94-007-4966-5_22.
short: H. de Vladar, J. Chela Flores, in:, Life on Earth and Other Planetary Bodies,
Springer, 2012, pp. 387–405.
date_created: 2018-12-11T12:02:25Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:20Z
day: '01'
department:
- _id: NiBa
doi: 10.1007/978-94-007-4966-5_22
intvolume: ' 24'
language:
- iso: eng
month: '01'
oa_version: None
page: 387 - 405
publication: Life on Earth and other planetary bodies
publication_status: published
publisher: Springer
publist_id: '3369'
quality_controlled: '1'
status: public
title: Can the evolution of multicellularity be anticipated in the exploration of
the solar system?
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2012'
...
---
_id: '3279'
abstract:
- lang: eng
text: "We show a hardness-preserving construction of a PRF from any length doubling
PRG which improves upon known constructions whenever we can put a non-trivial
upper bound q on the number of queries to the PRF. Our construction requires only
O(logq) invocations to the underlying PRG with each query. In comparison, the
number of invocations by the best previous hardness-preserving construction (GGM
using Levin's trick) is logarithmic in the hardness of the PRG. For example, starting
from an exponentially secure PRG {0,1} n → {0,1} 2n, we get a PRF which is exponentially
secure if queried at most q = exp(√n)times and where each invocation of the PRF
requires Θ(√n) queries to the underlying PRG. This is much less than the Θ(n)
required by known constructions. \r\n"
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: Abhishek
full_name: Jain, Abhishek
last_name: Jain
- 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: Aris
full_name: Tentes, Aris
last_name: Tentes
citation:
ama: 'Jain A, Pietrzak KZ, Tentes A. Hardness preserving constructions of pseudorandom
functions. In: Vol 7194. Springer; 2012:369-382. doi:10.1007/978-3-642-28914-9_21'
apa: 'Jain, A., Pietrzak, K. Z., & Tentes, A. (2012). Hardness preserving constructions
of pseudorandom functions (Vol. 7194, pp. 369–382). Presented at the TCC: Theory
of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_21'
chicago: Jain, Abhishek, Krzysztof Z Pietrzak, and Aris Tentes. “Hardness Preserving
Constructions of Pseudorandom Functions,” 7194:369–82. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_21.
ieee: 'A. Jain, K. Z. Pietrzak, and A. Tentes, “Hardness preserving constructions
of pseudorandom functions,” presented at the TCC: Theory of Cryptography Conference,
Taormina, Sicily, Italy, 2012, vol. 7194, pp. 369–382.'
ista: 'Jain A, Pietrzak KZ, Tentes A. 2012. Hardness preserving constructions of
pseudorandom functions. TCC: Theory of Cryptography Conference, LNCS, vol. 7194,
369–382.'
mla: Jain, Abhishek, et al. Hardness Preserving Constructions of Pseudorandom
Functions. Vol. 7194, Springer, 2012, pp. 369–82, doi:10.1007/978-3-642-28914-9_21.
short: A. Jain, K.Z. Pietrzak, A. Tentes, in:, Springer, 2012, pp. 369–382.
conference:
end_date: 2012-03-21
location: Taormina, Sicily, Italy
name: 'TCC: Theory of Cryptography Conference'
start_date: 2012-03-19
date_created: 2018-12-11T12:02:25Z
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_21
ec_funded: 1
intvolume: ' 7194'
language:
- iso: eng
main_file_link:
- url: http://www.iacr.org/archive/tcc2012/tcc2012-index.html
month: '05'
oa_version: None
page: 369 - 382
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: '3367'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hardness preserving constructions of pseudorandom functions
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7194
year: '2012'
...
---
_id: '3274'
abstract:
- lang: eng
text: A boundary element model of a tunnel running through horizontally layered
soil with anisotropic material properties is presented. Since there is no analytical
fundamental solution for wave propagation inside a layered orthotropic medium
in 3D, the fundamental displacements and stresses have to be calculated numerically.
In our model this is done in the Fourier domain with respect to space and time.
The assumption of a straight tunnel with infinite extension in the x direction
makes it possible to decouple the system for every wave number kx, leading to
a 2.5D-problem, which is suited for parallel computation. The special form of
the fundamental solution, resulting from our Fourier ansatz, and the fact, that
the calculation of the boundary integral equation is performed in the Fourier
domain, enhances the stability and efficiency of the numerical calculations.
acknowledgement: This work was supported by the Austrian Federal Ministry of Transport,
Innovation and Technology under the Grant Bmvit-isb2 and the FFG under the project
Pr. Nr. 809089.
author:
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Wolfgang
full_name: Kreuzer, Wolfgang
last_name: Kreuzer
- first_name: Holger
full_name: Waubke, Holger
last_name: Waubke
- first_name: Peter
full_name: Balazs, Peter
last_name: Balazs
citation:
ama: Rieckh G, Kreuzer W, Waubke H, Balazs P. A 2.5D-Fourier-BEM model for vibrations
in a tunnel running through layered anisotropic soil. Engineering Analysis
with Boundary Elements. 2012;36(6):960-967. doi:10.1016/j.enganabound.2011.12.014
apa: Rieckh, G., Kreuzer, W., Waubke, H., & Balazs, P. (2012). A 2.5D-Fourier-BEM
model for vibrations in a tunnel running through layered anisotropic soil.
Engineering Analysis with Boundary Elements. Elsevier. https://doi.org/10.1016/j.enganabound.2011.12.014
chicago: Rieckh, Georg, Wolfgang Kreuzer, Holger Waubke, and Peter Balazs. “A 2.5D-Fourier-BEM
Model for Vibrations in a Tunnel Running through Layered Anisotropic Soil.”
Engineering Analysis with Boundary Elements. Elsevier, 2012. https://doi.org/10.1016/j.enganabound.2011.12.014.
ieee: G. Rieckh, W. Kreuzer, H. Waubke, and P. Balazs, “A 2.5D-Fourier-BEM model
for vibrations in a tunnel running through layered anisotropic soil,” Engineering
Analysis with Boundary Elements, vol. 36, no. 6. Elsevier, pp. 960–967, 2012.
ista: Rieckh G, Kreuzer W, Waubke H, Balazs P. 2012. A 2.5D-Fourier-BEM model for
vibrations in a tunnel running through layered anisotropic soil. Engineering
Analysis with Boundary Elements. 36(6), 960–967.
mla: Rieckh, Georg, et al. “A 2.5D-Fourier-BEM Model for Vibrations in a Tunnel
Running through Layered Anisotropic Soil.” Engineering Analysis with Boundary
Elements, vol. 36, no. 6, Elsevier, 2012, pp. 960–67, doi:10.1016/j.enganabound.2011.12.014.
short: G. Rieckh, W. Kreuzer, H. Waubke, P. Balazs, Engineering Analysis with Boundary
Elements 36 (2012) 960–967.
date_created: 2018-12-11T12:02:24Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2021-01-12T07:42:19Z
day: '01'
department:
- _id: GaTk
doi: 10.1016/j.enganabound.2011.12.014
intvolume: ' 36'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 960 - 967
publication: ' Engineering Analysis with Boundary Elements'
publication_status: published
publisher: Elsevier
publist_id: '3372'
quality_controlled: '1'
scopus_import: 1
status: public
title: A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered
anisotropic soil
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2012'
...
---
_id: '3289'
abstract:
- lang: eng
text: "Viral manipulation of transduction pathways associated with key cellular
functions such as survival, response to microbial infection, and cytoskeleton
reorganization can provide the supportive milieu for a productive infection. Here,
we demonstrate that vaccinia virus (VACV) infection leads to activation of the
stress-activated protein kinase (SAPK)/extracellular signal-regulated kinase (ERK)
4/7 (MKK4/7)-c-Jun N-terminal protein kinase 1/2 (JNK1/2) pathway; further, the
stimulation of this pathway requires postpenetration, prereplicative events in
the viral replication cycle. Although the formation of intracellular mature virus
(IMV) was not affected in MKK4/7- or JNK1/2-knockout (KO) cells, we did note an
accentuated deregulation of microtubule and actin network organization in infected
JNK1/2-KO cells. This was followed by deregulated viral trafficking to the periphery
and enhanced enveloped particle release. Furthermore, VACV infection induced alterations
in the cell contractility and morphology, and cell migration was reduced in the
JNK-KO cells. In addition, phosphorylation of proteins implicated with early cell
contractility and cell migration, such as microtubule-associated protein 1B and
paxillin, respectively, was not detected in the VACV-infected KO cells. In sum,
our findings uncover a regulatory role played by the MKK4/7-JNK1/2 pathway in
cytoskeleton reorganization during VACV infection.\r\n"
acknowledgement: "This work was supported by grants from Fundação de Amparo a Pesquisa
do Estado de Minas Gerais (FAPEMIG), the Brazilian Federal Agency for Support and
Evaluation of Graduate Education (CAPES), and the National Council for Scientific
and Technological Development (CNPq). A.C.T.C.P., B.S.A.F.B., F.G.G.L., and J.A.P.S.-M.
were recipients of predoctoral fellowships from CNPq. C.A.B., E.G.K., T.S.-P., P.F.P.P.,
and P.C.P.F. are recipients of research fellowships from CNPq. \r\n\r\n\r\nWe are
grateful to Angela S. Lopes, Ilda M. V. Gama, João R. dos Santos, and Andreza A.
Carvalho for their secretarial/technical assistance and to Fernanda Gambogi for
help with immunofluorescence microscopy. We also thank M. C. Sogayar (Department
of Biochemistry, University of São Paulo, São Paulo, Brazil), who kindly provided
us with the A31 cell line, and R. Davis (Howard Hughes Medical Institute, University
of Massachusetts Medical School, Worcester, MA) for the WT and JNK1/2-, MKK4-, MKK7-,
and MKK4/7-KO cells. VACV WR was from C. Jungwirth (Universität Würzburg, Würzburg,
Germany). The recombinant VACV vF13L-GFP and the rabbit polyclonal antibodies against
viral proteins, B5R, D8L, L1R, and A36R, were from B. Moss (NIAID, Bethesda, MD).
The pcDNA3-Myc-JNK2-MKK7 WT plasmid was from Eugen Kerkhoff (Universität Würzburg,
Würzburg, Germany). We also thank Flávio G. da Fonseca (UFMG, Belo Horizonte, MG,
Brazil) and Kathleen A. Boyle (Medical College of Wisconsin, Milwaukee, WI) for
critically reading the manuscript."
author:
- first_name: Anna
full_name: Pereira, Anna
last_name: Pereira
- first_name: Flávia
full_name: Leite, Flávia
id: 36705F98-F248-11E8-B48F-1D18A9856A87
last_name: Leite
- first_name: Bruno
full_name: Brasil, Bruno
last_name: Brasil
- first_name: Jamaria
full_name: Soares Martins, Jamaria
last_name: Soares Martins
- first_name: Alice
full_name: Torres, Alice
last_name: Torres
- first_name: Paulo
full_name: Pimenta, Paulo
last_name: Pimenta
- first_name: Thais
full_name: Souto Padrón, Thais
last_name: Souto Padrón
- first_name: Paula
full_name: Tranktman, Paula
last_name: Tranktman
- first_name: Paulo
full_name: Ferreira, Paulo
last_name: Ferreira
- first_name: Erna
full_name: Kroon, Erna
last_name: Kroon
- first_name: Cláudio
full_name: Bonjardim, Cláudio
last_name: Bonjardim
citation:
ama: Pereira A, Leite F, Brasil B, et al. A vaccinia virus-driven interplay between
the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. Journal of Virology.
2012;86(1):172-184. doi:10.1128/JVI.05638-11
apa: Pereira, A., Leite, F., Brasil, B., Soares Martins, J., Torres, A., Pimenta,
P., … Bonjardim, C. (2012). A vaccinia virus-driven interplay between the MKK4/7-JNK1/2
pathway and cytoskeleton reorganization. Journal of Virology. ASM. https://doi.org/10.1128/JVI.05638-11
chicago: Pereira, Anna, Flávia Leite, Bruno Brasil, Jamaria Soares Martins, Alice
Torres, Paulo Pimenta, Thais Souto Padrón, et al. “A Vaccinia Virus-Driven Interplay
between the MKK4/7-JNK1/2 Pathway and Cytoskeleton Reorganization.” Journal
of Virology. ASM, 2012. https://doi.org/10.1128/JVI.05638-11.
ieee: A. Pereira et al., “A vaccinia virus-driven interplay between the MKK4/7-JNK1/2
pathway and cytoskeleton reorganization,” Journal of Virology, vol. 86,
no. 1. ASM, pp. 172–184, 2012.
ista: Pereira A, Leite F, Brasil B, Soares Martins J, Torres A, Pimenta P, Souto
Padrón T, Tranktman P, Ferreira P, Kroon E, Bonjardim C. 2012. A vaccinia virus-driven
interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. Journal
of Virology. 86(1), 172–184.
mla: Pereira, Anna, et al. “A Vaccinia Virus-Driven Interplay between the MKK4/7-JNK1/2
Pathway and Cytoskeleton Reorganization.” Journal of Virology, vol. 86,
no. 1, ASM, 2012, pp. 172–84, doi:10.1128/JVI.05638-11.
short: A. Pereira, F. Leite, B. Brasil, J. Soares Martins, A. Torres, P. Pimenta,
T. Souto Padrón, P. Tranktman, P. Ferreira, E. Kroon, C. Bonjardim, Journal of
Virology 86 (2012) 172–184.
date_created: 2018-12-11T12:02:29Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:25Z
day: '01'
department:
- _id: JoBo
doi: 10.1128/JVI.05638-11
external_id:
pmid:
- '22031940'
intvolume: ' 86'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255887/
month: '01'
oa: 1
oa_version: Submitted Version
page: 172 - 184
pmid: 1
publication: Journal of Virology
publication_status: published
publisher: ASM
publist_id: '3356'
quality_controlled: '1'
scopus_import: 1
status: public
title: A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton
reorganization
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 86
year: '2012'
...
---
_id: '3310'
abstract:
- lang: eng
text: The theory of persistent homology opens up the possibility to reason about
topological features of a space or a function quantitatively and in combinatorial
terms. We refer to this new angle at a classical subject within algebraic topology
as a point calculus, which we present for the family of interlevel sets of a real-valued
function. Our account of the subject is expository, devoid of proofs, and written
for non-experts in algebraic topology.
acknowledgement: Research by the third author is partially supported by the National
Science Foundation (NSF) under grant DBI-0820624.
author:
- first_name: Paul
full_name: Bendich, Paul
id: 43F6EC54-F248-11E8-B48F-1D18A9856A87
last_name: Bendich
- first_name: Sergio
full_name: Cabello, Sergio
last_name: Cabello
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Bendich P, Cabello S, Edelsbrunner H. A point calculus for interlevel set homology.
Pattern Recognition Letters. 2012;33(11):1436-1444. doi:10.1016/j.patrec.2011.10.007
apa: Bendich, P., Cabello, S., & Edelsbrunner, H. (2012). A point calculus for
interlevel set homology. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2011.10.007
chicago: Bendich, Paul, Sergio Cabello, and Herbert Edelsbrunner. “A Point Calculus
for Interlevel Set Homology.” Pattern Recognition Letters. Elsevier, 2012.
https://doi.org/10.1016/j.patrec.2011.10.007.
ieee: P. Bendich, S. Cabello, and H. Edelsbrunner, “A point calculus for interlevel
set homology,” Pattern Recognition Letters, vol. 33, no. 11. Elsevier,
pp. 1436–1444, 2012.
ista: Bendich P, Cabello S, Edelsbrunner H. 2012. A point calculus for interlevel
set homology. Pattern Recognition Letters. 33(11), 1436–1444.
mla: Bendich, Paul, et al. “A Point Calculus for Interlevel Set Homology.” Pattern
Recognition Letters, vol. 33, no. 11, Elsevier, 2012, pp. 1436–44, doi:10.1016/j.patrec.2011.10.007.
short: P. Bendich, S. Cabello, H. Edelsbrunner, Pattern Recognition Letters 33 (2012)
1436–1444.
date_created: 2018-12-11T12:02:36Z
date_published: 2012-08-01T00:00:00Z
date_updated: 2021-01-12T07:42:34Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1016/j.patrec.2011.10.007
file:
- access_level: open_access
checksum: d65f79775b51258a604ca5ec741297cc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:00Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5116'
file_name: IST-2016-542-v1+1_2012-J-01-Poinculus.pdf
file_size: 280280
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
intvolume: ' 33'
issue: '11'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 1436 - 1444
publication: Pattern Recognition Letters
publication_status: published
publisher: Elsevier
publist_id: '3330'
pubrep_id: '542'
quality_controlled: '1'
scopus_import: 1
status: public
title: A point calculus for interlevel set homology
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2012'
...
---
_id: '338'
abstract:
- lang: eng
text: The ample chemical and structural freedom of quaternary compounds permits
engineering materials that fulfill the requirements of a wide variety of applications.
In this work, the mechanisms to achieve unprecedented size, shape, and composition
control in quaternary nanocrystals are detailed. The described procedure allows
obtaining tetrahedral and penta-tetrahedral quaternary nanocrystals with tuned
size distributions and controlled compositions from a plethora of I 2-II-IV-VI
4 semiconductors.
acknowledgement: "This work was supported by the Spanish MICINN Projects MAT2008-05779,
MAT2008-03400-E/MAT, MAT2010-15138, ENE2008-03277-E/CON, CSD2009-00050, and CSD2009-00013.
M.I. thanks the Spanish MICINN for her Ph.D. grant. J.A. and R.Z. also acknowledge
Generalitat de Catalunya 2009-SGR-770 and XaRMAE. A.C. is grateful for financial
support through the Ramon y Cajal program of the Spanish MICINN.\r\n\r\n"
article_processing_charge: No
article_type: original
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: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- 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: Ibáñez M, Zamani R, Li W, et al. Extending the nanocrystal synthesis control
to quaternary compositions. Crystal Growth and Design . 2012;12(3):1085-1090.
doi:10.1021/cg201709c
apa: Ibáñez, M., Zamani, R., Li, W., Shavel, A., Arbiol, J., Morante, J., &
Cabot, A. (2012). Extending the nanocrystal synthesis control to quaternary compositions.
Crystal Growth and Design . American Chemical Society (ACS). https://doi.org/10.1021/cg201709c
chicago: Ibáñez, Maria, Reza Zamani, Wenhua Li, Alexey Shavel, Jordi Arbiol, Joan
Morante, and Andreu Cabot. “Extending the Nanocrystal Synthesis Control to Quaternary
Compositions.” Crystal Growth and Design . American Chemical Society (ACS),
2012. https://doi.org/10.1021/cg201709c.
ieee: M. Ibáñez et al., “Extending the nanocrystal synthesis control to quaternary
compositions,” Crystal Growth and Design , vol. 12, no. 3. American Chemical
Society (ACS), pp. 1085–1090, 2012.
ista: Ibáñez M, Zamani R, Li W, Shavel A, Arbiol J, Morante J, Cabot A. 2012. Extending
the nanocrystal synthesis control to quaternary compositions. Crystal Growth and
Design . 12(3), 1085–1090.
mla: Ibáñez, Maria, et al. “Extending the Nanocrystal Synthesis Control to Quaternary
Compositions.” Crystal Growth and Design , vol. 12, no. 3, American Chemical
Society (ACS), 2012, pp. 1085–90, doi:10.1021/cg201709c.
short: M. Ibáñez, R. Zamani, W. Li, A. Shavel, J. Arbiol, J. Morante, A. Cabot,
Crystal Growth and Design 12 (2012) 1085–1090.
date_created: 2018-12-11T11:45:54Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:05Z
day: '01'
doi: 10.1021/cg201709c
extern: '1'
intvolume: ' 12'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 1085 - 1090
publication: 'Crystal Growth and Design '
publication_status: published
publisher: American Chemical Society (ACS)
publist_id: '7488'
quality_controlled: '1'
status: public
title: Extending the nanocrystal synthesis control to quaternary compositions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2012'
...
---
_id: '339'
abstract:
- lang: eng
text: A high-yield and upscalable colloidal synthesis route for the production of
quaternary I 2-II-IV-VI 4 nanocrystals, particularly stannite Cu 2+xCd 1-xSnSe
4, with narrow size distribution and precisely controlled composition is presented.
It is also shown here how the diversity of valences in the constituent elements
allows an effective control of their electrical conductivity through the adjustment
of the cation ratios. At the same time, while the crystallographic complexity
of quaternary chalcogenides is associated with intrinsically low thermal conductivities,
the reduction of the lattice dimensions to the nanoscale further reduces the materials
thermal conductivity. In the specific case of the stannite crystal structure,
a convenient slab distribution of the valence band maximum states permits a partial
decoupling of the p-type electrical conductivity from both the Seebeck coefficient
and the thermal conductivity. Combining these features, we demonstrate how an
initial optimization of the nanocrystals Cd/Cu ratio allowed us to obtain low-temperature
solution-processed materials with ZT values up to 0.71 at 685 K.
acknowledgement: This work was supported by the Spanish MICINN Projects MAT2008-05779,
MAT2008-03400-E/MAT, MAT2010-15138, ENE2008-03277-E/CON, CSD2009-00050. and CSD2009-00013.
M.I. and N.G.-C. thank the Spanish MICINN for the PhD grant. J.A. and R.Z. also
acknowledge Generalitat de Catalunya 2009-SGR-770 and XaRMAE. A.C. is thankful for
financial support through the Ramon y Cajal program of the Spanish MICINN. N.G.-C.
and J.D.P. are thankful for the computer resources, technical expertise and assistance
provided by the Barcelona Supercomputing Center - Centro Nacional de Supercomputación.
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Reza
full_name: Zamani, Reza
last_name: Zamani
- first_name: Nuria
full_name: García Castelló, Nuria
last_name: García Castelló
- first_name: Victora
full_name: Izquierdo Roca, Victora
last_name: Izquierdo Roca
- first_name: Wenhua
full_name: Li, Wenhua
last_name: Li
- first_name: Andrew
full_name: Fairbrother, Andrew
last_name: Fairbrother
- first_name: Joan
full_name: Prades, Joan
last_name: Prades
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Alejandro
full_name: Pérez Rodríguez, Alejandro
last_name: Pérez Rodríguez
- first_name: Joan
full_name: Morante, Joan
last_name: Morante
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Ibáñez M, Cadavid D, Zamani R, et al. Composition control and thermoelectric
properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4.
Chemistry of Materials. 2012;24(3):562-570. doi:10.1021/cm2031812'
apa: 'Ibáñez, M., Cadavid, D., Zamani, R., García Castelló, N., Izquierdo Roca,
V., Li, W., … Cabot, A. (2012). Composition control and thermoelectric properties
of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4. Chemistry
of Materials. American Chemical Society. https://doi.org/10.1021/cm2031812'
chicago: 'Ibáñez, Maria, Doris Cadavid, Reza Zamani, Nuria García Castelló, Victora
Izquierdo Roca, Wenhua Li, Andrew Fairbrother, et al. “Composition Control and
Thermoelectric Properties of Quaternary Chalcogenide Nanocrystals: The Case of
Stannite Cu2CdSnSe4.” Chemistry of Materials. American Chemical Society,
2012. https://doi.org/10.1021/cm2031812.'
ieee: 'M. Ibáñez et al., “Composition control and thermoelectric properties
of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4,” Chemistry
of Materials, vol. 24, no. 3. American Chemical Society, pp. 562–570, 2012.'
ista: 'Ibáñez M, Cadavid D, Zamani R, García Castelló N, Izquierdo Roca V, Li W,
Fairbrother A, Prades J, Shavel A, Arbiol J, Pérez Rodríguez A, Morante J, Cabot
A. 2012. Composition control and thermoelectric properties of quaternary chalcogenide
nanocrystals: The case of stannite Cu2CdSnSe4. Chemistry of Materials. 24(3),
562–570.'
mla: 'Ibáñez, Maria, et al. “Composition Control and Thermoelectric Properties of
Quaternary Chalcogenide Nanocrystals: The Case of Stannite Cu2CdSnSe4.” Chemistry
of Materials, vol. 24, no. 3, American Chemical Society, 2012, pp. 562–70,
doi:10.1021/cm2031812.'
short: M. Ibáñez, D. Cadavid, R. Zamani, N. García Castelló, V. Izquierdo Roca,
W. Li, A. Fairbrother, J. Prades, A. Shavel, J. Arbiol, A. Pérez Rodríguez, J.
Morante, A. Cabot, Chemistry of Materials 24 (2012) 562–570.
date_created: 2018-12-11T11:45:54Z
date_published: 2012-01-31T00:00:00Z
date_updated: 2021-01-12T07:43:09Z
day: '31'
doi: 10.1021/cm2031812
extern: '1'
intvolume: ' 24'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 562 - 570
publication: Chemistry of Materials
publication_status: published
publisher: American Chemical Society
publist_id: '7489'
quality_controlled: '1'
status: public
title: 'Composition control and thermoelectric properties of quaternary chalcogenide
nanocrystals: The case of stannite Cu2CdSnSe4'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2012'
...
---
_id: '340'
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. '
acknowledgement: This work was supported by the Spanish MICINN Projects MAT2008-05779,
MAT2008-03400-E/MAT, CDS2009-00050, CSD2009-00013, and ENE2008-03277-E/CON. M.I.
thanks the Spanish MICINN for her Ph.D. grant. A.C. is thankful for financial support
through the Ramón y Cajal Program.
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: 2018-12-11T11:45:54Z
date_published: 2012-01-02T00:00:00Z
date_updated: 2021-01-12T07:43:13Z
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: '7490'
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: '345'
abstract:
- lang: eng
text: 'Nanocomposites are highly promising materials to enhance the efficiency of
current thermoelectric devices. A straightforward and at the same time highly
versatile and controllable approach to produce nanocomposites is the assembly
of solution-processed nanocrystal building blocks. The convenience of this bottom-up
approach to produce nanocomposites with homogeneous phase distributions and adjustable
composition is demonstrated here by blending Ag2Te and PbTe colloidal nanocrystals
to form Ag2Te–PbTe bulk nanocomposites. The thermoelectric properties of these
nanocomposites are analyzed in the temperature range from 300 to 700 K. The evolution
of their electrical conductivity and Seebeck coefficient is discussed in terms
of the blend composition and the characteristics of the constituent materials. '
acknowledgement: Acknowledgments The research was supported by the European Regional
Development Funds and the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT,
MAT2010-15138, MAT2010-21510, CSD2009-00050, and ENE2008-03277-E/CON. M.I. is grateful
to the Spanish MIC-INN for her PhD grant. A. Cirera acknowledges support from ICREA
Academia program. A. Cabot is grateful to the Spanish MICINN for financial support
through the Ramón y Cajal program.
article_processing_charge: No
article_type: original
author:
- 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: Stéphane
full_name: Gorsse, Stéphane
last_name: Gorsse
- first_name: Antonio
full_name: López, Antonio
last_name: López
- first_name: Albert
full_name: Cirera, Albert
last_name: Cirera
- first_name: Joan
full_name: Morante, Joan
last_name: Morante
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Cadavid D, Ibáñez M, Gorsse S, et al. Bottom-up processing of thermoelectric
nanocomposites from colloidal nanocrystal building blocks: The case of Ag2Te–PbTe.
Journal of Nanoparticle Research. 2012;14(12). doi:10.1007/s11051-012-1328-0'
apa: 'Cadavid, D., Ibáñez, M., Gorsse, S., López, A., Cirera, A., Morante, J., &
Cabot, A. (2012). Bottom-up processing of thermoelectric nanocomposites from colloidal
nanocrystal building blocks: The case of Ag2Te–PbTe. Journal of Nanoparticle
Research. Kluwer. https://doi.org/10.1007/s11051-012-1328-0'
chicago: 'Cadavid, Doris, Maria Ibáñez, Stéphane Gorsse, Antonio López, Albert Cirera,
Joan Morante, and Andreu Cabot. “Bottom-up Processing of Thermoelectric Nanocomposites
from Colloidal Nanocrystal Building Blocks: The Case of Ag2Te–PbTe.” Journal
of Nanoparticle Research. Kluwer, 2012. https://doi.org/10.1007/s11051-012-1328-0.'
ieee: 'D. Cadavid et al., “Bottom-up processing of thermoelectric nanocomposites
from colloidal nanocrystal building blocks: The case of Ag2Te–PbTe,” Journal
of Nanoparticle Research, vol. 14, no. 12. Kluwer, 2012.'
ista: 'Cadavid D, Ibáñez M, Gorsse S, López A, Cirera A, Morante J, Cabot A. 2012.
Bottom-up processing of thermoelectric nanocomposites from colloidal nanocrystal
building blocks: The case of Ag2Te–PbTe. Journal of Nanoparticle Research. 14(12).'
mla: 'Cadavid, Doris, et al. “Bottom-up Processing of Thermoelectric Nanocomposites
from Colloidal Nanocrystal Building Blocks: The Case of Ag2Te–PbTe.” Journal
of Nanoparticle Research, vol. 14, no. 12, Kluwer, 2012, doi:10.1007/s11051-012-1328-0.'
short: D. Cadavid, M. Ibáñez, S. Gorsse, A. López, A. Cirera, J. Morante, A. Cabot,
Journal of Nanoparticle Research 14 (2012).
date_created: 2018-12-11T11:45:56Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2021-01-12T07:43:32Z
day: '01'
doi: 10.1007/s11051-012-1328-0
extern: '1'
intvolume: ' 14'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
publication: Journal of Nanoparticle Research
publication_status: published
publisher: Kluwer
publist_id: '7485'
quality_controlled: '1'
status: public
title: 'Bottom-up processing of thermoelectric nanocomposites from colloidal nanocrystal
building blocks: The case of Ag2Te–PbTe'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2012'
...
---
_id: '347'
abstract:
- lang: eng
text: 'A synthetic route for producing Cu 2ZnGeSe 4 nanocrystals with narrow size
distributions and controlled composition is presented. These nanocrystals were
used to produce densely packed nanomaterials by hot-pressing. From the characterization
of the thermoelectric properties of these nanomaterials, Cu 2ZnGeSe 4 is demonstrated
to show excellent thermoelectric properties. A very preliminary adjustment of
the nanocrystal composition has already resulted in a figure of merit of up to
0.55 at 450°C. '
acknowledgement: This work was supported by the Spanish MICINN Projects MAT2008-05779,
MAT2008-03400-E/MAT, MAT2010-15138, ENE2008-03277-E/CON, CSD2009-00050, and CSD2009-00013.
M.I. thanks the Spanish MICINN for her Ph.D. Grant. J.A. and R.Z. also acknowledge
Generalitat de Catalunya 2009-SGR-770 and XaRMAE. A.C. is thankful for financial
support through the Ramon y Cajal Program of the Spanish MICINN.
article_processing_charge: No
article_type: original
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: Aaron
full_name: Lalonde, Aaron
last_name: Lalonde
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Wenhua
full_name: Li, Wenhua
last_name: Li
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Joan
full_name: Morante, Joan
last_name: Morante
- first_name: Stéphane
full_name: Gorsse, Stéphane
last_name: Gorsse
- first_name: G Jeffrey
full_name: Snyder, G Jeffrey
last_name: Snyder
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Ibáñez M, Zamani R, Lalonde A, et al. Cu 2ZnGeSe 4 nanocrystals: Synthesis
and thermoelectric properties. Journal of the American Chemical Society.
2012;134(9):4060-4063. doi:10.1021/ja211952z'
apa: 'Ibáñez, M., Zamani, R., Lalonde, A., Cadavid, D., Li, W., Shavel, A., … Cabot,
A. (2012). Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric properties.
Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja211952z'
chicago: 'Ibáñez, Maria, Reza Zamani, Aaron Lalonde, Doris Cadavid, Wenhua Li, Alexey
Shavel, Jordi Arbiol, et al. “Cu 2ZnGeSe 4 Nanocrystals: Synthesis and Thermoelectric
Properties.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja211952z.'
ieee: 'M. Ibáñez et al., “Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric
properties,” Journal of the American Chemical Society, vol. 134, no. 9.
ACS, pp. 4060–4063, 2012.'
ista: 'Ibáñez M, Zamani R, Lalonde A, Cadavid D, Li W, Shavel A, Arbiol J, Morante
J, Gorsse S, Snyder GJ, Cabot A. 2012. Cu 2ZnGeSe 4 nanocrystals: Synthesis and
thermoelectric properties. Journal of the American Chemical Society. 134(9), 4060–4063.'
mla: 'Ibáñez, Maria, et al. “Cu 2ZnGeSe 4 Nanocrystals: Synthesis and Thermoelectric
Properties.” Journal of the American Chemical Society, vol. 134, no. 9,
ACS, 2012, pp. 4060–63, doi:10.1021/ja211952z.'
short: M. Ibáñez, R. Zamani, A. Lalonde, D. Cadavid, W. Li, A. Shavel, J. Arbiol,
J. Morante, S. Gorsse, G.J. Snyder, A. Cabot, Journal of the American Chemical
Society 134 (2012) 4060–4063.
date_created: 2018-12-11T11:45:57Z
date_published: 2012-03-07T00:00:00Z
date_updated: 2021-01-12T07:43:40Z
day: '07'
doi: 10.1021/ja211952z
extern: '1'
intvolume: ' 134'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://authors.library.caltech.edu/30261/
month: '03'
oa: 1
oa_version: None
page: 4060 - 4063
publication: Journal of the American Chemical Society
publication_status: published
publisher: ACS
publist_id: '7487'
quality_controlled: '1'
status: public
title: 'Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric properties'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 134
year: '2012'
...
---
_id: '3836'
abstract:
- lang: eng
text: Hierarchical Timing Language (HTL) is a coordination language for distributed,
hard real-time applications. HTL is a hierarchical extension of Giotto and, like
its predecessor, based on the logical execution time (LET) paradigm of real-time
programming. Giotto is compiled into code for a virtual machine, called the EmbeddedMachine
(or E machine). If HTL is targeted to the E machine, then the hierarchicalprogram
structure needs to be flattened; the flattening makes separatecompilation difficult,
and may result in E machinecode of exponential size. In this paper, we propose
a generalization of the E machine, which supports a hierarchicalprogram structure
at runtime through real-time trigger mechanisms that are arranged in a tree. We
present the generalized E machine, and a modular compiler for HTL that generates
code of linear size. The compiler may generate code for any part of a given HTL
program separately in any order.
author:
- first_name: Arkadeb
full_name: Ghosal, Arkadeb
last_name: Ghosal
- first_name: Daniel
full_name: Iercan, Daniel
last_name: Iercan
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
- 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: Alberto
full_name: Sangiovanni Vincentelli, Alberto
last_name: Sangiovanni Vincentelli
citation:
ama: Ghosal A, Iercan D, Kirsch C, Henzinger TA, Sangiovanni Vincentelli A. Separate
compilation of hierarchical real-time programs into linear-bounded embedded machine
code. Science of Computer Programming. 2012;77(2):96-112. doi:10.1016/j.scico.2010.06.004
apa: Ghosal, A., Iercan, D., Kirsch, C., Henzinger, T. A., & Sangiovanni Vincentelli,
A. (2012). Separate compilation of hierarchical real-time programs into linear-bounded
embedded machine code. Science of Computer Programming. Elsevier. https://doi.org/10.1016/j.scico.2010.06.004
chicago: Ghosal, Arkadeb, Daniel Iercan, Christoph Kirsch, Thomas A Henzinger, and
Alberto Sangiovanni Vincentelli. “Separate Compilation of Hierarchical Real-Time
Programs into Linear-Bounded Embedded Machine Code.” Science of Computer Programming.
Elsevier, 2012. https://doi.org/10.1016/j.scico.2010.06.004.
ieee: A. Ghosal, D. Iercan, C. Kirsch, T. A. Henzinger, and A. Sangiovanni Vincentelli,
“Separate compilation of hierarchical real-time programs into linear-bounded embedded
machine code,” Science of Computer Programming, vol. 77, no. 2. Elsevier,
pp. 96–112, 2012.
ista: Ghosal A, Iercan D, Kirsch C, Henzinger TA, Sangiovanni Vincentelli A. 2012.
Separate compilation of hierarchical real-time programs into linear-bounded embedded
machine code. Science of Computer Programming. 77(2), 96–112.
mla: Ghosal, Arkadeb, et al. “Separate Compilation of Hierarchical Real-Time Programs
into Linear-Bounded Embedded Machine Code.” Science of Computer Programming,
vol. 77, no. 2, Elsevier, 2012, pp. 96–112, doi:10.1016/j.scico.2010.06.004.
short: A. Ghosal, D. Iercan, C. Kirsch, T.A. Henzinger, A. Sangiovanni Vincentelli,
Science of Computer Programming 77 (2012) 96–112.
date_created: 2018-12-11T12:05:26Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2021-01-12T07:52:32Z
day: '01'
department:
- _id: ToHe
doi: 10.1016/j.scico.2010.06.004
intvolume: ' 77'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 96 - 112
publication: Science of Computer Programming
publication_status: published
publisher: Elsevier
publist_id: '2370'
quality_controlled: '1'
scopus_import: 1
status: public
title: Separate compilation of hierarchical real-time programs into linear-bounded
embedded machine code
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2012'
...
---
_id: '2972'
abstract:
- lang: eng
text: 'Energy parity games are infinite two-player turn-based games played on weighted
graphs. The objective of the game combines a (qualitative) parity condition with
the (quantitative) requirement that the sum of the weights (i.e., the level of
energy in the game) must remain positive. Beside their own interest in the design
and synthesis of resource-constrained omega-regular specifications, energy parity
games provide one of the simplest model of games with combined qualitative and
quantitative objectives. Our main results are as follows: (a) exponential memory
is sufficient and may be necessary for winning strategies in energy parity games;
(b) the problem of deciding the winner in energy parity games can be solved in
NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to
energy games. We also show that the problem of deciding the winner in energy parity
games is logspace-equivalent to the problem of deciding the winner in mean-payoff
parity games, which can thus be solved in NP ∩ coNP. As a consequence we also
obtain a conceptually simple algorithm to solve mean-payoff parity games.'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: Chatterjee K, Doyen L. Energy parity games. Theoretical Computer Science.
2012;458:49-60. doi:10.1016/j.tcs.2012.07.038
apa: Chatterjee, K., & Doyen, L. (2012). Energy parity games. Theoretical
Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2012.07.038
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games.” Theoretical
Computer Science. Elsevier, 2012. https://doi.org/10.1016/j.tcs.2012.07.038.
ieee: K. Chatterjee and L. Doyen, “Energy parity games,” Theoretical Computer
Science, vol. 458. Elsevier, pp. 49–60, 2012.
ista: Chatterjee K, Doyen L. 2012. Energy parity games. Theoretical Computer Science.
458, 49–60.
mla: Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games.” Theoretical
Computer Science, vol. 458, Elsevier, 2012, pp. 49–60, doi:10.1016/j.tcs.2012.07.038.
short: K. Chatterjee, L. Doyen, Theoretical Computer Science 458 (2012) 49–60.
date_created: 2018-12-11T12:00:37Z
date_published: 2012-11-02T00:00:00Z
date_updated: 2023-02-23T11:45:29Z
day: '02'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1016/j.tcs.2012.07.038
ec_funded: 1
external_id:
arxiv:
- '1001.5183'
file:
- access_level: open_access
checksum: 719e4a5af5a01ad3f2f7f7f05b3c2b09
content_type: application/pdf
creator: kschuh
date_created: 2019-02-06T11:56:22Z
date_updated: 2020-07-14T12:45:57Z
file_id: '5935'
file_name: 2012_Elsevier_Chatterjee.pdf
file_size: 351271
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has_accepted_license: '1'
intvolume: ' 458'
language:
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license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 49 - 60
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: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '3736'
pubrep_id: '935'
quality_controlled: '1'
related_material:
record:
- id: '3851'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Energy parity games
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 458
year: '2012'
...
---
_id: '2967'
abstract:
- lang: eng
text: For programs whose data variables range over Boolean or finite domains, program
verification is decidable, and this forms the basis of recent tools for software
model checking. In this article, we consider algorithmic verification of programs
that use Boolean variables, and in addition, access a single read-only array whose
length is potentially unbounded, and whose elements range over an unbounded data
domain. We show that the reachability problem, while undecidable in general, is
(1) PSPACE-complete for programs in which the array-accessing for-loops are not
nested, (2) decidable for a restricted class of programs with doubly nested loops.
The second result establishes connections to automata and logics defining languages
over data words.
acknowledgement: This research was supported in part by the NSF Cybertrust award CNS
0524059, by the European Research Council (ERC) Advanced Investigator Grant QUAREM,
and by the Austrian Science Fund (FWF) project S11402-N23.
article_number: '27'
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Scott
full_name: Weinstein, Scott
last_name: Weinstein
citation:
ama: Alur R, Cerny P, Weinstein S. Algorithmic analysis of array-accessing programs.
ACM Transactions on Computational Logic (TOCL). 2012;13(3). doi:10.1145/2287718.2287727
apa: Alur, R., Cerny, P., & Weinstein, S. (2012). Algorithmic analysis of array-accessing
programs. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/2287718.2287727
chicago: Alur, Rajeev, Pavol Cerny, and Scott Weinstein. “Algorithmic Analysis of
Array-Accessing Programs.” ACM Transactions on Computational Logic (TOCL).
ACM, 2012. https://doi.org/10.1145/2287718.2287727.
ieee: R. Alur, P. Cerny, and S. Weinstein, “Algorithmic analysis of array-accessing
programs,” ACM Transactions on Computational Logic (TOCL), vol. 13, no.
3. ACM, 2012.
ista: Alur R, Cerny P, Weinstein S. 2012. Algorithmic analysis of array-accessing
programs. ACM Transactions on Computational Logic (TOCL). 13(3), 27.
mla: Alur, Rajeev, et al. “Algorithmic Analysis of Array-Accessing Programs.” ACM
Transactions on Computational Logic (TOCL), vol. 13, no. 3, 27, ACM, 2012,
doi:10.1145/2287718.2287727.
short: R. Alur, P. Cerny, S. Weinstein, ACM Transactions on Computational Logic
(TOCL) 13 (2012).
date_created: 2018-12-11T12:00:36Z
date_published: 2012-08-01T00:00:00Z
date_updated: 2023-02-23T12:09:43Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/2287718.2287727
ec_funded: 1
intvolume: ' 13'
issue: '3'
language:
- iso: eng
month: '08'
oa_version: None
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: ACM Transactions on Computational Logic (TOCL)
publication_status: published
publisher: ACM
publist_id: '3748'
quality_controlled: '1'
related_material:
record:
- id: '4403'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Algorithmic analysis of array-accessing programs
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2012'
...
---
_id: '492'
abstract:
- lang: eng
text: 'Background: Characterizing root system architecture (RSA) is essential to
understanding the development and function of vascular plants. Identifying RSA-associated
genes also represents an underexplored opportunity for crop improvement. Software
tools are needed to accelerate the pace at which quantitative traits of RSA are
estimated from images of root networks.Results: We have developed GiA Roots (General
Image Analysis of Roots), a semi-automated software tool designed specifically
for the high-throughput analysis of root system images. GiA Roots includes user-assisted
algorithms to distinguish root from background and a fully automated pipeline
that extracts dozens of root system phenotypes. Quantitative information on each
phenotype, along with intermediate steps for full reproducibility, is returned
to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line
interface for interweaving the software into large-scale workflows. GiA Roots
can also be extended to estimate novel phenotypes specified by the end-user.Conclusions:
We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing
12 genotypes from the species Oryza sativa. We validate trait measurements against
prior analyses of this image set that demonstrated that RSA traits are likely
heritable and associated with genotypic differences. Moreover, we demonstrate
that GiA Roots is extensible and an end-user can add functionality so that GiA
Roots can estimate novel RSA traits. In summary, we show that the software can
function as an efficient tool as part of a workflow to move from large numbers
of root images to downstream analysis.'
article_number: '116'
article_processing_charge: No
author:
- first_name: Taras
full_name: Galkovskyi, Taras
last_name: Galkovskyi
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
- first_name: Alexander
full_name: Bucksch, Alexander
last_name: Bucksch
- first_name: Brad
full_name: Moore, Brad
last_name: Moore
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
- first_name: Charles
full_name: Price, Charles
last_name: Price
- first_name: Chrostopher
full_name: Topp, Chrostopher
last_name: Topp
- first_name: Anjali
full_name: Iyer Pascuzzi, Anjali
last_name: Iyer Pascuzzi
- first_name: Paul
full_name: Zurek, Paul
last_name: Zurek
- first_name: Suqin
full_name: Fang, Suqin
last_name: Fang
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Philip
full_name: Benfey, Philip
last_name: Benfey
- first_name: Joshua
full_name: Weitz, Joshua
last_name: Weitz
citation:
ama: 'Galkovskyi T, Mileyko Y, Bucksch A, et al. GiA Roots: Software for the high
throughput analysis of plant root system architecture. BMC Plant Biology.
2012;12. doi:10.1186/1471-2229-12-116'
apa: 'Galkovskyi, T., Mileyko, Y., Bucksch, A., Moore, B., Symonova, O., Price,
C., … Weitz, J. (2012). GiA Roots: Software for the high throughput analysis of
plant root system architecture. BMC Plant Biology. BioMed Central. https://doi.org/10.1186/1471-2229-12-116'
chicago: 'Galkovskyi, Taras, Yuriy Mileyko, Alexander Bucksch, Brad Moore, Olga
Symonova, Charles Price, Chrostopher Topp, et al. “GiA Roots: Software for the
High Throughput Analysis of Plant Root System Architecture.” BMC Plant Biology.
BioMed Central, 2012. https://doi.org/10.1186/1471-2229-12-116.'
ieee: 'T. Galkovskyi et al., “GiA Roots: Software for the high throughput
analysis of plant root system architecture,” BMC Plant Biology, vol. 12.
BioMed Central, 2012.'
ista: 'Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price C, Topp C,
Iyer Pascuzzi A, Zurek P, Fang S, Harer J, Benfey P, Weitz J. 2012. GiA Roots:
Software for the high throughput analysis of plant root system architecture. BMC
Plant Biology. 12, 116.'
mla: 'Galkovskyi, Taras, et al. “GiA Roots: Software for the High Throughput Analysis
of Plant Root System Architecture.” BMC Plant Biology, vol. 12, 116, BioMed
Central, 2012, doi:10.1186/1471-2229-12-116.'
short: T. Galkovskyi, Y. Mileyko, A. Bucksch, B. Moore, O. Symonova, C. Price, C.
Topp, A. Iyer Pascuzzi, P. Zurek, S. Fang, J. Harer, P. Benfey, J. Weitz, BMC
Plant Biology 12 (2012).
date_created: 2018-12-11T11:46:46Z
date_published: 2012-07-26T00:00:00Z
date_updated: 2022-08-25T14:59:17Z
day: '26'
ddc:
- '005'
- '514'
- '516'
doi: 10.1186/1471-2229-12-116
extern: '1'
file:
- access_level: open_access
checksum: 0c629e36acd5f2878ff7dd088d67d494
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:35Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4953'
file_name: IST-2018-946-v1+1_2012_Symonova_GiA_Roots.pdf
file_size: 1691436
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: BMC Plant Biology
publication_status: published
publisher: BioMed Central
publist_id: '7328'
pubrep_id: '946'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'GiA Roots: Software for the high throughput analysis of plant root system
architecture'
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: 12
year: '2012'
...
---
_id: '493'
abstract:
- lang: eng
text: 'The BCI competition IV stands in the tradition of prior BCI competitions
that aim to provide high quality neuroscientific data for open access to the scientific
community. As experienced already in prior competitions not only scientists from
the narrow field of BCI compete, but scholars with a broad variety of backgrounds
and nationalities. They include high specialists as well as students.The goals
of all BCI competitions have always been to challenge with respect to novel paradigms
and complex data. We report on the following challenges: (1) asynchronous data,
(2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer,
(5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after
past competitions, our hope is that winning entries may enhance the analysis methods
of future BCIs.'
acknowledgement: "The studies were in part or completely supported by the Bundesministerium
für Bildung und Forschung (BMBF), Fkz 01IB001A, 01GQ0850, by the German Science
Foundation (DFG, contract MU 987/3-2), by the European ICT Programme Projects FP7-224631
and 216886, the World Class University Program through the National Research Foundation
of Korea funded by the Ministry of Education, Science, and Technology (Grant R31-10008),
the US Army Research Office [W911NF-08-1-0216 (Gerwin Schalk) and W911NF-07-1-0415
(Gerwin Schalk)] and the NIH [EB006356 (Gerwin Schalk) and EB000856 (Gerwin Schalk),
the WIN-Kolleg of the Heidelberg Academy of Sciences and Humanities, German Federal
Ministry of Education and Research grants 01GQ0420, 01GQ0761, 01GQ0762, and 01GQ0830,
German Research Foundation grants 550/B5 and C6, and by a scholarship from the German
National Academic Foundation. This paper only reflects the authors’ views and funding
agencies are not liable for any use that may be made of the information contained
herein.\r\n"
article_number: '55'
author:
- first_name: Michael
full_name: Tangermann, Michael
last_name: Tangermann
- first_name: Klaus
full_name: Müller, Klaus
last_name: Müller
- first_name: Ad
full_name: Aertsen, Ad
last_name: Aertsen
- first_name: Niels
full_name: Birbaumer, Niels
last_name: Birbaumer
- first_name: Christoph
full_name: Braun, Christoph
last_name: Braun
- first_name: Clemens
full_name: Brunner, Clemens
last_name: Brunner
- first_name: Robert
full_name: Leeb, Robert
last_name: Leeb
- first_name: Carsten
full_name: Mehring, Carsten
last_name: Mehring
- first_name: Kai
full_name: Miller, Kai
last_name: Miller
- first_name: Gernot
full_name: Müller Putz, Gernot
last_name: Müller Putz
- first_name: Guido
full_name: Nolte, Guido
last_name: Nolte
- first_name: Gert
full_name: Pfurtscheller, Gert
last_name: Pfurtscheller
- first_name: Hubert
full_name: Preissl, Hubert
last_name: Preissl
- first_name: Gerwin
full_name: Schalk, Gerwin
last_name: Schalk
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Carmen
full_name: Vidaurre, Carmen
last_name: Vidaurre
- first_name: Stephan
full_name: Waldert, Stephan
last_name: Waldert
- first_name: Benjamin
full_name: Blankertz, Benjamin
last_name: Blankertz
citation:
ama: Tangermann M, Müller K, Aertsen A, et al. Review of the BCI competition IV.
Frontiers in Neuroscience. 2012;6. doi:10.3389/fnins.2012.00055
apa: Tangermann, M., Müller, K., Aertsen, A., Birbaumer, N., Braun, C., Brunner,
C., … Blankertz, B. (2012). Review of the BCI competition IV. Frontiers in
Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnins.2012.00055
chicago: Tangermann, Michael, Klaus Müller, Ad Aertsen, Niels Birbaumer, Christoph
Braun, Clemens Brunner, Robert Leeb, et al. “Review of the BCI Competition IV.”
Frontiers in Neuroscience. Frontiers Research Foundation, 2012. https://doi.org/10.3389/fnins.2012.00055.
ieee: M. Tangermann et al., “Review of the BCI competition IV,” Frontiers
in Neuroscience, vol. 6. Frontiers Research Foundation, 2012.
ista: Tangermann M, Müller K, Aertsen A, Birbaumer N, Braun C, Brunner C, Leeb R,
Mehring C, Miller K, Müller Putz G, Nolte G, Pfurtscheller G, Preissl H, Schalk
G, Schlögl A, Vidaurre C, Waldert S, Blankertz B. 2012. Review of the BCI competition
IV. Frontiers in Neuroscience. 6, 55.
mla: Tangermann, Michael, et al. “Review of the BCI Competition IV.” Frontiers
in Neuroscience, vol. 6, 55, Frontiers Research Foundation, 2012, doi:10.3389/fnins.2012.00055.
short: M. Tangermann, K. Müller, A. Aertsen, N. Birbaumer, C. Braun, C. Brunner,
R. Leeb, C. Mehring, K. Miller, G. Müller Putz, G. Nolte, G. Pfurtscheller, H.
Preissl, G. Schalk, A. Schlögl, C. Vidaurre, S. Waldert, B. Blankertz, Frontiers
in Neuroscience 6 (2012).
date_created: 2018-12-11T11:46:46Z
date_published: 2012-07-13T00:00:00Z
date_updated: 2021-01-12T08:01:03Z
day: '13'
ddc:
- '004'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.3389/fnins.2012.00055
file:
- access_level: open_access
checksum: 195238221c4b0b0f4035f6f6c16ea17c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:34Z
date_updated: 2020-07-14T12:46:35Z
file_id: '5356'
file_name: IST-2018-945-v1+1_2012_Schloegl_Review_of.pdf
file_size: 2693701
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Frontiers in Neuroscience
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '7327'
pubrep_id: '945'
quality_controlled: '1'
scopus_import: 1
status: public
title: Review of the BCI competition IV
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2012'
...
---
_id: '495'
abstract:
- lang: eng
text: An automaton with advice is a finite state automaton which has access to an
additional fixed infinite string called an advice tape. We refine the Myhill-Nerode
theorem to characterize the languages of finite strings that are accepted by automata
with advice. We do the same for tree automata with advice.
alternative_title:
- EPTCS
author:
- first_name: Alex
full_name: Kruckman, Alex
last_name: Kruckman
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
- first_name: John
full_name: Sheridan, John
last_name: Sheridan
- first_name: Ben
full_name: Zax, Ben
last_name: Zax
citation:
ama: 'Kruckman A, Rubin S, Sheridan J, Zax B. A Myhill Nerode theorem for automata
with advice. In: Proceedings GandALF 2012. Vol 96. Open Publishing Association;
2012:238-246. doi:10.4204/EPTCS.96.18'
apa: 'Kruckman, A., Rubin, S., Sheridan, J., & Zax, B. (2012). A Myhill Nerode
theorem for automata with advice. In Proceedings GandALF 2012 (Vol. 96,
pp. 238–246). Napoli, Italy: Open Publishing Association. https://doi.org/10.4204/EPTCS.96.18'
chicago: Kruckman, Alex, Sasha Rubin, John Sheridan, and Ben Zax. “A Myhill Nerode
Theorem for Automata with Advice.” In Proceedings GandALF 2012, 96:238–46.
Open Publishing Association, 2012. https://doi.org/10.4204/EPTCS.96.18.
ieee: A. Kruckman, S. Rubin, J. Sheridan, and B. Zax, “A Myhill Nerode theorem for
automata with advice,” in Proceedings GandALF 2012, Napoli, Italy, 2012,
vol. 96, pp. 238–246.
ista: 'Kruckman A, Rubin S, Sheridan J, Zax B. 2012. A Myhill Nerode theorem for
automata with advice. Proceedings GandALF 2012. GandALF: Games, Automata, Logics
and Formal Verification, EPTCS, vol. 96, 238–246.'
mla: Kruckman, Alex, et al. “A Myhill Nerode Theorem for Automata with Advice.”
Proceedings GandALF 2012, vol. 96, Open Publishing Association, 2012, pp.
238–46, doi:10.4204/EPTCS.96.18.
short: A. Kruckman, S. Rubin, J. Sheridan, B. Zax, in:, Proceedings GandALF 2012,
Open Publishing Association, 2012, pp. 238–246.
conference:
end_date: 2012-09-08
location: Napoli, Italy
name: 'GandALF: Games, Automata, Logics and Formal Verification'
start_date: 2012-09-06
date_created: 2018-12-11T11:46:47Z
date_published: 2012-10-07T00:00:00Z
date_updated: 2021-01-12T08:01:04Z
day: '07'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4204/EPTCS.96.18
ec_funded: 1
file:
- access_level: open_access
checksum: 56277f95edc9d531fa3bdc5f9579fda8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:31Z
date_updated: 2020-07-14T12:46:35Z
file_id: '5152'
file_name: IST-2018-944-v1+1_2012_Rubin_A_Myhill.pdf
file_size: 97736
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 96'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 238 - 246
project:
- _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'
publication: Proceedings GandALF 2012
publication_status: published
publisher: Open Publishing Association
publist_id: '7325'
pubrep_id: '944'
quality_controlled: '1'
scopus_import: 1
status: public
title: A Myhill Nerode theorem for automata with advice
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: 96
year: '2012'
...
---
_id: '498'
abstract:
- lang: eng
text: Understanding patterns and correlates of local adaptation in heterogeneous
landscapes can provide important information in the selection of appropriate seed
sources for restoration. We assessed the extent of local adaptation of fitness
components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides
(Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance,
quantitative (QST) and neutral (FST) genetic differentiation, and size of the
local and foreign populations could predict patterns of adaptive differentiation.
Local adaptation varied among populations and fitness components. Including all
population pairs, local adaptation was observed for seedling survival, but not
for biomass, while foreign genotype advantage was observed for reproduction (number
of inflorescences). Among population pairs, local adaptation increased with QST
and local population size for biomass. QST was associated with environmental distance,
suggesting ecological selection for phenotypic divergence. However, low FST and
variation in population structure in small populations demonstrates the interaction
of gene flow and drift in constraining local adaptation in R. leptorrhynchoides.
Our study indicates that for species in heterogeneous landscapes, collecting seed
from large populations from similar environments to candidate sites is likely
to provide the most appropriate seed sources for restoration.
acknowledgement: "We thank Graham Pickup, David Steer, Linda Broadhurst, Lan Li and
Carole Elliott for technical assistance. The New\r\nSouth Wales Department of Environment
and Climate Change, ACT Parks, Conservation and Lands and the\r\nDepartment of Sustainability
and Environment in Victoria provided permits for seed and soil collection. We thank\r\nSpencer
C. H. Barrett for comments that improved the quality of the manuscript.\r\n"
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: David
full_name: Rowell, David
last_name: Rowell
- first_name: Andrew
full_name: Young, Andrew
last_name: Young
citation:
ama: 'Pickup M, Field D, Rowell D, Young A. Predicting local adaptation in fragmented
plant populations: Implications for restoration genetics. Evolutionary Applications.
2012;5(8):913-924. doi:10.1111/j.1752-4571.2012.00284.x'
apa: 'Pickup, M., Field, D., Rowell, D., & Young, A. (2012). Predicting local
adaptation in fragmented plant populations: Implications for restoration genetics.
Evolutionary Applications. Wiley-Blackwell. https://doi.org/10.1111/j.1752-4571.2012.00284.x'
chicago: 'Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Predicting
Local Adaptation in Fragmented Plant Populations: Implications for Restoration
Genetics.” Evolutionary Applications. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1752-4571.2012.00284.x.'
ieee: 'M. Pickup, D. Field, D. Rowell, and A. Young, “Predicting local adaptation
in fragmented plant populations: Implications for restoration genetics,” Evolutionary
Applications, vol. 5, no. 8. Wiley-Blackwell, pp. 913–924, 2012.'
ista: 'Pickup M, Field D, Rowell D, Young A. 2012. Predicting local adaptation in
fragmented plant populations: Implications for restoration genetics. Evolutionary
Applications. 5(8), 913–924.'
mla: 'Pickup, Melinda, et al. “Predicting Local Adaptation in Fragmented Plant Populations:
Implications for Restoration Genetics.” Evolutionary Applications, vol.
5, no. 8, Wiley-Blackwell, 2012, pp. 913–24, doi:10.1111/j.1752-4571.2012.00284.x.'
short: M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012)
913–924.
date_created: 2018-12-11T11:46:48Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:06Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/j.1752-4571.2012.00284.x
file:
- access_level: open_access
checksum: 233007138606aca5a2f75f7ae1742f43
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:33Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4821'
file_name: IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf
file_size: 396136
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 913 - 924
publication: Evolutionary Applications
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7322'
pubrep_id: '942'
quality_controlled: '1'
status: public
title: 'Predicting local adaptation in fragmented plant populations: Implications
for restoration genetics'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2012'
...
---
_id: '496'
abstract:
- lang: eng
text: 'We study the expressive power of logical interpretations on the class of
scattered trees, namely those with countably many infinite branches. Scattered
trees can be thought of as the tree analogue of scattered linear orders. Every
scattered tree has an ordinal rank that reflects the structure of its infinite
branches. We prove, roughly, that trees and orders of large rank cannot be interpreted
in scattered trees of small rank. We consider a quite general notion of interpretation:
each element of the interpreted structure is represented by a set of tuples of
subsets of the interpreting tree. Our trees are countable, not necessarily finitely
branching, and may have finitely many unary predicates as labellings. We also
show how to replace injective set-interpretations in (not necessarily scattered)
trees by ''finitary'' set-interpretations.'
alternative_title:
- LICS
article_number: '6280474'
author:
- first_name: Alexander
full_name: Rabinovich, Alexander
last_name: Rabinovich
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
citation:
ama: 'Rabinovich A, Rubin S. Interpretations in trees with countably many branches.
In: IEEE; 2012. doi:10.1109/LICS.2012.65'
apa: 'Rabinovich, A., & Rubin, S. (2012). Interpretations in trees with countably
many branches. Presented at the LICS: Symposium on Logic in Computer Science,
Dubrovnik, Croatia: IEEE. https://doi.org/10.1109/LICS.2012.65'
chicago: Rabinovich, Alexander, and Sasha Rubin. “Interpretations in Trees with
Countably Many Branches.” IEEE, 2012. https://doi.org/10.1109/LICS.2012.65.
ieee: 'A. Rabinovich and S. Rubin, “Interpretations in trees with countably many
branches,” presented at the LICS: Symposium on Logic in Computer Science, Dubrovnik,
Croatia, 2012.'
ista: 'Rabinovich A, Rubin S. 2012. Interpretations in trees with countably many
branches. LICS: Symposium on Logic in Computer Science, LICS, , 6280474.'
mla: Rabinovich, Alexander, and Sasha Rubin. Interpretations in Trees with Countably
Many Branches. 6280474, IEEE, 2012, doi:10.1109/LICS.2012.65.
short: A. Rabinovich, S. Rubin, in:, IEEE, 2012.
conference:
end_date: 2012-06-28
location: Dubrovnik, Croatia
name: 'LICS: Symposium on Logic in Computer Science'
start_date: 2012-06-25
date_created: 2018-12-11T11:46:47Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T08:01:05Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/LICS.2012.65
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arise.or.at/pubpdf/Interpretations_in_Trees_with_Countably_Many_Branches.pdf
month: '01'
oa: 1
oa_version: Preprint
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: IEEE
publist_id: '7324'
quality_controlled: '1'
scopus_import: 1
status: public
title: Interpretations in trees with countably many branches
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '494'
abstract:
- lang: eng
text: We solve the longstanding open problems of the blow-up involved in the translations,
when possible, of a nondeterministic Büchi word automaton (NBW) to a nondeterministic
co-Büchi word automaton (NCW) and to a deterministic co-Büchi word automaton (DCW).
For the NBW to NCW translation, the currently known upper bound is 2o(nlog n)
and the lower bound is 1.5n. We improve the upper bound to n2n and describe a
matching lower bound of 2ω(n). For the NBW to DCW translation, the currently known
upper bound is 2o(nlog n). We improve it to 2 o(n), which is asymptotically tight.
Both of our upper-bound constructions are based on a simple subset construction,
do not involve intermediate automata with richer acceptance conditions, and can
be implemented symbolically. We continue and solve the open problems of translating
nondeterministic Streett, Rabin, Muller, and parity word automata to NCW and to
DCW. Going via an intermediate NBW is not optimal and we describe direct, simple,
and asymptotically tight constructions, involving a 2o(n) blow-up. The constructions
are variants of the subset construction, providing a unified approach for translating
all common classes of automata to NCW and DCW. Beyond the theoretical importance
of the results, we point to numerous applications of the new constructions. In
particular, they imply a simple subset-construction based translation, when possible,
of LTL to deterministic Büchi word automata.
article_number: '29'
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: Boker U, Kupferman O. Translating to Co-Büchi made tight, unified, and useful.
ACM Transactions on Computational Logic (TOCL). 2012;13(4). doi:10.1145/2362355.2362357
apa: Boker, U., & Kupferman, O. (2012). Translating to Co-Büchi made tight,
unified, and useful. ACM Transactions on Computational Logic (TOCL). ACM.
https://doi.org/10.1145/2362355.2362357
chicago: Boker, Udi, and Orna Kupferman. “Translating to Co-Büchi Made Tight, Unified,
and Useful.” ACM Transactions on Computational Logic (TOCL). ACM, 2012.
https://doi.org/10.1145/2362355.2362357.
ieee: U. Boker and O. Kupferman, “Translating to Co-Büchi made tight, unified, and
useful,” ACM Transactions on Computational Logic (TOCL), vol. 13, no. 4.
ACM, 2012.
ista: Boker U, Kupferman O. 2012. Translating to Co-Büchi made tight, unified, and
useful. ACM Transactions on Computational Logic (TOCL). 13(4), 29.
mla: Boker, Udi, and Orna Kupferman. “Translating to Co-Büchi Made Tight, Unified,
and Useful.” ACM Transactions on Computational Logic (TOCL), vol. 13, no.
4, 29, ACM, 2012, doi:10.1145/2362355.2362357.
short: U. Boker, O. Kupferman, ACM Transactions on Computational Logic (TOCL) 13
(2012).
date_created: 2018-12-11T11:46:47Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2021-01-12T08:01:03Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/2362355.2362357
intvolume: ' 13'
issue: '4'
language:
- iso: eng
month: '10'
oa_version: None
publication: ACM Transactions on Computational Logic (TOCL)
publication_status: published
publisher: ACM
publist_id: '7326'
quality_controlled: '1'
scopus_import: 1
status: public
title: Translating to Co-Büchi made tight, unified, and useful
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2012'
...
---
_id: '506'
article_processing_charge: No
article_type: original
author:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Sixt MK. Cell migration: Fibroblasts find a new way to get ahead. Journal
of Cell Biology. 2012;197(3):347-349. doi:10.1083/jcb.201204039'
apa: 'Sixt, M. K. (2012). Cell migration: Fibroblasts find a new way to get ahead.
Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201204039'
chicago: 'Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.”
Journal of Cell Biology. Rockefeller University Press, 2012. https://doi.org/10.1083/jcb.201204039.'
ieee: 'M. K. Sixt, “Cell migration: Fibroblasts find a new way to get ahead,” Journal
of Cell Biology, vol. 197, no. 3. Rockefeller University Press, pp. 347–349,
2012.'
ista: 'Sixt MK. 2012. Cell migration: Fibroblasts find a new way to get ahead. Journal
of Cell Biology. 197(3), 347–349.'
mla: 'Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.”
Journal of Cell Biology, vol. 197, no. 3, Rockefeller University Press,
2012, pp. 347–49, doi:10.1083/jcb.201204039.'
short: M.K. Sixt, Journal of Cell Biology 197 (2012) 347–349.
date_created: 2018-12-11T11:46:51Z
date_published: 2012-04-30T00:00:00Z
date_updated: 2021-01-12T08:01:11Z
day: '30'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1083/jcb.201204039
file:
- access_level: open_access
checksum: 45c02be33ebd99fc3077d60b9c90bdfa
content_type: application/pdf
creator: kschuh
date_created: 2019-02-12T09:03:09Z
date_updated: 2020-07-14T12:46:36Z
file_id: '5957'
file_name: 2012_CellBiology_Sixt.pdf
file_size: 986566
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 197'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 347 - 349
publication: Journal of Cell Biology
publication_status: published
publisher: Rockefeller University Press
publist_id: '7314'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Cell migration: Fibroblasts find a new way to get ahead'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 197
year: '2012'
...
---
_id: '497'
abstract:
- lang: eng
text: 'One central issue in the formal design and analysis of reactive systems is
the notion of refinement that asks whether all behaviors of the implementation
is allowed by the specification. The local interpretation of behavior leads to
the notion of simulation. Alternating transition systems (ATSs) provide a general
model for composite reactive systems, and the simulation relation for ATSs is
known as alternating simulation. The simulation relation for fair transition systems
is called fair simulation. In this work our main contributions are as follows:
(1) We present an improved algorithm for fair simulation with Büchi fairness constraints;
our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time
algorithm, where n is the number of states and m is the number of transitions.
(2) We present a game based algorithm for alternating simulation that requires
O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n
is the number of states and m is the size of transition relation. (3) We present
an iterative algorithm for alternating simulation that matches the time complexity
of the game based algorithm, but is more space efficient than the game based algorithm.
© Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.'
alternative_title:
- LIPIcs
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Siddhesh
full_name: Chaubal, Siddhesh
last_name: Chaubal
- first_name: Pritish
full_name: Kamath, Pritish
last_name: Kamath
citation:
ama: 'Chatterjee K, Chaubal S, Kamath P. Faster algorithms for alternating refinement
relations. In: Vol 16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2012:167-182.
doi:10.4230/LIPIcs.CSL.2012.167'
apa: 'Chatterjee, K., Chaubal, S., & Kamath, P. (2012). Faster algorithms for
alternating refinement relations (Vol. 16, pp. 167–182). Presented at the EACSL:
European Association for Computer Science Logic, Fontainebleau, France: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2012.167'
chicago: Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. “Faster Algorithms
for Alternating Refinement Relations,” 16:167–82. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2012. https://doi.org/10.4230/LIPIcs.CSL.2012.167.
ieee: 'K. Chatterjee, S. Chaubal, and P. Kamath, “Faster algorithms for alternating
refinement relations,” presented at the EACSL: European Association for Computer
Science Logic, Fontainebleau, France, 2012, vol. 16, pp. 167–182.'
ista: 'Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating
refinement relations. EACSL: European Association for Computer Science Logic,
LIPIcs, vol. 16, 167–182.'
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Alternating Refinement
Relations. Vol. 16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012,
pp. 167–82, doi:10.4230/LIPIcs.CSL.2012.167.
short: K. Chatterjee, S. Chaubal, P. Kamath, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2012, pp. 167–182.
conference:
end_date: 2012-09-06
location: Fontainebleau, France
name: 'EACSL: European Association for Computer Science Logic'
start_date: 2012-09-03
date_created: 2018-12-11T11:46:48Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2023-02-23T12:23:32Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.CSL.2012.167
ec_funded: 1
file:
- access_level: open_access
checksum: f1b0dd99240800db2d7dbf9b5131fe5e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:50Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4712'
file_name: IST-2018-943-v1+1_2012_Chatterjee_Faster_Algorithms.pdf
file_size: 471236
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 16'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 167 - 182
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: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7323'
pubrep_id: '943'
quality_controlled: '1'
related_material:
record:
- id: '5378'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Faster algorithms for alternating refinement relations
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2012'
...
---
_id: '3165'
abstract:
- lang: eng
text: Computing the winning set for Büchi objectives in alternating games on graphs
is a central problem in computer aided verification with a large number of applications.
The long standing best known upper bound for solving the problem is Õ(n·m), where
n is the number of vertices and m is the number of edges in the graph. We are
the first to break the Õ(n·m) boundary by presenting a new technique that reduces
the running time to O(n 2). This bound also leads to O(n 2) time algorithms for
computing the set of almost-sure winning vertices for Büchi objectives (1) in
alternating games with probabilistic transitions (improving an earlier bound of
Õ(n·m)), (2) in concurrent graph games with constant actions (improving an earlier
bound of O(n 3)), and (3) in Markov decision processes (improving for m > n
4/3 an earlier bound of O(min(m 1.5, m·n 2/3)). We also show that the same technique
can be used to compute the maximal end-component decomposition of a graph in time
O(n 2), which is an improvement over earlier bounds for m > n 4/3. Finally,
we show how to maintain the winning set for Büchi objectives in alternating games
under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized
time per operation. This is the first dynamic algorithm for this problem.
acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant
No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, Vienna
Science and Technology Fund (WWTF) Grant ICT10-002, FWF NFN Grant No S11407-N23
(RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.'
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: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Chatterjee K, Henzinger MH. An O(n2) time algorithm for alternating Büchi
games. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
SIAM; 2012:1386-1399. doi:10.1137/1.9781611973099.109'
apa: 'Chatterjee, K., & Henzinger, M. H. (2012). An O(n2) time algorithm for
alternating Büchi games. In Proceedings of the Annual ACM-SIAM Symposium on
Discrete Algorithms (pp. 1386–1399). Kyoto, Japan: SIAM. https://doi.org/10.1137/1.9781611973099.109'
chicago: Chatterjee, Krishnendu, and Monika H Henzinger. “An O(N2) Time Algorithm
for Alternating Büchi Games.” In Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms, 1386–99. SIAM, 2012. https://doi.org/10.1137/1.9781611973099.109.
ieee: K. Chatterjee and M. H. Henzinger, “An O(n2) time algorithm for alternating
Büchi games,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms,
Kyoto, Japan, 2012, pp. 1386–1399.
ista: 'Chatterjee K, Henzinger MH. 2012. An O(n2) time algorithm for alternating
Büchi games. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
SODA: Symposium on Discrete Algorithms, 1386–1399.'
mla: Chatterjee, Krishnendu, and Monika H. Henzinger. “An O(N2) Time Algorithm for
Alternating Büchi Games.” Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms, SIAM, 2012, pp. 1386–99, doi:10.1137/1.9781611973099.109.
short: K. Chatterjee, M.H. Henzinger, in:, Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms, SIAM, 2012, pp. 1386–1399.
conference:
end_date: 2012-01-19
location: Kyoto, Japan
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2012-01-17
date_created: 2018-12-11T12:01:46Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2023-02-23T12:23:35Z
day: '01'
department:
- _id: KrCh
doi: 10.1137/1.9781611973099.109
ec_funded: 1
external_id:
arxiv:
- '1109.5018'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1109.5018
month: '01'
oa: 1
oa_version: None
page: 1386 - 1399
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
publication_status: published
publisher: SIAM
publist_id: '3519'
pubrep_id: '15'
quality_controlled: '1'
related_material:
record:
- id: '2141'
relation: later_version
status: public
- id: '5379'
relation: earlier_version
status: public
status: public
title: An O(n2) time algorithm for alternating Büchi games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '2956'
abstract:
- lang: eng
text: 'Two-player games on graphs are central in many problems in formal verification
and program analysis such as synthesis and verification of open systems. In this
work we consider solving recursive game graphs (or pushdown game graphs) that
can model the control flow of sequential programs with recursion. While pushdown
games have been studied before with qualitative objectives, such as reachability
and parity objectives, in this work we study for the first time such games with
the most well-studied quantitative objective, namely, mean payoff objectives.
In pushdown games two types of strategies are relevant: (1) global strategies,
that depend on the entire global history; and (2) modular strategies, that have
only local memory and thus do not depend on the context of invocation, but only
on the history of the current invocation of the module. Our main results are as
follows: (1) One-player pushdown games with mean-payoff objectives under global
strategies are decidable in polynomial time. (2) Two-player pushdown games with
mean-payoff objectives under global strategies are undecidable. (3) One-player
pushdown games with mean-payoff objectives under modular strategies are NP-hard.
(4) Two-player pushdown games with mean-payoff objectives under modular strategies
can be solved in NP (i.e., both one-player and two-player pushdown games with
mean-payoff objectives under modular strategies are NP-complete). We also establish
the optimal strategy complexity showing that global strategies for mean-payoff
objectives require infinite memory even in one-player pushdown games; and memoryless
modular strategies are sufficient in two-player pushdown games. Finally we also
show that all the problems have the same computational complexity if the stack
boundedness condition is added, where along with the mean-payoff objective the
player must also ensure that the stack height is bounded.'
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), Microsoft faculty fellows award, the Israeli Centers of Research Excellence
(ICORE) program, (Center No. 4/11), the RICH Model Toolkit (ICT COST Action IC0901),
and was carried out in partial fulfillment of the requirements for the Ph.D. degree
of the second author.\r\nA Technical Report of this paper is available via internal
link."
article_number: '6280438'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: 'Chatterjee K, Velner Y. Mean payoff pushdown games. In: Proceedings of
the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE;
2012. doi:10.1109/LICS.2012.30'
apa: 'Chatterjee, K., & Velner, Y. (2012). Mean payoff pushdown games. In Proceedings
of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. Dubrovnik,
Croatia : IEEE. https://doi.org/10.1109/LICS.2012.30'
chicago: Chatterjee, Krishnendu, and Yaron Velner. “Mean Payoff Pushdown Games.”
In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer
Science. IEEE, 2012. https://doi.org/10.1109/LICS.2012.30.
ieee: K. Chatterjee and Y. Velner, “Mean payoff pushdown games,” in Proceedings
of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, Dubrovnik,
Croatia , 2012.
ista: 'Chatterjee K, Velner Y. 2012. Mean payoff pushdown games. Proceedings of
the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic
in Computer Science, 6280438.'
mla: Chatterjee, Krishnendu, and Yaron Velner. “Mean Payoff Pushdown Games.” Proceedings
of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, 6280438,
IEEE, 2012, doi:10.1109/LICS.2012.30.
short: K. Chatterjee, Y. Velner, in:, Proceedings of the 2012 27th Annual ACM/IEEE
Symposium on Logic in Computer Science, IEEE, 2012.
conference:
end_date: 2012-06-28
location: 'Dubrovnik, Croatia '
name: 'LICS: Logic in Computer Science'
start_date: 2012-06-25
date_created: 2018-12-11T12:00:32Z
date_published: 2012-08-23T00:00:00Z
date_updated: 2023-02-23T12:23:30Z
day: '23'
department:
- _id: KrCh
doi: 10.1109/LICS.2012.30
ec_funded: 1
language:
- iso: eng
month: '08'
oa_version: None
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: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer
Science
publication_status: published
publisher: IEEE
publist_id: '3770'
quality_controlled: '1'
related_material:
record:
- id: '5377'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Mean payoff pushdown games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...