---
_id: '2824'
abstract:
- lang: eng
text: We study synthesis of controllers for real-time systems, where the objective
is to stay in a given safe set. The problem is solved by obtaining winning strategies
in the setting of concurrent two player timed automaton games with safety objectives.
To prevent a player from winning by blocking time, we restrict each player to
strategies that ensure that the player cannot be responsible for causing a Zeno
run. We construct winning strategies for the controller which require access only
to (1) the system clocks (thus, controllers which require their own internal infinitely
precise clocks are not necessary), and (2) a logarithmic (in the number of clocks)
number of memory bits (i.e. a linear number of memory states). Precisely, we show
that for safety objectives, a memory of size (3 + lg (| C | + 1)) bits suffices
for winning controller strategies, where C is the set of clocks of the timed automaton
game, significantly improving the previous known exponential memory states bound.
We also settle the open question of whether winning region-based strategies require
memory for safety objectives by showing with an example the necessity of memory
for such strategies to win for safety objectives. Finally, we show that the decision
problem of determining if there exists a receptive player-1 winning strategy for
safety objectives is EXPTIME-complete over timed automaton games.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vinayak
full_name: Prabhu, Vinayak
last_name: Prabhu
citation:
ama: Chatterjee K, Prabhu V. Synthesis of memory-efficient, clock-memory free, and
non-Zeno safety controllers for timed systems. Information and Computation.
2013;228-229:83-119. doi:10.1016/j.ic.2013.04.003
apa: Chatterjee, K., & Prabhu, V. (2013). Synthesis of memory-efficient, clock-memory
free, and non-Zeno safety controllers for timed systems. Information and Computation.
Elsevier. https://doi.org/10.1016/j.ic.2013.04.003
chicago: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient,
Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information
and Computation. Elsevier, 2013. https://doi.org/10.1016/j.ic.2013.04.003.
ieee: K. Chatterjee and V. Prabhu, “Synthesis of memory-efficient, clock-memory
free, and non-Zeno safety controllers for timed systems,” Information and Computation,
vol. 228–229. Elsevier, pp. 83–119, 2013.
ista: Chatterjee K, Prabhu V. 2013. Synthesis of memory-efficient, clock-memory
free, and non-Zeno safety controllers for timed systems. Information and Computation.
228–229, 83–119.
mla: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient,
Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information
and Computation, vol. 228–229, Elsevier, 2013, pp. 83–119, doi:10.1016/j.ic.2013.04.003.
short: K. Chatterjee, V. Prabhu, Information and Computation 228–229 (2013) 83–119.
date_created: 2018-12-11T11:59:47Z
date_published: 2013-04-24T00:00:00Z
date_updated: 2021-01-12T06:59:58Z
day: '24'
department:
- _id: KrCh
doi: 10.1016/j.ic.2013.04.003
ec_funded: 1
language:
- iso: eng
month: '04'
oa_version: None
page: 83-119
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '3977'
quality_controlled: '1'
scopus_import: 1
status: public
title: Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers
for timed systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 228-229
year: '2013'
...
---
_id: '2832'
abstract:
- lang: eng
text: PIN-FORMED (PIN) proteins localize asymmetrically at the plasma membrane and
mediate intercellular polar transport of the plant hormone auxin that is crucial
for a multitude of developmental processes in plants. PIN localization is under
extensive control by environmental or developmental cues, but mechanisms regulating
PIN localization are not fully understood. Here we show that early endosomal components
ARF GEF BEN1 and newly identified Sec1/Munc18 family protein BEN2 are involved
in distinct steps of early endosomal trafficking. BEN1 and BEN2 are collectively
required for polar PIN localization, for their dynamic repolarization, and consequently
for auxin activity gradient formation and auxin-related developmental processes
including embryonic patterning, organogenesis, and vasculature venation patterning.
These results show that early endosomal trafficking is crucial for cell polarity
and auxin-dependent regulation of plant architecture.
article_number: e1003540
author:
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Tomohiro
full_name: Uemura, Tomohiro
last_name: Uemura
- first_name: Mugurel
full_name: Feraru, Mugurel
last_name: Feraru
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Tatsuo
full_name: Kakimoto, Tatsuo
last_name: Kakimoto
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tanaka H, Kitakura S, Rakusová H, et al. Cell polarity and patterning by PIN
trafficking through early endosomal compartments in arabidopsis thaliana. PLoS
Genetics. 2013;9(5). doi:10.1371/journal.pgen.1003540
apa: Tanaka, H., Kitakura, S., Rakusová, H., Uemura, T., Feraru, M., De Rycke, R.,
… Friml, J. (2013). Cell polarity and patterning by PIN trafficking through early
endosomal compartments in arabidopsis thaliana. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1003540
chicago: Tanaka, Hirokazu, Saeko Kitakura, Hana Rakusová, Tomohiro Uemura, Mugurel
Feraru, Riet De Rycke, Stéphanie Robert, Tatsuo Kakimoto, and Jiří Friml. “Cell
Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments
in Arabidopsis Thaliana.” PLoS Genetics. Public Library of Science, 2013.
https://doi.org/10.1371/journal.pgen.1003540.
ieee: H. Tanaka et al., “Cell polarity and patterning by PIN trafficking
through early endosomal compartments in arabidopsis thaliana,” PLoS Genetics,
vol. 9, no. 5. Public Library of Science, 2013.
ista: Tanaka H, Kitakura S, Rakusová H, Uemura T, Feraru M, De Rycke R, Robert S,
Kakimoto T, Friml J. 2013. Cell polarity and patterning by PIN trafficking through
early endosomal compartments in arabidopsis thaliana. PLoS Genetics. 9(5), e1003540.
mla: Tanaka, Hirokazu, et al. “Cell Polarity and Patterning by PIN Trafficking through
Early Endosomal Compartments in Arabidopsis Thaliana.” PLoS Genetics, vol.
9, no. 5, e1003540, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003540.
short: H. Tanaka, S. Kitakura, H. Rakusová, T. Uemura, M. Feraru, R. De Rycke, S.
Robert, T. Kakimoto, J. Friml, PLoS Genetics 9 (2013).
date_created: 2018-12-11T11:59:50Z
date_published: 2013-05-05T00:00:00Z
date_updated: 2021-01-12T07:00:03Z
day: '05'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1371/journal.pgen.1003540
ec_funded: 1
file:
- access_level: open_access
checksum: 050237d6c53e8d1601b26808ee1dd6d8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:39Z
date_updated: 2020-07-14T12:45:50Z
file_id: '4957'
file_name: IST-2016-411-v1+1_journal.pgen.1003540.pdf
file_size: 3813091
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '3967'
pubrep_id: '411'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cell polarity and patterning by PIN trafficking through early endosomal compartments
in arabidopsis thaliana
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '2828'
abstract:
- lang: eng
text: 'We study the complexity of valued constraint satisfaction problems (VCSPs)
parametrized 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 minimize the sum. Under the unique games conjecture,
the approximability of finite-valued VCSPs is well understood, see Raghavendra
[2008]. However, there is no characterization of finite-valued VCSPs, let alone
general-valued VCSPs, that can be solved exactly in polynomial time, thus giving
insights from a combinatorial optimization 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 [2003, 2011] and recently
by Barto [2011]. 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. [2006] for languages
over Boolean domains, by Deineko et al. [2008] for {0, 1}-valued languages (a.k.a
Max-CSP), and by Takhanov [2010a] 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 multimor-phisms), then any instance can be solved in polynomial time (via
a new algorithm developed in this article), 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 are significantly harder
than the Boolean cases. The polynomial-time algorithm we present for the tractable
cases is a generalization of the submodular minimization problem and a result
of Cohen et al. [2008]. Our results generalize previous results by Takhanov [2010a]
and (a subset of results) by Cohen et al. [2006] and Deineko et al. [2008]. Moreover,
our results do not rely on any computer-assisted search as in Deineko et al. [2008],
and provide a powerful tool for proving hardness of finite-valued and general-valued
languages.'
article_number: '10'
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
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. Journal
of the ACM. 2013;60(2). doi:10.1145/2450142.2450146
apa: Kolmogorov, V., & Živný, S. (2013). The complexity of conservative valued
CSPs. Journal of the ACM. ACM. https://doi.org/10.1145/2450142.2450146
chicago: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative
Valued CSPs.” Journal of the ACM. ACM, 2013. https://doi.org/10.1145/2450142.2450146.
ieee: V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,”
Journal of the ACM, vol. 60, no. 2. ACM, 2013.
ista: Kolmogorov V, Živný S. 2013. The complexity of conservative valued CSPs. Journal
of the ACM. 60(2), 10.
mla: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative
Valued CSPs.” Journal of the ACM, vol. 60, no. 2, 10, ACM, 2013, doi:10.1145/2450142.2450146.
short: V. Kolmogorov, S. Živný, Journal of the ACM 60 (2013).
date_created: 2018-12-11T11:59:48Z
date_published: 2013-04-02T00:00:00Z
date_updated: 2021-01-12T07:00:00Z
day: '02'
department:
- _id: VlKo
doi: 10.1145/2450142.2450146
external_id:
arxiv:
- '1110.2809'
intvolume: ' 60'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1110.2809
month: '04'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '3971'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of conservative valued CSPs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2013'
...
---
_id: '2829'
abstract:
- lang: eng
text: Laminar-turbulent intermittency is intrinsic to the transitional regime of
a wide range of fluid flows including pipe, channel, boundary layer, and Couette
flow. In the latter turbulent spots can grow and form continuous stripes, yet
in the stripe-normal direction they remain interspersed by laminar fluid. We carry
out direct numerical simulations in a long narrow domain and observe that individual
turbulent stripes are transient. In agreement with recent observations in pipe
flow, we find that turbulence becomes sustained at a distinct critical point once
the spatial proliferation outweighs the inherent decaying process. By resolving
the asymptotic size distributions close to criticality we can for the first time
demonstrate scale invariance at the onset of turbulence.
article_number: '204502'
author:
- first_name: Liang
full_name: Shi, Liang
id: 374A3F1A-F248-11E8-B48F-1D18A9856A87
last_name: Shi
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Shi L, Avila M, Hof B. Scale invariance at the onset of turbulence in couette
flow. Physical Review Letters. 2013;110(20). doi:10.1103/PhysRevLett.110.204502
apa: Shi, L., Avila, M., & Hof, B. (2013). Scale invariance at the onset of
turbulence in couette flow. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.110.204502
chicago: Shi, Liang, Marc Avila, and Björn Hof. “Scale Invariance at the Onset of
Turbulence in Couette Flow.” Physical Review Letters. American Physical
Society, 2013. https://doi.org/10.1103/PhysRevLett.110.204502.
ieee: L. Shi, M. Avila, and B. Hof, “Scale invariance at the onset of turbulence
in couette flow,” Physical Review Letters, vol. 110, no. 20. American Physical
Society, 2013.
ista: Shi L, Avila M, Hof B. 2013. Scale invariance at the onset of turbulence in
couette flow. Physical Review Letters. 110(20), 204502.
mla: Shi, Liang, et al. “Scale Invariance at the Onset of Turbulence in Couette
Flow.” Physical Review Letters, vol. 110, no. 20, 204502, American Physical
Society, 2013, doi:10.1103/PhysRevLett.110.204502.
short: L. Shi, M. Avila, B. Hof, Physical Review Letters 110 (2013).
date_created: 2018-12-11T11:59:49Z
date_published: 2013-05-13T00:00:00Z
date_updated: 2021-01-12T07:00:00Z
day: '13'
department:
- _id: BjHo
doi: 10.1103/PhysRevLett.110.204502
ec_funded: 1
external_id:
arxiv:
- '1304.5446'
intvolume: ' 110'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.5446
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
- _id: 2511D90C-B435-11E9-9278-68D0E5697425
grant_number: SFB 963 TP A8
name: Astrophysical instability of currents and turbulences
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '3970'
quality_controlled: '1'
scopus_import: 1
status: public
title: Scale invariance at the onset of turbulence in couette flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2834'
abstract:
- lang: eng
text: Although the equations governing fluid flow are well known, there are no analytical
expressions that describe the complexity of turbulent motion. A recent proposition
is that in analogy to low dimensional chaotic systems, turbulence is organized
around unstable solutions of the governing equations which provide the building
blocks of the disordered dynamics. We report the discovery of periodic solutions
which just like intermittent turbulence are spatially localized and show that
turbulent transients arise from one such solution branch.
article_number: '224502'
author:
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Fernando
full_name: Mellibovsky, Fernando
last_name: Mellibovsky
- first_name: Nicolas
full_name: Roland, Nicolas
last_name: Roland
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Avila M, Mellibovsky F, Roland N, Hof B. Streamwise-localized solutions at
the onset of turbulence in pipe flow. Physical Review Letters. 2013;110(22).
doi:10.1103/PhysRevLett.110.224502
apa: Avila, M., Mellibovsky, F., Roland, N., & Hof, B. (2013). Streamwise-localized
solutions at the onset of turbulence in pipe flow. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.110.224502
chicago: Avila, Marc, Fernando Mellibovsky, Nicolas Roland, and Björn Hof. “Streamwise-Localized
Solutions at the Onset of Turbulence in Pipe Flow.” Physical Review Letters.
American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.224502.
ieee: M. Avila, F. Mellibovsky, N. Roland, and B. Hof, “Streamwise-localized solutions
at the onset of turbulence in pipe flow,” Physical Review Letters, vol.
110, no. 22. American Physical Society, 2013.
ista: Avila M, Mellibovsky F, Roland N, Hof B. 2013. Streamwise-localized solutions
at the onset of turbulence in pipe flow. Physical Review Letters. 110(22), 224502.
mla: Avila, Marc, et al. “Streamwise-Localized Solutions at the Onset of Turbulence
in Pipe Flow.” Physical Review Letters, vol. 110, no. 22, 224502, American
Physical Society, 2013, doi:10.1103/PhysRevLett.110.224502.
short: M. Avila, F. Mellibovsky, N. Roland, B. Hof, Physical Review Letters 110
(2013).
date_created: 2018-12-11T11:59:50Z
date_published: 2013-05-29T00:00:00Z
date_updated: 2021-01-12T07:00:05Z
day: '29'
department:
- _id: BjHo
doi: 10.1103/PhysRevLett.110.224502
ec_funded: 1
external_id:
arxiv:
- '1212.0230'
intvolume: ' 110'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1212.0230
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '3965'
quality_controlled: '1'
scopus_import: 1
status: public
title: Streamwise-localized solutions at the onset of turbulence in pipe flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2833'
abstract:
- lang: eng
text: During development, mechanical forces cause changes in size, shape, number,
position, and gene expression of cells. They are therefore integral to any morphogenetic
processes. Force generation by actin-myosin networks and force transmission through
adhesive complexes are two self-organizing phenomena driving tissue morphogenesis.
Coordination and integration of forces by long-range force transmission and mechanosensing
of cells within tissues produce large-scale tissue shape changes. Extrinsic mechanical
forces also control tissue patterning by modulating cell fate specification and
differentiation. Thus, the interplay between tissue mechanics and biochemical
signaling orchestrates tissue morphogenesis and patterning in development.
acknowledgement: C.-P.H. is supported by the Institute of Science and Technology Austria
and grants from the Deutsche Forschungsgemeinschaft (DFG) and Fonds zur Förderung
der wissenschaftlichen Forschung (FWF).
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: Yohanns
full_name: Bellaïche, Yohanns
last_name: Bellaïche
citation:
ama: Heisenberg C-PJ, Bellaïche Y. Forces in tissue morphogenesis and patterning.
Cell. 2013;153(5):948-962. doi:10.1016/j.cell.2013.05.008
apa: Heisenberg, C.-P. J., & Bellaïche, Y. (2013). Forces in tissue morphogenesis
and patterning. Cell. Cell Press. https://doi.org/10.1016/j.cell.2013.05.008
chicago: Heisenberg, Carl-Philipp J, and Yohanns Bellaïche. “Forces in Tissue Morphogenesis
and Patterning.” Cell. Cell Press, 2013. https://doi.org/10.1016/j.cell.2013.05.008.
ieee: C.-P. J. Heisenberg and Y. Bellaïche, “Forces in tissue morphogenesis and
patterning,” Cell, vol. 153, no. 5. Cell Press, pp. 948–962, 2013.
ista: Heisenberg C-PJ, Bellaïche Y. 2013. Forces in tissue morphogenesis and patterning.
Cell. 153(5), 948–962.
mla: Heisenberg, Carl-Philipp J., and Yohanns Bellaïche. “Forces in Tissue Morphogenesis
and Patterning.” Cell, vol. 153, no. 5, Cell Press, 2013, pp. 948–62, doi:10.1016/j.cell.2013.05.008.
short: C.-P.J. Heisenberg, Y. Bellaïche, Cell 153 (2013) 948–962.
date_created: 2018-12-11T11:59:50Z
date_published: 2013-05-23T00:00:00Z
date_updated: 2021-01-12T07:00:04Z
day: '23'
department:
- _id: CaHe
doi: 10.1016/j.cell.2013.05.008
intvolume: ' 153'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 948 - 962
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3966'
quality_controlled: '1'
scopus_import: 1
status: public
title: Forces in tissue morphogenesis and patterning
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 153
year: '2013'
...
---
_id: '2830'
author:
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- 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: Moussion C, Sixt MK. A conduit to amplify innate immunity. Immunity.
2013;38(5):853-854. doi:10.1016/j.immuni.2013.05.005
apa: Moussion, C., & Sixt, M. K. (2013). A conduit to amplify innate immunity.
Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2013.05.005
chicago: Moussion, Christine, and Michael K Sixt. “A Conduit to Amplify Innate Immunity.”
Immunity. Cell Press, 2013. https://doi.org/10.1016/j.immuni.2013.05.005.
ieee: C. Moussion and M. K. Sixt, “A conduit to amplify innate immunity,” Immunity,
vol. 38, no. 5. Cell Press, pp. 853–854, 2013.
ista: Moussion C, Sixt MK. 2013. A conduit to amplify innate immunity. Immunity.
38(5), 853–854.
mla: Moussion, Christine, and Michael K. Sixt. “A Conduit to Amplify Innate Immunity.”
Immunity, vol. 38, no. 5, Cell Press, 2013, pp. 853–54, doi:10.1016/j.immuni.2013.05.005.
short: C. Moussion, M.K. Sixt, Immunity 38 (2013) 853–854.
date_created: 2018-12-11T11:59:49Z
date_published: 2013-05-23T00:00:00Z
date_updated: 2021-01-12T07:00:01Z
day: '23'
department:
- _id: MiSi
doi: 10.1016/j.immuni.2013.05.005
intvolume: ' 38'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 853 - 854
publication: Immunity
publication_status: published
publisher: Cell Press
publist_id: '3969'
quality_controlled: '1'
scopus_import: 1
status: public
title: A conduit to amplify innate immunity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2013'
...
---
_id: '2842'
abstract:
- lang: eng
text: 'We outline two approaches to inference of neighbourhood size, N, and dispersal
rate, σ2, based on either allele frequencies or on the lengths of sequence blocks
that are shared between genomes. Over intermediate timescales (10-100 generations,
say), populations that live in two dimensions approach a quasi-equilibrium that
is independent of both their local structure and their deeper history. Over such
scales, the standardised covariance of allele frequencies (i.e. pairwise FS T)
falls with the logarithm of distance, and depends only on neighbourhood size,
N, and a ''local scale'', κ; the rate of gene flow, σ2, cannot be inferred. We
show how spatial correlations can be accounted for, assuming a Gaussian distribution
of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively,
inferences can be based on the distribution of the lengths of sequence that are
identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about
intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood
size, the distribution of long blocks is given directly by the classical Wright-Malécot
formula; this relationship can be used to infer both N and σ2. With small neighbourhood
size, there is an appreciable chance that recombinant lineages will coalesce back
before escaping into the distant past. For this case, we show that if genomes
are sampled from some distance apart, then the distribution of lengths of blocks
that are identical in state is geometric, with a mean that depends on N and σ2.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: 'Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions:
Allele frequencies versus lengths of shared sequence blocks. Theoretical Population
Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001'
apa: 'Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference
in two dimensions: Allele frequencies versus lengths of shared sequence blocks.
Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001'
chicago: 'Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber.
“Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence
Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.'
ieee: 'N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two
dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical
Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.'
ista: 'Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions:
Allele frequencies versus lengths of shared sequence blocks. Theoretical Population
Biology. 87(1), 105–119.'
mla: 'Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies
versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology,
vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.'
short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population
Biology 87 (2013) 105–119.
date_created: 2018-12-11T11:59:53Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T07:00:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2013.03.001
ec_funded: 1
file:
- access_level: open_access
checksum: 9bf9d9a6fd03dd9df50906891f393bf8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:33Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5288'
file_name: IST-2016-558-v1+1_inference_revised3101NB.pdf
file_size: 1554712
relation: main_file
- access_level: open_access
checksum: 2bceddb76edacd0cd5fad73051e2a928
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:34Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5289'
file_name: IST-2016-558-v1+2_inference_revised3101NBApp.pdf
file_size: 822964
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 87'
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 105 - 119
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Elsevier
publist_id: '3953'
pubrep_id: '558'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Inference in two dimensions: Allele frequencies versus lengths of shared sequence
blocks'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2013'
...
---
_id: '2838'
abstract:
- lang: eng
text: Individuals with Down syndrome (DS) present important motor deficits that
derive from altered motor development of infants and young children. DYRK1A, a
candidate gene for DS abnormalities has been implicated in motor function due
to its expression in motor nuclei in the adult brain, and its overexpression in
DS mouse models leads to hyperactivity and altered motor learning. However, its
precise role in the adult motor system, or its possible involvement in postnatal
locomotor development has not yet been clarified. During the postnatal period
we observed time-specific expression of Dyrk1A in discrete subsets of brainstem
nuclei and spinal cord motor neurons. Interestingly, we describe for the first
time the presence of Dyrk1A in the presynaptic terminal of the neuromuscular junctions
and its axonal transport from the facial nucleus, suggesting a function for Dyrk1A
in these structures. Relevant to DS, Dyrk1A overexpression in transgenic mice
(TgDyrk1A) produces motor developmental alterations possibly contributing to DS
motor phenotypes and modifies the numbers of motor cholinergic neurons, suggesting
that the kinase may have a role in the development of the brainstem and spinal
cord motor system.
article_number: e54285
author:
- first_name: Gloria
full_name: Arquè Fuste, Gloria
id: 3CF33908-F248-11E8-B48F-1D18A9856A87
last_name: Arquè Fuste
- first_name: Anna
full_name: Casanovas, Anna
last_name: Casanovas
- first_name: Mara
full_name: Dierssen, Mara
last_name: Dierssen
citation:
ama: 'Arquè Fuste G, Casanovas A, Dierssen M. Dyrk1A is dynamically expressed on
subsets of motor neurons and in the neuromuscular junction: Possible role in Down
syndrome. PLoS One. 2013;8(1). doi:10.1371/journal.pone.0054285'
apa: 'Arquè Fuste, G., Casanovas, A., & Dierssen, M. (2013). Dyrk1A is dynamically
expressed on subsets of motor neurons and in the neuromuscular junction: Possible
role in Down syndrome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0054285'
chicago: 'Arquè Fuste, Gloria, Anna Casanovas, and Mara Dierssen. “Dyrk1A Is Dynamically
Expressed on Subsets of Motor Neurons and in the Neuromuscular Junction: Possible
Role in Down Syndrome.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0054285.'
ieee: 'G. Arquè Fuste, A. Casanovas, and M. Dierssen, “Dyrk1A is dynamically expressed
on subsets of motor neurons and in the neuromuscular junction: Possible role in
Down syndrome,” PLoS One, vol. 8, no. 1. Public Library of Science, 2013.'
ista: 'Arquè Fuste G, Casanovas A, Dierssen M. 2013. Dyrk1A is dynamically expressed
on subsets of motor neurons and in the neuromuscular junction: Possible role in
Down syndrome. PLoS One. 8(1), e54285.'
mla: 'Arquè Fuste, Gloria, et al. “Dyrk1A Is Dynamically Expressed on Subsets of
Motor Neurons and in the Neuromuscular Junction: Possible Role in Down Syndrome.”
PLoS One, vol. 8, no. 1, e54285, Public Library of Science, 2013, doi:10.1371/journal.pone.0054285.'
short: G. Arquè Fuste, A. Casanovas, M. Dierssen, PLoS One 8 (2013).
date_created: 2018-12-11T11:59:52Z
date_published: 2013-01-16T00:00:00Z
date_updated: 2021-01-12T07:00:07Z
day: '16'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1371/journal.pone.0054285
file:
- access_level: open_access
checksum: 512733b21419574a45f10cabef3d7f81
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:38Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5160'
file_name: IST-2016-407-v1+1_journal.pone.0054285.pdf
file_size: 4795977
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3960'
pubrep_id: '407'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular
junction: Possible role in Down syndrome'
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: '2013'
...
---
_id: '2839'
abstract:
- lang: eng
text: Directional guidance of cells via gradients of chemokines is considered crucial
for embryonic development, cancer dissemination, and immune responses. Nevertheless,
the concept still lacks direct experimental confirmation in vivo. Here, we identify
endogenous gradients of the chemokine CCL21 within mouse skin and show that they
guide dendritic cells toward lymphatic vessels. Quantitative imaging reveals depots
of CCL21 within lymphatic endothelial cells and steeply decaying gradients within
the perilymphatic interstitium. These gradients match the migratory patterns of
the dendritic cells, which directionally approach vessels from a distance of up
to 90-micrometers. Interstitial CCL21 is immobilized to heparan sulfates, and
its experimental delocalization or swamping the endogenous gradients abolishes
directed migration. These findings functionally establish the concept of haptotaxis,
directed migration along immobilized gradients, in tissues.
acknowledgement: We thank M. Frank for technical assistance and S. Cremer, P. Schmalhorst,
and E. Kiermaier for critical reading of the manuscript. This work was supported
by a Humboldt Foundation postdoctoral fellowship (to M.W.), the German Research
Foundation (Si1323 1,2 to M.S.), the Human Frontier Science Program (HFSP RGP0058/2011
to M.S.), the European Research Council (ERC StG 281556 to M.S.), and the Swiss
National Science Foundation (31003A 127474 to D.F.L., 130488 to S.A.L.).
article_processing_charge: No
article_type: original
author:
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Daniel
full_name: Legler, Daniel
last_name: Legler
- first_name: Sanjiv
full_name: Luther, Sanjiv
last_name: Luther
- 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: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Weber M, Hauschild R, Schwarz J, et al. Interstitial dendritic cell guidance
by haptotactic chemokine gradients. Science. 2013;339(6117):328-332. doi:10.1126/science.1228456
apa: Weber, M., Hauschild, R., Schwarz, J., Moussion, C., de Vries, I., Legler,
D., … Sixt, M. K. (2013). Interstitial dendritic cell guidance by haptotactic
chemokine gradients. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1228456
chicago: Weber, Michele, Robert Hauschild, Jan Schwarz, Christine Moussion, Ingrid
de Vries, Daniel Legler, Sanjiv Luther, Mark Tobias Bollenbach, and Michael K
Sixt. “Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients.”
Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1228456.
ieee: M. Weber et al., “Interstitial dendritic cell guidance by haptotactic
chemokine gradients,” Science, vol. 339, no. 6117. American Association
for the Advancement of Science, pp. 328–332, 2013.
ista: Weber M, Hauschild R, Schwarz J, Moussion C, de Vries I, Legler D, Luther
S, Bollenbach MT, Sixt MK. 2013. Interstitial dendritic cell guidance by haptotactic
chemokine gradients. Science. 339(6117), 328–332.
mla: Weber, Michele, et al. “Interstitial Dendritic Cell Guidance by Haptotactic
Chemokine Gradients.” Science, vol. 339, no. 6117, American Association
for the Advancement of Science, 2013, pp. 328–32, doi:10.1126/science.1228456.
short: M. Weber, R. Hauschild, J. Schwarz, C. Moussion, I. de Vries, D. Legler,
S. Luther, M.T. Bollenbach, M.K. Sixt, Science 339 (2013) 328–332.
date_created: 2018-12-11T11:59:52Z
date_published: 2013-01-18T00:00:00Z
date_updated: 2022-06-10T10:21:40Z
day: '18'
department:
- _id: MiSi
- _id: Bio
doi: 10.1126/science.1228456
ec_funded: 1
intvolume: ' 339'
issue: '6117'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://kops.uni-konstanz.de/bitstream/123456789/26341/2/Weber_263418.pdf
month: '01'
oa: 1
oa_version: Published Version
page: 328 - 332
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25ABD200-B435-11E9-9278-68D0E5697425
grant_number: RGP0058/2011
name: 'Cell migration in complex environments: from in vivo experiments to theoretical
models'
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '3959'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interstitial dendritic cell guidance by haptotactic chemokine gradients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2013'
...
---
_id: '2837'
abstract:
- lang: eng
text: We consider a general class of N × N random matrices whose entries hij are
independent up to a symmetry constraint, but not necessarily identically distributed.
Our main result is a local semicircle law which improves previous results [17]
both in the bulk and at the edge. The error bounds are given in terms of the basic
small parameter of the model, maxi,j E|hij|2. As a consequence, we prove the universality
of the local n-point correlation functions in the bulk spectrum for a class of
matrices whose entries do not have comparable variances, including random band
matrices with band width W ≫N1-εn with some εn > 0 and with a negligible mean-field
component. In addition, we provide a coherent and pedagogical proof of the local
semicircle law, streamlining and strengthening previous arguments from [17, 19,
6].
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Antti
full_name: Knowles, Antti
last_name: Knowles
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
- first_name: Jun
full_name: Yin, Jun
last_name: Yin
citation:
ama: Erdös L, Knowles A, Yau H, Yin J. The local semicircle law for a general class
of random matrices. Electronic Journal of Probability. 2013;18(59):1-58.
doi:10.1214/EJP.v18-2473
apa: Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). The local semicircle
law for a general class of random matrices. Electronic Journal of Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v18-2473
chicago: Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “The Local Semicircle
Law for a General Class of Random Matrices.” Electronic Journal of Probability.
Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/EJP.v18-2473.
ieee: L. Erdös, A. Knowles, H. Yau, and J. Yin, “The local semicircle law for a
general class of random matrices,” Electronic Journal of Probability, vol.
18, no. 59. Institute of Mathematical Statistics, pp. 1–58, 2013.
ista: Erdös L, Knowles A, Yau H, Yin J. 2013. The local semicircle law for a general
class of random matrices. Electronic Journal of Probability. 18(59), 1–58.
mla: Erdös, László, et al. “The Local Semicircle Law for a General Class of Random
Matrices.” Electronic Journal of Probability, vol. 18, no. 59, Institute
of Mathematical Statistics, 2013, pp. 1–58, doi:10.1214/EJP.v18-2473.
short: L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of Probability 18
(2013) 1–58.
date_created: 2018-12-11T11:59:51Z
date_published: 2013-05-29T00:00:00Z
date_updated: 2021-01-12T07:00:06Z
day: '29'
ddc:
- '530'
department:
- _id: LaEr
doi: 10.1214/EJP.v18-2473
file:
- access_level: open_access
checksum: aac9e52a00cb2f5149dc9e362b5ccf44
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:46Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5169'
file_name: IST-2016-406-v1+1_2473-13759-1-PB.pdf
file_size: 651497
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '59'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1-58
publication: Electronic Journal of Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '3962'
pubrep_id: '406'
quality_controlled: '1'
scopus_import: 1
status: public
title: The local semicircle law for a general class of random matrices
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: 18
year: '2013'
...
---
_id: '2835'
abstract:
- lang: eng
text: The phytohormone auxin regulates virtually every aspect of plant development.
To identify new genes involved in auxin activity, a genetic screen was performed
for Arabidopsis (Arabidopsis thaliana) mutants with altered expression of the
auxin-responsive reporter DR5rev:GFP. One of the mutants recovered in the screen,
designated as weak auxin response3 (wxr3), exhibits much lower DR5rev:GFP expression
when treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid and displays
severe defects in root development. The wxr3 mutant decreases polar auxin transport
and results in a disruption of the asymmetric auxin distribution. The levels of
the auxin transporters AUXIN1 and PIN-FORMED are dramatically reduced in the wxr3
root tip. Molecular analyses demonstrate that WXR3 is ROOT ULTRAVIOLET B-SENSITIVE1
(RUS1), a member of the conserved Domain of Unknown Function647 protein family
found in diverse eukaryotic organisms. Our data suggest that RUS1/WXR3 plays an
essential role in the regulation of polar auxin transport by maintaining the proper
level of auxin transporters on the plasma membrane.
author:
- first_name: Hong
full_name: Yu, Hong
last_name: Yu
- first_name: Michael
full_name: Karampelias, Michael
last_name: Karampelias
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Wendy
full_name: Peer, Wendy
last_name: Peer
- first_name: Ranjan
full_name: Swarup, Ranjan
last_name: Swarup
- first_name: Songqing
full_name: Ye, Songqing
last_name: Ye
- first_name: Lei
full_name: Ge, Lei
last_name: Ge
- first_name: Jerry
full_name: Cohen, Jerry
last_name: Cohen
- first_name: Angus
full_name: Murphy, Angus
last_name: Murphy
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Mark
full_name: Estelle, Mark
last_name: Estelle
citation:
ama: Yu H, Karampelias M, Robert S, et al. Root ultraviolet b-sensitive1/weak auxin
response3 is essential for polar auxin transport in arabidopsis. Plant Physiology.
2013;162(2):965-976. doi:10.1104/pp.113.217018
apa: Yu, H., Karampelias, M., Robert, S., Peer, W., Swarup, R., Ye, S., … Estelle,
M. (2013). Root ultraviolet b-sensitive1/weak auxin response3 is essential for
polar auxin transport in arabidopsis. Plant Physiology. American Society
of Plant Biologists. https://doi.org/10.1104/pp.113.217018
chicago: Yu, Hong, Michael Karampelias, Stéphanie Robert, Wendy Peer, Ranjan Swarup,
Songqing Ye, Lei Ge, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3
Is Essential for Polar Auxin Transport in Arabidopsis.” Plant Physiology.
American Society of Plant Biologists, 2013. https://doi.org/10.1104/pp.113.217018.
ieee: H. Yu et al., “Root ultraviolet b-sensitive1/weak auxin response3 is
essential for polar auxin transport in arabidopsis,” Plant Physiology,
vol. 162, no. 2. American Society of Plant Biologists, pp. 965–976, 2013.
ista: Yu H, Karampelias M, Robert S, Peer W, Swarup R, Ye S, Ge L, Cohen J, Murphy
A, Friml J, Estelle M. 2013. Root ultraviolet b-sensitive1/weak auxin response3
is essential for polar auxin transport in arabidopsis. Plant Physiology. 162(2),
965–976.
mla: Yu, Hong, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3 Is Essential
for Polar Auxin Transport in Arabidopsis.” Plant Physiology, vol. 162,
no. 2, American Society of Plant Biologists, 2013, pp. 965–76, doi:10.1104/pp.113.217018.
short: H. Yu, M. Karampelias, S. Robert, W. Peer, R. Swarup, S. Ye, L. Ge, J. Cohen,
A. Murphy, J. Friml, M. Estelle, Plant Physiology 162 (2013) 965–976.
date_created: 2018-12-11T11:59:51Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2021-01-12T07:00:05Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.113.217018
external_id:
pmid:
- '23580592'
intvolume: ' 162'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668084/
month: '06'
oa: 1
oa_version: Submitted Version
page: 965 - 976
pmid: 1
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3964'
quality_controlled: '1'
scopus_import: 1
status: public
title: Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin
transport in arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 162
year: '2013'
...
---
_id: '2836'
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 and the trusted third
party as path formulas in linear temporal logic and prove that the satisfaction
of these objectives imply fairness; a property required of fair exchange protocols.
We then show that weak (co-operative) co-synthesis and classical (strictly competitive)
co-synthesis fail, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate
the success of AGS as follows: (a) any solution of AGS is attack-free; no subset
of participants can violate the objectives of the other participants; (b) the
Asokan-Shoup-Waidner certified mail protocol that has known vulnerabilities is
not a solution of AGS; (c) the Kremer-Markowitch non-repudiation protocol is a
solution of AGS; and (d) AGS presents a new and symmetric fair non-repudiation
protocol that is attack-free. To our knowledge this is the first application of
synthesis to fair non-repudiation protocols, and our results show how synthesis
can both automatically discover vulnerabilities in protocols and generate correct
protocols. The solution to AGS can be computed efficiently as the secure equilibrium
solution of three-player graph games. '
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vishwanath
full_name: Raman, Vishwanath
last_name: Raman
citation:
ama: Chatterjee K, Raman V. Assume-guarantee synthesis for digital contract signing.
Formal Aspects of Computing. 2013;26(4):825-859. doi:10.1007/s00165-013-0283-6
apa: Chatterjee, K., & Raman, V. (2013). Assume-guarantee synthesis for digital
contract signing. Formal Aspects of Computing. Springer. https://doi.org/10.1007/s00165-013-0283-6
chicago: Chatterjee, Krishnendu, and Vishwanath Raman. “Assume-Guarantee Synthesis
for Digital Contract Signing.” Formal Aspects of Computing. Springer, 2013.
https://doi.org/10.1007/s00165-013-0283-6.
ieee: K. Chatterjee and V. Raman, “Assume-guarantee synthesis for digital contract
signing,” Formal Aspects of Computing, vol. 26, no. 4. Springer, pp. 825–859,
2013.
ista: Chatterjee K, Raman V. 2013. Assume-guarantee synthesis for digital contract
signing. Formal Aspects of Computing. 26(4), 825–859.
mla: Chatterjee, Krishnendu, and Vishwanath Raman. “Assume-Guarantee Synthesis for
Digital Contract Signing.” Formal Aspects of Computing, vol. 26, no. 4,
Springer, 2013, pp. 825–59, doi:10.1007/s00165-013-0283-6.
short: K. Chatterjee, V. Raman, Formal Aspects of Computing 26 (2013) 825–859.
date_created: 2018-12-11T11:59:51Z
date_published: 2013-07-04T00:00:00Z
date_updated: 2021-01-12T07:00:06Z
day: '04'
department:
- _id: KrCh
doi: 10.1007/s00165-013-0283-6
ec_funded: 1
external_id:
arxiv:
- '1004.2697'
intvolume: ' 26'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1004.2697
month: '07'
oa: 1
oa_version: Preprint
page: 825 - 859
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Formal Aspects of Computing
publication_status: published
publisher: Springer
publist_id: '3963'
quality_controlled: '1'
scopus_import: 1
status: public
title: Assume-guarantee synthesis for digital contract signing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2013'
...
---
_id: '2840'
abstract:
- lang: eng
text: It is known that the entorhinal cortex plays a crucial role in spatial cognition
in rodents. Neuroanatomical and electrophysiological data suggest that there is
a functional distinction between 2 subregions within the entorhinal cortex, the
medial entorhinal cortex (MEC), and the lateral entorhinal cortex (LEC). Rats
with MEC or LEC lesions were trained in 2 navigation tasks requiring allothetic
(water maze task) or idiothetic (path integration) information processing and
2-object exploration tasks allowing testing of spatial and nonspatial processing
of intramaze objects. MEC lesions mildly affected place navigation in the water
maze and produced a path integration deficit. They also altered the processing
of spatial information in both exploration tasks while sparing the processing
of nonspatial information. LEC lesions did not affect navigation abilities in
both the water maze and the path integration tasks. They altered spatial and nonspatial
processing in the object exploration task but not in the one-trial recognition
task. Overall, these results indicate that the MEC is important for spatial processing
and path integration. The LEC has some influence on both spatial and nonspatial
processes, suggesting that the 2 kinds of information interact at the level of
the EC.
author:
- first_name: Tiffany
full_name: Van Cauter, Tiffany
last_name: Van Cauter
- first_name: Jeremy
full_name: Camon, Jeremy
last_name: Camon
- first_name: Alice
full_name: Alvernhe, Alice
id: 467FB3D4-F248-11E8-B48F-1D18A9856A87
last_name: Alvernhe
- first_name: Coralie
full_name: Elduayen, Coralie
last_name: Elduayen
- first_name: Francesca
full_name: Sargolini, Francesca
last_name: Sargolini
- first_name: Étienne
full_name: Save, Étienne
last_name: Save
citation:
ama: Van Cauter T, Camon J, Alvernhe A, Elduayen C, Sargolini F, Save É. Distinct
roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral
Cortex. 2013;23(2):451-459. doi:10.1093/cercor/bhs033
apa: Van Cauter, T., Camon, J., Alvernhe, A., Elduayen, C., Sargolini, F., &
Save, É. (2013). Distinct roles of medial and lateral entorhinal cortex in spatial
cognition. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhs033
chicago: Van Cauter, Tiffany, Jeremy Camon, Alice Alvernhe, Coralie Elduayen, Francesca
Sargolini, and Étienne Save. “Distinct Roles of Medial and Lateral Entorhinal
Cortex in Spatial Cognition.” Cerebral Cortex. Oxford University Press,
2013. https://doi.org/10.1093/cercor/bhs033.
ieee: T. Van Cauter, J. Camon, A. Alvernhe, C. Elduayen, F. Sargolini, and É. Save,
“Distinct roles of medial and lateral entorhinal cortex in spatial cognition,”
Cerebral Cortex, vol. 23, no. 2. Oxford University Press, pp. 451–459,
2013.
ista: Van Cauter T, Camon J, Alvernhe A, Elduayen C, Sargolini F, Save É. 2013.
Distinct roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral
Cortex. 23(2), 451–459.
mla: Van Cauter, Tiffany, et al. “Distinct Roles of Medial and Lateral Entorhinal
Cortex in Spatial Cognition.” Cerebral Cortex, vol. 23, no. 2, Oxford University
Press, 2013, pp. 451–59, doi:10.1093/cercor/bhs033.
short: T. Van Cauter, J. Camon, A. Alvernhe, C. Elduayen, F. Sargolini, É. Save,
Cerebral Cortex 23 (2013) 451–459.
date_created: 2018-12-11T11:59:52Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T07:00:08Z
day: '01'
department:
- _id: JoCs
doi: 10.1093/cercor/bhs033
intvolume: ' 23'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 451 - 459
publication: Cerebral Cortex
publication_status: published
publisher: Oxford University Press
publist_id: '3958'
quality_controlled: '1'
scopus_import: 1
status: public
title: Distinct roles of medial and lateral entorhinal cortex in spatial cognition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2013'
...
---
_id: '2841'
abstract:
- lang: eng
text: In zebrafish early development, blastoderm cells undergo extensive radial
intercalations, triggering the spreading of the blastoderm over the yolk cell
and thereby initiating embryonic body axis formation. Now reporting in Developmental
Cell, Song et al. (2013) demonstrate a critical function for EGF-dependent E-cadherin
endocytosis in promoting blastoderm cell intercalations.
author:
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- 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: 'Morita H, Heisenberg C-PJ. Holding on and letting go: Cadherin turnover in
cell intercalation. Developmental Cell. 2013;24(6):567-569. doi:10.1016/j.devcel.2013.03.007'
apa: 'Morita, H., & Heisenberg, C.-P. J. (2013). Holding on and letting go:
Cadherin turnover in cell intercalation. Developmental Cell. Cell Press.
https://doi.org/10.1016/j.devcel.2013.03.007'
chicago: 'Morita, Hitoshi, and Carl-Philipp J Heisenberg. “Holding on and Letting
Go: Cadherin Turnover in Cell Intercalation.” Developmental Cell. Cell
Press, 2013. https://doi.org/10.1016/j.devcel.2013.03.007.'
ieee: 'H. Morita and C.-P. J. Heisenberg, “Holding on and letting go: Cadherin turnover
in cell intercalation,” Developmental Cell, vol. 24, no. 6. Cell Press,
pp. 567–569, 2013.'
ista: 'Morita H, Heisenberg C-PJ. 2013. Holding on and letting go: Cadherin turnover
in cell intercalation. Developmental Cell. 24(6), 567–569.'
mla: 'Morita, Hitoshi, and Carl-Philipp J. Heisenberg. “Holding on and Letting Go:
Cadherin Turnover in Cell Intercalation.” Developmental Cell, vol. 24,
no. 6, Cell Press, 2013, pp. 567–69, doi:10.1016/j.devcel.2013.03.007.'
short: H. Morita, C.-P.J. Heisenberg, Developmental Cell 24 (2013) 567–569.
date_created: 2018-12-11T11:59:52Z
date_published: 2013-05-25T00:00:00Z
date_updated: 2021-01-12T07:00:09Z
day: '25'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2013.03.007
intvolume: ' 24'
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 567 - 569
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3956'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Holding on and letting go: Cadherin turnover in cell intercalation'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2013'
...
---
_id: '2846'
abstract:
- lang: eng
text: The Red Queen hypothesis proposes that coevolving parasites select for outcrossing
in the host. Outcrossing relies on males, which often show lower immune investment
due to, for example, sexual selection. Here, we demonstrate that such sex differences
in immunity interfere with parasite-mediated selection for outcrossing. Two independent
coevolution experiments with Caenorhabditis elegans and its microparasite Bacillus
thuringiensis produced decreased yet stable frequencies of outcrossing male hosts.
A subsequent systematic analysis verified that male C. elegans suffered from a
direct selective disadvantage under parasite pressure (i.e. lower resistance,
decreased sexual activity, increased escape behaviour), which can reduce outcrossing
and thus male frequencies. At the same time, males offered an indirect selective
benefit, because male-mediated outcrossing increased offspring resistance, thus
favouring male persistence in the evolving populations. As sex differences in
immunity are widespread, such interference of opposing selective constraints is
likely of central importance during host adaptation to a coevolving parasite.
article_processing_charge: No
author:
- first_name: Leila
full_name: El Masri, Leila
id: 349A6E66-F248-11E8-B48F-1D18A9856A87
last_name: El Masri
- first_name: Rebecca
full_name: Schulte, Rebecca
last_name: Schulte
- first_name: Nadine
full_name: Timmermeyer, Nadine
last_name: Timmermeyer
- first_name: Stefanie
full_name: Thanisch, Stefanie
last_name: Thanisch
- first_name: Lena
full_name: Crummenerl, Lena
last_name: Crummenerl
- first_name: Gunther
full_name: Jansen, Gunther
last_name: Jansen
- first_name: Nico
full_name: Michiels, Nico
last_name: Michiels
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
citation:
ama: El Masri L, Schulte R, Timmermeyer N, et al. Sex differences in host defence
interfere with parasite-mediated selection for outcrossing during host-parasite
coevolution. Ecology Letters. 2013;16(4):461-468. doi:10.1111/ele.12068
apa: El Masri, L., Schulte, R., Timmermeyer, N., Thanisch, S., Crummenerl, L., Jansen,
G., … Schulenburg, H. (2013). Sex differences in host defence interfere with parasite-mediated
selection for outcrossing during host-parasite coevolution. Ecology Letters.
Wiley-Blackwell. https://doi.org/10.1111/ele.12068
chicago: El Masri, Leila, Rebecca Schulte, Nadine Timmermeyer, Stefanie Thanisch,
Lena Crummenerl, Gunther Jansen, Nico Michiels, and Hinrich Schulenburg. “Sex
Differences in Host Defence Interfere with Parasite-Mediated Selection for Outcrossing
during Host-Parasite Coevolution.” Ecology Letters. Wiley-Blackwell, 2013.
https://doi.org/10.1111/ele.12068.
ieee: L. El Masri et al., “Sex differences in host defence interfere with
parasite-mediated selection for outcrossing during host-parasite coevolution,”
Ecology Letters, vol. 16, no. 4. Wiley-Blackwell, pp. 461–468, 2013.
ista: El Masri L, Schulte R, Timmermeyer N, Thanisch S, Crummenerl L, Jansen G,
Michiels N, Schulenburg H. 2013. Sex differences in host defence interfere with
parasite-mediated selection for outcrossing during host-parasite coevolution.
Ecology Letters. 16(4), 461–468.
mla: El Masri, Leila, et al. “Sex Differences in Host Defence Interfere with Parasite-Mediated
Selection for Outcrossing during Host-Parasite Coevolution.” Ecology Letters,
vol. 16, no. 4, Wiley-Blackwell, 2013, pp. 461–68, doi:10.1111/ele.12068.
short: L. El Masri, R. Schulte, N. Timmermeyer, S. Thanisch, L. Crummenerl, G. Jansen,
N. Michiels, H. Schulenburg, Ecology Letters 16 (2013) 461–468.
date_created: 2018-12-11T11:59:54Z
date_published: 2013-04-04T00:00:00Z
date_updated: 2022-08-25T14:51:57Z
day: '04'
ddc:
- '570'
doi: 10.1111/ele.12068
extern: '1'
file:
- access_level: open_access
checksum: aa7db788f7da7d7f102539a249ebce50
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:52Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5176'
file_name: IST-2016-404-v1+1_ele12068.pdf
file_size: 763731
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 16'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 461 - 468
publication: Ecology Letters
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3948'
pubrep_id: '404'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sex differences in host defence interfere with parasite-mediated selection
for outcrossing during host-parasite coevolution
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: 16
year: '2013'
...
---
_id: '2844'
abstract:
- lang: eng
text: As soon as a seed germinates, plant growth relates to gravity to ensure that
the root penetrates the soil and the shoot expands aerially. Whereas mechanisms
of positive and negative orthogravitropism of primary roots and shoots are relatively
well understood [1-3], lateral organs often show more complex growth behavior
[4]. Lateral roots (LRs) seemingly suppress positive gravitropic growth and show
a defined gravitropic set-point angle (GSA) that allows radial expansion of the
root system (plagiotropism) [3, 4]. Despite its eminent importance for root architecture,
it so far remains completely unknown how lateral organs partially suppress positive
orthogravitropism. Here we show that the phytohormone auxin steers GSA formation
and limits positive orthogravitropism in LR. Low and high auxin levels/signaling
lead to radial or axial root systems, respectively. At a cellular level, it is
the auxin transport-dependent regulation of asymmetric growth in the elongation
zone that determines GSA. Our data suggest that strong repression of PIN4/PIN7
and transient PIN3 expression limit auxin redistribution in young LR columella
cells. We conclude that PIN activity, by temporally limiting the asymmetric auxin
fluxes in the tip of LRs, induces transient, differential growth responses in
the elongation zone and, consequently, controls root architecture.
author:
- first_name: Michel
full_name: Rosquete, Michel
last_name: Rosquete
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Elke
full_name: Barbez, Elke
last_name: Barbez
- first_name: Ernst
full_name: Stelzer, Ernst
last_name: Stelzer
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Alexis
full_name: Maizel, Alexis
last_name: Maizel
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
citation:
ama: Rosquete M, von Wangenheim D, Marhavý P, et al. An auxin transport mechanism
restricts positive orthogravitropism in lateral roots. Current Biology.
2013;23(9):817-822. doi:10.1016/j.cub.2013.03.064
apa: Rosquete, M., von Wangenheim, D., Marhavý, P., Barbez, E., Stelzer, E., Benková,
E., … Kleine Vehn, J. (2013). An auxin transport mechanism restricts positive
orthogravitropism in lateral roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.03.064
chicago: Rosquete, Michel, Daniel von Wangenheim, Peter Marhavý, Elke Barbez, Ernst
Stelzer, Eva Benková, Alexis Maizel, and Jürgen Kleine Vehn. “An Auxin Transport
Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” Current Biology.
Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.03.064.
ieee: M. Rosquete et al., “An auxin transport mechanism restricts positive
orthogravitropism in lateral roots,” Current Biology, vol. 23, no. 9. Cell
Press, pp. 817–822, 2013.
ista: Rosquete M, von Wangenheim D, Marhavý P, Barbez E, Stelzer E, Benková E, Maizel
A, Kleine Vehn J. 2013. An auxin transport mechanism restricts positive orthogravitropism
in lateral roots. Current Biology. 23(9), 817–822.
mla: Rosquete, Michel, et al. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism
in Lateral Roots.” Current Biology, vol. 23, no. 9, Cell Press, 2013, pp.
817–22, doi:10.1016/j.cub.2013.03.064.
short: M. Rosquete, D. von Wangenheim, P. Marhavý, E. Barbez, E. Stelzer, E. Benková,
A. Maizel, J. Kleine Vehn, Current Biology 23 (2013) 817–822.
date_created: 2018-12-11T11:59:53Z
date_published: 2013-05-06T00:00:00Z
date_updated: 2021-01-12T07:00:10Z
day: '06'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1016/j.cub.2013.03.064
ec_funded: 1
intvolume: ' 23'
issue: '9'
language:
- iso: eng
month: '05'
oa_version: None
page: 817 - 822
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3950'
quality_controlled: '1'
scopus_import: 1
status: public
title: An auxin transport mechanism restricts positive orthogravitropism in lateral
roots
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2013'
...
---
_id: '2843'
abstract:
- lang: eng
text: 'Mathematical objects can be measured unambiguously, but not so objects from
our physical world. Even the total length of tubelike shapes has its difficulties.
We introduce a combination of geometric, probabilistic, and topological methods
to design a stable length estimate for tube-like shapes; that is: one that is
insensitive to small shape changes.'
alternative_title:
- LNCS
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: 'Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes.
In: 17th IAPR International Conference on Discrete Geometry for Computer Imagery.
Vol 7749. Springer; 2013:XV-XIX. doi:10.1007/978-3-642-37067-0'
apa: 'Edelsbrunner, H., & Pausinger, F. (2013). Stable length estimates of tube-like
shapes. In 17th IAPR International Conference on Discrete Geometry for Computer
Imagery (Vol. 7749, pp. XV–XIX). Seville, Spain: Springer. https://doi.org/10.1007/978-3-642-37067-0'
chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates
of Tube-like Shapes.” In 17th IAPR International Conference on Discrete Geometry
for Computer Imagery, 7749:XV–XIX. Springer, 2013. https://doi.org/10.1007/978-3-642-37067-0.
ieee: H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,”
in 17th IAPR International Conference on Discrete Geometry for Computer Imagery,
Seville, Spain, 2013, vol. 7749, pp. XV–XIX.
ista: 'Edelsbrunner H, Pausinger F. 2013. Stable length estimates of tube-like shapes.
17th IAPR International Conference on Discrete Geometry for Computer Imagery.
DGCI: Discrete Geometry for Computer Imagery, LNCS, vol. 7749, XV–XIX.'
mla: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like
Shapes.” 17th IAPR International Conference on Discrete Geometry for Computer
Imagery, vol. 7749, Springer, 2013, pp. XV–XIX, doi:10.1007/978-3-642-37067-0.
short: H. Edelsbrunner, F. Pausinger, in:, 17th IAPR International Conference on
Discrete Geometry for Computer Imagery, Springer, 2013, pp. XV–XIX.
conference:
end_date: 2013-03-22
location: Seville, Spain
name: 'DGCI: Discrete Geometry for Computer Imagery'
start_date: 2013-03-20
date_created: 2018-12-11T11:59:53Z
date_published: 2013-02-21T00:00:00Z
date_updated: 2023-02-23T10:35:00Z
day: '21'
department:
- _id: HeEd
doi: 10.1007/978-3-642-37067-0
intvolume: ' 7749'
language:
- iso: eng
month: '02'
oa_version: None
page: XV - XIX
publication: 17th IAPR International Conference on Discrete Geometry for Computer
Imagery
publication_status: published
publisher: Springer
publist_id: '3952'
quality_controlled: '1'
related_material:
record:
- id: '2255'
relation: later_version
status: public
scopus_import: 1
status: public
title: Stable length estimates of tube-like shapes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7749
year: '2013'
...
---
_id: '2845'
abstract:
- lang: eng
text: At synapses formed between dissociated neurons, about half of all synaptic
vesicles are refractory to evoked release, forming the so-called "resting
pool." Here, we use optical measurements of vesicular pH to study developmental
changes in pool partitioning and vesicle cycling in cultured hippocampal slices.
Two-photon imaging of a genetically encoded two-color release sensor (ratio-sypHy)
allowed us to perform calibrated measurements at individual Schaffer collateral
boutons. Mature boutons released a large fraction of their vesicles during simulated
place field activity, and vesicle retrieval rates were 7-fold higher compared
to immature boutons. Saturating stimulation mobilized essentially all vesicles
at mature synapses. Resting pool formation and a concomitant reduction in evoked
release was induced by chronic depolarization but not by acute inhibition of the
protein phosphatase calcineurin. We conclude that synapses in CA1 undergo a prominent
refinement of vesicle use during early postnatal development that is not recapitulated
in dissociated neuronal culture.
author:
- first_name: Tobias
full_name: Rose, Tobias
last_name: Rose
- first_name: Philipp
full_name: Schönenberger, Philipp
id: 3B9D816C-F248-11E8-B48F-1D18A9856A87
last_name: Schönenberger
- first_name: Karel
full_name: Jezek, Karel
last_name: Jezek
- first_name: Thomas
full_name: Oertner, Thomas
last_name: Oertner
citation:
ama: Rose T, Schönenberger P, Jezek K, Oertner T. Developmental refinement of vesicle
cycling at Schaffer collateral synapses. Neuron. 2013;77(6):1109-1121.
doi:10.1016/j.neuron.2013.01.021
apa: Rose, T., Schönenberger, P., Jezek, K., & Oertner, T. (2013). Developmental
refinement of vesicle cycling at Schaffer collateral synapses. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2013.01.021
chicago: Rose, Tobias, Philipp Schönenberger, Karel Jezek, and Thomas Oertner. “Developmental
Refinement of Vesicle Cycling at Schaffer Collateral Synapses.” Neuron.
Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.01.021.
ieee: T. Rose, P. Schönenberger, K. Jezek, and T. Oertner, “Developmental refinement
of vesicle cycling at Schaffer collateral synapses,” Neuron, vol. 77, no.
6. Elsevier, pp. 1109–1121, 2013.
ista: Rose T, Schönenberger P, Jezek K, Oertner T. 2013. Developmental refinement
of vesicle cycling at Schaffer collateral synapses. Neuron. 77(6), 1109–1121.
mla: Rose, Tobias, et al. “Developmental Refinement of Vesicle Cycling at Schaffer
Collateral Synapses.” Neuron, vol. 77, no. 6, Elsevier, 2013, pp. 1109–21,
doi:10.1016/j.neuron.2013.01.021.
short: T. Rose, P. Schönenberger, K. Jezek, T. Oertner, Neuron 77 (2013) 1109–1121.
date_created: 2018-12-11T11:59:54Z
date_published: 2013-03-20T00:00:00Z
date_updated: 2021-01-12T07:00:11Z
day: '20'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2013.01.021
intvolume: ' 77'
issue: '6'
language:
- iso: eng
month: '03'
oa_version: None
page: 1109 - 1121
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '3949'
quality_controlled: '1'
scopus_import: 1
status: public
title: Developmental refinement of vesicle cycling at Schaffer collateral synapses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2013'
...
---
_id: '2854'
abstract:
- lang: eng
text: We consider concurrent games played on graphs. At every round of a game, each
player simultaneously and independently selects a move; the moves jointly determine
the transition to a successor state. Two basic objectives are the safety objective
to stay forever in a given set of states, and its dual, the reachability objective
to reach a given set of states. First, we present a simple proof of the fact that
in concurrent reachability games, for all ε>0, memoryless ε-optimal strategies
exist. A memoryless strategy is independent of the history of plays, and an ε-optimal
strategy achieves the objective with probability within ε of the value of the
game. In contrast to previous proofs of this fact, our proof is more elementary
and more combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration)
algorithm for concurrent games with reachability objectives. Finally, we present
a strategy-improvement algorithm for turn-based stochastic games (where each player
selects moves in turns) with safety objectives. Our algorithms yield sequences
of player-1 strategies which ensure probabilities of winning that converge monotonically
(from below) to the value of the game. © 2012 Elsevier Inc.
acknowledgement: This work was partially supported in part by the NSF grants CCR-0132780,
CNS-0720884, CCR-0225610, by the Swiss National Science Foundation, ERC Start Grant
Graph Games (Project No. 279307), FWF NFN Grant S11407-N23 (RiSE), and a Microsoft
faculty fellows
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: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- 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, De Alfaro L, Henzinger TA. Strategy improvement for concurrent
reachability and turn based stochastic safety games. Journal of Computer and
System Sciences. 2013;79(5):640-657. doi:10.1016/j.jcss.2012.12.001
apa: Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2013). Strategy improvement
for concurrent reachability and turn based stochastic safety games. Journal
of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2012.12.001
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy
Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.”
Journal of Computer and System Sciences. Elsevier, 2013. https://doi.org/10.1016/j.jcss.2012.12.001.
ieee: K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for
concurrent reachability and turn based stochastic safety games,” Journal of
Computer and System Sciences, vol. 79, no. 5. Elsevier, pp. 640–657, 2013.
ista: Chatterjee K, De Alfaro L, Henzinger TA. 2013. Strategy improvement for concurrent
reachability and turn based stochastic safety games. Journal of Computer and System
Sciences. 79(5), 640–657.
mla: Chatterjee, Krishnendu, et al. “Strategy Improvement for Concurrent Reachability
and Turn Based Stochastic Safety Games.” Journal of Computer and System Sciences,
vol. 79, no. 5, Elsevier, 2013, pp. 640–57, doi:10.1016/j.jcss.2012.12.001.
short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, Journal of Computer and System
Sciences 79 (2013) 640–657.
date_created: 2018-12-11T11:59:57Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T07:00:16Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.jcss.2012.12.001
ec_funded: 1
file:
- access_level: open_access
checksum: 6d3ee12cceb946a0abe69594b6a22409
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:48Z
date_updated: 2020-07-14T12:45:51Z
file_id: '5370'
file_name: IST-2015-388-v1+1_1-s2.0-S0022000012001778-main.pdf
file_size: 425488
relation: main_file
file_date_updated: 2020-07-14T12:45:51Z
has_accepted_license: '1'
intvolume: ' 79'
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: 640 - 657
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Elsevier
publist_id: '3938'
pubrep_id: '388'
quality_controlled: '1'
scopus_import: 1
status: public
title: Strategy improvement for concurrent reachability and turn based stochastic
safety 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: 79
year: '2013'
...
---
_id: '2850'
abstract:
- lang: eng
text: "Recent work emphasizes that the maximum entropy principle provides a bridge
between statistical mechanics models for collective behavior in neural networks
and experiments on networks of real neurons. Most of this work has focused on
capturing the measured correlations among pairs of neurons. Here we suggest an
alternative, constructing models that are consistent with the distribution of
global network activity, i.e. the probability that K out of N cells in the network
generate action potentials in the same small time bin. The inverse problem that
we need to solve in constructing the model is analytically tractable, and provides
a natural 'thermodynamics' for the network in the limit of large N. We analyze
the responses of neurons in a small patch of the retina to naturalistic stimuli,
and find that the implied thermodynamics is very close to an unusual critical
point, in which the entropy (in proper units) is exactly equal to the energy.
© 2013 IOP Publishing Ltd and SISSA Medialab srl.\r\n"
acknowledgement: "his work was supported in part by NSF Grants IIS-0613435 and PHY-0957573,
by NIH Grants R01 EY14196 and P50 GM071508, by the Fannie and John Hertz Foundation,
by the Human Frontiers Science Program, by the Swartz Foundation, and by the WM
Keck Foundation.\r\n"
article_number: P03011
article_processing_charge: No
article_type: original
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
- first_name: Dario
full_name: Amodei, Dario
last_name: Amodei
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. The simplest maximum
entropy model for collective behavior in a neural network. Journal of Statistical
Mechanics Theory and Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03011
apa: Tkačik, G., Marre, O., Mora, T., Amodei, D., Berry, M., & Bialek, W. (2013).
The simplest maximum entropy model for collective behavior in a neural network.
Journal of Statistical Mechanics Theory and Experiment. IOP Publishing
Ltd. https://doi.org/10.1088/1742-5468/2013/03/P03011
chicago: Tkačik, Gašper, Olivier Marre, Thierry Mora, Dario Amodei, Michael Berry,
and William Bialek. “The Simplest Maximum Entropy Model for Collective Behavior
in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/03/P03011.
ieee: G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, and W. Bialek, “The simplest
maximum entropy model for collective behavior in a neural network,” Journal
of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3. IOP Publishing
Ltd., 2013.
ista: Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. 2013. The simplest
maximum entropy model for collective behavior in a neural network. Journal of
Statistical Mechanics Theory and Experiment. 2013(3), P03011.
mla: Tkačik, Gašper, et al. “The Simplest Maximum Entropy Model for Collective Behavior
in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment,
vol. 2013, no. 3, P03011, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03011.
short: G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of
Statistical Mechanics Theory and Experiment 2013 (2013).
date_created: 2018-12-11T11:59:55Z
date_published: 2013-03-12T00:00:00Z
date_updated: 2021-01-12T07:00:14Z
day: '12'
department:
- _id: GaTk
doi: 10.1088/1742-5468/2013/03/P03011
external_id:
arxiv:
- '1207.6319'
intvolume: ' 2013'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.6319
month: '03'
oa: 1
oa_version: Preprint
publication: Journal of Statistical Mechanics Theory and Experiment
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '3942'
quality_controlled: '1'
scopus_import: 1
status: public
title: The simplest maximum entropy model for collective behavior in a neural network
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2013
year: '2013'
...
---
_id: '2851'
abstract:
- lang: eng
text: The number of possible activity patterns in a population of neurons grows
exponentially with the size of the population. Typical experiments explore only
a tiny fraction of the large space of possible activity patterns in the case of
populations with more than 10 or 20 neurons. It is thus impossible, in this undersampled
regime, to estimate the probabilities with which most of the activity patterns
occur. As a result, the corresponding entropy - which is a measure of the computational
power of the neural population - cannot be estimated directly. We propose a simple
scheme for estimating the entropy in the undersampled regime, which bounds its
value from both below and above. The lower bound is the usual 'naive' entropy
of the experimental frequencies. The upper bound results from a hybrid approximation
of the entropy which makes use of the naive estimate, a maximum entropy fit, and
a coverage adjustment. We apply our simple scheme to artificial data, in order
to check their accuracy; we also compare its performance to those of several previously
defined entropy estimators. We then apply it to actual measurements of neural
activity in populations with up to 100 cells. Finally, we discuss the similarities
and differences between the proposed simple estimation scheme and various earlier
methods. © 2013 IOP Publishing Ltd and SISSA Medialab srl.
article_number: P03015
author:
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Julien
full_name: Dubuis, Julien
last_name: Dubuis
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Ravá
full_name: Da Silveira, Ravá
last_name: Da Silveira
citation:
ama: Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. A simple method for estimating
the entropy of neural activity. Journal of Statistical Mechanics Theory and
Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03015
apa: Berry, M., Tkačik, G., Dubuis, J., Marre, O., & Da Silveira, R. (2013).
A simple method for estimating the entropy of neural activity. Journal of Statistical
Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/03/P03015
chicago: Berry, Michael, Gašper Tkačik, Julien Dubuis, Olivier Marre, and Ravá Da
Silveira. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal
of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013.
https://doi.org/10.1088/1742-5468/2013/03/P03015.
ieee: M. Berry, G. Tkačik, J. Dubuis, O. Marre, and R. Da Silveira, “A simple method
for estimating the entropy of neural activity,” Journal of Statistical Mechanics
Theory and Experiment, vol. 2013, no. 3. IOP Publishing Ltd., 2013.
ista: Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. 2013. A simple method
for estimating the entropy of neural activity. Journal of Statistical Mechanics
Theory and Experiment. 2013(3), P03015.
mla: Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural
Activity.” Journal of Statistical Mechanics Theory and Experiment, vol.
2013, no. 3, P03015, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03015.
short: M. Berry, G. Tkačik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical
Mechanics Theory and Experiment 2013 (2013).
date_created: 2018-12-11T11:59:56Z
date_published: 2013-03-12T00:00:00Z
date_updated: 2021-01-12T07:00:14Z
day: '12'
department:
- _id: GaTk
doi: 10.1088/1742-5468/2013/03/P03015
intvolume: ' 2013'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: Journal of Statistical Mechanics Theory and Experiment
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '3941'
quality_controlled: '1'
scopus_import: 1
status: public
title: A simple method for estimating the entropy of neural activity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2013
year: '2013'
...
---
_id: '2857'
abstract:
- lang: eng
text: In the vibrant field of optogenetics, optics and genetic targeting are combined
to commandeer cellular functions, such as the neuronal action potential, by optically
stimulating light-sensitive ion channels expressed in the cell membrane. One broadly
applicable manifestation of this approach are covalently attached photochromic
tethered ligands (PTLs) that allow activating ligand-gated ion channels with outstanding
spatial and temporal resolution. Here, we describe all steps towards the successful
development and application of PTL-gated ion channels in cell lines and primary
cells. The basis for these experiments forms a combination of molecular modeling,
genetic engineering, cell culture, and electrophysiology. The light-gated glutamate
receptor (LiGluR), which consists of the PTL-functionalized GluK2 receptor, serves
as a model.
alternative_title:
- MIMB
author:
- first_name: Stephanie
full_name: Szobota, Stephanie
last_name: Szobota
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Szobota S, Mckenzie C, Janovjak HL. Optical control of ligand-gated ion channels.
Methods in Molecular Biology. 2013;998:417-435. doi:10.1007/978-1-62703-351-0_32
apa: Szobota, S., Mckenzie, C., & Janovjak, H. L. (2013). Optical control of
ligand-gated ion channels. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-62703-351-0_32
chicago: Szobota, Stephanie, Catherine Mckenzie, and Harald L Janovjak. “Optical
Control of Ligand-Gated Ion Channels.” Methods in Molecular Biology. Springer,
2013. https://doi.org/10.1007/978-1-62703-351-0_32.
ieee: S. Szobota, C. Mckenzie, and H. L. Janovjak, “Optical control of ligand-gated
ion channels,” Methods in Molecular Biology, vol. 998. Springer, pp. 417–435,
2013.
ista: Szobota S, Mckenzie C, Janovjak HL. 2013. Optical control of ligand-gated
ion channels. Methods in Molecular Biology. 998, 417–435.
mla: Szobota, Stephanie, et al. “Optical Control of Ligand-Gated Ion Channels.”
Methods in Molecular Biology, vol. 998, Springer, 2013, pp. 417–35, doi:10.1007/978-1-62703-351-0_32.
short: S. Szobota, C. Mckenzie, H.L. Janovjak, Methods in Molecular Biology 998
(2013) 417–435.
date_created: 2018-12-11T11:59:57Z
date_published: 2013-02-22T00:00:00Z
date_updated: 2021-01-12T07:00:17Z
day: '22'
ddc:
- '570'
department:
- _id: HaJa
doi: 10.1007/978-1-62703-351-0_32
ec_funded: 1
file:
- access_level: open_access
checksum: 1701f0d989f27ddac471b19a894ec0d1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:34Z
date_updated: 2020-07-14T12:45:51Z
file_id: '4952'
file_name: IST-2017-834-v1+1_szobota.pdf
file_size: 336734
relation: main_file
file_date_updated: 2020-07-14T12:45:51Z
has_accepted_license: '1'
intvolume: ' 998'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Submitted Version
page: 417 - 435
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
publication: Methods in Molecular Biology
publication_status: published
publisher: Springer
publist_id: '3932'
pubrep_id: '834'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optical control of ligand-gated ion channels
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 998
year: '2013'
...
---
_id: '2860'
abstract:
- lang: eng
text: 'In the hippocampus, cell assemblies forming mnemonic representations of space
are thought to arise as a result of changes in functional connections of pyramidal
cells. We have found that CA1 interneuron circuits are also reconfigured during
goal-oriented spatial learning through modification of inputs from pyramidal cells.
As learning progressed, new pyramidal assemblies expressed in theta cycles alternated
with previously established ones, and eventually overtook them. The firing patterns
of interneurons developed a relationship to new, learning-related assemblies:
some interneurons associated their activity with new pyramidal assemblies while
some others dissociated from them. These firing associations were explained by
changes in the weight of monosynaptic inputs received by interneurons from new
pyramidal assemblies, as these predicted the associational changes. Spatial learning
thus engages circuit modifications in the hippocampus that incorporate a redistribution
of inhibitory activity that might assist in the segregation of competing pyramidal
cell assembly patterns in space and time.'
acknowledgement: D.D. and J.C. were supported by a MRC Intramural Programme Grant
U138197111
author:
- first_name: David
full_name: Dupret, David
last_name: Dupret
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- 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: Dupret D, O’Neill J, Csicsvari JL. Dynamic reconfiguration of hippocampal interneuron
circuits during spatial learning. Neuron. 2013;78(1):166-180. doi:10.1016/j.neuron.2013.01.033
apa: Dupret, D., O’Neill, J., & Csicsvari, J. L. (2013). Dynamic reconfiguration
of hippocampal interneuron circuits during spatial learning. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2013.01.033
chicago: Dupret, David, Joseph O’Neill, and Jozsef L Csicsvari. “Dynamic Reconfiguration
of Hippocampal Interneuron Circuits during Spatial Learning.” Neuron. Elsevier,
2013. https://doi.org/10.1016/j.neuron.2013.01.033.
ieee: D. Dupret, J. O’Neill, and J. L. Csicsvari, “Dynamic reconfiguration of hippocampal
interneuron circuits during spatial learning,” Neuron, vol. 78, no. 1.
Elsevier, pp. 166–180, 2013.
ista: Dupret D, O’Neill J, Csicsvari JL. 2013. Dynamic reconfiguration of hippocampal
interneuron circuits during spatial learning. Neuron. 78(1), 166–180.
mla: Dupret, David, et al. “Dynamic Reconfiguration of Hippocampal Interneuron Circuits
during Spatial Learning.” Neuron, vol. 78, no. 1, Elsevier, 2013, pp. 166–80,
doi:10.1016/j.neuron.2013.01.033.
short: D. Dupret, J. O’Neill, J.L. Csicsvari, Neuron 78 (2013) 166–180.
date_created: 2018-12-11T11:59:59Z
date_published: 2013-03-21T00:00:00Z
date_updated: 2021-01-12T07:00:19Z
day: '21'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2013.01.033
ec_funded: 1
file:
- access_level: open_access
checksum: 0e18cb8561153ddb50bb5af16e7c9e97
content_type: application/pdf
creator: dernst
date_created: 2019-01-23T08:08:07Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5877'
file_name: 2013_Neuron_Dupret.pdf
file_size: 2637837
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 78'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 166 - 180
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: Neuron
publication_status: published
publisher: Elsevier
publist_id: '3929'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dynamic reconfiguration of hippocampal interneuron circuits during spatial
learning
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: 78
year: '2013'
...
---
_id: '2855'
abstract:
- lang: eng
text: Genomic imprinting leads to preferred expression of either the maternal or
paternal alleles of a subset of genes. Imprinting is essential for mammalian development,
and its deregulation causes many diseases. However, the functional relevance of
imprinting at the cellular level is poorly understood for most imprinted genes.
We used mosaic analysis with double markers (MADM) in mice to create uniparental
disomies (UPDs) and to visualize imprinting effects with single-cell resolution.
Although chromosome 12 UPD did not produce detectable phenotypes, chromosome 7
UPD caused highly significant paternal growth dominance in the liver and lung,
but not in the brain or heart. A single gene on chromosome 7, encoding the secreted
insulin-like growth factor 2 (IGF2), accounts for most of the paternal dominance
effect. Mosaic analyses implied additional imprinted loci on chromosome 7 acting
cell autonomously to transmit the IGF2 signal. Our study reveals chromosome- and
cell-type specificity of genomic imprinting effects.
author:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Randy
full_name: Johnson, Randy
last_name: Johnson
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: Hippenmeyer S, Johnson R, Luo L. Mosaic analysis with double markers reveals
cell type specific paternal growth dominance. Cell Reports. 2013;3(3):960-967.
doi:10.1016/j.celrep.2013.02.002
apa: Hippenmeyer, S., Johnson, R., & Luo, L. (2013). Mosaic analysis with double
markers reveals cell type specific paternal growth dominance. Cell Reports.
Cell Press. https://doi.org/10.1016/j.celrep.2013.02.002
chicago: Hippenmeyer, Simon, Randy Johnson, and Liqun Luo. “Mosaic Analysis with
Double Markers Reveals Cell Type Specific Paternal Growth Dominance.” Cell
Reports. Cell Press, 2013. https://doi.org/10.1016/j.celrep.2013.02.002.
ieee: S. Hippenmeyer, R. Johnson, and L. Luo, “Mosaic analysis with double markers
reveals cell type specific paternal growth dominance,” Cell Reports, vol.
3, no. 3. Cell Press, pp. 960–967, 2013.
ista: Hippenmeyer S, Johnson R, Luo L. 2013. Mosaic analysis with double markers
reveals cell type specific paternal growth dominance. Cell Reports. 3(3), 960–967.
mla: Hippenmeyer, Simon, et al. “Mosaic Analysis with Double Markers Reveals Cell
Type Specific Paternal Growth Dominance.” Cell Reports, vol. 3, no. 3,
Cell Press, 2013, pp. 960–67, doi:10.1016/j.celrep.2013.02.002.
short: S. Hippenmeyer, R. Johnson, L. Luo, Cell Reports 3 (2013) 960–967.
date_created: 2018-12-11T11:59:57Z
date_published: 2013-03-28T00:00:00Z
date_updated: 2021-01-12T07:00:16Z
day: '28'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.celrep.2013.02.002
file:
- access_level: open_access
checksum: 6e977b918e81384cd571ec5a9d812289
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:20Z
date_updated: 2020-07-14T12:45:51Z
file_id: '5274'
file_name: IST-2016-405-v1+1_1-s2.0-S2211124713000612-main.pdf
file_size: 1907211
relation: main_file
file_date_updated: 2020-07-14T12:45:51Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 960 - 967
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '3937'
pubrep_id: '405'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mosaic analysis with double markers reveals cell type specific paternal growth
dominance
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: 3
year: '2013'
...
---
_id: '2856'
abstract:
- lang: eng
text: 'G protein–coupled receptors (GPCRs), the largest family of membrane signaling
proteins, respond to neurotransmitters, hormones and small environmental molecules.
The neuronal function of many GPCRs has been difficult to resolve because of an
inability to gate them with subtype specificity, spatial precision, speed and
reversibility. To address this, we developed an approach for opto-chemical engineering
of native GPCRs. We applied this to the metabotropic glutamate receptors (mGluRs)
to generate light-agonized and light-antagonized mGluRs (LimGluRs). The light-agonized
LimGluR2, on which we focused, was fast, bistable and supported multiple rounds
of on/off switching. Light gated two of the primary neuronal functions of mGluR2:
suppression of excitability and inhibition of neurotransmitter release. We found
that the light-antagonized tool LimGluR2-block was able to manipulate negative
feedback of synaptically released glutamate on transmitter release. We generalized
the optical control to two additional family members: mGluR3 and mGluR6. This
system worked in rodent brain slices and in zebrafish in vivo, where we found
that mGluR2 modulated the threshold for escape behavior. These light-gated mGluRs
pave the way for determining the roles of mGluRs in synaptic plasticity, memory
and disease.'
acknowledgement: National Science Foundation grants CHE-0233882 and CHE-0840505 (to
the College of Chemistry at the University of California, Berkeley), a postdoctoral
fellowship of the European Molecular Biology Organization (H.J.)
author:
- first_name: Joshua
full_name: Levitz, Joshua
last_name: Levitz
- first_name: Carlos
full_name: Pantoja, Carlos
last_name: Pantoja
- first_name: Benjamin
full_name: Gaub, Benjamin
last_name: Gaub
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Andreas
full_name: Reiner, Andreas
last_name: Reiner
- first_name: Adam
full_name: Hoagland, Adam
last_name: Hoagland
- first_name: David
full_name: Schoppik, David
last_name: Schoppik
- first_name: Brian
full_name: Kane, Brian
last_name: Kane
- first_name: Philipp
full_name: Stawski, Philipp
last_name: Stawski
- first_name: Alexander
full_name: Schier, Alexander
last_name: Schier
- first_name: Dirk
full_name: Trauner, Dirk
last_name: Trauner
- first_name: Ehud
full_name: Isacoff, Ehud
last_name: Isacoff
citation:
ama: Levitz J, Pantoja C, Gaub B, et al. Optical control of metabotropic glutamate
receptors. Nature Neuroscience. 2013;16:507-516. doi:10.1038/nn.3346
apa: Levitz, J., Pantoja, C., Gaub, B., Janovjak, H. L., Reiner, A., Hoagland, A.,
… Isacoff, E. (2013). Optical control of metabotropic glutamate receptors. Nature
Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3346
chicago: Levitz, Joshua, Carlos Pantoja, Benjamin Gaub, Harald L Janovjak, Andreas
Reiner, Adam Hoagland, David Schoppik, et al. “Optical Control of Metabotropic
Glutamate Receptors.” Nature Neuroscience. Nature Publishing Group, 2013.
https://doi.org/10.1038/nn.3346.
ieee: J. Levitz et al., “Optical control of metabotropic glutamate receptors,”
Nature Neuroscience, vol. 16. Nature Publishing Group, pp. 507–516, 2013.
ista: Levitz J, Pantoja C, Gaub B, Janovjak HL, Reiner A, Hoagland A, Schoppik D,
Kane B, Stawski P, Schier A, Trauner D, Isacoff E. 2013. Optical control of metabotropic
glutamate receptors. Nature Neuroscience. 16, 507–516.
mla: Levitz, Joshua, et al. “Optical Control of Metabotropic Glutamate Receptors.”
Nature Neuroscience, vol. 16, Nature Publishing Group, 2013, pp. 507–16,
doi:10.1038/nn.3346.
short: J. Levitz, C. Pantoja, B. Gaub, H.L. Janovjak, A. Reiner, A. Hoagland, D.
Schoppik, B. Kane, P. Stawski, A. Schier, D. Trauner, E. Isacoff, Nature Neuroscience
16 (2013) 507–516.
date_created: 2018-12-11T11:59:57Z
date_published: 2013-03-03T00:00:00Z
date_updated: 2021-01-12T07:00:16Z
day: '03'
department:
- _id: HaJa
doi: 10.1038/nn.3346
external_id:
pmid:
- '23455609'
intvolume: ' 16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681425/
month: '03'
oa: 1
oa_version: Submitted Version
page: 507 - 516
pmid: 1
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '3936'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optical control of metabotropic glutamate receptors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2013'
...
---
_id: '2859'
abstract:
- lang: eng
text: Given a continuous function f:X-R on a topological space, we consider the
preimages of intervals and their homology groups and show how to read the ranks
of these groups from the extended persistence diagram of f. In addition, we quantify
the robustness of the homology classes under perturbations of f using well groups,
and we show how to read the ranks of these groups from the same extended persistence
diagram. The special case X=R3 has ramifications in the fields of medical imaging
and scientific visualization.
author:
- first_name: Paul
full_name: Bendich, Paul
id: 43F6EC54-F248-11E8-B48F-1D18A9856A87
last_name: Bendich
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: Bendich P, Edelsbrunner H, Morozov D, Patel A. Homology and robustness of level
and interlevel sets. Homology, Homotopy and Applications. 2013;15(1):51-72.
doi:10.4310/HHA.2013.v15.n1.a3
apa: Bendich, P., Edelsbrunner, H., Morozov, D., & Patel, A. (2013). Homology
and robustness of level and interlevel sets. Homology, Homotopy and Applications.
International Press. https://doi.org/10.4310/HHA.2013.v15.n1.a3
chicago: Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “Homology
and Robustness of Level and Interlevel Sets.” Homology, Homotopy and Applications.
International Press, 2013. https://doi.org/10.4310/HHA.2013.v15.n1.a3.
ieee: P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “Homology and robustness
of level and interlevel sets,” Homology, Homotopy and Applications, vol.
15, no. 1. International Press, pp. 51–72, 2013.
ista: Bendich P, Edelsbrunner H, Morozov D, Patel A. 2013. Homology and robustness
of level and interlevel sets. Homology, Homotopy and Applications. 15(1), 51–72.
mla: Bendich, Paul, et al. “Homology and Robustness of Level and Interlevel Sets.”
Homology, Homotopy and Applications, vol. 15, no. 1, International Press,
2013, pp. 51–72, doi:10.4310/HHA.2013.v15.n1.a3.
short: P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, Homology, Homotopy and
Applications 15 (2013) 51–72.
date_created: 2018-12-11T11:59:58Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2021-01-12T07:00:18Z
day: '01'
department:
- _id: HeEd
doi: 10.4310/HHA.2013.v15.n1.a3
external_id:
arxiv:
- '1102.3389'
intvolume: ' 15'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1102.3389v1
month: '05'
oa: 1
oa_version: Preprint
page: 51 - 72
publication: Homology, Homotopy and Applications
publication_status: published
publisher: International Press
publist_id: '3930'
quality_controlled: '1'
scopus_import: 1
status: public
title: Homology and robustness of level and interlevel sets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2013'
...
---
_id: '2863'
abstract:
- lang: eng
text: Neural populations encode information about their stimulus in a collective
fashion, by joint activity patterns of spiking and silence. A full account of
this mapping from stimulus to neural activity is given by the conditional probability
distribution over neural codewords given the sensory input. For large populations,
direct sampling of these distributions is impossible, and so we must rely on constructing
appropriate models. We show here that in a population of 100 retinal ganglion
cells in the salamander retina responding to temporal white-noise stimuli, dependencies
between cells play an important encoding role. We introduce the stimulus-dependent
maximum entropy (SDME) model—a minimal extension of the canonical linear-nonlinear
model of a single neuron, to a pairwise-coupled neural population. We find that
the SDME model gives a more accurate account of single cell responses and in particular
significantly outperforms uncoupled models in reproducing the distributions of
population codewords emitted in response to a stimulus. We show how the SDME model,
in conjunction with static maximum entropy models of population vocabulary, can
be used to estimate information-theoretic quantities like average surprise and
information transmission in a neural population.
article_number: e1002922
author:
- first_name: Einat
full_name: Granot Atedgi, Einat
last_name: Granot Atedgi
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Ronen
full_name: Segev, Ronen
last_name: Segev
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum
entropy models of neural population codes. PLoS Computational Biology.
2013;9(3). doi:10.1371/journal.pcbi.1002922
apa: Granot Atedgi, E., Tkačik, G., Segev, R., & Schneidman, E. (2013). Stimulus-dependent
maximum entropy models of neural population codes. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1002922
chicago: Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman.
“Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS
Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1002922.
ieee: E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent
maximum entropy models of neural population codes,” PLoS Computational Biology,
vol. 9, no. 3. Public Library of Science, 2013.
ista: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. 2013. Stimulus-dependent
maximum entropy models of neural population codes. PLoS Computational Biology.
9(3), e1002922.
mla: Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of
Neural Population Codes.” PLoS Computational Biology, vol. 9, no. 3, e1002922,
Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922.
short: E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational
Biology 9 (2013).
date_created: 2018-12-11T12:00:00Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2021-01-12T07:00:20Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1002922
file:
- access_level: open_access
checksum: 5a30876c193209fa05b26db71845dd16
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:45Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5099'
file_name: IST-2013-120-v1+1_journal.pcbi.1002922.pdf
file_size: 1548120
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3926'
pubrep_id: '120'
quality_controlled: '1'
scopus_import: 1
status: public
title: Stimulus-dependent maximum entropy models of neural population codes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '2862'
abstract:
- lang: eng
text: Motile cilia perform crucial functions during embryonic development and throughout
adult life. Development of organs containing motile cilia involves regulation
of cilia formation (ciliogenesis) and formation of a luminal space (lumenogenesis)
in which cilia generate fluid flows. Control of ciliogenesis and lumenogenesis
is not yet fully understood, and it remains unclear whether these processes are
coupled. In the zebrafish embryo, lethal giant larvae 2 (lgl2) is expressed prominently
in ciliated organs. Lgl proteins are involved in establishing cell polarity and
have been implicated in vesicle trafficking. Here, we identified a role for Lgl2
in development of ciliated epithelia in Kupffer's vesicle, which directs left-right
asymmetry of the embryo; the otic vesicles, which give rise to the inner ear;
and the pronephric ducts of the kidney. Using Kupffer's vesicle as a model ciliated
organ, we found that depletion of Lgl2 disrupted lumen formation and reduced cilia
number and length. Immunofluorescence and time-lapse imaging of Kupffer's vesicle
morphogenesis in Lgl2-deficient embryos suggested cell adhesion defects and revealed
loss of the adherens junction component E-cadherin at lateral membranes. Genetic
interaction experiments indicate that Lgl2 interacts with Rab11a to regulate E-cadherin
and mediate lumen formation that is uncoupled from cilia formation. These results
uncover new roles and interactions for Lgl2 that are crucial for both lumenogenesis
and ciliogenesis and indicate that these processes are genetically separable in
zebrafish.
acknowledgement: Deposited in PMC for release after 12 months. We thank members of
the Amack lab for helpful discussions and Mahendra Sonawane for donating reagents.
author:
- first_name: Hwee
full_name: Tay, Hwee
last_name: Tay
- first_name: Sabrina
full_name: Schulze, Sabrina
last_name: Schulze
- first_name: Julien
full_name: Compagnon, Julien
id: 2E3E0988-F248-11E8-B48F-1D18A9856A87
last_name: Compagnon
- first_name: Fiona
full_name: Foley, Fiona
last_name: Foley
- 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: H Joseph
full_name: Yost, H Joseph
last_name: Yost
- first_name: Salim
full_name: Abdelilah Seyfried, Salim
last_name: Abdelilah Seyfried
- first_name: Jeffrey
full_name: Amack, Jeffrey
last_name: Amack
citation:
ama: Tay H, Schulze S, Compagnon J, et al. Lethal giant larvae 2 regulates development
of the ciliated organ Kupffer’s vesicle. Development. 2013;140(7):1550-1559.
doi:10.1242/dev.087130
apa: Tay, H., Schulze, S., Compagnon, J., Foley, F., Heisenberg, C.-P. J., Yost,
H. J., … Amack, J. (2013). Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle. Development. Company of Biologists. https://doi.org/10.1242/dev.087130
chicago: Tay, Hwee, Sabrina Schulze, Julien Compagnon, Fiona Foley, Carl-Philipp
J Heisenberg, H Joseph Yost, Salim Abdelilah Seyfried, and Jeffrey Amack. “Lethal
Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.”
Development. Company of Biologists, 2013. https://doi.org/10.1242/dev.087130.
ieee: H. Tay et al., “Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle,” Development, vol. 140, no. 7. Company
of Biologists, pp. 1550–1559, 2013.
ista: Tay H, Schulze S, Compagnon J, Foley F, Heisenberg C-PJ, Yost HJ, Abdelilah
Seyfried S, Amack J. 2013. Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle. Development. 140(7), 1550–1559.
mla: Tay, Hwee, et al. “Lethal Giant Larvae 2 Regulates Development of the Ciliated
Organ Kupffer’s Vesicle.” Development, vol. 140, no. 7, Company of Biologists,
2013, pp. 1550–59, doi:10.1242/dev.087130.
short: H. Tay, S. Schulze, J. Compagnon, F. Foley, C.-P.J. Heisenberg, H.J. Yost,
S. Abdelilah Seyfried, J. Amack, Development 140 (2013) 1550–1559.
date_created: 2018-12-11T11:59:59Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2021-01-12T07:00:20Z
day: '01'
department:
- _id: CaHe
doi: 10.1242/dev.087130
external_id:
pmid:
- '23482490'
intvolume: ' 140'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596994/
month: '04'
oa: 1
oa_version: Submitted Version
page: 1550 - 1559
pmid: 1
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3927'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s
vesicle
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 140
year: '2013'
...
---
_id: '2861'
abstract:
- lang: eng
text: We consider a two-parameter family of piecewise linear maps in which the moduli
of the two slopes take different values. We provide numerical evidence of the
existence of some parameter regions in which the Lyapunov exponent and the topological
entropy remain constant. Analytical proof of this phenomenon is also given for
certain cases. Surprisingly however, the systems with that property are not conjugate
as we prove by using kneading theory.
article_number: '125101'
author:
- first_name: Vicente
full_name: Botella Soler, Vicente
id: 421234E8-F248-11E8-B48F-1D18A9856A87
last_name: Botella Soler
orcid: 0000-0002-8790-1914
- first_name: José
full_name: Oteo, José
last_name: Oteo
- first_name: Javier
full_name: Ros, Javier
last_name: Ros
- first_name: Paul
full_name: Glendinning, Paul
last_name: Glendinning
citation:
ama: 'Botella Soler V, Oteo J, Ros J, Glendinning P. Lyapunov exponent and topological
entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical
and Theoretical. 2013;46(12). doi:10.1088/1751-8113/46/12/125101'
apa: 'Botella Soler, V., Oteo, J., Ros, J., & Glendinning, P. (2013). Lyapunov
exponent and topological entropy plateaus in piecewise linear maps. Journal
of Physics A: Mathematical and Theoretical. IOP Publishing Ltd. https://doi.org/10.1088/1751-8113/46/12/125101'
chicago: 'Botella Soler, Vicente, José Oteo, Javier Ros, and Paul Glendinning. “Lyapunov
Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” Journal
of Physics A: Mathematical and Theoretical. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1751-8113/46/12/125101.'
ieee: 'V. Botella Soler, J. Oteo, J. Ros, and P. Glendinning, “Lyapunov exponent
and topological entropy plateaus in piecewise linear maps,” Journal of Physics
A: Mathematical and Theoretical, vol. 46, no. 12. IOP Publishing Ltd., 2013.'
ista: 'Botella Soler V, Oteo J, Ros J, Glendinning P. 2013. Lyapunov exponent and
topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical
and Theoretical. 46(12), 125101.'
mla: 'Botella Soler, Vicente, et al. “Lyapunov Exponent and Topological Entropy
Plateaus in Piecewise Linear Maps.” Journal of Physics A: Mathematical and
Theoretical, vol. 46, no. 12, 125101, IOP Publishing Ltd., 2013, doi:10.1088/1751-8113/46/12/125101.'
short: 'V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A:
Mathematical and Theoretical 46 (2013).'
date_created: 2018-12-11T11:59:59Z
date_published: 2013-03-29T00:00:00Z
date_updated: 2021-01-12T07:00:19Z
day: '29'
department:
- _id: GaTk
doi: 10.1088/1751-8113/46/12/125101
intvolume: ' 46'
issue: '12'
language:
- iso: eng
month: '03'
oa_version: None
publication: 'Journal of Physics A: Mathematical and Theoretical'
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '3928'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lyapunov exponent and topological entropy plateaus in piecewise linear maps
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2013'
...
---
_id: '2877'
abstract:
- lang: eng
text: 'Premise of the study: To reach favorable conditions for photosynthesis, seedlings
grow upward when deprived of light upon underground germination. To direct their
growth, they use their negative gravitropic capacity. Negative gravitropism is
under tight control of multiple hormones. • Methods: By counting the number of
standing plants in a population or by real time monitoring of the reorientation
of gravistimulated seedlings of Arabidopsis thaliana, we evaluated the negative
gravitropism of ethylene or brassinosteroid (BR) treated plants. Meta-analysis
of transcriptomic data on AUX / IAA genes was gathered, and subsequent mutant
analysis was performed. • Key results: Ethylene and BR have opposite effects in
regulating shoot gravitropism. Lack of BR enhances gravitropic reorientation in
2-d-old seedlings, whereas ethylene does not. Lack of ethylene signaling results
in enhanced BR sensitivity. Ethylene and BRs regulate overlapping sets of AUX
/ IAA genes. BRs regulate a wider range of auxin signaling components than ethylene.
• Conclusions: Upward growth in seedlings depends strongly on the internal hormonal
balance. Endogenous ethylene stimulates, whereas BRs reduce negative gravitropism
in a manner that depends on the function of different, yet overlapping sets of
auxin signaling components.'
author:
- first_name: Filip
full_name: Vandenbussche, Filip
last_name: Vandenbussche
- first_name: Pieter
full_name: Callebert, Pieter
last_name: Callebert
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
citation:
ama: Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D. Brassinosteroid
control of shoot gravitropism interacts with ethylene and depends on auxin signaling
components. American Journal of Botany. 2013;100(1):215-225. doi:10.3732/ajb.1200264
apa: Vandenbussche, F., Callebert, P., Žádníková, P., Benková, E., & Van Der
Straeten, D. (2013). Brassinosteroid control of shoot gravitropism interacts with
ethylene and depends on auxin signaling components. American Journal of Botany.
Botanical Society of America. https://doi.org/10.3732/ajb.1200264
chicago: Vandenbussche, Filip, Pieter Callebert, Petra Žádníková, Eva Benková, and
Dominique Van Der Straeten. “Brassinosteroid Control of Shoot Gravitropism Interacts
with Ethylene and Depends on Auxin Signaling Components.” American Journal
of Botany. Botanical Society of America, 2013. https://doi.org/10.3732/ajb.1200264.
ieee: F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, and D. Van Der Straeten,
“Brassinosteroid control of shoot gravitropism interacts with ethylene and depends
on auxin signaling components,” American Journal of Botany, vol. 100, no.
1. Botanical Society of America, pp. 215–225, 2013.
ista: Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D.
2013. Brassinosteroid control of shoot gravitropism interacts with ethylene and
depends on auxin signaling components. American Journal of Botany. 100(1), 215–225.
mla: Vandenbussche, Filip, et al. “Brassinosteroid Control of Shoot Gravitropism
Interacts with Ethylene and Depends on Auxin Signaling Components.” American
Journal of Botany, vol. 100, no. 1, Botanical Society of America, 2013, pp.
215–25, doi:10.3732/ajb.1200264.
short: F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, D. Van Der Straeten,
American Journal of Botany 100 (2013) 215–225.
date_created: 2018-12-11T12:00:06Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:25Z
day: '01'
doi: 10.3732/ajb.1200264
extern: 1
intvolume: ' 100'
issue: '1'
month: '01'
page: 215 - 225
publication: American Journal of Botany
publication_status: published
publisher: Botanical Society of America
publist_id: '3883'
quality_controlled: 0
status: public
title: Brassinosteroid control of shoot gravitropism interacts with ethylene and depends
on auxin signaling components
type: journal_article
volume: 100
year: '2013'
...
---
_id: '2883'
abstract:
- lang: eng
text: Plant architecture is influenced by the polar, cell-to-cell transport of auxin
that is primarily provided and regulated by plasma membrane efflux catalysts of
the PIN-FORMED and B family of ABC transporter (ABCB) classes. The latter were
shown to require the functionality of the FK506 binding protein42 TWISTED DWARF1
(TWD1), although underlying mechanisms are unclear. By genetic manipulation of
TWD1 expression, we show here that TWD1 affects shootward root auxin reflux and,
thus, downstream developmental traits, such as epidermal twisting and gravitropism
of the root. Using immunological assays, we demonstrate a predominant lateral,
mainly outward-facing, plasma membrane location for TWD1 in the root epidermis
characterized by the lateral marker ABC transporter G36/PLEIOTROPIC DRUG-RESISTANCE8/PENETRATION3.
At these epidermal plasma membrane domains, TWD1 colocalizes with nonpolar ABCB1.
In planta bioluminescence resonance energy transfer analysis was used to verify
specific ABC transporter B1 (ABCB1)-TWD1 interaction. Our data support a model
in which TWD1 promotes lateral ABCB-mediated auxin efflux via protein-protein
interaction at the plasma membrane, minimizing reflux from the root apoplast into
the cytoplasm.
acknowledgement: We would thank Vincent Vincenzetti and Laurence Charrier for excellent
technical assistance, A. von Arnim for the donation of BRET vectors, E. Spalding
for TWD1-CFP, TWD1-CFP/29-1-GFP/ER-YFP, and ABCB4-GFP lines, M. Palmgren for discussion
and support, and E. Martinoia for TT12 cDNA, support, and mentorship. Imaging data
were partially collected at the Center for Advanced Bioimaging, University of Copenhagen,
Denmark. This work was supported by grants from the Novartis Foundation (to M.G.),
from the Danish Research School for Biotechnology (to M.G. and A.S.), from the Forschungskredit
of the University of Zurich (to A.B.), from the Pool de Recherche of the University
of Fribourg (to M.G.), and from the Swiss National Funds (to M.G.). M.G. dedicates
this work to his father, who passed away during the resubmission process.
author:
- first_name: Bangjun
full_name: Wang, Bangjun
last_name: Wang
- first_name: Aurélien
full_name: Bailly, Aurélien
last_name: Bailly
- first_name: Marta
full_name: Zwiewk, Marta
last_name: Zwiewk
- first_name: Sina
full_name: Henrichs, Sina
last_name: Henrichs
- first_name: Elisa
full_name: Azzarello, Elisa
last_name: Azzarello
- first_name: Stefano
full_name: Mancuso, Stefano
last_name: Mancuso
- first_name: Masayoshi
full_name: Maeshima, Masayoshi
last_name: Maeshima
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Alexander
full_name: Schulz, Alexander
last_name: Schulz
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
citation:
ama: Wang B, Bailly A, Zwiewk M, et al. Arabidopsis TWISTED DWARF1 functionally
interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell.
2013;25(1):202-214. doi:10.1105/tpc.112.105999
apa: Wang, B., Bailly, A., Zwiewk, M., Henrichs, S., Azzarello, E., Mancuso, S.,
… Geisler, M. (2013). Arabidopsis TWISTED DWARF1 functionally interacts with auxin
exporter ABCB1 on the root plasma membrane. Plant Cell. American Society
of Plant Biologists. https://doi.org/10.1105/tpc.112.105999
chicago: Wang, Bangjun, Aurélien Bailly, Marta Zwiewk, Sina Henrichs, Elisa Azzarello,
Stefano Mancuso, Masayoshi Maeshima, Jiří Friml, Alexander Schulz, and Markus
Geisler. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter
ABCB1 on the Root Plasma Membrane.” Plant Cell. American Society of Plant
Biologists, 2013. https://doi.org/10.1105/tpc.112.105999.
ieee: B. Wang et al., “Arabidopsis TWISTED DWARF1 functionally interacts
with auxin exporter ABCB1 on the root plasma membrane,” Plant Cell, vol.
25, no. 1. American Society of Plant Biologists, pp. 202–214, 2013.
ista: Wang B, Bailly A, Zwiewk M, Henrichs S, Azzarello E, Mancuso S, Maeshima M,
Friml J, Schulz A, Geisler M. 2013. Arabidopsis TWISTED DWARF1 functionally interacts
with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. 25(1), 202–214.
mla: Wang, Bangjun, et al. “Arabidopsis TWISTED DWARF1 Functionally Interacts with
Auxin Exporter ABCB1 on the Root Plasma Membrane.” Plant Cell, vol. 25,
no. 1, American Society of Plant Biologists, 2013, pp. 202–14, doi:10.1105/tpc.112.105999.
short: B. Wang, A. Bailly, M. Zwiewk, S. Henrichs, E. Azzarello, S. Mancuso, M.
Maeshima, J. Friml, A. Schulz, M. Geisler, Plant Cell 25 (2013) 202–214.
date_created: 2018-12-11T12:00:08Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:28Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.112.105999
external_id:
pmid:
- '23321285'
intvolume: ' 25'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584535/
month: '01'
oa: 1
oa_version: Submitted Version
page: 202 - 214
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3878'
quality_controlled: '1'
scopus_import: 1
status: public
title: Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1
on the root plasma membrane
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '2880'
abstract:
- lang: eng
text: Lateral root (LR) formation is initiated when pericycle cells accumulate auxin,
thereby acquiring founder cell (FC) status and triggering asymmetric cell divisions,
giving rise to a new primordium. How this auxin maximum in pericycle cells builds
up and remains focused is not understood. We report that the endodermis plays
an active role in the regulation of auxin accumulation and is instructive for
FCs to progress during the LR initiation (LRI) phase. We describe the functional
importance of a PIN3 (PIN-formed) auxin efflux carrier-dependent hormone reflux
pathway between overlaying endodermal and pericycle FCs. Disrupting this reflux
pathway causes dramatic defects in the progress of FCs towards the next initiation
phase. Our data identify an unexpected regulatory function for the endodermis
in LRI as part of the fine-tuning mechanism that appears to act as a check point
in LR organogenesis after FCs are specified.
author:
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Ding
full_name: Zhaojun, Ding
last_name: Zhaojun
- first_name: Malcolm
full_name: Bennett, Malcolm
last_name: Bennett
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Vanstraelen M, De Rybel B, et al. Auxin reflux between the endodermis
and pericycle promotes lateral root initiation. EMBO Journal. 2013;32(1):149-158.
doi:10.1038/emboj.2012.303
apa: Marhavý, P., Vanstraelen, M., De Rybel, B., Zhaojun, D., Bennett, M., Beeckman,
T., & Benková, E. (2013). Auxin reflux between the endodermis and pericycle
promotes lateral root initiation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.303
chicago: Marhavý, Peter, Marleen Vanstraelen, Bert De Rybel, Ding Zhaojun, Malcolm
Bennett, Tom Beeckman, and Eva Benková. “Auxin Reflux between the Endodermis and
Pericycle Promotes Lateral Root Initiation.” EMBO Journal. Wiley-Blackwell,
2013. https://doi.org/10.1038/emboj.2012.303.
ieee: P. Marhavý et al., “Auxin reflux between the endodermis and pericycle
promotes lateral root initiation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell,
pp. 149–158, 2013.
ista: Marhavý P, Vanstraelen M, De Rybel B, Zhaojun D, Bennett M, Beeckman T, Benková
E. 2013. Auxin reflux between the endodermis and pericycle promotes lateral root
initiation. EMBO Journal. 32(1), 149–158.
mla: Marhavý, Peter, et al. “Auxin Reflux between the Endodermis and Pericycle Promotes
Lateral Root Initiation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell,
2013, pp. 149–58, doi:10.1038/emboj.2012.303.
short: P. Marhavý, M. Vanstraelen, B. De Rybel, D. Zhaojun, M. Bennett, T. Beeckman,
E. Benková, EMBO Journal 32 (2013) 149–158.
date_created: 2018-12-11T12:00:07Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2021-01-12T07:00:27Z
day: '09'
department:
- _id: EvBe
doi: 10.1038/emboj.2012.303
ec_funded: 1
external_id:
pmid:
- '23178590'
intvolume: ' 32'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545298/
month: '01'
oa: 1
oa_version: Submitted Version
page: 149 - 158
pmid: 1
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3882'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin reflux between the endodermis and pericycle promotes lateral root initiation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2882'
abstract:
- lang: eng
text: Gravitropic bending of plant organs is mediated by an asymmetric signaling
of the plant hormone auxin between the upper and lower side of the respective
organ. Here, we show that also another plant hormone, gibberellic acid (GA), shows
asymmetric action during gravitropic responses. Immunodetection using an antibody
against GA and monitoring GA signaling output by downstream degradation of DELLA
proteins revealed an asymmetric GA distribution and response with the maximum
at the lower side of gravistimulated roots. Genetic or pharmacological manipulation
of GA levels or response affects gravity-mediated auxin redistribution and root
bending response. The higher GA levels at the lower side of the root correlate
with increased amounts of PIN-FORMED2 (PIN2) auxin transporter at the plasma membrane.
The observed increase in PIN2 stability is caused by a specific GA effect on trafficking
of PIN proteins to lytic vacuoles that presumably occurs downstream of brefeldin
A-sensitive endosomes. Our results suggest that asymmetric auxin distribution
instructive for gravity-induced differential growth is consolidated by the asymmetric
action of GA that stabilizes the PIN-dependent auxin stream along the lower side
of gravistimulated roots.
author:
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Ingo
full_name: Heilmann, Ingo
last_name: Heilmann
- first_name: Marc
full_name: Van Montagu, Marc
last_name: Van Montagu
- first_name: Thomas
full_name: Teichmann, Thomas
last_name: Teichmann
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. Asymmetric
gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters
during root gravitropism. PNAS. 2013;110(9):3627-3632. doi:10.1073/pnas.1300107110
apa: Löfke, C., Zwiewka, M., Heilmann, I., Van Montagu, M., Teichmann, T., &
Friml, J. (2013). Asymmetric gibberellin signaling regulates vacuolar trafficking
of PIN auxin transporters during root gravitropism. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1300107110
chicago: Löfke, Christian, Marta Zwiewka, Ingo Heilmann, Marc Van Montagu, Thomas
Teichmann, and Jiří Friml. “Asymmetric Gibberellin Signaling Regulates Vacuolar
Trafficking of PIN Auxin Transporters during Root Gravitropism.” PNAS.
National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1300107110.
ieee: C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, and J. Friml,
“Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin
transporters during root gravitropism,” PNAS, vol. 110, no. 9. National
Academy of Sciences, pp. 3627–3632, 2013.
ista: Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. 2013.
Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters
during root gravitropism. PNAS. 110(9), 3627–3632.
mla: Löfke, Christian, et al. “Asymmetric Gibberellin Signaling Regulates Vacuolar
Trafficking of PIN Auxin Transporters during Root Gravitropism.” PNAS,
vol. 110, no. 9, National Academy of Sciences, 2013, pp. 3627–32, doi:10.1073/pnas.1300107110.
short: C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml,
PNAS 110 (2013) 3627–3632.
date_created: 2018-12-11T12:00:07Z
date_published: 2013-02-26T00:00:00Z
date_updated: 2021-01-12T07:00:27Z
day: '26'
department:
- _id: JiFr
doi: 10.1073/pnas.1300107110
external_id:
pmid:
- '23391733'
intvolume: ' 110'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/
month: '02'
oa: 1
oa_version: Submitted Version
page: 3627 - 3632
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3879'
quality_controlled: '1'
scopus_import: 1
status: public
title: Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin
transporters during root gravitropism
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2885'
abstract:
- lang: eng
text: 'This volume contains the post-proceedings of the 8th Doctoral Workshop on
Mathematical and Engineering Methods in Computer Science, MEMICS 2012, held in
Znojmo, Czech Republic, in October, 2012. The 13 thoroughly revised papers were
carefully selected out of 31 submissions and are presented together with 6 invited
papers. The topics covered by the papers include: computer-aided analysis and
verification, applications of game theory in computer science, networks and security,
modern trends of graph theory in computer science, electronic systems design and
testing, and quantum information processing.'
acknowledgement: Red Hat Czech Republic, Y Soft
alternative_title:
- LNCS
citation:
ama: Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D, eds. Mathematical
and Engineering Methods in Computer Science. Vol 7721. Springer; 2013:1-228.
doi:10.1007/978-3-642-36046-6
apa: 'Kucera, A., Henzinger, T. A., Nesetril, J., Vojnar, T., & Antos, D. (Eds.).
(2013). Mathematical and Engineering Methods in Computer Science (Vol.
7721, pp. 1–228). Presented at the MEMICS: Mathematical and Engineering methods
in computer science, Znojmo, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-36046-6'
chicago: Kucera, Antonin, Thomas A Henzinger, Jaroslav Nesetril, Tomas Vojnar, and
David Antos, eds. Mathematical and Engineering Methods in Computer Science.
Vol. 7721. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36046-6.
ieee: A. Kucera, T. A. Henzinger, J. Nesetril, T. Vojnar, and D. Antos, Eds., Mathematical
and Engineering Methods in Computer Science, vol. 7721. Springer, 2013, pp.
1–228.
ista: Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D eds. 2013. Mathematical
and Engineering Methods in Computer Science, Springer,p.
mla: Kucera, Antonin, et al., editors. Mathematical and Engineering Methods in
Computer Science. Vol. 7721, Springer, 2013, pp. 1–228, doi:10.1007/978-3-642-36046-6.
short: A. Kucera, T.A. Henzinger, J. Nesetril, T. Vojnar, D. Antos, eds., Mathematical
and Engineering Methods in Computer Science, Springer, 2013.
conference:
end_date: 2012-10-28
location: Znojmo, Czech Republic
name: 'MEMICS: Mathematical and Engineering methods in computer science'
start_date: 2012-10-25
date_created: 2018-12-11T12:00:08Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2019-08-02T12:37:55Z
day: '09'
department:
- _id: ToHe
doi: 10.1007/978-3-642-36046-6
editor:
- first_name: Antonin
full_name: Kucera, Antonin
last_name: Kucera
- 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: Jaroslav
full_name: Nesetril, Jaroslav
last_name: Nesetril
- first_name: Tomas
full_name: Vojnar, Tomas
last_name: Vojnar
- first_name: David
full_name: Antos, David
last_name: Antos
intvolume: ' 7721'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 228
publication_status: published
publisher: Springer
publist_id: '3874'
quality_controlled: '1'
series_title: Lecture Notes in Computer Science
status: public
title: Mathematical and Engineering Methods in Computer Science
type: conference_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7721
year: '2013'
...
---
_id: '2881'
abstract:
- lang: eng
text: The puzzle piece-shaped Arabidopsis leaf pavement cells (PCs) with interdigitated
lobes and indents is a good model system to investigate the mechanisms that coordinate
cell polarity and shape formation within a tissue. Auxin has been shown to coordinate
the interdigitation by activating ROP GTPase-dependent signaling pathways. To
identify additional components or mechanisms, we screened for mutants with abnormal
PC morphogenesis and found that cytokinin signaling regulates the PC interdigitation
pattern. Reduction in cytokinin accumulation and defects in cytokinin signaling
(such as in ARR7-over-expressing lines, the ahk3cre1 cytokinin receptor mutant,
and the ahp12345 cytokinin signaling mutant) enhanced PC interdigitation, whereas
over-production of cytokinin and over-activation of cytokinin signaling in an
ARR20 over-expression line delayed or abolished PC interdigitation throughout
the cotyledon. Genetic and biochemical analyses suggest that cytokinin signaling
acts upstream of ROPs to suppress the formation of interdigitated pattern. Our
results provide novel mechanistic understanding of the pathways controlling PC
shape and uncover a new role for cytokinin signaling in cell morphogenesis.
acknowledgement: is work was supported by grants from the US National Institute of
General Medical Sciences (GM081451 and GM081451-03S2) to ZY. We thank National Science
Foundation grant (IOS-1147250) to GVR and MX. HL and DL were partially supported
by the Chinese Scholarship Council.
author:
- first_name: Hongjiang
full_name: Hongjiang Li
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Deshu
full_name: Lin, Deshu
last_name: Lin
- first_name: Mingzhang
full_name: Wen, Mingzhang
last_name: Wen
- first_name: Mingtang
full_name: Xie, Mingtang
last_name: Xie
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Jungmook
full_name: Kim, Jungmook
last_name: Kim
- first_name: G Venugopala
full_name: Reddy, G Venugopala
last_name: Reddy
- first_name: Jianru
full_name: Zuo, Jianru
last_name: Zuo
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Hongwei
full_name: Guo, Hongwei
last_name: Guo
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
citation:
ama: Li H, Xu T, Lin D, et al. Cytokinin signaling regulates pavement cell morphogenesis
in Arabidopsis. Cell Research. 2013;23(2):290-299. doi:10.1038/cr.2012.146
apa: Li, H., Xu, T., Lin, D., Wen, M., Xie, M., Duclercq, J., … Yang, Z. (2013).
Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell
Research. Nature Publishing Group. https://doi.org/10.1038/cr.2012.146
chicago: Li, Hongjiang, Tongda Xu, Deshu Lin, Mingzhang Wen, Mingtang Xie, Jérôme
Duclercq, Agnieszka Bielach, et al. “Cytokinin Signaling Regulates Pavement Cell
Morphogenesis in Arabidopsis.” Cell Research. Nature Publishing Group,
2013. https://doi.org/10.1038/cr.2012.146.
ieee: H. Li et al., “Cytokinin signaling regulates pavement cell morphogenesis
in Arabidopsis,” Cell Research, vol. 23, no. 2. Nature Publishing Group,
pp. 290–299, 2013.
ista: Li H, Xu T, Lin D, Wen M, Xie M, Duclercq J, Bielach A, Kim J, Reddy GV, Zuo
J, Benková E, Friml J, Guo H, Yang Z. 2013. Cytokinin signaling regulates pavement
cell morphogenesis in Arabidopsis. Cell Research. 23(2), 290–299.
mla: Li, Hongjiang, et al. “Cytokinin Signaling Regulates Pavement Cell Morphogenesis
in Arabidopsis.” Cell Research, vol. 23, no. 2, Nature Publishing Group,
2013, pp. 290–99, doi:10.1038/cr.2012.146.
short: H. Li, T. Xu, D. Lin, M. Wen, M. Xie, J. Duclercq, A. Bielach, J. Kim, G.V.
Reddy, J. Zuo, E. Benková, J. Friml, H. Guo, Z. Yang, Cell Research 23 (2013)
290–299.
date_created: 2018-12-11T12:00:07Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T07:00:27Z
day: '01'
doi: 10.1038/cr.2012.146
extern: 1
intvolume: ' 23'
issue: '2'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567823/
month: '02'
oa: 1
page: 290 - 299
publication: Cell Research
publication_status: published
publisher: Nature Publishing Group
publist_id: '3881'
quality_controlled: 0
status: public
title: Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis
type: journal_article
volume: 23
year: '2013'
...
---
_id: '2884'
author:
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- first_name: Hélène
full_name: Berthoumieux, Hélène
last_name: Berthoumieux
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Ewa
full_name: Paluch, Ewa
last_name: Paluch
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Maître J-L, Berthoumieux H, Krens G, et al. Cell adhesion mechanics of zebrafish
gastrulation. Medecine Sciences. 2013;29(2):147-150. doi:10.1051/medsci/2013292011
apa: Maître, J.-L., Berthoumieux, H., Krens, G., Salbreux, G., Julicher, F., Paluch,
E., & Heisenberg, C.-P. J. (2013). Cell adhesion mechanics of zebrafish gastrulation.
Medecine Sciences. Éditions Médicales et Scientifiques. https://doi.org/10.1051/medsci/2013292011
chicago: Maître, Jean-Léon, Hélène Berthoumieux, Gabriel Krens, Guillaume Salbreux,
Frank Julicher, Ewa Paluch, and Carl-Philipp J Heisenberg. “Cell Adhesion Mechanics
of Zebrafish Gastrulation.” Medecine Sciences. Éditions Médicales et Scientifiques,
2013. https://doi.org/10.1051/medsci/2013292011.
ieee: J.-L. Maître et al., “Cell adhesion mechanics of zebrafish gastrulation,”
Medecine Sciences, vol. 29, no. 2. Éditions Médicales et Scientifiques,
pp. 147–150, 2013.
ista: Maître J-L, Berthoumieux H, Krens G, Salbreux G, Julicher F, Paluch E, Heisenberg
C-PJ. 2013. Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences.
29(2), 147–150.
mla: Maître, Jean-Léon, et al. “Cell Adhesion Mechanics of Zebrafish Gastrulation.”
Medecine Sciences, vol. 29, no. 2, Éditions Médicales et Scientifiques,
2013, pp. 147–50, doi:10.1051/medsci/2013292011.
short: J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch,
C.-P.J. Heisenberg, Medecine Sciences 29 (2013) 147–150.
date_created: 2018-12-11T12:00:08Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T07:00:28Z
day: '01'
department:
- _id: CaHe
doi: 10.1051/medsci/2013292011
intvolume: ' 29'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 147 - 150
project:
- _id: 252064B8-B435-11E9-9278-68D0E5697425
grant_number: HE_3231/6-1
name: Analysis of the Formation and Function of Different Cell Protusion Types During
Cell Migration in Vivo
- _id: 2527D5CC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 812-B12
name: Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation
publication: Medecine Sciences
publication_status: published
publisher: Éditions Médicales et Scientifiques
publist_id: '3877'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cell adhesion mechanics of zebrafish gastrulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2013'
...
---
_id: '2886'
abstract:
- lang: eng
text: We focus on the realizability problem of Message Sequence Graphs (MSG), i.e.
the problem whether a given MSG specification is correctly distributable among
parallel components communicating via messages. This fundamental problem of MSG
is known to be undecidable. We introduce a well motivated restricted class of
MSG, so called controllable-choice MSG, and show that all its models are realizable
and moreover it is decidable whether a given MSG model is a member of this class.
In more detail, this class of MSG specifications admits a deadlock-free realization
by overloading existing messages with additional bounded control data. We also
show that the presented class is the largest known subclass of MSG that allows
for deadlock-free realization.
alternative_title:
- LNCS
author:
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Vojtěch
full_name: Řehák, Vojtěch
last_name: Řehák
citation:
ama: Chmelik M, Řehák V. Controllable-choice message sequence graphs. 2013;7721:118-130.
doi:10.1007/978-3-642-36046-6_12
apa: 'Chmelik, M., & Řehák, V. (2013). Controllable-choice message sequence
graphs. Presented at the MEMICS: Mathematical and Engineering Methods in Computer
Science, Znojmo, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-36046-6_12'
chicago: Chmelik, Martin, and Vojtěch Řehák. “Controllable-Choice Message Sequence
Graphs.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36046-6_12.
ieee: M. Chmelik and V. Řehák, “Controllable-choice message sequence graphs,” vol.
7721. Springer, pp. 118–130, 2013.
ista: Chmelik M, Řehák V. 2013. Controllable-choice message sequence graphs. 7721,
118–130.
mla: Chmelik, Martin, and Vojtěch Řehák. Controllable-Choice Message Sequence
Graphs. Vol. 7721, Springer, 2013, pp. 118–30, doi:10.1007/978-3-642-36046-6_12.
short: M. Chmelik, V. Řehák, 7721 (2013) 118–130.
conference:
end_date: 2012-10-28
location: Znojmo, Czech Republic
name: 'MEMICS: Mathematical and Engineering Methods in Computer Science'
start_date: 2012-10-25
date_created: 2018-12-11T12:00:09Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2020-08-11T10:09:52Z
day: '09'
department:
- _id: KrCh
doi: 10.1007/978-3-642-36046-6_12
ec_funded: 1
intvolume: ' 7721'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1209.4499
month: '01'
oa: 1
oa_version: Submitted Version
page: 118 - 130
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '3873'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Controllable-choice message sequence graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7721
year: '2013'
...
---
_id: '2887'
abstract:
- lang: eng
text: 'Root system growth and development is highly plastic and is influenced by
the surrounding environment. Roots frequently grow in heterogeneous environments
that include interactions from neighboring plants and physical impediments in
the rhizosphere. To investigate how planting density and physical objects affect
root system growth, we grew rice in a transparent gel system in close proximity
with another plant or a physical object. Root systems were imaged and reconstructed
in three dimensions. Root-root interaction strength was calculated using quantitative
metrics that characterize the extent towhich the reconstructed root systems overlap
each other. Surprisingly, we found the overlap of root systems of the same genotype
was significantly higher than that of root systems of different genotypes. Root
systems of the same genotype tended to grow toward each other but those of different
genotypes appeared to avoid each other. Shoot separation experiments excluded
the possibility of aerial interactions, suggesting root communication. Staggered
plantings indicated that interactions likely occur at root tips in close proximity.
Recognition of obstacles also occurred through root tips, but through physical
contact in a size-dependent manner. These results indicate that root systems use
two different forms of communication to recognize objects and alter root architecture:
root-root recognition, possibly mediated through root exudates, and root-object
recognition mediated by physical contact at the root tips. This finding suggests
that root tips act as local sensors that integrate rhizosphere information into
global root architectural changes.'
article_processing_charge: No
article_type: original
author:
- first_name: Suqin
full_name: Fang, Suqin
last_name: Fang
- first_name: Randy
full_name: Clark, Randy
last_name: Clark
- first_name: Ying
full_name: Zheng, Ying
last_name: Zheng
- first_name: Anjali
full_name: Iyer Pascuzzi, Anjali
last_name: Iyer Pascuzzi
- first_name: Joshua
full_name: Weitz, Joshua
last_name: Weitz
- first_name: Leon
full_name: Kochian, Leon
last_name: Kochian
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Hong
full_name: Liao, Hong
last_name: Liao
- first_name: Philip
full_name: Benfey, Philip
last_name: Benfey
citation:
ama: Fang S, Clark R, Zheng Y, et al. Genotypic recognition and spatial responses
by rice roots. PNAS. 2013;110(7):2670-2675. doi:10.1073/pnas.1222821110
apa: Fang, S., Clark, R., Zheng, Y., Iyer Pascuzzi, A., Weitz, J., Kochian, L.,
… Benfey, P. (2013). Genotypic recognition and spatial responses by rice roots.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1222821110
chicago: Fang, Suqin, Randy Clark, Ying Zheng, Anjali Iyer Pascuzzi, Joshua Weitz,
Leon Kochian, Herbert Edelsbrunner, Hong Liao, and Philip Benfey. “Genotypic Recognition
and Spatial Responses by Rice Roots.” PNAS. National Academy of Sciences,
2013. https://doi.org/10.1073/pnas.1222821110.
ieee: S. Fang et al., “Genotypic recognition and spatial responses by rice
roots,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2670–2675,
2013.
ista: Fang S, Clark R, Zheng Y, Iyer Pascuzzi A, Weitz J, Kochian L, Edelsbrunner
H, Liao H, Benfey P. 2013. Genotypic recognition and spatial responses by rice
roots. PNAS. 110(7), 2670–2675.
mla: Fang, Suqin, et al. “Genotypic Recognition and Spatial Responses by Rice Roots.”
PNAS, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2670–75,
doi:10.1073/pnas.1222821110.
short: S. Fang, R. Clark, Y. Zheng, A. Iyer Pascuzzi, J. Weitz, L. Kochian, H. Edelsbrunner,
H. Liao, P. Benfey, PNAS 110 (2013) 2670–2675.
date_created: 2018-12-11T12:00:09Z
date_published: 2013-02-12T00:00:00Z
date_updated: 2021-01-12T07:00:29Z
day: '12'
department:
- _id: HeEd
doi: 10.1073/pnas.1222821110
external_id:
pmid:
- '23362379'
intvolume: ' 110'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/
month: '02'
oa: 1
oa_version: Published Version
page: 2670 - 2675
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3872'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genotypic recognition and spatial responses by rice roots
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2901'
abstract:
- lang: eng
text: ' We introduce the M-modes problem for graphical models: predicting the M
label configurations of highest probability that are at the same time local maxima
of the probability landscape. M-modes have multiple possible applications: because
they are intrinsically diverse, they provide a principled alternative to non-maximum
suppression techniques for structured prediction, they can act as codebook vectors
for quantizing the configuration space, or they can form component centers for
mixture model approximation. We present two algorithms for solving the M-modes
problem. The first algorithm solves the problem in polynomial time when the underlying
graphical model is a simple chain. The second algorithm solves the problem for
junction chains. In synthetic and real dataset, we demonstrate how M-modes can
improve the performance of prediction. We also use the generated modes as a tool
to understand the topography of the probability distribution of configurations,
for example with relation to the training set size and amount of noise in the
data. '
alternative_title:
- ' JMLR: W&CP'
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Zhu
full_name: Yan, Zhu
last_name: Yan
- first_name: Dimitris
full_name: Metaxas, Dimitris
last_name: Metaxas
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. Computing the M most probable
modes of a graphical model. In: Vol 31. JMLR; 2013:161-169.'
apa: 'Chen, C., Kolmogorov, V., Yan, Z., Metaxas, D., & Lampert, C. (2013).
Computing the M most probable modes of a graphical model (Vol. 31, pp. 161–169).
Presented at the AISTATS: Conference on Uncertainty in Artificial Intelligence,
Scottsdale, AZ, United States: JMLR.'
chicago: Chen, Chao, Vladimir Kolmogorov, Zhu Yan, Dimitris Metaxas, and Christoph
Lampert. “Computing the M Most Probable Modes of a Graphical Model,” 31:161–69.
JMLR, 2013.
ieee: 'C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, and C. Lampert, “Computing the
M most probable modes of a graphical model,” presented at the AISTATS: Conference
on Uncertainty in Artificial Intelligence, Scottsdale, AZ, United States, 2013,
vol. 31, pp. 161–169.'
ista: 'Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. 2013. Computing the M
most probable modes of a graphical model. AISTATS: Conference on Uncertainty
in Artificial Intelligence, JMLR: W&CP, vol. 31, 161–169.'
mla: Chen, Chao, et al. Computing the M Most Probable Modes of a Graphical Model.
Vol. 31, JMLR, 2013, pp. 161–69.
short: C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, C. Lampert, in:, JMLR, 2013,
pp. 161–169.
conference:
end_date: 2013-05-01
location: Scottsdale, AZ, United States
name: ' AISTATS: Conference on Uncertainty in Artificial Intelligence'
start_date: 2013-04-29
date_created: 2018-12-11T12:00:14Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:35Z
day: '01'
department:
- _id: HeEd
- _id: VlKo
- _id: ChLa
intvolume: ' 31'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://jmlr.org/proceedings/papers/v31/chen13a.html
month: '01'
oa: 1
oa_version: None
page: 161 - 169
publication_status: published
publisher: JMLR
publist_id: '3846'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing the M most probable modes of a graphical model
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2013'
...
---
_id: '2900'
author:
- first_name: Ricardo
full_name: Azevedo, Ricardo B
last_name: Azevedo
- first_name: Rolf
full_name: Lohaus, Rolf
last_name: Lohaus
- first_name: Tiago
full_name: Tiago Paixao
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Azevedo R, Lohaus R, Paixao T. Networking networks. Evolution & Development.
2013;10(5):514-515.
apa: Azevedo, R., Lohaus, R., & Paixao, T. (2013). Networking networks. Evolution
& Development. Wiley-Blackwell.
chicago: Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.”
Evolution & Development. Wiley-Blackwell, 2013.
ieee: R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” Evolution
& Development, vol. 10, no. 5. Wiley-Blackwell, pp. 514–515, 2013.
ista: Azevedo R, Lohaus R, Paixao T. 2013. Networking networks. Evolution &
Development. 10(5), 514–515.
mla: Azevedo, Ricardo, et al. “Networking Networks.” Evolution & Development,
vol. 10, no. 5, Wiley-Blackwell, 2013, pp. 514–15.
short: R. Azevedo, R. Lohaus, T. Paixao, Evolution & Development 10 (2013) 514–515.
date_created: 2018-12-11T12:00:14Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:34Z
day: '01'
extern: 1
intvolume: ' 10'
issue: '5'
main_file_link:
- open_access: '0'
url: http://onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2008.00265.x/abstract
month: '01'
page: 514 - 515
publication: Evolution & Development
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3858'
quality_controlled: 0
status: public
title: Networking networks
type: journal_article
volume: 10
year: '2013'
...
---
_id: '2906'
abstract:
- lang: eng
text: "Motivated by an application in cell biology, we describe an extension of
the kinetic data structures framework from Delaunay triangulations to fixed-radius
alpha complexes. Our algorithm is implemented\r\nusing CGAL, following the exact
geometric computation paradigm. We report on several\r\ntechniques to accelerate
the computation that turn our implementation applicable to the underlying biological\r\nproblem."
alternative_title:
- ALENEX
author:
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Kerber M, Edelsbrunner H. 3D kinetic alpha complexes and their implementation.
In: 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments.
Society of Industrial and Applied Mathematics; 2013:70-77. doi:10.1137/1.9781611972931.6'
apa: 'Kerber, M., & Edelsbrunner, H. (2013). 3D kinetic alpha complexes and
their implementation. In 2013 Proceedings of the 15th Workshop on Algorithm
Engineering and Experiments (pp. 70–77). New Orleans, LA, United States: Society
of Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611972931.6'
chicago: Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes
and Their Implementation.” In 2013 Proceedings of the 15th Workshop on Algorithm
Engineering and Experiments, 70–77. Society of Industrial and Applied Mathematics,
2013. https://doi.org/10.1137/1.9781611972931.6.
ieee: M. Kerber and H. Edelsbrunner, “3D kinetic alpha complexes and their implementation,”
in 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments,
New Orleans, LA, United States, 2013, pp. 70–77.
ista: 'Kerber M, Edelsbrunner H. 2013. 3D kinetic alpha complexes and their implementation.
2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments.
ALENEX: Algorithm Engineering and Experiments, ALENEX, , 70–77.'
mla: Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and
Their Implementation.” 2013 Proceedings of the 15th Workshop on Algorithm Engineering
and Experiments, Society of Industrial and Applied Mathematics, 2013, pp.
70–77, doi:10.1137/1.9781611972931.6.
short: M. Kerber, H. Edelsbrunner, in:, 2013 Proceedings of the 15th Workshop on
Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics,
2013, pp. 70–77.
conference:
end_date: 2013-01-07
location: New Orleans, LA, United States
name: 'ALENEX: Algorithm Engineering and Experiments'
start_date: 2013-01-07
date_created: 2018-12-11T12:00:16Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:36Z
day: '01'
ddc:
- '500'
department:
- _id: HeEd
doi: 10.1137/1.9781611972931.6
file:
- access_level: open_access
checksum: a15a3ba22df9445731507f3e06c9fcee
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:57Z
date_updated: 2020-07-14T12:45:52Z
file_id: '4720'
file_name: IST-2016-547-v1+1_2013-P-08-MedusaII.pdf
file_size: 403013
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 70 - 77
publication: 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments
publication_status: published
publisher: Society of Industrial and Applied Mathematics
publist_id: '3841'
pubrep_id: '547'
quality_controlled: '1'
scopus_import: 1
status: public
title: 3D kinetic alpha complexes and their implementation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2910'
abstract:
- lang: eng
text: "Coalescent simulation has become an indispensable tool in population genetics
and many complex evolutionary scenarios have been incorporated into the basic
algorithm. Despite many years of intense interest in spatial structure, however,
there are no available methods to simulate the ancestry of a sample of genes that
occupy a spatial continuum. This is mainly due to the severe technical problems
encountered by the classical model of isolation\r\nby distance. A recently introduced
model solves these technical problems and provides a solid theoretical basis for
the study of populations evolving in continuous space. We present a detailed algorithm
to simulate the coalescent process in this model, and provide an efficient implementation
of a generalised version of this algorithm as a freely available Python module."
author:
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space.
Bioinformatics. 2013;29(7):955-956. doi:10.1093/bioinformatics/btt067
apa: Kelleher, J., Barton, N. H., & Etheridge, A. (2013). Coalescent simulation
in continuous space. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btt067
chicago: Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent
Simulation in Continuous Space.” Bioinformatics. Oxford University Press,
2013. https://doi.org/10.1093/bioinformatics/btt067.
ieee: J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous
space,” Bioinformatics, vol. 29, no. 7. Oxford University Press, pp. 955–956,
2013.
ista: Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous
space. Bioinformatics. 29(7), 955–956.
mla: Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” Bioinformatics,
vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:10.1093/bioinformatics/btt067.
short: J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956.
date_created: 2018-12-11T12:00:17Z
date_published: 2013-02-07T00:00:00Z
date_updated: 2021-01-12T07:00:38Z
day: '07'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/bioinformatics/btt067
ec_funded: 1
file:
- access_level: open_access
checksum: a3b54d7477fac923815ac082403d9bd0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:04Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5189'
file_name: IST-2016-556-v1+1_bioinformatics-2013.pdf
file_size: 170197
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 29'
issue: '7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 955 - 956
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Bioinformatics
publication_status: published
publisher: Oxford University Press
publist_id: '3833'
pubrep_id: '556'
quality_controlled: '1'
scopus_import: 1
status: public
title: Coalescent simulation in continuous space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2013'
...
---
_id: '2909'
abstract:
- lang: eng
text: "We survey a class of models for spatially structured populations\r\nwhich
we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework
for modelling in which the key innovation is that random genetic drift\r\nis driven
by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes
some of the obstructions to modelling populations which evolve in two-\r\n(and
higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved
in data and how it fits with classical models. Finally we outline some\r\ndirections
for future research."
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum.
Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002
apa: Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in
a spatial continuum. Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/01/P01002
chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution
in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/01/P01002.
ieee: N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial
continuum,” Journal of Statistical Mechanics Theory and Experiment, vol.
2013, no. 1. IOP Publishing Ltd., 2013.
ista: Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum.
Journal of Statistical Mechanics Theory and Experiment. 2013(1).
mla: Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal
of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing
Ltd., 2013, doi:10.1088/1742-5468/2013/01/P01002.
short: N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory
and Experiment 2013 (2013).
date_created: 2018-12-11T12:00:17Z
date_published: 2013-01-16T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '16'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1088/1742-5468/2013/01/P01002
ec_funded: 1
file:
- access_level: open_access
checksum: ce8a4424385b3086138a1e054e16e0e3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:52Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5242'
file_name: IST-2016-557-v1+1_BEVrevised.pdf
file_size: 702583
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 2013'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted 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: Journal of Statistical Mechanics Theory and Experiment
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '3834'
pubrep_id: '557'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modelling evolution in a spatial continuum
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2013
year: '2013'
...
---
_id: '2908'
abstract:
- lang: eng
text: 'Hybridization is an almost inevitable component of speciation, and its study
can tell us much about that process. However, hybridization itself may have a
negligible influence on the origin of species: on the one hand, universally favoured
alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous
selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional
hybridisation may hardly affect the process of divergence.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Does hybridisation influence speciation? . Journal of Evolutionary
Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015
apa: Barton, N. H. (2013). Does hybridisation influence speciation? . Journal
of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015
chicago: Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal
of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015.
ieee: N. H. Barton, “Does hybridisation influence speciation? ,” Journal of
Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.
ista: Barton NH. 2013. Does hybridisation influence speciation? . Journal of Evolutionary
Biology. 26(2), 267–269.
mla: Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal
of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69,
doi:10.1111/jeb.12015.
short: N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.
date_created: 2018-12-11T12:00:17Z
date_published: 2013-01-17T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '17'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/jeb.12015
file:
- access_level: open_access
checksum: 716e88714c3411cd0bd70928b14ea692
content_type: text/rtf
creator: system
date_created: 2018-12-12T10:09:38Z
date_updated: 2020-07-14T12:45:52Z
file_id: '4762'
file_name: IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf
file_size: 13339
relation: main_file
- access_level: open_access
checksum: 957fd07c71c1b1eac2c65ae3311aca78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:39Z
date_updated: 2020-07-14T12:45:52Z
file_id: '4763'
file_name: IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf
file_size: 103437
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 26'
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 267 - 269
publication: Journal of Evolutionary Biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3835'
pubrep_id: '111'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Does hybridisation influence speciation? '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2013'
...
---
_id: '2907'
abstract:
- lang: eng
text: 'Sex and recombination are among the most striking features of the living
world, and they play a crucial role in allowing the evolution of complex adaptation.
The sharing of genomes through the sexual union of different individuals requires
elaborate behavioral and physiological adaptations. At the molecular level, the
alignment of two DNA double helices, followed by their precise cutting and rejoining,
is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary
consequences: distinct sexes, elaborate mating displays, selfish genetic elements,
and so on.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Recombination and sex. In: The Princeton Guide to Evolution.
Princeton University Press; 2013:328-333.'
apa: Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution
(pp. 328–333). Princeton University Press.
chicago: Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide
to Evolution, 328–33. Princeton University Press, 2013.
ieee: N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution,
Princeton University Press, 2013, pp. 328–333.
ista: 'Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution.
, 328–333.'
mla: Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution,
Princeton University Press, 2013, pp. 328–33.
short: N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University
Press, 2013, pp. 328–333.
date_created: 2018-12-11T12:00:16Z
date_published: 2013-11-04T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '04'
ddc:
- '576'
department:
- _id: NiBa
file:
- access_level: open_access
checksum: 8332ca9cb40f7e66d1006b175ce36b60
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: system
date_created: 2018-12-12T10:16:47Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5237'
file_name: IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx
file_size: 79838
relation: main_file
- access_level: open_access
checksum: 849f418620fb78d6ba23bb4f488ee93f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:48Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5238'
file_name: IST-2017-119-v1+2_Barton_Recombination_Sex.pdf
file_size: 144131
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 328 - 333
publication: The Princeton Guide to Evolution
publication_identifier:
isbn:
- '9780691149776'
publication_status: published
publisher: Princeton University Press
publist_id: '3839'
pubrep_id: '119'
quality_controlled: '1'
status: public
title: Recombination and sex
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2913'
abstract:
- lang: eng
text: 'The ability of an organism to distinguish between various stimuli is limited
by the structure and noise in the population code of its sensory neurons. Here
we infer a distance measure on the stimulus space directly from the recorded activity
of 100 neurons in the salamander retina. In contrast to previously used measures
of stimulus similarity, this "neural metric" tells us how distinguishable
a pair of stimulus clips is to the retina, based on the similarity between the
induced distributions of population responses. We show that the retinal distance
strongly deviates from Euclidean, or any static metric, yet has a simple structure:
we identify the stimulus features that the neural population is jointly sensitive
to, and show the support-vector-machine- like kernel function relating the stimulus
and neural response spaces. We show that the non-Euclidean nature of the retinal
distance has important consequences for neural decoding.'
article_number: '058104'
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Einat
full_name: Granot Atedgi, Einat
last_name: Granot Atedgi
- first_name: Ronen
full_name: Segev, Ronen
last_name: Segev
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: 'Tkačik G, Granot Atedgi E, Segev R, Schneidman E. Retinal metric: a stimulus
distance measure derived from population neural responses. Physical Review
Letters. 2013;110(5). doi:10.1103/PhysRevLett.110.058104'
apa: 'Tkačik, G., Granot Atedgi, E., Segev, R., & Schneidman, E. (2013). Retinal
metric: a stimulus distance measure derived from population neural responses.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.058104'
chicago: 'Tkačik, Gašper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman.
“Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.”
Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.058104.'
ieee: 'G. Tkačik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric:
a stimulus distance measure derived from population neural responses,” Physical
Review Letters, vol. 110, no. 5. American Physical Society, 2013.'
ista: 'Tkačik G, Granot Atedgi E, Segev R, Schneidman E. 2013. Retinal metric: a
stimulus distance measure derived from population neural responses. Physical Review
Letters. 110(5), 058104.'
mla: 'Tkačik, Gašper, et al. “Retinal Metric: A Stimulus Distance Measure Derived
from Population Neural Responses.” Physical Review Letters, vol. 110, no.
5, 058104, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.058104.'
short: G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters
110 (2013).
date_created: 2018-12-11T12:00:18Z
date_published: 2013-01-28T00:00:00Z
date_updated: 2021-01-12T07:00:39Z
day: '28'
department:
- _id: GaTk
doi: 10.1103/PhysRevLett.110.058104
intvolume: ' 110'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1205.6598
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '3830'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Retinal metric: a stimulus distance measure derived from population neural
responses'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2918'
abstract:
- lang: eng
text: "Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar
cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems,
including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during
zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however,
unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a
(Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic
A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms
an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2.
Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts
with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically,
Antxr2a functions as a Wnt-dependent polarized determinant, which, through the
action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V
axis.\r\n"
acknowledgement: This work was supported by the SNSF, the Swiss SystemsX.ch initiative
and LipidX-2008/011 (M.G-G. and F.G.v.d.G.), by the Fondation SANTE-Vaduz/Aide au
Soutien des Nouvelles Thérapies (F.G.v.d.G.) and by the ERC, the NCCR Frontiers
in Genetics and Chemical Biology programmes and the Polish–Swiss research program
(M.G-G.).
author:
- first_name: Irinka
full_name: Castanon, Irinka
last_name: Castanon
- first_name: Laurence
full_name: Abrami, Laurence
last_name: Abrami
- first_name: Laurent
full_name: Holtzer, Laurent
last_name: Holtzer
- 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: Françoise
full_name: Van Der Goot, Françoise
last_name: Van Der Goot
- first_name: Marcos
full_name: González Gaitán, Marcos
last_name: González Gaitán
citation:
ama: Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González
Gaitán M. Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature
Cell Biology. 2013;15(1):28-39. doi:10.1038/ncb2632
apa: Castanon, I., Abrami, L., Holtzer, L., Heisenberg, C.-P. J., Van Der Goot,
F., & González Gaitán, M. (2013). Anthrax toxin receptor 2a controls mitotic
spindle positioning. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2632
chicago: Castanon, Irinka, Laurence Abrami, Laurent Holtzer, Carl-Philipp J Heisenberg,
Françoise Van Der Goot, and Marcos González Gaitán. “Anthrax Toxin Receptor 2a
Controls Mitotic Spindle Positioning.” Nature Cell Biology. Nature Publishing
Group, 2013. https://doi.org/10.1038/ncb2632.
ieee: I. Castanon, L. Abrami, L. Holtzer, C.-P. J. Heisenberg, F. Van Der Goot,
and M. González Gaitán, “Anthrax toxin receptor 2a controls mitotic spindle positioning,”
Nature Cell Biology, vol. 15, no. 1. Nature Publishing Group, pp. 28–39,
2013.
ista: Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González
Gaitán M. 2013. Anthrax toxin receptor 2a controls mitotic spindle positioning.
Nature Cell Biology. 15(1), 28–39.
mla: Castanon, Irinka, et al. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle
Positioning.” Nature Cell Biology, vol. 15, no. 1, Nature Publishing Group,
2013, pp. 28–39, doi:10.1038/ncb2632.
short: I. Castanon, L. Abrami, L. Holtzer, C.-P.J. Heisenberg, F. Van Der Goot,
M. González Gaitán, Nature Cell Biology 15 (2013) 28–39.
date_created: 2018-12-11T12:00:20Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:41Z
day: '01'
department:
- _id: CaHe
doi: 10.1038/ncb2632
intvolume: ' 15'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 28 - 39
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3819'
quality_controlled: '1'
scopus_import: 1
status: public
title: Anthrax toxin receptor 2a controls mitotic spindle positioning
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2013'
...
---
_id: '2919'
abstract:
- lang: eng
text: The distribution of the phytohormone auxin regulates many aspects of plant
development including growth response to gravity. Gravitropic root curvature involves
coordinated and asymmetric cell elongation between the lower and upper side of
the root, mediated by differential cellular auxin levels. The asymmetry in the
auxin distribution is established and maintained by a spatio-temporal regulation
of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights
into the complex regulation of PIN abundance and activity during root gravitropism.
We show that PIN2 turnover is differentially regulated on the upper and lower
side of gravistimulated roots by distinct but partially overlapping auxin feedback
mechanisms. In addition to regulating transcription and clathrin-mediated internalization,
auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar
targeting and degradation. This effect of elevated auxin levels requires the activity
of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also
suboptimal auxin levels mediate PIN degradation utilizing the same signalling
pathway. These feedback mechanisms are functionally important during gravitropic
response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating
asymmetric growth.
author:
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Urszula
full_name: Kania, Urszula
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Baster P, Robert S, Kleine Vehn J, et al. SCF^TIR1 AFB-auxin signalling regulates
PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal.
2013;32(2):260-274. doi:10.1038/emboj.2012.310
apa: Baster, P., Robert, S., Kleine Vehn, J., Vanneste, S., Kania, U., Grunewald,
W., … Friml, J. (2013). SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking
and auxin fluxes during root gravitropism. EMBO Journal. Wiley-Blackwell.
https://doi.org/10.1038/emboj.2012.310
chicago: Baster, Pawel, Stéphanie Robert, Jürgen Kleine Vehn, Steffen Vanneste,
Urszula Kania, Wim Grunewald, Bert De Rybel, Tom Beeckman, and Jiří Friml. “SCF^TIR1
AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during
Root Gravitropism.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2012.310.
ieee: P. Baster et al., “SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar
trafficking and auxin fluxes during root gravitropism,” EMBO Journal, vol.
32, no. 2. Wiley-Blackwell, pp. 260–274, 2013.
ista: Baster P, Robert S, Kleine Vehn J, Vanneste S, Kania U, Grunewald W, De Rybel
B, Beeckman T, Friml J. 2013. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar
trafficking and auxin fluxes during root gravitropism. EMBO Journal. 32(2), 260–274.
mla: Baster, Pawel, et al. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar
Trafficking and Auxin Fluxes during Root Gravitropism.” EMBO Journal, vol.
32, no. 2, Wiley-Blackwell, 2013, pp. 260–74, doi:10.1038/emboj.2012.310.
short: P. Baster, S. Robert, J. Kleine Vehn, S. Vanneste, U. Kania, W. Grunewald,
B. De Rybel, T. Beeckman, J. Friml, EMBO Journal 32 (2013) 260–274.
date_created: 2018-12-11T12:00:20Z
date_published: 2013-01-23T00:00:00Z
date_updated: 2021-01-12T07:00:41Z
day: '23'
department:
- _id: JiFr
doi: 10.1038/emboj.2012.310
external_id:
pmid:
- '23211744'
intvolume: ' 32'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553380/
month: '01'
oa: 1
oa_version: Submitted Version
page: 260 - 274
pmid: 1
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3818'
quality_controlled: '1'
scopus_import: 1
status: public
title: SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin
fluxes during root gravitropism
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2920'
abstract:
- lang: eng
text: Cell polarisation in development is a common and fundamental process underlying
embryo patterning and morphogenesis, and has been extensively studied over the
past years. Our current knowledge of cell polarisation in development is predominantly
based on studies that have analysed polarisation of single cells, such as eggs,
or cellular aggregates with a stable polarising interface, such as cultured epithelial
cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly
of vertebrates, cell polarisation processes often encompass large numbers of cells
that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial
transitions with a highly complex spatiotemporal choreography. How such intricate
cell polarisation processes in embryonic development are achieved has only started
to be analysed. By using live imaging of neurulation in the transparent zebrafish
embryo, Buckley et al (2012) now describe a novel polarisation strategy by which
cells assemble an apical domain in the part of their cell body that intersects
with the midline of the forming neural rod. This mechanism, along with the previously
described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger
formation of both neural rod midline and lumen.
author:
- first_name: Julien
full_name: Compagnon, Julien
id: 2E3E0988-F248-11E8-B48F-1D18A9856A87
last_name: Compagnon
- 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: Compagnon J, Heisenberg C-PJ. Neurulation coordinating cell polarisation and
lumen formation. EMBO Journal. 2013;32(1):1-3. doi:10.1038/emboj.2012.325
apa: Compagnon, J., & Heisenberg, C.-P. J. (2013). Neurulation coordinating
cell polarisation and lumen formation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.325
chicago: Compagnon, Julien, and Carl-Philipp J Heisenberg. “Neurulation Coordinating
Cell Polarisation and Lumen Formation.” EMBO Journal. Wiley-Blackwell,
2013. https://doi.org/10.1038/emboj.2012.325.
ieee: J. Compagnon and C.-P. J. Heisenberg, “Neurulation coordinating cell polarisation
and lumen formation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell, pp.
1–3, 2013.
ista: Compagnon J, Heisenberg C-PJ. 2013. Neurulation coordinating cell polarisation
and lumen formation. EMBO Journal. 32(1), 1–3.
mla: Compagnon, Julien, and Carl-Philipp J. Heisenberg. “Neurulation Coordinating
Cell Polarisation and Lumen Formation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell,
2013, pp. 1–3, doi:10.1038/emboj.2012.325.
short: J. Compagnon, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 1–3.
date_created: 2018-12-11T12:00:20Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2021-01-12T07:00:42Z
day: '09'
department:
- _id: CaHe
doi: 10.1038/emboj.2012.325
external_id:
pmid:
- '23211745'
intvolume: ' 32'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545307/
month: '01'
oa: 1
oa_version: Submitted Version
page: 1 - 3
pmid: 1
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3817'
quality_controlled: '1'
scopus_import: 1
status: public
title: Neurulation coordinating cell polarisation and lumen formation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2940'
abstract:
- lang: eng
text: "A chain rule for an entropy notion H(.) states that the entropy H(X) of a
variable X decreases by at most l if conditioned on an l-bit string A, i.e., H(X|A)>=
H(X)-l. More generally, it satisfies a chain rule for conditional entropy if H(X|Y,A)>=
H(X|Y)-l.\r\n\r\nAll natural information theoretic entropy notions we are aware
of (like Shannon or min-entropy) satisfy some kind of chain rule for conditional
entropy. Moreover, many computational entropy notions (like Yao entropy, unpredictability
entropy and several variants of HILL entropy) satisfy the chain rule for conditional
entropy, though here not only the quantity decreases by l, but also the quality
of the entropy decreases exponentially in l. However, for \r\nthe standard notion
of conditional HILL entropy (the computational equivalent of min-entropy) the
existence of such a rule was unknown so far.\r\n\r\nIn this paper, we prove that
for conditional HILL entropy no meaningful chain rule exists, assuming the existence
of one-way permutations: there exist distributions X,Y,A, where A is a distribution
over a single bit, but $H(X|Y)>>H(X|Y,A)$, even if we simultaneously allow
for a massive degradation in the quality of the entropy.\r\n\r\nThe idea underlying
our construction is based on a surprising connection between the chain rule for
HILL entropy and deniable encryption. "
alternative_title:
- LNCS
author:
- 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: Akshay
full_name: Wadia, Akshay
last_name: Wadia
citation:
ama: 'Krenn S, Pietrzak KZ, Wadia A. A counterexample to the chain rule for conditional
HILL entropy, and what deniable encryption has to do with it. In: Sahai A, ed.
Vol 7785. Springer; 2013:23-39. doi:10.1007/978-3-642-36594-2_2'
apa: 'Krenn, S., Pietrzak, K. Z., & Wadia, A. (2013). A counterexample to the
chain rule for conditional HILL entropy, and what deniable encryption has to do
with it. In A. Sahai (Ed.) (Vol. 7785, pp. 23–39). Presented at the TCC: Theory
of Cryptography Conference, Tokyo, Japan: Springer. https://doi.org/10.1007/978-3-642-36594-2_2'
chicago: Krenn, Stephan, Krzysztof Z Pietrzak, and Akshay Wadia. “A Counterexample
to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has
to Do with It.” edited by Amit Sahai, 7785:23–39. Springer, 2013. https://doi.org/10.1007/978-3-642-36594-2_2.
ieee: 'S. Krenn, K. Z. Pietrzak, and A. Wadia, “A counterexample to the chain rule
for conditional HILL entropy, and what deniable encryption has to do with it,”
presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan, 2013, vol.
7785, pp. 23–39.'
ista: 'Krenn S, Pietrzak KZ, Wadia A. 2013. A counterexample to the chain rule for
conditional HILL entropy, and what deniable encryption has to do with it. TCC:
Theory of Cryptography Conference, LNCS, vol. 7785, 23–39.'
mla: Krenn, Stephan, et al. A Counterexample to the Chain Rule for Conditional
HILL Entropy, and What Deniable Encryption Has to Do with It. Edited by Amit
Sahai, vol. 7785, Springer, 2013, pp. 23–39, doi:10.1007/978-3-642-36594-2_2.
short: S. Krenn, K.Z. Pietrzak, A. Wadia, in:, A. Sahai (Ed.), Springer, 2013, pp.
23–39.
conference:
end_date: 2013-03-06
location: Tokyo, Japan
name: 'TCC: Theory of Cryptography Conference'
start_date: 2013-03-03
date_created: 2018-12-11T12:00:27Z
date_published: 2013-01-29T00:00:00Z
date_updated: 2023-02-23T10:00:43Z
day: '29'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.1007/978-3-642-36594-2_2
ec_funded: 1
editor:
- first_name: Amit
full_name: Sahai, Amit
last_name: Sahai
file:
- access_level: open_access
checksum: beb0cc1c0579da2d2e84394230a5da78
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T14:11:11Z
date_updated: 2020-07-14T12:45:54Z
file_id: '5875'
file_name: 2013_LNCS_Krenn.pdf
file_size: 414823
relation: main_file
file_date_updated: 2020-07-14T12:45:54Z
has_accepted_license: '1'
intvolume: ' 7785'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 23 - 39
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: '3795'
quality_controlled: '1'
related_material:
record:
- id: '1479'
relation: later_version
status: public
scopus_import: 1
status: public
title: A counterexample to the chain rule for conditional HILL entropy, and what deniable
encryption has to do with it
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7785
year: '2013'
...
---
_id: '2948'
abstract:
- lang: eng
text: 'Many visual datasets are traditionally used to analyze the performance of
different learning techniques. The evaluation is usually done within each dataset,
therefore it is questionable if such results are a reliable indicator of true
generalization ability. We propose here an algorithm to exploit the existing data
resources when learning on a new multiclass problem. Our main idea is to identify
an image representation that decomposes orthogonally into two subspaces: a part
specific to each dataset, and a part generic to, and therefore shared between,
all the considered source sets. This allows us to use the generic representation
as un-biased reference knowledge for a novel classification task. By casting the
method in the multi-view setting, we also make it possible to use different features
for different databases. We call the algorithm MUST, Multitask Unaligned Shared
knowledge Transfer. Through extensive experiments on five public datasets, we
show that MUST consistently improves the cross-datasets generalization performance.'
acknowledgement: This work was supported by the PASCAL 2 Network of Excellence (TT)
and by the Newton International Fellowship (NQ)
alternative_title:
- LNCS
author:
- first_name: Tatiana
full_name: Tommasi, Tatiana
last_name: Tommasi
- first_name: Novi
full_name: Quadrianto, Novi
last_name: Quadrianto
- first_name: Barbara
full_name: Caputo, Barbara
last_name: Caputo
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Tommasi T, Quadrianto N, Caputo B, Lampert C. Beyond dataset bias: Multi-task
unaligned shared knowledge transfer. 2013;7724:1-15. doi:10.1007/978-3-642-37331-2_1'
apa: 'Tommasi, T., Quadrianto, N., Caputo, B., & Lampert, C. (2013). Beyond
dataset bias: Multi-task unaligned shared knowledge transfer. Presented at the
ACCV: Asian Conference on Computer Vision, Daejeon, Korea: Springer. https://doi.org/10.1007/978-3-642-37331-2_1'
chicago: 'Tommasi, Tatiana, Novi Quadrianto, Barbara Caputo, and Christoph Lampert.
“Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer.” Lecture
Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-37331-2_1.'
ieee: 'T. Tommasi, N. Quadrianto, B. Caputo, and C. Lampert, “Beyond dataset bias:
Multi-task unaligned shared knowledge transfer,” vol. 7724. Springer, pp. 1–15,
2013.'
ista: 'Tommasi T, Quadrianto N, Caputo B, Lampert C. 2013. Beyond dataset bias:
Multi-task unaligned shared knowledge transfer. 7724, 1–15.'
mla: 'Tommasi, Tatiana, et al. Beyond Dataset Bias: Multi-Task Unaligned Shared
Knowledge Transfer. Vol. 7724, Springer, 2013, pp. 1–15, doi:10.1007/978-3-642-37331-2_1.'
short: T. Tommasi, N. Quadrianto, B. Caputo, C. Lampert, 7724 (2013) 1–15.
conference:
end_date: 2012-11-09
location: Daejeon, Korea
name: 'ACCV: Asian Conference on Computer Vision'
start_date: 2012-11-05
date_created: 2018-12-11T12:00:30Z
date_published: 2013-04-04T00:00:00Z
date_updated: 2020-08-11T10:09:54Z
day: '04'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1007/978-3-642-37331-2_1
file:
- access_level: open_access
checksum: a0a7234a89e2192af655b0d0ae3bf445
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T14:03:11Z
date_updated: 2020-07-14T12:45:55Z
file_id: '5874'
file_name: 2012_ACCV_Tommasi.pdf
file_size: 1513620
relation: main_file
file_date_updated: 2020-07-14T12:45:55Z
has_accepted_license: '1'
intvolume: ' 7724'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 1 - 15
publication_status: published
publisher: Springer
publist_id: '3784'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: 'Beyond dataset bias: Multi-task unaligned shared knowledge transfer'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7724
year: '2013'
...
---
_id: '2973'
abstract:
- lang: eng
text: "Efficient zero-knowledge proofs of knowledge (ZK-PoK) are basic building
blocks of many practical cryptographic applications such as identification schemes,
group signatures, and secure multiparty computation. Currently, first applications
that critically rely on ZK-PoKs are being deployed in the real world. The most
prominent example is Direct Anonymous Attestation (DAA), which was adopted by
the Trusted Computing Group (TCG) and implemented as one of the functionalities
of the cryptographic Trusted Platform Module (TPM) chip.\n\nImplementing systems
using ZK-PoK turns out to be challenging, since ZK-PoK are, loosely speaking,
significantly more complex than standard crypto primitives, such as encryption
and signature schemes. As a result, implementation cycles of ZK-PoK are time-consuming
and error-prone, in particular for developers with minor or no cryptographic skills.
\n\nIn this paper we report on our ongoing and future research vision with the
goal to bring ZK-PoK to practice by making them accessible to crypto and security
engineers. To this end we are developing compilers and related tools that support
and partially automate the design, implementation, verification and secure implementation
of ZK-PoK protocols."
acknowledgement: This work is being performed within the FP7 EU project CACE (Computer
Aided Cryptography Engineering).
alternative_title:
- LNCS
author:
- first_name: Endre
full_name: Bangerter, Endre
last_name: Bangerter
- first_name: Stefania
full_name: Barzan, Stefania
last_name: Barzan
- first_name: Stephan
full_name: Stephan Krenn
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- first_name: Ahmad
full_name: Sadeghi, Ahmad-Reza
last_name: Sadeghi
- first_name: Thomas
full_name: Schneider, Thomas
last_name: Schneider
- first_name: Joe
full_name: Tsay, Joe-Kai
last_name: Tsay
citation:
ama: 'Bangerter E, Barzan S, Krenn S, Sadeghi A, Schneider T, Tsay J. Bringing Zero-Knowledge
Proofs of Knowledge to Practice. In: Christianson B, Malcolm J, Matyas V, Roe
M, eds. Vol 7028. Springer; 2013:51-62. doi:10.1007/978-3-642-36213-2_9'
apa: 'Bangerter, E., Barzan, S., Krenn, S., Sadeghi, A., Schneider, T., & Tsay,
J. (2013). Bringing Zero-Knowledge Proofs of Knowledge to Practice. In B. Christianson,
J. Malcolm, V. Matyas, & M. Roe (Eds.) (Vol. 7028, pp. 51–62). Presented at
the SPW: Security Protocols Workshop, Springer. https://doi.org/10.1007/978-3-642-36213-2_9'
chicago: Bangerter, Endre, Stefania Barzan, Stephan Krenn, Ahmad Sadeghi, Thomas
Schneider, and Joe Tsay. “Bringing Zero-Knowledge Proofs of Knowledge to Practice.”
edited by Bruce Christianson, James Malcolm, Vashek Matyas, and Michael Roe, 7028:51–62.
Springer, 2013. https://doi.org/10.1007/978-3-642-36213-2_9.
ieee: 'E. Bangerter, S. Barzan, S. Krenn, A. Sadeghi, T. Schneider, and J. Tsay,
“Bringing Zero-Knowledge Proofs of Knowledge to Practice,” presented at the SPW:
Security Protocols Workshop, 2013, vol. 7028, pp. 51–62.'
ista: 'Bangerter E, Barzan S, Krenn S, Sadeghi A, Schneider T, Tsay J. 2013. Bringing
Zero-Knowledge Proofs of Knowledge to Practice. SPW: Security Protocols Workshop,
LNCS, vol. 7028, 51–62.'
mla: Bangerter, Endre, et al. Bringing Zero-Knowledge Proofs of Knowledge to
Practice. Edited by Bruce Christianson et al., vol. 7028, Springer, 2013,
pp. 51–62, doi:10.1007/978-3-642-36213-2_9.
short: E. Bangerter, S. Barzan, S. Krenn, A. Sadeghi, T. Schneider, J. Tsay, in:,
B. Christianson, J. Malcolm, V. Matyas, M. Roe (Eds.), Springer, 2013, pp. 51–62.
conference:
name: 'SPW: Security Protocols Workshop'
date_created: 2018-12-11T12:00:38Z
date_published: 2013-01-08T00:00:00Z
date_updated: 2021-01-12T07:40:10Z
day: '08'
doi: 10.1007/978-3-642-36213-2_9
editor:
- first_name: Bruce
full_name: Christianson, Bruce
last_name: Christianson
- first_name: James
full_name: Malcolm, James A.
last_name: Malcolm
- first_name: Vashek
full_name: Matyas, Vashek
last_name: Matyas
- first_name: Michael
full_name: Roe, Michael
last_name: Roe
extern: 1
intvolume: ' 7028'
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2009/211.pdf
month: '01'
oa: 1
page: 51 - 62
publication_status: published
publisher: Springer
publist_id: '3732'
quality_controlled: 0
status: public
title: Bringing Zero-Knowledge Proofs of Knowledge to Practice
type: conference
volume: 7028
year: '2013'
...
---
_id: '3116'
abstract:
- lang: eng
text: Multithreaded programs coordinate their interaction through synchronization
primitives like mutexes and semaphores, which are managed by an OS-provided resource
manager. We propose algorithms for the automatic construction of code-aware resource
managers for multithreaded embedded applications. Such managers use knowledge
about the structure and resource usage (mutex and semaphore usage) of the threads
to guarantee deadlock freedom and progress while managing resources in an efficient
way. Our algorithms compute managers as winning strategies in certain infinite
games, and produce a compact code description of these strategies. We have implemented
the algorithms in the tool Cynthesis. Given a multithreaded program in C, the
tool produces C code implementing a code-aware resource manager. We show in experiments
that Cynthesis produces compact resource managers within a few minutes on a set
of embedded benchmarks with up to 6 threads. © 2012 Springer Science+Business
Media, LLC.
acknowledgement: This research was supported in part by the National Science Foundation
CAREER award CCR-0132780, by the ONR grant N00014-02-1-0671, by the National Science
Foundation grants CCR-0427202 and CCR-0234690, and by the ARP award TO.030.MM.D.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Marco
full_name: Faella, Marco
last_name: Faella
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
- first_name: Vishwanath
full_name: Raman, Vishwanath
last_name: Raman
citation:
ama: Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. Code aware resource
management. Formal Methods in System Design. 2013;42(2):142-174. doi:10.1007/s10703-012-0170-4
apa: Chatterjee, K., De Alfaro, L., Faella, M., Majumdar, R., & Raman, V. (2013).
Code aware resource management. Formal Methods in System Design. Springer.
https://doi.org/10.1007/s10703-012-0170-4
chicago: Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, Ritankar Majumdar,
and Vishwanath Raman. “Code Aware Resource Management.” Formal Methods in System
Design. Springer, 2013. https://doi.org/10.1007/s10703-012-0170-4.
ieee: K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, and V. Raman, “Code aware
resource management,” Formal Methods in System Design, vol. 42, no. 2.
Springer, pp. 142–174, 2013.
ista: Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. 2013. Code aware
resource management. Formal Methods in System Design. 42(2), 142–174.
mla: Chatterjee, Krishnendu, et al. “Code Aware Resource Management.” Formal
Methods in System Design, vol. 42, no. 2, Springer, 2013, pp. 142–74, doi:10.1007/s10703-012-0170-4.
short: K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, V. Raman, Formal Methods
in System Design 42 (2013) 142–174.
date_created: 2018-12-11T12:01:29Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2021-01-12T07:41:10Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/s10703-012-0170-4
intvolume: ' 42'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 142 - 174
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '3583'
quality_controlled: '1'
scopus_import: 1
status: public
title: Code aware resource management
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2013'
...
---
_id: '2815'
abstract:
- lang: eng
text: The fact that a sum of isotropic Gaussian kernels can have more modes than
kernels is surprising. Extra (ghost) modes do not exist in ℝ1 and are generally
not well studied in higher dimensions. We study a configuration of n+1 Gaussian
kernels for which there are exactly n+2 modes. We show that all modes lie on a
finite set of lines, which we call axes, and study the restriction of the Gaussian
mixture to these axes in order to discover that there are an exponential number
of critical points in this configuration. Although the existence of ghost modes
remained unknown due to the difficulty of finding examples in ℝ2, we show that
the resilience of ghost modes grows like the square root of the dimension. In
addition, we exhibit finite configurations of isotropic Gaussian kernels with
superlinearly many modes.
acknowledgement: This research is partially supported by the National Science Foundation
(NSF) under Grant DBI-0820624, by the European Science Foundation under the Research
Networking Programme, and the Russian Government Project 11.G34.31.0053.
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Brittany Terese
full_name: Fasy, Brittany Terese
id: F65D502E-E68D-11E9-9252-C644099818F6
last_name: Fasy
- first_name: Günter
full_name: Rote, Günter
last_name: Rote
citation:
ama: 'Edelsbrunner H, Fasy BT, Rote G. Add isotropic Gaussian kernels at own risk:
More and more resilient modes in higher dimensions. Discrete & Computational
Geometry. 2013;49(4):797-822. doi:10.1007/s00454-013-9517-x'
apa: 'Edelsbrunner, H., Fasy, B. T., & Rote, G. (2013). Add isotropic Gaussian
kernels at own risk: More and more resilient modes in higher dimensions. Discrete
& Computational Geometry. Springer. https://doi.org/10.1007/s00454-013-9517-x'
chicago: 'Edelsbrunner, Herbert, Brittany Terese Fasy, and Günter Rote. “Add Isotropic
Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.”
Discrete & Computational Geometry. Springer, 2013. https://doi.org/10.1007/s00454-013-9517-x.'
ieee: 'H. Edelsbrunner, B. T. Fasy, and G. Rote, “Add isotropic Gaussian kernels
at own risk: More and more resilient modes in higher dimensions,” Discrete
& Computational Geometry, vol. 49, no. 4. Springer, pp. 797–822, 2013.'
ista: 'Edelsbrunner H, Fasy BT, Rote G. 2013. Add isotropic Gaussian kernels at
own risk: More and more resilient modes in higher dimensions. Discrete & Computational
Geometry. 49(4), 797–822.'
mla: 'Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk:
More and More Resilient Modes in Higher Dimensions.” Discrete & Computational
Geometry, vol. 49, no. 4, Springer, 2013, pp. 797–822, doi:10.1007/s00454-013-9517-x.'
short: H. Edelsbrunner, B.T. Fasy, G. Rote, Discrete & Computational Geometry
49 (2013) 797–822.
date_created: 2018-12-11T11:59:44Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2023-02-23T11:13:49Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00454-013-9517-x
intvolume: ' 49'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00454-013-9517-x
month: '06'
oa: 1
oa_version: Published Version
page: 797 - 822
publication: Discrete & Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer
publist_id: '3991'
quality_controlled: '1'
related_material:
record:
- id: '3134'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Add isotropic Gaussian kernels at own risk: More and more resilient modes
in higher dimensions'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 49
year: '2013'
...
---
_id: '2939'
abstract:
- lang: eng
text: In this paper, we present the first output-sensitive algorithm to compute
the persistence diagram of a filtered simplicial complex. For any Γ > 0, it
returns only those homology classes with persistence at least Γ. Instead of the
classical reduction via column operations, our algorithm performs rank computations
on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0, 1), the
running time is O (C (1 - δ) Γ R d (n) log n), where C (1 - δ) Γ is the number
of homology classes with persistence at least (1 - δ) Γ, n is the total number
of simplices in the complex, d its dimension, and R d (n) is the complexity of
computing the rank of an n × n matrix with O (d n) nonzero entries. Depending
on the choice of the rank algorithm, this yields a deterministic O (C (1 - δ)
Γ n 2.376) algorithm, an O (C (1 - δ) Γ n 2.28) Las-Vegas algorithm, or an O (C
(1 - δ) Γ n 2 + ε{lunate}) Monte-Carlo algorithm for an arbitrary ε{lunate} >
0. The space complexity of the Monte-Carlo version is bounded by O (d n) = O (n
log n).
acknowledgement: The authors thank Herbert Edelsbrunner for many helpful discussions
and suggestions. Moreover, they are grateful for the careful reviews that helped
to improve the quality of the paper.
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
citation:
ama: 'Chen C, Kerber M. An output sensitive algorithm for persistent homology. Computational
Geometry: Theory and Applications. 2013;46(4):435-447. doi:10.1016/j.comgeo.2012.02.010'
apa: 'Chen, C., & Kerber, M. (2013). An output sensitive algorithm for persistent
homology. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2012.02.010'
chicago: 'Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent
Homology.” Computational Geometry: Theory and Applications. Elsevier, 2013.
https://doi.org/10.1016/j.comgeo.2012.02.010.'
ieee: 'C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,”
Computational Geometry: Theory and Applications, vol. 46, no. 4. Elsevier,
pp. 435–447, 2013.'
ista: 'Chen C, Kerber M. 2013. An output sensitive algorithm for persistent homology.
Computational Geometry: Theory and Applications. 46(4), 435–447.'
mla: 'Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent
Homology.” Computational Geometry: Theory and Applications, vol. 46, no.
4, Elsevier, 2013, pp. 435–47, doi:10.1016/j.comgeo.2012.02.010.'
short: 'C. Chen, M. Kerber, Computational Geometry: Theory and Applications 46 (2013)
435–447.'
date_created: 2018-12-11T12:00:27Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2023-02-23T11:24:10Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2012.02.010
intvolume: ' 46'
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 435 - 447
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '3796'
quality_controlled: '1'
related_material:
record:
- id: '3367'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: An output sensitive algorithm for persistent homology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2013'
...
---
_id: '344'
abstract:
- lang: eng
text: Copper-based selenides are attracting increasing interest due to their outstanding
optoelectronic and thermoelectric properties. Herein a novel colloidal synthetic
route to prepare Cu2SnSe3 nanocrystals with controlled size, shape and composition
is presented. The high yield of the developed procedure allowed its up-scaling
to the production of grams of colloidal Cu2SnSe3 nanocrystals. These nanocrystals
were used as building blocks for the production of Cu2SnSe3 bulk nanostructured
materials by spark plasma sintering. The thermoelectric properties of the prepared
nanocrystalline Cu2SnSe3 pellets were characterized in the temperature range from
300 to 720 K. The obtained results show the bottom-up production of nanocrystalline
materials from solution-processed nanocrystals to be a potentially advantageous
alternative to conventional methods of production of efficient thermoelectric
materials.
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: Umberto
full_name: Anselmi Tamburini, Umberto
last_name: Anselmi Tamburini
- first_name: Reza
full_name: Zamani, Reza
last_name: Zamani
- first_name: Stéphane
full_name: Gorsse, Stéphane
last_name: Gorsse
- first_name: Wenhua
full_name: Li, Wenhua
last_name: Li
- first_name: Antonio
full_name: López, Antonio
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, Cadavid D, Anselmi Tamburini U, et al. Colloidal synthesis and thermoelectric
properties of Cu 2SnSe3 nanocrystals. Journal of Materials Chemistry A.
2013;1(4):1421-1426. doi:10.1039/C2TA00419D
apa: Ibáñez, M., Cadavid, D., Anselmi Tamburini, U., Zamani, R., Gorsse, S., Li,
W., … Cabot, A. (2013). Colloidal synthesis and thermoelectric properties of Cu
2SnSe3 nanocrystals. Journal of Materials Chemistry A. Royal Society of
Chemistry. https://doi.org/10.1039/C2TA00419D
chicago: Ibáñez, Maria, Doris Cadavid, Umberto Anselmi Tamburini, Reza Zamani, Stéphane
Gorsse, Wenhua Li, Antonio López, Joan Morante, Jordi Arbiol, and Andreu Cabot.
“Colloidal Synthesis and Thermoelectric Properties of Cu 2SnSe3 Nanocrystals.”
Journal of Materials Chemistry A. Royal Society of Chemistry, 2013. https://doi.org/10.1039/C2TA00419D.
ieee: M. Ibáñez et al., “Colloidal synthesis and thermoelectric properties
of Cu 2SnSe3 nanocrystals,” Journal of Materials Chemistry A, vol. 1, no.
4. Royal Society of Chemistry, pp. 1421–1426, 2013.
ista: Ibáñez M, Cadavid D, Anselmi Tamburini U, Zamani R, Gorsse S, Li W, López
A, Morante J, Arbiol J, Cabot A. 2013. Colloidal synthesis and thermoelectric
properties of Cu 2SnSe3 nanocrystals. Journal of Materials Chemistry A. 1(4),
1421–1426.
mla: Ibáñez, Maria, et al. “Colloidal Synthesis and Thermoelectric Properties of
Cu 2SnSe3 Nanocrystals.” Journal of Materials Chemistry A, vol. 1, no.
4, Royal Society of Chemistry, 2013, pp. 1421–26, doi:10.1039/C2TA00419D.
short: M. Ibáñez, D. Cadavid, U. Anselmi Tamburini, R. Zamani, S. Gorsse, W. Li,
A. López, J. Morante, J. Arbiol, A. Cabot, Journal of Materials Chemistry A 1
(2013) 1421–1426.
date_created: 2018-12-11T11:45:56Z
date_published: 2013-01-28T00:00:00Z
date_updated: 2021-01-12T07:43:28Z
day: '28'
doi: 10.1039/C2TA00419D
extern: '1'
intvolume: ' 1'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-00917429/
month: '01'
oa: 1
oa_version: Submitted Version
page: 1421 - 1426
publication: Journal of Materials Chemistry A
publication_status: published
publisher: Royal Society of Chemistry
publist_id: '7484'
quality_controlled: '1'
status: public
title: Colloidal synthesis and thermoelectric properties of Cu 2SnSe3 nanocrystals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2013'
...
---
_id: '352'
abstract:
- lang: eng
text: The presence of organic ligands on the surface of colloidal nanoparticles
strongly limits their performance in technological applications where charge carrier
transfer/transport plays an important role. We use metal salts, matched with the
nanoparticle composition, to eliminate the surface organic ligands without introducing
extrinsic impurities in the final nanomaterial. The potential of the simple, general
and scalable processes presented here is demonstrated by characterizing the thermoelectric
properties of nanostructured Ag2Te produced by the bottom up assembly of Ag2Te
nanocrystals. A 6-fold increase of the thermoelectric figure of merit of Ag2Te
was obtained when organic ligands were displaced by AgNO3. The same procedure
can enhance the performance of nanocrystals and nanocrystal-based devices in a
broad range of applications, from photovoltaics and thermoelectrics to catalysis.
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: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Oscar
full_name: Durá, Oscar
last_name: Durá
- first_name: Marco
full_name: López De La Torre, Marco
last_name: López De La Torre
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Cadavid D, Ibáñez M, Shavel A, Durá O, López De La Torre M, Cabot A. Organic
ligand displacement by metal salts to enhance nanoparticle functionality: Thermoelectric
properties of Ag inf 2 inf Te. Journal of Materials Chemistry A. 2013;1(15):4864-4870.
doi:10.1039/C3TA01455J'
apa: 'Cadavid, D., Ibáñez, M., Shavel, A., Durá, O., López De La Torre, M., &
Cabot, A. (2013). Organic ligand displacement by metal salts to enhance nanoparticle
functionality: Thermoelectric properties of Ag inf 2 inf Te. Journal of Materials
Chemistry A. Royal Society of Chemistry. https://doi.org/10.1039/C3TA01455J'
chicago: 'Cadavid, Doris, Maria Ibáñez, Alexey Shavel, Oscar Durá, Marco López De
La Torre, and Andreu Cabot. “Organic Ligand Displacement by Metal Salts to Enhance
Nanoparticle Functionality: Thermoelectric Properties of Ag Inf 2 Inf Te.” Journal
of Materials Chemistry A. Royal Society of Chemistry, 2013. https://doi.org/10.1039/C3TA01455J.'
ieee: 'D. Cadavid, M. Ibáñez, A. Shavel, O. Durá, M. López De La Torre, and A. Cabot,
“Organic ligand displacement by metal salts to enhance nanoparticle functionality:
Thermoelectric properties of Ag inf 2 inf Te,” Journal of Materials Chemistry
A, vol. 1, no. 15. Royal Society of Chemistry, pp. 4864–4870, 2013.'
ista: 'Cadavid D, Ibáñez M, Shavel A, Durá O, López De La Torre M, Cabot A. 2013.
Organic ligand displacement by metal salts to enhance nanoparticle functionality:
Thermoelectric properties of Ag inf 2 inf Te. Journal of Materials Chemistry A.
1(15), 4864–4870.'
mla: 'Cadavid, Doris, et al. “Organic Ligand Displacement by Metal Salts to Enhance
Nanoparticle Functionality: Thermoelectric Properties of Ag Inf 2 Inf Te.” Journal
of Materials Chemistry A, vol. 1, no. 15, Royal Society of Chemistry, 2013,
pp. 4864–70, doi:10.1039/C3TA01455J.'
short: D. Cadavid, M. Ibáñez, A. Shavel, O. Durá, M. López De La Torre, A. Cabot,
Journal of Materials Chemistry A 1 (2013) 4864–4870.
date_created: 2018-12-11T11:45:58Z
date_published: 2013-02-13T00:00:00Z
date_updated: 2021-01-12T07:44:02Z
day: '13'
doi: 10.1039/C3TA01455J
extern: '1'
intvolume: ' 1'
issue: '15'
language:
- iso: eng
month: '02'
oa_version: None
page: 4864 - 4870
publication: Journal of Materials Chemistry A
publication_status: published
publisher: Royal Society of Chemistry
publist_id: '7481'
quality_controlled: '1'
status: public
title: 'Organic ligand displacement by metal salts to enhance nanoparticle functionality:
Thermoelectric properties of Ag inf 2 inf Te'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2013'
...
---
_id: '378'
abstract:
- lang: eng
text: Until recently, to prepare nanocrystals of a new material, scientists searched
their shelves for the appropriate molecular precursors, surfactants, and solvents.
They then optimized the reaction conditions for the atoms to self-assemble into
monodisperse nanocrystals (1). This approach is being replaced by a simpler strategy,
in which preformed nanocrystals serve as templates to produce nanoparticles with
a different composition through chemical transformation. On page 964 of this issue,
Oh et al. (2) report a powerful mechanism that allows the composition of oxide
nanoparticles to be transformed in solution and at low temperatures.
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: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Ibáñez M, Cabot A. All change for nanocrystals. Science. 2013;340(6135):935-936.
doi:10.1126/science.1239221
apa: Ibáñez, M., & Cabot, A. (2013). All change for nanocrystals. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1239221
chicago: Ibáñez, Maria, and Andreu Cabot. “All Change for Nanocrystals.” Science.
American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1239221.
ieee: M. Ibáñez and A. Cabot, “All change for nanocrystals,” Science, vol.
340, no. 6135. American Association for the Advancement of Science, pp. 935–936,
2013.
ista: Ibáñez M, Cabot A. 2013. All change for nanocrystals. Science. 340(6135),
935–936.
mla: Ibáñez, Maria, and Andreu Cabot. “All Change for Nanocrystals.” Science,
vol. 340, no. 6135, American Association for the Advancement of Science, 2013,
pp. 935–36, doi:10.1126/science.1239221.
short: M. Ibáñez, A. Cabot, Science 340 (2013) 935–936.
date_created: 2018-12-11T11:46:08Z
date_published: 2013-05-24T00:00:00Z
date_updated: 2021-01-12T07:52:09Z
day: '24'
doi: 10.1126/science.1239221
extern: '1'
intvolume: ' 340'
issue: '6135'
language:
- iso: eng
month: '05'
oa_version: None
page: 935 - 936
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7451'
status: public
title: All change for nanocrystals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 340
year: '2013'
...
---
_id: '3261'
abstract:
- lang: eng
text: Cells in a developing embryo have no direct way of "measuring" their
physical position. Through a variety of processes, however, the expression levels
of multiple genes come to be correlated with position, and these expression levels
thus form a code for "positional information." We show how to measure
this information, in bits, using the gap genes in the Drosophila embryo as an
example. Individual genes carry nearly two bits of information, twice as much
as expected if the expression patterns consisted only of on/off domains separated
by sharp boundaries. Taken together, four gap genes carry enough information to
define a cell's location with an error bar of ~1% along the anterior-posterior
axis of the embryo. This precision is nearly enough for each cell to have a unique
identity, which is the maximum information the system can use, and is nearly constant
along the length of the embryo. We argue that this constancy is a signature of
optimality in the transmission of information from primary morphogen inputs to
the output of the gap gene network.
author:
- first_name: Julien
full_name: Dubuis, Julien
last_name: Dubuis
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Eric
full_name: Wieschaus, Eric
last_name: Wieschaus
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. Positional information,
in bits. PNAS. 2013;110(41):16301-16308. doi:10.1073/pnas.1315642110
apa: Dubuis, J., Tkačik, G., Wieschaus, E., Gregor, T., & Bialek, W. (2013).
Positional information, in bits. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315642110
chicago: Dubuis, Julien, Gašper Tkačik, Eric Wieschaus, Thomas Gregor, and William
Bialek. “Positional Information, in Bits.” PNAS. National Academy of Sciences,
2013. https://doi.org/10.1073/pnas.1315642110.
ieee: J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional
information, in bits,” PNAS, vol. 110, no. 41. National Academy of Sciences,
pp. 16301–16308, 2013.
ista: Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. 2013. Positional information,
in bits. PNAS. 110(41), 16301–16308.
mla: Dubuis, Julien, et al. “Positional Information, in Bits.” PNAS, vol.
110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:10.1073/pnas.1315642110.
short: J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013)
16301–16308.
date_created: 2018-12-11T12:02:19Z
date_published: 2013-10-08T00:00:00Z
date_updated: 2021-01-12T07:42:13Z
day: '08'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.1315642110
external_id:
pmid:
- '24089448'
file:
- access_level: open_access
checksum: ecd859fe52a562193027d428b5524a8d
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T13:53:23Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5873'
file_name: 2013_PNAS_Dubuis.pdf
file_size: 1670548
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
intvolume: ' 110'
issue: '41'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 16301 - 16308
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3387'
quality_controlled: '1'
scopus_import: 1
status: public
title: Positional information, in bits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '331'
abstract:
- lang: eng
text: We report a procedure to prepare highly monodisperse copper telluride nanocubes,
nanoplates, and nanorods. The procedure is based on the reaction of a copper salt
with trioctylphosphine telluride in the presence of lithium bis(trimethylsilyl)amide
and oleylamine. CuTe nanocrystals display a strong near-infrared optical absorption
associated with localized surface plasmon resonances. We exploit this plasmon
resonance for the design of surface-enhanced Raman scattering sensors for unconventional
optical probes. Furthermore, we also report here our preliminary analysis of the
use of CuTe nanocrystals as cytotoxic and photothermal agents.
article_processing_charge: No
article_type: original
author:
- first_name: Wenhua
full_name: Li, Wenhua
last_name: Li
- first_name: Reza
full_name: Zamani, Reza
last_name: Zamani
- first_name: Pilar
full_name: Rivera Gil, Pilar
last_name: Rivera Gil
- first_name: Beatriz
full_name: Pelaz, Beatriz
last_name: Pelaz
- 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: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Ramon
full_name: Alvarez Puebla, Ramon
last_name: Alvarez Puebla
- first_name: Wolfgang
full_name: Parak, Wolfgang
last_name: Parak
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Li W, Zamani R, Rivera Gil P, et al. CuTe nanocrystals: Shape and size control,
plasmonic properties, and use as SERS probes and photothermal agents. Journal
of the American Chemical Society. 2013;135(19):7098-7101. doi:10.1021/ja401428e'
apa: 'Li, W., Zamani, R., Rivera Gil, P., Pelaz, B., Ibáñez, M., Cadavid, D., …
Cabot, A. (2013). CuTe nanocrystals: Shape and size control, plasmonic properties,
and use as SERS probes and photothermal agents. Journal of the American Chemical
Society. ACS. https://doi.org/10.1021/ja401428e'
chicago: 'Li, Wenhua, Reza Zamani, Pilar Rivera Gil, Beatriz Pelaz, Maria Ibáñez,
Doris Cadavid, Alexey Shavel, et al. “CuTe Nanocrystals: Shape and Size Control,
Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” Journal
of the American Chemical Society. ACS, 2013. https://doi.org/10.1021/ja401428e.'
ieee: 'W. Li et al., “CuTe nanocrystals: Shape and size control, plasmonic
properties, and use as SERS probes and photothermal agents,” Journal of the
American Chemical Society, vol. 135, no. 19. ACS, pp. 7098–7101, 2013.'
ista: 'Li W, Zamani R, Rivera Gil P, Pelaz B, Ibáñez M, Cadavid D, Shavel A, Alvarez
Puebla R, Parak W, Arbiol J, Cabot A. 2013. CuTe nanocrystals: Shape and size
control, plasmonic properties, and use as SERS probes and photothermal agents.
Journal of the American Chemical Society. 135(19), 7098–7101.'
mla: 'Li, Wenhua, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties,
and Use as SERS Probes and Photothermal Agents.” Journal of the American Chemical
Society, vol. 135, no. 19, ACS, 2013, pp. 7098–101, doi:10.1021/ja401428e.'
short: W. Li, R. Zamani, P. Rivera Gil, B. Pelaz, M. Ibáñez, D. Cadavid, A. Shavel,
R. Alvarez Puebla, W. Parak, J. Arbiol, A. Cabot, Journal of the American Chemical
Society 135 (2013) 7098–7101.
date_created: 2018-12-11T11:45:51Z
date_published: 2013-04-30T00:00:00Z
date_updated: 2021-01-12T07:42:33Z
day: '30'
doi: 10.1021/ja401428e
extern: '1'
intvolume: ' 135'
issue: '19'
language:
- iso: eng
month: '04'
oa_version: None
page: 7098 - 7101
publication: Journal of the American Chemical Society
publication_status: published
publisher: ACS
publist_id: '7521'
quality_controlled: '1'
status: public
title: 'CuTe nanocrystals: Shape and size control, plasmonic properties, and use as
SERS probes and photothermal agents'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2013'
...
---
_id: '3321'
author:
- 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: 'Quadrianto N, Lampert C. Kernel based learning. In: Dubitzky W, Wolkenhauer
O, Cho K, Yokota H, eds. Encyclopedia of Systems Biology. Vol 3. Springer;
2013:1069-1069. doi:10.1007/978-1-4419-9863-7_604'
apa: Quadrianto, N., & Lampert, C. (2013). Kernel based learning. In W. Dubitzky,
O. Wolkenhauer, K. Cho, & H. Yokota (Eds.), Encyclopedia of Systems Biology
(Vol. 3, pp. 1069–1069). Springer. https://doi.org/10.1007/978-1-4419-9863-7_604
chicago: Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” In Encyclopedia
of Systems Biology, edited by Werner Dubitzky, Olaf Wolkenhauer, Kwang Cho,
and Hiroki Yokota, 3:1069–1069. Springer, 2013. https://doi.org/10.1007/978-1-4419-9863-7_604.
ieee: N. Quadrianto and C. Lampert, “Kernel based learning,” in Encyclopedia
of Systems Biology, vol. 3, W. Dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota,
Eds. Springer, 2013, pp. 1069–1069.
ista: 'Quadrianto N, Lampert C. 2013.Kernel based learning. In: Encyclopedia of
Systems Biology. vol. 3, 1069–1069.'
mla: Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” Encyclopedia
of Systems Biology, edited by Werner Dubitzky et al., vol. 3, Springer, 2013,
pp. 1069–1069, doi:10.1007/978-1-4419-9863-7_604.
short: N. Quadrianto, C. Lampert, in:, W. Dubitzky, O. Wolkenhauer, K. Cho, H. Yokota
(Eds.), Encyclopedia of Systems Biology, Springer, 2013, pp. 1069–1069.
date_created: 2018-12-11T12:02:39Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:38Z
day: '01'
department:
- _id: ChLa
doi: 10.1007/978-1-4419-9863-7_604
editor:
- first_name: Werner
full_name: Dubitzky, Werner
last_name: Dubitzky
- first_name: Olaf
full_name: Wolkenhauer, Olaf
last_name: Wolkenhauer
- first_name: Kwang
full_name: Cho, Kwang
last_name: Cho
- first_name: Hiroki
full_name: Yokota, Hiroki
last_name: Yokota
intvolume: ' 3'
language:
- iso: eng
month: '01'
oa_version: None
page: 1069 - 1069
publication: Encyclopedia of Systems Biology
publication_status: published
publisher: Springer
publist_id: '3314'
quality_controlled: '1'
status: public
title: Kernel based learning
type: encyclopedia_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2013'
...
---
_id: '2831'
abstract:
- lang: eng
text: 'We consider Markov decision processes (MDPs) with Büchi (liveness) objectives.
We consider the problem of computing the set of almost-sure winning states from
where the objective can be ensured with probability 1. Our contributions are as
follows: First, we present the first subquadratic symbolic algorithm to compute
the almost-sure winning set for MDPs with Büchi objectives; our algorithm takes
O(n · √ m) symbolic steps as compared to the previous known algorithm that takes
O(n 2) symbolic steps, where n is the number of states and m is the number of
edges of the MDP. In practice MDPs have constant out-degree, and then our symbolic
algorithm takes O(n · √ n) symbolic steps, as compared to the previous known O(n
2) symbolic steps algorithm. Second, we present a new algorithm, namely win-lose
algorithm, with the following two properties: (a) the algorithm iteratively computes
subsets of the almost-sure winning set and its complement, as compared to all
previous algorithms that discover the almost-sure winning set upon termination;
and (b) requires O(n · √ K) symbolic steps, where K is the maximal number of edges
of strongly connected components (scc''s) of the MDP. The win-lose algorithm requires
symbolic computation of scc''s. Third, we improve the algorithm for symbolic scc
computation; the previous known algorithm takes linear symbolic steps, and our
new algorithm improves the constants associated with the linear number of steps.
In the worst case the previous known algorithm takes 5×n symbolic steps, whereas
our new algorithm takes 4×n symbolic steps.'
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
- first_name: Manas
full_name: Joglekar, Manas
last_name: Joglekar
- first_name: Nisarg
full_name: Shah, Nisarg
last_name: Shah
citation:
ama: Chatterjee K, Henzinger MH, Joglekar M, Shah N. Symbolic algorithms for qualitative
analysis of Markov decision processes with Büchi objectives. Formal Methods
in System Design. 2013;42(3):301-327. doi:10.1007/s10703-012-0180-2
apa: Chatterjee, K., Henzinger, M. H., Joglekar, M., & Shah, N. (2013). Symbolic
algorithms for qualitative analysis of Markov decision processes with Büchi objectives.
Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-012-0180-2
chicago: Chatterjee, Krishnendu, Monika H Henzinger, Manas Joglekar, and Nisarg
Shah. “Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes
with Büchi Objectives.” Formal Methods in System Design. Springer, 2013.
https://doi.org/10.1007/s10703-012-0180-2.
ieee: K. Chatterjee, M. H. Henzinger, M. Joglekar, and N. Shah, “Symbolic algorithms
for qualitative analysis of Markov decision processes with Büchi objectives,”
Formal Methods in System Design, vol. 42, no. 3. Springer, pp. 301–327,
2013.
ista: Chatterjee K, Henzinger MH, Joglekar M, Shah N. 2013. Symbolic algorithms
for qualitative analysis of Markov decision processes with Büchi objectives. Formal
Methods in System Design. 42(3), 301–327.
mla: Chatterjee, Krishnendu, et al. “Symbolic Algorithms for Qualitative Analysis
of Markov Decision Processes with Büchi Objectives.” Formal Methods in System
Design, vol. 42, no. 3, Springer, 2013, pp. 301–27, doi:10.1007/s10703-012-0180-2.
short: K. Chatterjee, M.H. Henzinger, M. Joglekar, N. Shah, Formal Methods in System
Design 42 (2013) 301–327.
date_created: 2018-12-11T11:59:49Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2023-02-23T11:23:04Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/s10703-012-0180-2
ec_funded: 1
external_id:
arxiv:
- '1104.3348'
intvolume: ' 42'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1104.3348
month: '06'
oa: 1
oa_version: Preprint
page: 301 - 327
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '3968'
quality_controlled: '1'
related_material:
record:
- id: '3342'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Symbolic algorithms for qualitative analysis of Markov decision processes with
Büchi objectives
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 42
year: '2013'
...
---
_id: '342'
abstract:
- lang: eng
text: Morphology is a key parameter in the design of novel nanocrystals and nanomaterials
with controlled functional properties. Here, we demonstrate the potential of foreign
metal ions to tune the morphology of colloidal semiconductor nanoparticles. We
illustrate the underlying mechanism by preparing copper selenide nanocubes in
the presence of Al ions. We further characterize the plasmonic properties of the
obtained nanocrystals and demonstrate their potential as a platform to produce
cubic nanoparticles with different composition by cation exchange. © 2013 American
Chemical Society.
acknowledgement: The research was supported by the European Regional Development Funds.
M.I. thanks the Spanish MICINN for her Ph.D. grant. J.A. and R.Z. also acknowledge
MAT2010-15138.
article_processing_charge: No
article_type: original
author:
- first_name: Wenhua
full_name: Li, Wenhua
last_name: Li
- first_name: Reza
full_name: Zamani, Reza
last_name: Zamani
- 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: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- 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: 'Li W, Zamani R, Ibáñez M, et al. Metal ions to control the morphology of semiconductor
nanoparticles: Copper selenide nanocubes. Journal of the American Chemical
Society. 2013;135(12):4664-4667. doi:10.1021/ja400472m'
apa: 'Li, W., Zamani, R., Ibáñez, M., Cadavid, D., Shavel, A., Morante, J., … Cabot,
A. (2013). Metal ions to control the morphology of semiconductor nanoparticles:
Copper selenide nanocubes. Journal of the American Chemical Society. American
Chemical Society. https://doi.org/10.1021/ja400472m'
chicago: 'Li, Wenhua, Reza Zamani, Maria Ibáñez, Doris Cadavid, Alexey Shavel, Joan
Morante, Jordi Arbiol, and Andreu Cabot. “Metal Ions to Control the Morphology
of Semiconductor Nanoparticles: Copper Selenide Nanocubes.” Journal of the
American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja400472m.'
ieee: 'W. Li et al., “Metal ions to control the morphology of semiconductor
nanoparticles: Copper selenide nanocubes,” Journal of the American Chemical
Society, vol. 135, no. 12. American Chemical Society, pp. 4664–4667, 2013.'
ista: 'Li W, Zamani R, Ibáñez M, Cadavid D, Shavel A, Morante J, Arbiol J, Cabot
A. 2013. Metal ions to control the morphology of semiconductor nanoparticles:
Copper selenide nanocubes. Journal of the American Chemical Society. 135(12),
4664–4667.'
mla: 'Li, Wenhua, et al. “Metal Ions to Control the Morphology of Semiconductor
Nanoparticles: Copper Selenide Nanocubes.” Journal of the American Chemical
Society, vol. 135, no. 12, American Chemical Society, 2013, pp. 4664–67, doi:10.1021/ja400472m.'
short: W. Li, R. Zamani, M. Ibáñez, D. Cadavid, A. Shavel, J. Morante, J. Arbiol,
A. Cabot, Journal of the American Chemical Society 135 (2013) 4664–4667.
date_created: 2018-12-11T11:45:55Z
date_published: 2013-03-07T00:00:00Z
date_updated: 2021-01-12T07:43:21Z
day: '07'
doi: 10.1021/ja400472m
extern: '1'
intvolume: ' 135'
issue: '12'
language:
- iso: eng
month: '03'
oa_version: None
page: 4664 - 4667
publication: Journal of the American Chemical Society
publication_status: published
publisher: American Chemical Society
publist_id: '7482'
quality_controlled: '1'
status: public
title: 'Metal ions to control the morphology of semiconductor nanoparticles: Copper
selenide nanocubes'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2013'
...
---
_id: '343'
abstract:
- lang: eng
text: The bottom-up assembly of nanocrystals provides access to a three-dimensional
composition control at the nanoscale not attainable by any other technology. In
particular, colloidal nanoheterostructures, with intrinsic multiphase organization,
are especially appealing building blocks for the bottom-up production of nanocomposites.
In the present work, we use PbTe-PbS as the model material system and thermoelectricity
as the paradigmatic application to investigate the potential of the bottom-up
assembly of core-shell nanoparticles to produce functional nanocomposites. With
this goal in mind, a rapid, high-yield and scalable colloidal synthetic route
to prepare grams of PbTe@PbS core-shell nanoparticles with unprecedented narrow
size distributions and exceptional composition control is detailed. PbTe@PbS nanoparticles
were used as building blocks for the bottom-up production of PbTe-PbS nanocomposites
with tuned composition. In such PbTe-PbS nanocomposites, synergistic nanocrystal
doping effects result in up to 10-fold higher electrical conductivities than in
pure PbTe and PbS nanomaterials. At the same time, the acoustic impedance mismatch
between PbTe and PbS phases and a partial phase alloying provide PbTe-PbS nanocomposites
with strongly reduced thermal conductivities. As a result, record thermoelectric
figures of merit (ZT) of ∼1.1 were obtained from undoped PbTe and PbS phases at
710 K. These high ZT values prove the potential of the proposed processes to produce
efficient functional nanomaterials with programmable properties. © 2013 American
Chemical Society.
acknowledgement: "The research was supported by the European Regional Development
Funds (ERDF, “FEDER Programa Competitivitat de Catalunya 2007-2013”) and the Spanish
MICINN Projects MAT2008-05779, MAT2010-15138, 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.\r\n\r\nThe authors declare no
competing financial interest."
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: Stéphane
full_name: Gorsse, Stéphane
last_name: Gorsse
- first_name: Jiandong
full_name: Fan, Jiandong
last_name: Fan
- first_name: Silvia
full_name: Ortega, Silvia
last_name: Ortega
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- 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, Gorsse S, et al. Core shell nanoparticles as building
blocks for the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric
properties. ACS Nano. 2013;7(3):2573-2586. doi:10.1021/nn305971v'
apa: 'Ibáñez, M., Zamani, R., Gorsse, S., Fan, J., Ortega, S., Cadavid, D., … Cabot,
A. (2013). Core shell nanoparticles as building blocks for the bottom-up production
of functional nanocomposites: PbTe PbS thermoelectric properties. ACS Nano.
American Chemical Society. https://doi.org/10.1021/nn305971v'
chicago: 'Ibáñez, Maria, Reza Zamani, Stéphane Gorsse, Jiandong Fan, Silvia Ortega,
Doris Cadavid, Joan Morante, Jordi Arbiol, and Andreu Cabot. “Core Shell Nanoparticles
as Building Blocks for the Bottom-up Production of Functional Nanocomposites:
PbTe PbS Thermoelectric Properties.” ACS Nano. American Chemical Society,
2013. https://doi.org/10.1021/nn305971v.'
ieee: 'M. Ibáñez et al., “Core shell nanoparticles as building blocks for
the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric
properties,” ACS Nano, vol. 7, no. 3. American Chemical Society, pp. 2573–2586,
2013.'
ista: 'Ibáñez M, Zamani R, Gorsse S, Fan J, Ortega S, Cadavid D, Morante J, Arbiol
J, Cabot A. 2013. Core shell nanoparticles as building blocks for the bottom-up
production of functional nanocomposites: PbTe PbS thermoelectric properties. ACS
Nano. 7(3), 2573–2586.'
mla: 'Ibáñez, Maria, et al. “Core Shell Nanoparticles as Building Blocks for the
Bottom-up Production of Functional Nanocomposites: PbTe PbS Thermoelectric Properties.”
ACS Nano, vol. 7, no. 3, American Chemical Society, 2013, pp. 2573–86,
doi:10.1021/nn305971v.'
short: M. Ibáñez, R. Zamani, S. Gorsse, J. Fan, S. Ortega, D. Cadavid, J. Morante,
J. Arbiol, A. Cabot, ACS Nano 7 (2013) 2573–2586.
date_created: 2018-12-11T11:45:55Z
date_published: 2013-02-28T00:00:00Z
date_updated: 2021-01-12T07:43:25Z
day: '28'
doi: 10.1021/nn305971v
extern: '1'
intvolume: ' 7'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
page: 2573 - 2586
publication: ACS Nano
publication_status: published
publisher: American Chemical Society
publist_id: '7483'
quality_controlled: '1'
status: public
title: 'Core shell nanoparticles as building blocks for the bottom-up production of
functional nanocomposites: PbTe PbS thermoelectric properties'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2013'
...
---
_id: '351'
abstract:
- lang: eng
text: 'A multistrategy approach to overcome the main challenges of nanoparticle-based
solution-processed Cu2ZnSnSe4 thin film solar cells is presented. We developed
an efficient ligand exchange strategy, using an antimony salt, to displace organic
ligands from the surface of Cu 2ZnSnS4 nanoparticles. An automated pulsed spray-deposition
system was used to deposit the nanoparticles into homogeneous and crack-free films
with controlled thickness. After annealing the film in a Se-rich atmosphere, carbon-free
and crystalline Cu2ZnSnSe4 absorber layers were obtained. Not only was crystallization
promoted by the complete removal of organics, but also Sb itself played a critical
role. The Sb-assisted crystal growth is associated with the formation of a Sb-based
compound at the grain boundaries, which locally reduces the melting point, thus
promoting the film diffusion-limited crystallization. '
acknowledgement: This work was supported by the European Regional Development Funds
and the Framework 7 program under project SCALENANO (FP7-NMP-ENERGY-2011-284486).
E.S. thanks the Spanish government for the “Ramon y Cajal” fellowship (RYC-2011-09212).
article_processing_charge: No
article_type: original
author:
- first_name: Alex
full_name: Carrete, Alex
last_name: Carrete
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Xavier
full_name: Fontané, Xavier
last_name: Fontané
- first_name: Joana
full_name: Montserrat, Joana
last_name: Montserrat
- first_name: Jiandong
full_name: Fan, Jiandong
last_name: Fan
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Edgardo
full_name: Saucedo, Edgardo
last_name: Saucedo
- first_name: Alejandro
full_name: Pérez Rodríguez, Alejandro
last_name: Pérez Rodríguez
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Carrete A, Shavel A, Fontané X, et al. Antimony-based ligand exchange to promote
crystallization in spray-deposited Cu2ZnSnSe4 solar cells. Journal of the American
Chemical Society. 2013;135(43):15982-15985. doi:10.1021/ja4068639
apa: Carrete, A., Shavel, A., Fontané, X., Montserrat, J., Fan, J., Ibáñez, M.,
… Cabot, A. (2013). Antimony-based ligand exchange to promote crystallization
in spray-deposited Cu2ZnSnSe4 solar cells. Journal of the American Chemical
Society. American Chemical Society. https://doi.org/10.1021/ja4068639
chicago: Carrete, Alex, Alexey Shavel, Xavier Fontané, Joana Montserrat, Jiandong
Fan, Maria Ibáñez, Edgardo Saucedo, Alejandro Pérez Rodríguez, and Andreu Cabot.
“Antimony-Based Ligand Exchange to Promote Crystallization in Spray-Deposited
Cu2ZnSnSe4 Solar Cells.” Journal of the American Chemical Society. American
Chemical Society, 2013. https://doi.org/10.1021/ja4068639.
ieee: A. Carrete et al., “Antimony-based ligand exchange to promote crystallization
in spray-deposited Cu2ZnSnSe4 solar cells,” Journal of the American Chemical
Society, vol. 135, no. 43. American Chemical Society, pp. 15982–15985, 2013.
ista: Carrete A, Shavel A, Fontané X, Montserrat J, Fan J, Ibáñez M, Saucedo E,
Pérez Rodríguez A, Cabot A. 2013. Antimony-based ligand exchange to promote crystallization
in spray-deposited Cu2ZnSnSe4 solar cells. Journal of the American Chemical Society.
135(43), 15982–15985.
mla: Carrete, Alex, et al. “Antimony-Based Ligand Exchange to Promote Crystallization
in Spray-Deposited Cu2ZnSnSe4 Solar Cells.” Journal of the American Chemical
Society, vol. 135, no. 43, American Chemical Society, 2013, pp. 15982–85,
doi:10.1021/ja4068639.
short: A. Carrete, A. Shavel, X. Fontané, J. Montserrat, J. Fan, M. Ibáñez, E. Saucedo,
A. Pérez Rodríguez, A. Cabot, Journal of the American Chemical Society 135 (2013)
15982–15985.
date_created: 2018-12-11T11:45:58Z
date_published: 2013-10-30T00:00:00Z
date_updated: 2021-01-12T07:43:57Z
day: '30'
doi: 10.1021/ja4068639
extern: '1'
intvolume: ' 135'
issue: '43'
language:
- iso: eng
month: '10'
oa_version: None
page: 15982 - 15985
publication: Journal of the American Chemical Society
publication_status: published
publisher: American Chemical Society
publist_id: '7479'
quality_controlled: '1'
status: public
title: Antimony-based ligand exchange to promote crystallization in spray-deposited
Cu2ZnSnSe4 solar cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2013'
...
---
_id: '353'
abstract:
- lang: eng
text: We report a procedure to prepare highly monodisperse copper telluride nanocubes,
nanoplates, and nanorods. The procedure is based on the reaction of a copper salt
with trioctylphosphine telluride in the presence of lithium bis(trimethylsilyl)amide
and oleylamine. CuTe nanocrystals display a strong near-infrared optical absorption
associated with localized surface plasmon resonances. We exploit this plasmon
resonance for the design of surface-enhanced Raman scattering sensors for unconventional
optical probes. Furthermore, we also report here our preliminary analysis of the
use of CuTe nanocrystals as cytotoxic and photothermal agents.
acknowledgement: This research was supported by the European Regional Development
Funds. J.A. and R.Z. acknowledge MAT2010-15138. Part of this work was supported
by HFSP grant RGP0052/2012 to W.J.P.
article_processing_charge: No
article_type: original
author:
- first_name: Wenhua
full_name: Li, Wenhua
last_name: Li
- first_name: Reza
full_name: Zamani, Reza
last_name: Zamani
- first_name: Pilar
full_name: Rivera Gil, Pilar
last_name: Rivera Gil
- first_name: Beatriz
full_name: Pelaz, Beatriz
last_name: Pelaz
- 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: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Ramon
full_name: Alvarez Puebla, Ramon
last_name: Alvarez Puebla
- first_name: Wolfgang
full_name: Parak, Wolfgang
last_name: Parak
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Li W, Zamani R, Rivera Gil P, et al. CuTe nanocrystals: Shape and size control,
plasmonic properties, and use as SERS probes and photothermal agents. Journal
of the American Chemical Society. 2013;135(19):7098-7101. doi:10.1021/ja401428e'
apa: 'Li, W., Zamani, R., Rivera Gil, P., Pelaz, B., Ibáñez, M., Cadavid, D., …
Cabot, A. (2013). CuTe nanocrystals: Shape and size control, plasmonic properties,
and use as SERS probes and photothermal agents. Journal of the American Chemical
Society. American Chemical Society. https://doi.org/10.1021/ja401428e'
chicago: 'Li, Wenhua, Reza Zamani, Pilar Rivera Gil, Beatriz Pelaz, Maria Ibáñez,
Doris Cadavid, Alexey Shavel, et al. “CuTe Nanocrystals: Shape and Size Control,
Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” Journal
of the American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja401428e.'
ieee: 'W. Li et al., “CuTe nanocrystals: Shape and size control, plasmonic
properties, and use as SERS probes and photothermal agents,” Journal of the
American Chemical Society, vol. 135, no. 19. American Chemical Society, pp.
7098–7101, 2013.'
ista: 'Li W, Zamani R, Rivera Gil P, Pelaz B, Ibáñez M, Cadavid D, Shavel A, Alvarez
Puebla R, Parak W, Arbiol J, Cabot A. 2013. CuTe nanocrystals: Shape and size
control, plasmonic properties, and use as SERS probes and photothermal agents.
Journal of the American Chemical Society. 135(19), 7098–7101.'
mla: 'Li, Wenhua, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties,
and Use as SERS Probes and Photothermal Agents.” Journal of the American Chemical
Society, vol. 135, no. 19, American Chemical Society, 2013, pp. 7098–101,
doi:10.1021/ja401428e.'
short: W. Li, R. Zamani, P. Rivera Gil, B. Pelaz, M. Ibáñez, D. Cadavid, A. Shavel,
R. Alvarez Puebla, W. Parak, J. Arbiol, A. Cabot, Journal of the American Chemical
Society 135 (2013) 7098–7101.
date_created: 2018-12-11T11:45:59Z
date_published: 2013-04-30T00:00:00Z
date_updated: 2021-01-12T07:44:06Z
day: '30'
doi: 10.1021/ja401428e
extern: '1'
intvolume: ' 135'
issue: '19'
language:
- iso: eng
month: '04'
oa_version: None
page: 7098 - 7101
publication: Journal of the American Chemical Society
publication_status: published
publisher: American Chemical Society
publist_id: '7480'
quality_controlled: '1'
status: public
title: 'CuTe nanocrystals: Shape and size control, plasmonic properties, and use as
SERS probes and photothermal agents'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2013'
...
---
_id: '376'
abstract:
- lang: eng
text: The compositional versatility of I2–II–IV–VI4 tetrahedrally-coordinated compounds
allows for accommodating their functional properties to numerous technological
applications. Among them, Cu2ZnSnSe4 is an emerging photovoltaic material and
Cu2CdSnSe4 displays excellent thermoelectric properties. The third compound of
this family, Cu2HgSnSe4, remains relatively unexplored. Herein, a synthetic route
to produce Cu2HgSnSe4 nanoparticles with narrow size distribution and controlled
composition is presented. Cu2HgSnSe4 nanoparticles were subsequently used as building
blocks to produce bulk nanocrystalline materials, whose thermoelectric properties
were analyzed. A very preliminary adjustment of the material composition yielded
Seebeck coefficients up to 160 μV K−1, electrical conductivities close to 104
S m−1 and thermal conductivities down to 0.5 W m−1 K−1.
author:
- first_name: Wenhua
full_name: Li, Wenhua
last_name: Li
- 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: Nuria
full_name: García Castelló, Nuria
last_name: García Castelló
- first_name: Grosse
full_name: Stéphane, Grosse
last_name: Stéphane
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Joan
full_name: Prades, Joan
last_name: Prades
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Li W, Ibáñez M, Zamani R, et al. Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric
properties. CrystEngComm. 2013;44:8966-8971. doi:10.1039/C3CE41583J'
apa: 'Li, W., Ibáñez, M., Zamani, R., García Castelló, N., Stéphane, G., Cadavid,
D., … Cabot, A. (2013). Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric
properties. CrystEngComm. Royal Society of Chemistry. https://doi.org/10.1039/C3CE41583J'
chicago: 'Li, Wenhua, Maria Ibáñez, Reza Zamani, Nuria García Castelló, Grosse Stéphane,
Doris Cadavid, Joan Prades, Jordi Arbiol, and Andreu Cabot. “Cu2HgSnSe4 Nanoparticles:
Synthesis and Thermoelectric Properties.” CrystEngComm. Royal Society of
Chemistry, 2013. https://doi.org/10.1039/C3CE41583J.'
ieee: 'W. Li et al., “Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric
properties,” CrystEngComm, vol. 44. Royal Society of Chemistry, pp. 8966–8971,
2013.'
ista: 'Li W, Ibáñez M, Zamani R, García Castelló N, Stéphane G, Cadavid D, Prades
J, Arbiol J, Cabot A. 2013. Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric
properties. CrystEngComm. 44, 8966–8971.'
mla: 'Li, Wenhua, et al. “Cu2HgSnSe4 Nanoparticles: Synthesis and Thermoelectric
Properties.” CrystEngComm, vol. 44, Royal Society of Chemistry, 2013, pp.
8966–71, doi:10.1039/C3CE41583J.'
short: W. Li, M. Ibáñez, R. Zamani, N. García Castelló, G. Stéphane, D. Cadavid,
J. Prades, J. Arbiol, A. Cabot, CrystEngComm 44 (2013) 8966–8971.
date_created: 2018-12-11T11:46:07Z
date_published: 2013-09-23T00:00:00Z
date_updated: 2021-01-12T07:52:00Z
day: '23'
doi: 10.1039/C3CE41583J
extern: '1'
intvolume: ' 44'
language:
- iso: eng
month: '09'
oa_version: None
page: 8966 - 8971
publication: CrystEngComm
publication_status: published
publisher: Royal Society of Chemistry
publist_id: '7453'
quality_controlled: '1'
status: public
title: 'Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric properties'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2013'
...
---
_id: '450'
abstract:
- lang: eng
text: Understanding the relative importance of heterosis and outbreeding depression
over multiple generations is a key question in evolutionary biology and is essential
for identifying appropriate genetic sources for population and ecosystem restoration.
Here we use 2455 experimental crosses between 12 population pairs of the rare
perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational
(F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no
evidence of outbreeding depression, with inter-population hybrids and backcrosses
showing either similar fitness or significant heterosis for fitness components
across the three generations. Variation in heterosis among population pairs was
best explained by characteristics of the foreign source or home population, and
was greatest when the source population was large, with high genetic diversity
and low inbreeding, and the home population was small and inbred. Our results
indicate that the primary consideration for maximizing progeny fitness following
population augmentation or restoration is the use of seed from large, genetically
diverse populations.
article_number: '2058'
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. Source population characteristics affect
heterosis following genetic rescue of fragmented plant populations. Proceedings
of the Royal Society of London Series B Biological Sciences. 2013;280(1750).
doi:10.1098/rspb.2012.2058
apa: Pickup, M., Field, D., Rowell, D., & Young, A. (2013). Source population
characteristics affect heterosis following genetic rescue of fragmented plant
populations. Proceedings of the Royal Society of London Series B Biological
Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.2058
chicago: Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population
Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant
Populations.” Proceedings of the Royal Society of London Series B Biological
Sciences. Royal Society, The, 2013. https://doi.org/10.1098/rspb.2012.2058.
ieee: M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics
affect heterosis following genetic rescue of fragmented plant populations,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 280, no.
1750. Royal Society, The, 2013.
ista: Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics
affect heterosis following genetic rescue of fragmented plant populations. Proceedings
of the Royal Society of London Series B Biological Sciences. 280(1750), 2058.
mla: Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis
Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the
Royal Society of London Series B Biological Sciences, vol. 280, no. 1750,
2058, Royal Society, The, 2013, doi:10.1098/rspb.2012.2058.
short: M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society
of London Series B Biological Sciences 280 (2013).
date_created: 2018-12-11T11:46:32Z
date_published: 2013-01-07T00:00:00Z
date_updated: 2021-01-12T07:57:25Z
day: '07'
department:
- _id: NiBa
doi: 10.1098/rspb.2012.2058
external_id:
pmid:
- '23173202'
intvolume: ' 280'
issue: '1750'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '7372'
quality_controlled: '1'
status: public
title: Source population characteristics affect heterosis following genetic rescue
of fragmented plant populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 280
year: '2013'
...
---
_id: '476'
abstract:
- lang: eng
text: 'Maternal exposure to infection occurring mid-gestation produces a three-fold
increase in the risk of schizophrenia in the offspring. The critical initiating
factor appears to be the maternal immune activation (MIA) that follows infection.
This process can be induced in rodents by exposure of pregnant dams to the viral
mimic Poly I:C, which triggers an immune response that results in structural,
functional, behavioral, and electrophysiological phenotypes in the adult offspring
that model those seen in schizophrenia. We used this model to explore the role
of synchronization in brain neural networks, a process thought to be dysfunctional
in schizophrenia and previously associated with positive, negative, and cognitive
symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced
an impairment in long-range neural synchrony in adult offspring between two regions
implicated in schizophrenia pathology; the hippocampus and the medial prefrontal
cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the
antipsychotic clozapine. MIA animals have previously been shown to have impaired
pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits
in animal models. Our data showed that deficits in synchrony were positively correlated
with the impairments in PPI. Subsequent analysis of LFP activity during the PPI
response also showed that reduced coupling between the mPFC and the hippocampus
following processing of the pre-pulse was associated with reduced PPI. The ability
of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology
provides a useful platform from which to investigate the ontogeny of aberrant
synchronous processes. Further, the way in which the model expresses translatable
deficits such as aberrant synchrony and reduced PPI will allow researchers to
explore novel intervention strategies targeted to these changes. '
author:
- first_name: Desiree
full_name: Dickerson, Desiree
id: 444EB89E-F248-11E8-B48F-1D18A9856A87
last_name: Dickerson
- first_name: David
full_name: Bilkey, David
last_name: Bilkey
citation:
ama: 'Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation
model: Using translatable measures to explore targeted interventions. Frontiers
in Behavioral Neuroscience. 2013;7(DEC). doi:10.3389/fnbeh.2013.00217'
apa: 'Dickerson, D., & Bilkey, D. (2013). Aberrant neural synchrony in the maternal
immune activation model: Using translatable measures to explore targeted interventions.
Frontiers in Behavioral Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnbeh.2013.00217'
chicago: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the
Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted
Interventions.” Frontiers in Behavioral Neuroscience. Frontiers Research
Foundation, 2013. https://doi.org/10.3389/fnbeh.2013.00217.'
ieee: 'D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune
activation model: Using translatable measures to explore targeted interventions,”
Frontiers in Behavioral Neuroscience, vol. 7, no. DEC. Frontiers Research
Foundation, 2013.'
ista: 'Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune
activation model: Using translatable measures to explore targeted interventions.
Frontiers in Behavioral Neuroscience. 7(DEC).'
mla: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal
Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.”
Frontiers in Behavioral Neuroscience, vol. 7, no. DEC, Frontiers Research
Foundation, 2013, doi:10.3389/fnbeh.2013.00217.'
short: D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013).
date_created: 2018-12-11T11:46:41Z
date_published: 2013-12-27T00:00:00Z
date_updated: 2021-01-12T08:00:53Z
day: '27'
ddc:
- '571'
department:
- _id: JoCs
doi: 10.3389/fnbeh.2013.00217
file:
- access_level: open_access
checksum: cd7183121e56251176100ccac165c95c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:10Z
date_updated: 2020-07-14T12:46:35Z
file_id: '5128'
file_name: IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf
file_size: 530134
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 7'
issue: DEC
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Frontiers in Behavioral Neuroscience
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '7346'
pubrep_id: '953'
quality_controlled: '1'
status: public
title: 'Aberrant neural synchrony in the maternal immune activation model: Using translatable
measures to explore targeted interventions'
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: 7
year: '2013'
...
---
_id: '499'
abstract:
- lang: eng
text: Exposure of an isogenic bacterial population to a cidal antibiotic typically
fails to eliminate a small fraction of refractory cells. Historically, fractional
killing has been attributed to infrequently dividing or nondividing "persisters."
Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium
smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although
persistence in these studies was characterized by stable numbers of cells, this
apparent stability was actually a dynamic state of balanced division and death.
Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic
pulses that were negatively correlated with cell survival. These behaviors may
reflect epigenetic effects, because KatG pulsing and death were correlated between
sibling cells. Selection of lineages characterized by infrequent KatG pulsing
could allow nonresponsive adaptation during prolonged drug exposure.
author:
- first_name: Yurichi
full_name: Wakamoto, Yurichi
last_name: Wakamoto
- first_name: Neraaj
full_name: Dhar, Neraaj
last_name: Dhar
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Katrin
full_name: Schneider, Katrin
last_name: Schneider
- first_name: François
full_name: Signorino Gelo, François
last_name: Signorino Gelo
- first_name: Stanislas
full_name: Leibler, Stanislas
last_name: Leibler
- first_name: John
full_name: Mckinney, John
last_name: Mckinney
citation:
ama: Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed
mycobacteria. Science. 2013;339(6115):91-95. doi:10.1126/science.1229858
apa: Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler,
S., & Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1229858
chicago: Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François
Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of
Antibiotic-Stressed Mycobacteria.” Science. American Association for the
Advancement of Science, 2013. https://doi.org/10.1126/science.1229858.
ieee: Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,”
Science, vol. 339, no. 6115. American Association for the Advancement of
Science, pp. 91–95, 2013.
ista: Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney
J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115),
91–95.
mla: Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.”
Science, vol. 339, no. 6115, American Association for the Advancement of
Science, 2013, pp. 91–95, doi:10.1126/science.1229858.
short: Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler,
J. Mckinney, Science 339 (2013) 91–95.
date_created: 2018-12-11T11:46:48Z
date_published: 2013-01-04T00:00:00Z
date_updated: 2021-01-12T08:01:06Z
day: '04'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1126/science.1229858
intvolume: ' 339'
issue: '6115'
language:
- iso: eng
month: '01'
oa_version: None
page: 91 - 95
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7321'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dynamic persistence of antibiotic-stressed mycobacteria
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2013'
...
---
_id: '500'
abstract:
- lang: eng
text: 'Background: Reassortment between the RNA segments encoding haemagglutinin
(HA) and neuraminidase (NA), the major antigenic influenza proteins, produces
viruses with novel HA and NA subtype combinations and has preceded the emergence
of pandemic strains. It has been suggested that productive viral infection requires
a balance in the level of functional activity of HA and NA, arising from their
closely interacting roles in the viral life cycle, and that this functional balance
could be mediated by genetic changes in the HA and NA. Here, we investigate how
the selective pressure varies for H7 avian influenza HA on different NA subtype
backgrounds. Results: By extending Bayesian stochastic mutational mapping methods
to calculate the ratio of the rate of non-synonymous change to the rate of synonymous
change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1
region to be significantly greater on an N2 NA subtype background than on an N1,
N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different
NA subtype backgrounds could not be attributed to underlying differences between
avian host species or virus pathogenicity. Examination of d N/d S values for each
subtype on a site-by-site basis indicated that the elevated d N/d S on the N2
NA background was a result of increased selection, rather than a relaxation of
selective constraint. Conclusions: Our results are consistent with the hypothesis
that reassortment exposes influenza HA to significant changes in selective pressure
through genetic interactions with NA. Such epistatic effects might be explicitly
accounted for in future models of influenza evolution.'
acknowledgement: "This work was supported by the Biotechnology and Biological Sciences
Research Council, the Government of the Republic of Panama, the Interdisciplinary
Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the
Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC
BY 2.0\r\n"
article_number: '222'
author:
- first_name: Melissa
full_name: Ward, Melissa
last_name: Ward
- first_name: Samantha
full_name: Lycett, Samantha
last_name: Lycett
- first_name: Dorita
full_name: Avila, Dorita
last_name: Avila
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Andrew
full_name: Leigh Brown, Andrew
last_name: Leigh Brown
citation:
ama: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions
between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary
Biology. 2013;13(1). doi:10.1186/1471-2148-13-222
apa: Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013).
Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza.
BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-222
chicago: Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and
Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase
in Avian Influenza.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-222.
ieee: M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary
interactions between haemagglutinin and neuraminidase in avian influenza,” BMC
Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.
ista: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary
interactions between haemagglutinin and neuraminidase in avian influenza. BMC
Evolutionary Biology. 13(1), 222.
mla: Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and
Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no.
1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222.
short: M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary
Biology 13 (2013).
date_created: 2018-12-11T11:46:49Z
date_published: 2013-10-09T00:00:00Z
date_updated: 2021-01-12T08:01:08Z
day: '09'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1471-2148-13-222
file:
- access_level: open_access
checksum: 52cf48a7c1794676ae8b0029573a84a9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:59Z
date_updated: 2020-07-14T12:46:36Z
file_id: '4722'
file_name: IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf
file_size: 1150052
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '7320'
pubrep_id: '941'
quality_controlled: '1'
scopus_import: 1
status: public
title: Evolutionary interactions between haemagglutinin and neuraminidase in avian
influenza
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: 13
year: '2013'
...
---
_id: '501'
abstract:
- lang: eng
text: 'All known species of extant tapirs are allopatric: 1 in southeastern Asia
and 3 in Central and South America. The fossil record for tapirs, however, is
much wider in geographical range, including Europe, Asia, and North and South
America, going back to the late Oligocene, making the present distribution a relict
of the original one. We here describe a new species of living Tapirus from the
Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla
in more than 100 years, from both morphological and molecular characters. It is
shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull
morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque
(Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia,
where the biota faces increasing threats. Local peoples have long recognized our
new species, suggesting a key role for traditional knowledge in understanding
the biodiversity of the region.'
author:
- first_name: Mario
full_name: Cozzuol, Mario
last_name: Cozzuol
- first_name: Camila
full_name: Clozato, Camila
last_name: Clozato
- first_name: Elizete
full_name: Holanda, Elizete
last_name: Holanda
- first_name: Flávio
full_name: Rodrigues, Flávio
last_name: Rodrigues
- first_name: Samuel
full_name: Nienow, Samuel
last_name: Nienow
- first_name: Benoit
full_name: De Thoisy, Benoit
last_name: De Thoisy
- 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: Fabrício
full_name: Santos, Fabrício
last_name: Santos
citation:
ama: Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon.
Journal of Mammalogy. 2013;94(6):1331-1345. doi:10.1644/12-MAMM-A-169.1
apa: Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy,
B., … Santos, F. (2013). A new species of tapir from the Amazon. Journal of
Mammalogy. Oxford University Press. https://doi.org/10.1644/12-MAMM-A-169.1
chicago: Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel
Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A
New Species of Tapir from the Amazon.” Journal of Mammalogy. Oxford University
Press, 2013. https://doi.org/10.1644/12-MAMM-A-169.1.
ieee: M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal
of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.
ista: Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes
Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of
Mammalogy. 94(6), 1331–1345.
mla: Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” Journal
of Mammalogy, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45,
doi:10.1644/12-MAMM-A-169.1.
short: M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy,
R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.
date_created: 2018-12-11T11:46:49Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:09Z
day: '01'
ddc:
- '570'
department:
- _id: JoBo
doi: 10.1644/12-MAMM-A-169.1
file:
- access_level: open_access
checksum: 8007815078dccac21ecd1cf73a269dc6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:59Z
date_updated: 2020-07-14T12:46:36Z
file_id: '4980'
file_name: IST-2018-940-v1+1_2013_Redondo_A_new.pdf
file_size: 1040765
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 94'
issue: '6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 1331 - 1345
publication: Journal of Mammalogy
publication_status: published
publisher: Oxford University Press
publist_id: '7319'
pubrep_id: '940'
quality_controlled: '1'
scopus_import: 1
status: public
title: A new species of tapir from the Amazon
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: 94
year: '2013'
...
---
_id: '505'
abstract:
- lang: eng
text: Alkyd resins are polyesters containing unsaturated fatty acids that are used
as binding agents in paints and coatings. Chemical drying of these polyesters
is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid
moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective,
yet they have been proven to be carcinogenic. Therefore, strategies to replace
the cobalt-based catalyst by environmentally friendlier and less toxic alternatives
are under development. Here, we demonstrate for the first time that a laccase-mediator
system can effectively replace the heavy-metal catalyst and cross-link alkyd resins.
Interestingly, the biocatalytic reaction does not only work in aqueous media,
but also in a solid film, where enzyme diffusion is limited. Within the catalytic
cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase,
which is uniformly distributed within the drying film as evidenced by confocal
laser scanning microscopy. During gradual build-up of molecular weight, there
is a concomitant decrease of the oxygen content in the film. A new optical sensor
to follow oxygen consumption during the cross-linking reaction was developed and
validated with state of the art techniques. A remarkable feature is the low sample
amount required, which allows faster screening of new catalysts.
acknowledgement: "This study was performed within the Austrian Centre of Indus-\r\ntrial
Biotechnology ACIB and the COST Action 868. This work\r\nhas been supported by the
Federal Ministry of Economy,\r\nFamily and Youth (BMWFJ), the Federal Ministry of
Tra\r\nffi\r\nc,\r\nInnovation and Technology (bmvit), the Styrian Business\r\nPromotion
Agency SFG, the Standortagentur Tirol and ZIT\r\n–\r\nTechnology Agency of the
\ City of Vienna through the\r\nCOMET-Funding Program managed by the Austrian
Research\r\nPromotion Agency FFG. Dr Massimiliano Cardinale (Institute of\r\nEnvironmental
Biotechnology, TU Graz) is gratefully acknowl-\r\nedged for technical support with
the CLSM measurements."
author:
- first_name: Katrin
full_name: Greimel, Katrin
last_name: Greimel
- first_name: Veronika
full_name: Perz, Veronika
last_name: Perz
- first_name: Klaus
full_name: Koren, Klaus
id: 382FBD6A-F248-11E8-B48F-1D18A9856A87
last_name: Koren
- first_name: Roland
full_name: Feola, Roland
last_name: Feola
- first_name: Armin
full_name: Temel, Armin
last_name: Temel
- first_name: Christian
full_name: Sohar, Christian
last_name: Sohar
- first_name: Enrique
full_name: Herrero Acero, Enrique
last_name: Herrero Acero
- first_name: Ingo
full_name: Klimant, Ingo
last_name: Klimant
- first_name: Georg
full_name: Guebitz, Georg
last_name: Guebitz
citation:
ama: 'Greimel K, Perz V, Koren K, et al. Banning toxic heavy-metal catalysts from
paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 2013;15(2):381-388.
doi:10.1039/c2gc36666e'
apa: 'Greimel, K., Perz, V., Koren, K., Feola, R., Temel, A., Sohar, C., … Guebitz,
G. (2013). Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking
of alkyd resins. Green Chemistry. Royal Society of Chemistry. https://doi.org/10.1039/c2gc36666e'
chicago: 'Greimel, Katrin, Veronika Perz, Klaus Koren, Roland Feola, Armin Temel,
Christian Sohar, Enrique Herrero Acero, Ingo Klimant, and Georg Guebitz. “Banning
Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.”
Green Chemistry. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c2gc36666e.'
ieee: 'K. Greimel et al., “Banning toxic heavy-metal catalysts from paints:
Enzymatic cross-linking of alkyd resins,” Green Chemistry, vol. 15, no.
2. Royal Society of Chemistry, pp. 381–388, 2013.'
ista: 'Greimel K, Perz V, Koren K, Feola R, Temel A, Sohar C, Herrero Acero E, Klimant
I, Guebitz G. 2013. Banning toxic heavy-metal catalysts from paints: Enzymatic
cross-linking of alkyd resins. Green Chemistry. 15(2), 381–388.'
mla: 'Greimel, Katrin, et al. “Banning Toxic Heavy-Metal Catalysts from Paints:
Enzymatic Cross-Linking of Alkyd Resins.” Green Chemistry, vol. 15, no.
2, Royal Society of Chemistry, 2013, pp. 381–88, doi:10.1039/c2gc36666e.'
short: K. Greimel, V. Perz, K. Koren, R. Feola, A. Temel, C. Sohar, E. Herrero Acero,
I. Klimant, G. Guebitz, Green Chemistry 15 (2013) 381–388.
date_created: 2018-12-11T11:46:51Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T08:01:11Z
day: '01'
department:
- _id: HaJa
doi: 10.1039/c2gc36666e
intvolume: ' 15'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 381 - 388
publication: Green Chemistry
publication_status: published
publisher: Royal Society of Chemistry
publist_id: '7313'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of
alkyd resins'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2013'
...
---
_id: '502'
abstract:
- lang: eng
text: 'Blind signatures allow users to obtain signatures on messages hidden from
the signer; moreover, the signer cannot link the resulting message/signature pair
to the signing session. This paper presents blind signature schemes, in which
the number of interactions between the user and the signer is minimal and whose
blind signatures are short. Our schemes are defined over bilinear groups and are
proved secure in the common-reference-string model without random oracles and
under standard assumptions: CDH and the decision-linear assumption. (We also give
variants over asymmetric groups based on similar assumptions.) The blind signatures
are Waters signatures, which consist of 2 group elements. Moreover, we instantiate
partially blind signatures, where the message consists of a part hidden from the
signer and a commonly known public part, and schemes achieving perfect blindness.
We propose new variants of blind signatures, such as signer-friendly partially
blind signatures, where the public part can be chosen by the signer without prior
agreement, 3-party blind signatures, as well as blind signatures on multiple aggregated
messages provided by independent sources. We also extend Waters signatures to
non-binary alphabets by proving a new result on the underlying hash function. '
author:
- first_name: Olivier
full_name: Blazy, Olivier
last_name: Blazy
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: David
full_name: Pointcheval, David
last_name: Pointcheval
- first_name: Damien
full_name: Vergnaud, Damien
last_name: Vergnaud
citation:
ama: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. Short blind signatures. Journal
of Computer Security. 2013;21(5):627-661. doi:10.3233/JCS-130477
apa: Blazy, O., Fuchsbauer, G., Pointcheval, D., & Vergnaud, D. (2013). Short
blind signatures. Journal of Computer Security. IOS Press. https://doi.org/10.3233/JCS-130477
chicago: Blazy, Olivier, Georg Fuchsbauer, David Pointcheval, and Damien Vergnaud.
“Short Blind Signatures.” Journal of Computer Security. IOS Press, 2013.
https://doi.org/10.3233/JCS-130477.
ieee: O. Blazy, G. Fuchsbauer, D. Pointcheval, and D. Vergnaud, “Short blind signatures,”
Journal of Computer Security, vol. 21, no. 5. IOS Press, pp. 627–661, 2013.
ista: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. 2013. Short blind signatures.
Journal of Computer Security. 21(5), 627–661.
mla: Blazy, Olivier, et al. “Short Blind Signatures.” Journal of Computer Security,
vol. 21, no. 5, IOS Press, 2013, pp. 627–61, doi:10.3233/JCS-130477.
short: O. Blazy, G. Fuchsbauer, D. Pointcheval, D. Vergnaud, Journal of Computer
Security 21 (2013) 627–661.
date_created: 2018-12-11T11:46:50Z
date_published: 2013-11-22T00:00:00Z
date_updated: 2021-01-12T08:01:09Z
day: '22'
department:
- _id: KrPi
doi: 10.3233/JCS-130477
intvolume: ' 21'
issue: '5'
language:
- iso: eng
month: '11'
oa_version: None
page: 627 - 661
publication: Journal of Computer Security
publication_status: published
publisher: IOS Press
publist_id: '7318'
quality_controlled: '1'
scopus_import: 1
status: public
title: Short blind signatures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2013'
...
---
_id: '508'
abstract:
- lang: eng
text: The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen
species with microbicidal activity. It is composed of two membrane-spanning subunits,
gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic
subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively).
Mutations in any of these genes can result in chronic granulomatous disease, a
primary immunodeficiency characterized by recurrent infections. Using evolutionary
mapping, we determined that episodes of adaptive natural selection have shaped
the extracellular portion of gp91-phox during the evolution of mammals, which
suggests that this region may have a function in host-pathogen interactions. On
the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2,
and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of
European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the
pattern of CYBA diversity is compatible with balancing natural selection, perhaps
mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern
of diversity characterized by a differentiated haplotype structure. Our study
provides insight into the role of pathogen-driven natural selection in an innate
immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic
NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other
complex diseases.
author:
- first_name: Eduardo
full_name: Tarazona Santos, Eduardo
last_name: Tarazona Santos
- first_name: Moara
full_name: Machado, Moara
last_name: Machado
- first_name: Wagner
full_name: Magalhães, Wagner
last_name: Magalhães
- first_name: Renee
full_name: Chen, Renee
last_name: Chen
- first_name: Fernanda
full_name: Lyon, Fernanda
last_name: Lyon
- first_name: Laurie
full_name: Burdett, Laurie
last_name: Burdett
- first_name: Andrew
full_name: Crenshaw, Andrew
last_name: Crenshaw
- first_name: Cristina
full_name: Fabbri, Cristina
last_name: Fabbri
- first_name: Latife
full_name: Pereira, Latife
last_name: Pereira
- first_name: Laelia
full_name: Pinto, Laelia
last_name: Pinto
- 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: Ben
full_name: Sestanovich, Ben
last_name: Sestanovich
- first_name: Meredith
full_name: Yeager, Meredith
last_name: Yeager
- first_name: Stephen
full_name: Chanock, Stephen
last_name: Chanock
citation:
ama: 'Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of
the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications.
Molecular Biology and Evolution. 2013;30(9):2157-2167. doi:10.1093/molbev/mst119'
apa: 'Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett,
L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes
CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and
Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst119'
chicago: 'Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen,
Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics
of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.”
Molecular Biology and Evolution. Oxford University Press, 2013. https://doi.org/10.1093/molbev/mst119.'
ieee: 'E. Tarazona Santos et al., “Evolutionary dynamics of the human NADPH
oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” Molecular
Biology and Evolution, vol. 30, no. 9. Oxford University Press, pp. 2157–2167,
2013.'
ista: 'Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw
A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M,
Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB,
CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution.
30(9), 2157–2167.'
mla: 'Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH
Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular
Biology and Evolution, vol. 30, no. 9, Oxford University Press, 2013, pp.
2157–67, doi:10.1093/molbev/mst119.'
short: E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett,
A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich,
M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T08:01:12Z
day: '01'
department:
- _id: JoBo
doi: 10.1093/molbev/mst119
external_id:
pmid:
- '23821607'
intvolume: ' 30'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/
month: '09'
oa: 1
oa_version: Submitted Version
page: 2157 - 2167
pmid: 1
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '7310'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and
NCF4: Functional implications'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2013'
...
---
_id: '509'
abstract:
- lang: eng
text: 'Clathrin-mediated endocytosis (CME) regulates many aspects of plant development,
including hormone signaling and responses to environmental stresses. Despite the
importance of this process, the machinery that regulates CME in plants is largely
unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is
required for the formation of clathrin-coated vesicles at the plasma membrane
(PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana,
the biochemistry and functionality of the complex is still uncharacterized. Here,
we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification
and found that one of the large AP-2 subunits, AP2A1, localized at the PM and
interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat
receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2.
Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative
version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced
the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis
is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. '
author:
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Niloufer
full_name: Irani, Niloufer
last_name: Irani
- first_name: Soo
full_name: Kim, Soo
last_name: Kim
- first_name: Zheng
full_name: Xu, Zheng
last_name: Xu
- first_name: Astrid
full_name: Gadeyne, Astrid
last_name: Gadeyne
- first_name: Wim
full_name: Dejonghe, Wim
last_name: Dejonghe
- first_name: Isabelle
full_name: Vanhoutte, Isabelle
last_name: Vanhoutte
- first_name: Geert
full_name: Persiau, Geert
last_name: Persiau
- first_name: Dominique
full_name: Eeckhout, Dominique
last_name: Eeckhout
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Kyungyoung
full_name: Song, Kyungyoung
last_name: Song
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Inhwan
full_name: Hwang, Inhwan
last_name: Hwang
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Di Rubbo S, Irani N, Kim S, et al. The clathrin adaptor complex AP-2 mediates
endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell.
2013;25(8):2986-2997. doi:10.1105/tpc.113.114058
apa: Di Rubbo, S., Irani, N., Kim, S., Xu, Z., Gadeyne, A., Dejonghe, W., … Russinova,
E. (2013). The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid
INSENSITIVE1 in arabidopsis. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.113.114058
chicago: Di Rubbo, Simone, Niloufer Irani, Soo Kim, Zheng Xu, Astrid Gadeyne, Wim
Dejonghe, Isabelle Vanhoutte, et al. “The Clathrin Adaptor Complex AP-2 Mediates
Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell.
American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114058.
ieee: S. Di Rubbo et al., “The clathrin adaptor complex AP-2 mediates endocytosis
of brassinosteroid INSENSITIVE1 in arabidopsis,” Plant Cell, vol. 25, no.
8. American Society of Plant Biologists, pp. 2986–2997, 2013.
ista: Di Rubbo S, Irani N, Kim S, Xu Z, Gadeyne A, Dejonghe W, Vanhoutte I, Persiau
G, Eeckhout D, Simon S, Song K, Kleine Vehn J, Friml J, De Jaeger G, Van Damme
D, Hwang I, Russinova E. 2013. The clathrin adaptor complex AP-2 mediates endocytosis
of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 25(8), 2986–2997.
mla: Di Rubbo, Simone, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis
of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell, vol. 25, no.
8, American Society of Plant Biologists, 2013, pp. 2986–97, doi:10.1105/tpc.113.114058.
short: S. Di Rubbo, N. Irani, S. Kim, Z. Xu, A. Gadeyne, W. Dejonghe, I. Vanhoutte,
G. Persiau, D. Eeckhout, S. Simon, K. Song, J. Kleine Vehn, J. Friml, G. De Jaeger,
D. Van Damme, I. Hwang, E. Russinova, Plant Cell 25 (2013) 2986–2997.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:01:13Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.113.114058
external_id:
pmid:
- '23975899'
intvolume: ' 25'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784593/
month: '08'
oa: 1
oa_version: Submitted Version
page: 2986 - 2997
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7311'
quality_controlled: '1'
scopus_import: 1
status: public
title: The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1
in arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '507'
abstract:
- lang: eng
text: Fertilization in flowering plants requires the temporal and spatial coordination
of many developmental processes, including pollen production, anther dehiscence,
ovule production, and pollen tube elongation. However, it remains elusive as to
how this coordination occurs during reproduction. Here, we present evidence that
endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays
a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays
multiple defects in pollen production and viability, as well as elongation of
staminal filaments and pollen tubes, all of which are pivotal processes needed
for fertilization. Of these abnormalities, the defects in elongation of staminal
filaments and pollen tubes were partially rescued by exogenous auxin. Moreover,
DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments
and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed
defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl)
pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar
localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments.
Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an
inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent
endocytosis plays a crucial role in coordinating the multiple developmental aspects
of male reproductive organs by modulating cellular auxin level through the regulation
of the amount and polarity of PINs.
author:
- first_name: Soo
full_name: Kim, Soo
last_name: Kim
- first_name: Zheng
full_name: Xu, Zheng
last_name: Xu
- first_name: Kyungyoung
full_name: Song, Kyungyoung
last_name: Song
- first_name: Dae
full_name: Kim, Dae
last_name: Kim
- first_name: Hyangju
full_name: Kang, Hyangju
last_name: Kang
- first_name: Ilka
full_name: Reichardt, Ilka
last_name: Reichardt
- first_name: Eun
full_name: Sohn, Eun
last_name: Sohn
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Gerd
full_name: Juergens, Gerd
last_name: Juergens
- first_name: Inhwan
full_name: Hwang, Inhwan
last_name: Hwang
citation:
ama: Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis
is crucial for male reproductive organ development in arabidopsis. Plant Cell.
2013;25(8):2970-2985. doi:10.1105/tpc.113.114264
apa: Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013).
Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive
organ development in arabidopsis. Plant Cell. American Society of Plant
Biologists. https://doi.org/10.1105/tpc.113.114264
chicago: Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt,
Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex
2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.”
Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114264.
ieee: S. Kim et al., “Adaptor protein complex 2-mediated endocytosis is crucial
for male reproductive organ development in arabidopsis,” Plant Cell, vol.
25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013.
ista: Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens
G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for
male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985.
mla: Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial
for Male Reproductive Organ Development in Arabidopsis.” Plant Cell, vol.
25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:10.1105/tpc.113.114264.
short: S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml,
G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:01:12Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.113.114264
external_id:
pmid:
- '23975898'
intvolume: ' 25'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/
month: '08'
oa: 1
oa_version: Submitted Version
page: 2970 - 2985
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7312'
quality_controlled: '1'
scopus_import: 1
status: public
title: Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive
organ development in arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '511'
abstract:
- lang: eng
text: The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant
growth and development. Its nonuniform distribution between cells and tissues
underlies the spatiotemporal coordination of many developmental events and responses
to environmental stimuli. The regulation of auxin gradients and the formation
of auxin maxima/minima most likely involve the regulation of both metabolic and
transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic
acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana
root tissues. OxIAA had little biological activity and was formed rapidly and
irreversibly in response to increases in auxin levels. We further showed that
there is cell type-specific regulation of oxIAA levels in the Arabidopsis root
apex. We propose that oxIAA is an important element in the regulation of output
from auxin gradients and, therefore, in the regulation of auxin homeostasis and
response mechanisms.
author:
- first_name: Aleš
full_name: Pěnčík, Aleš
last_name: Pěnčík
- first_name: Biljana
full_name: Simonovik, Biljana
last_name: Simonovik
- first_name: Sara
full_name: Petersson, Sara
last_name: Petersson
- first_name: Eva
full_name: Henyková, Eva
last_name: Henyková
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Kathleen
full_name: Greenham, Kathleen
last_name: Greenham
- first_name: Yi
full_name: Zhang, Yi
last_name: Zhang
- first_name: Mariusz
full_name: Kowalczyk, Mariusz
last_name: Kowalczyk
- first_name: Mark
full_name: Estelle, Mark
last_name: Estelle
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Göran
full_name: Sandberg, Göran
last_name: Sandberg
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
citation:
ama: Pěnčík A, Simonovik B, Petersson S, et al. Regulation of auxin homeostasis
and gradients in Arabidopsis roots through the formation of the indole-3-acetic
acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 2013;25(10):3858-3870.
doi:10.1105/tpc.113.114421
apa: Pěnčík, A., Simonovik, B., Petersson, S., Henyková, E., Simon, S., Greenham,
K., … Ljung, K. (2013). Regulation of auxin homeostasis and gradients in Arabidopsis
roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic
acid. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114421
chicago: Pěnčík, Aleš, Biljana Simonovik, Sara Petersson, Eva Henyková, Sibu Simon,
Kathleen Greenham, Yi Zhang, et al. “Regulation of Auxin Homeostasis and Gradients
in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite
2-Oxindole-3-Acetic Acid.” Plant Cell. American Society of Plant Biologists,
2013. https://doi.org/10.1105/tpc.113.114421.
ieee: A. Pěnčík et al., “Regulation of auxin homeostasis and gradients in
Arabidopsis roots through the formation of the indole-3-acetic acid catabolite
2-oxindole-3-acetic acid,” Plant Cell, vol. 25, no. 10. American Society
of Plant Biologists, pp. 3858–3870, 2013.
ista: Pěnčík A, Simonovik B, Petersson S, Henyková E, Simon S, Greenham K, Zhang
Y, Kowalczyk M, Estelle M, Zažímalová E, Novák O, Sandberg G, Ljung K. 2013. Regulation
of auxin homeostasis and gradients in Arabidopsis roots through the formation
of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 25(10),
3858–3870.
mla: Pěnčík, Aleš, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis
Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic
Acid.” Plant Cell, vol. 25, no. 10, American Society of Plant Biologists,
2013, pp. 3858–70, doi:10.1105/tpc.113.114421.
short: A. Pěnčík, B. Simonovik, S. Petersson, E. Henyková, S. Simon, K. Greenham,
Y. Zhang, M. Kowalczyk, M. Estelle, E. Zažímalová, O. Novák, G. Sandberg, K. Ljung,
Plant Cell 25 (2013) 3858–3870.
date_created: 2018-12-11T11:46:53Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2021-01-12T08:01:15Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.113.114421
external_id:
pmid:
- '24163311'
intvolume: ' 25'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: www.doi.org/10.1105/tpc.113.114421
month: '10'
oa: 1
oa_version: Published Version
page: 3858 - 3870
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7309'
quality_controlled: '1'
scopus_import: 1
status: public
title: Regulation of auxin homeostasis and gradients in Arabidopsis roots through
the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '516'
abstract:
- lang: eng
text: In plants, changes in local auxin concentrations can trigger a range of developmental
processes as distinct tissues respond differently to the same auxin stimulus.
However, little is known about how auxin is interpreted by individual cell types.
We performed a transcriptomic analysis of responses to auxin within four distinct
tissues of the Arabidopsis thaliana root and demonstrate that different cell types
show competence for discrete responses. The majority of auxin‐responsive genes
displayed a spatial bias in their induction or repression. The novel data set
was used to examine how auxin influences tissue‐specific transcriptional regulation
of cell‐identity markers. Additionally, the data were used in combination with
spatial expression maps of the root to plot a transcriptomic auxin‐response gradient
across the apical and basal meristem. The readout revealed a strong correlation
for thousands of genes between the relative response to auxin and expression along
the longitudinal axis of the root. This data set and comparative analysis provide
a transcriptome‐level spatial breakdown of the response to auxin within an organ
where this hormone mediates many aspects of development.
article_number: '688'
article_processing_charge: No
author:
- first_name: Bastiaan
full_name: Bargmann, Bastiaan
last_name: Bargmann
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Gabriel
full_name: Krouk, Gabriel
last_name: Krouk
- first_name: Tal
full_name: Nawy, Tal
last_name: Nawy
- first_name: Idan
full_name: Efroni, Idan
last_name: Efroni
- first_name: Eilon
full_name: Shani, Eilon
last_name: Shani
- first_name: Goh
full_name: Choe, Goh
last_name: Choe
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dominique
full_name: Bergmann, Dominique
last_name: Bergmann
- first_name: Mark
full_name: Estelle, Mark
last_name: Estelle
- first_name: Kenneth
full_name: Birnbaum, Kenneth
last_name: Birnbaum
citation:
ama: Bargmann B, Vanneste S, Krouk G, et al. A map of cell type‐specific auxin responses.
Molecular Systems Biology. 2013;9(1). doi:10.1038/msb.2013.40
apa: Bargmann, B., Vanneste, S., Krouk, G., Nawy, T., Efroni, I., Shani, E., … Birnbaum,
K. (2013). A map of cell type‐specific auxin responses. Molecular Systems Biology.
Nature Publishing Group. https://doi.org/10.1038/msb.2013.40
chicago: Bargmann, Bastiaan, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efroni,
Eilon Shani, Goh Choe, et al. “A Map of Cell Type‐specific Auxin Responses.” Molecular
Systems Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/msb.2013.40.
ieee: B. Bargmann et al., “A map of cell type‐specific auxin responses,”
Molecular Systems Biology, vol. 9, no. 1. Nature Publishing Group, 2013.
ista: Bargmann B, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml
J, Bergmann D, Estelle M, Birnbaum K. 2013. A map of cell type‐specific auxin
responses. Molecular Systems Biology. 9(1), 688.
mla: Bargmann, Bastiaan, et al. “A Map of Cell Type‐specific Auxin Responses.” Molecular
Systems Biology, vol. 9, no. 1, 688, Nature Publishing Group, 2013, doi:10.1038/msb.2013.40.
short: B. Bargmann, S. Vanneste, G. Krouk, T. Nawy, I. Efroni, E. Shani, G. Choe,
J. Friml, D. Bergmann, M. Estelle, K. Birnbaum, Molecular Systems Biology 9 (2013).
date_created: 2018-12-11T11:46:55Z
date_published: 2013-09-10T00:00:00Z
date_updated: 2021-01-12T08:01:17Z
day: '10'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1038/msb.2013.40
file:
- access_level: open_access
checksum: 9c4fbe793af4bb22b3fe50cc677a39bf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:46Z
date_updated: 2020-07-14T12:46:36Z
file_id: '4644'
file_name: IST-2018-936-v1+1_2008_Barton_A_map.pdf
file_size: 3257692
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '09'
oa: 1
oa_version: Published Version
publication: Molecular Systems Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7303'
pubrep_id: '936'
quality_controlled: '1'
scopus_import: 1
status: public
title: A map of cell type‐specific auxin responses
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '522'
abstract:
- lang: eng
text: Podoplanin, a mucin-like plasma membrane protein, is expressed by lymphatic
endothelial cells and responsible for separation of blood and lymphatic circulation
through activation of platelets. Here we show that podoplanin is also expressed
by thymic fibroblastic reticular cells (tFRC), a novel thymic medulla stroma cell
type associated with thymic conduits, and involved in development of natural regulatory
T cells (nTreg). Young mice deficient in podoplanin lack nTreg owing to retardation
of CD4+CD25+ thymocytes in the cortex and missing differentiation of Foxp3+ thymocytes
in the medulla. This might be due to CCL21 that delocalizes upon deletion of the
CCL21-binding podoplanin from medullar tFRC to cortex areas. The animals do not
remain devoid of nTreg but generate them delayed within the first month resulting
in Th2-biased hypergammaglobulinemia but not in the death-causing autoimmune phenotype
of Foxp3-deficient Scurfy mice.
author:
- first_name: Elke
full_name: Fuertbauer, Elke
last_name: Fuertbauer
- first_name: Jan
full_name: Zaujec, Jan
last_name: Zaujec
- first_name: Pavel
full_name: Uhrin, Pavel
last_name: Uhrin
- first_name: Ingrid
full_name: Raab, Ingrid
last_name: Raab
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
- first_name: Helga
full_name: Schachner, Helga
last_name: Schachner
- first_name: Miroslav
full_name: Bauer, Miroslav
last_name: Bauer
- first_name: Gerhard
full_name: Schütz, Gerhard
last_name: Schütz
- first_name: Bernd
full_name: Binder, Bernd
last_name: Binder
- 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: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
- first_name: Hannes
full_name: Stockinger, Hannes
last_name: Stockinger
citation:
ama: Fuertbauer E, Zaujec J, Uhrin P, et al. Thymic medullar conduits-associated
podoplanin promotes natural regulatory T cells. Immunology Letters. 2013;154(1-2):31-41.
doi:10.1016/j.imlet.2013.07.007
apa: Fuertbauer, E., Zaujec, J., Uhrin, P., Raab, I., Weber, M., Schachner, H.,
… Stockinger, H. (2013). Thymic medullar conduits-associated podoplanin promotes
natural regulatory T cells. Immunology Letters. Elsevier. https://doi.org/10.1016/j.imlet.2013.07.007
chicago: Fuertbauer, Elke, Jan Zaujec, Pavel Uhrin, Ingrid Raab, Michele Weber,
Helga Schachner, Miroslav Bauer, et al. “Thymic Medullar Conduits-Associated Podoplanin
Promotes Natural Regulatory T Cells.” Immunology Letters. Elsevier, 2013.
https://doi.org/10.1016/j.imlet.2013.07.007.
ieee: E. Fuertbauer et al., “Thymic medullar conduits-associated podoplanin
promotes natural regulatory T cells,” Immunology Letters, vol. 154, no.
1–2. Elsevier, pp. 31–41, 2013.
ista: Fuertbauer E, Zaujec J, Uhrin P, Raab I, Weber M, Schachner H, Bauer M, Schütz
G, Binder B, Sixt MK, Kerjaschki D, Stockinger H. 2013. Thymic medullar conduits-associated
podoplanin promotes natural regulatory T cells. Immunology Letters. 154(1–2),
31–41.
mla: Fuertbauer, Elke, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes
Natural Regulatory T Cells.” Immunology Letters, vol. 154, no. 1–2, Elsevier,
2013, pp. 31–41, doi:10.1016/j.imlet.2013.07.007.
short: E. Fuertbauer, J. Zaujec, P. Uhrin, I. Raab, M. Weber, H. Schachner, M. Bauer,
G. Schütz, B. Binder, M.K. Sixt, D. Kerjaschki, H. Stockinger, Immunology Letters
154 (2013) 31–41.
date_created: 2018-12-11T11:46:57Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T08:01:22Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/j.imlet.2013.07.007
intvolume: ' 154'
issue: 1-2
language:
- iso: eng
month: '07'
oa_version: None
page: 31 - 41
publication: Immunology Letters
publication_status: published
publisher: Elsevier
publist_id: '7300'
quality_controlled: '1'
scopus_import: 1
status: public
title: Thymic medullar conduits-associated podoplanin promotes natural regulatory
T cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 154
year: '2013'
...
---
_id: '2279'
abstract:
- lang: eng
text: We consider two-player games played on weighted directed graphs with mean-payoff
and total-payoff objectives, two classical quantitative objectives. While for
single-dimensional games the complexity and memory bounds for both objectives
coincide, we show that in contrast to multi-dimensional mean-payoff games that
are known to be coNP-complete, multi-dimensional total-payoff games are undecidable.
We introduce conservative approximations of these objectives, where the payoff
is considered over a local finite window sliding along a play, instead of the
whole play. For single dimension, we show that (i) if the window size is polynomial,
deciding the winner takes polynomial time, and (ii) the existence of a bounded
window can be decided in NP ∩ coNP, and is at least as hard as solving mean-payoff
games. For multiple dimensions, we show that (i) the problem with fixed window
size is EXPTIME-complete, and (ii) there is no primitive-recursive algorithm to
decide the existence of a bounded window.
acknowledgement: 279307; ERC; Fonds National de la Reserche Luxembourg; 279499; ERC;
Fonds National de la Reserche Luxembourg
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: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Mickael
full_name: Randour, Mickael
last_name: Randour
- first_name: Jean
full_name: Raskin, Jean
last_name: Raskin
citation:
ama: Chatterjee K, Doyen L, Randour M, Raskin J. Looking at mean-payoff and total-payoff
through windows. 2013;8172:118-132. doi:10.1007/978-3-319-02444-8_10
apa: 'Chatterjee, K., Doyen, L., Randour, M., & Raskin, J. (2013). Looking at
mean-payoff and total-payoff through windows. Presented at the ATVA: Automated
Technology for Verification and Analysis, Hanoi, Vietnam: Springer. https://doi.org/10.1007/978-3-319-02444-8_10'
chicago: Chatterjee, Krishnendu, Laurent Doyen, Mickael Randour, and Jean Raskin.
“Looking at Mean-Payoff and Total-Payoff through Windows.” Lecture Notes in Computer
Science. Springer, 2013. https://doi.org/10.1007/978-3-319-02444-8_10.
ieee: K. Chatterjee, L. Doyen, M. Randour, and J. Raskin, “Looking at mean-payoff
and total-payoff through windows,” vol. 8172. Springer, pp. 118–132, 2013.
ista: Chatterjee K, Doyen L, Randour M, Raskin J. 2013. Looking at mean-payoff and
total-payoff through windows. 8172, 118–132.
mla: Chatterjee, Krishnendu, et al. Looking at Mean-Payoff and Total-Payoff through
Windows. Vol. 8172, Springer, 2013, pp. 118–32, doi:10.1007/978-3-319-02444-8_10.
short: K. Chatterjee, L. Doyen, M. Randour, J. Raskin, 8172 (2013) 118–132.
conference:
end_date: 2013-10-18
location: Hanoi, Vietnam
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2013-10-15
date_created: 2018-12-11T11:56:44Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2023-02-23T12:22:51Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-319-02444-8_10
ec_funded: 1
intvolume: ' 8172'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1302.4248
month: '01'
oa: 1
oa_version: Preprint
page: 118 - 132
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: Springer
publist_id: '4656'
quality_controlled: '1'
related_material:
record:
- id: '523'
relation: later_version
status: public
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Looking at mean-payoff and total-payoff through windows
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8172
year: '2013'
...
---
_id: '528'
abstract:
- lang: eng
text: Establishment of the embryonic axis foreshadows the main body axis of adults
both in plants and in animals, but underlying mechanisms are considered distinct.
Plants utilize directional, cell-to-cell transport of the growth hormone auxin
[1, 2] to generate an asymmetric auxin response that specifies the embryonic apical-basal
axis [3-6]. The auxin flow directionality depends on the polarized subcellular
localization of PIN-FORMED (PIN) auxin transporters [7, 8]. It remains unknown
which mechanisms and spatial cues guide cell polarization and axis orientation
in early embryos. Herein, we provide conceptually novel insights into the formation
of embryonic axis in Arabidopsis by identifying a crucial role of localized tryptophan-dependent
auxin biosynthesis [9-12]. Local auxin production at the base of young embryos
and the accompanying PIN7-mediated auxin flow toward the proembryo are required
for the apical auxin response maximum and the specification of apical embryonic
structures. Later in embryogenesis, the precisely timed onset of localized apical
auxin biosynthesis mediates PIN1 polarization, basal auxin response maximum, and
specification of the root pole. Thus, the tight spatiotemporal control of distinct
local auxin sources provides a necessary, non-cell-autonomous trigger for the
coordinated cell polarization and subsequent apical-basal axis orientation during
embryogenesis and, presumably, also for other polarization events during postembryonic
plant life [13, 14].
author:
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Anna
full_name: Stepanova, Anna
last_name: Stepanova
- first_name: Linda
full_name: Robles, Linda
last_name: Robles
- first_name: Annemarie
full_name: Lokerse, Annemarie
last_name: Lokerse
- first_name: Jose
full_name: Alonso, Jose
last_name: Alonso
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Robert H, Grones P, Stepanova A, et al. Local auxin sources orient the apical
basal axis in arabidopsis embryos. Current Biology. 2013;23(24):2506-2512.
doi:10.1016/j.cub.2013.09.039
apa: Robert, H., Grones, P., Stepanova, A., Robles, L., Lokerse, A., Alonso, J.,
… Friml, J. (2013). Local auxin sources orient the apical basal axis in arabidopsis
embryos. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.09.039
chicago: Robert, Hélène, Peter Grones, Anna Stepanova, Linda Robles, Annemarie Lokerse,
Jose Alonso, Dolf Weijers, and Jiří Friml. “Local Auxin Sources Orient the Apical
Basal Axis in Arabidopsis Embryos.” Current Biology. Cell Press, 2013.
https://doi.org/10.1016/j.cub.2013.09.039.
ieee: H. Robert et al., “Local auxin sources orient the apical basal axis
in arabidopsis embryos,” Current Biology, vol. 23, no. 24. Cell Press,
pp. 2506–2512, 2013.
ista: Robert H, Grones P, Stepanova A, Robles L, Lokerse A, Alonso J, Weijers D,
Friml J. 2013. Local auxin sources orient the apical basal axis in arabidopsis
embryos. Current Biology. 23(24), 2506–2512.
mla: Robert, Hélène, et al. “Local Auxin Sources Orient the Apical Basal Axis in
Arabidopsis Embryos.” Current Biology, vol. 23, no. 24, Cell Press, 2013,
pp. 2506–12, doi:10.1016/j.cub.2013.09.039.
short: H. Robert, P. Grones, A. Stepanova, L. Robles, A. Lokerse, J. Alonso, D.
Weijers, J. Friml, Current Biology 23 (2013) 2506–2512.
date_created: 2018-12-11T11:46:59Z
date_published: 2013-12-16T00:00:00Z
date_updated: 2021-01-12T08:01:25Z
day: '16'
department:
- _id: JiFr
doi: 10.1016/j.cub.2013.09.039
ec_funded: 1
intvolume: ' 23'
issue: '24'
language:
- iso: eng
month: '12'
oa_version: None
page: 2506 - 2512
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '7291'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local auxin sources orient the apical basal axis in arabidopsis embryos
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2013'
...
---
_id: '527'
abstract:
- lang: eng
text: The apical-basal axis of the early plant embryo determines the body plan of
the adult organism. To establish a polarized embryonic axis, plants evolved a
unique mechanism that involves directional, cell-to-cell transport of the growth
regulator auxin. Auxin transport relies on PIN auxin transporters [1], whose polar
subcellular localization determines the flow directionality. PIN-mediated auxin
transport mediates the spatial and temporal activity of the auxin response machinery
[2-7] that contributes to embryo patterning processes, including establishment
of the apical (shoot) and basal (root) embryo poles [8]. However, little is known
of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis
[9]. Here, we developed a model of plant embryogenesis that correctly generates
emergent cell polarities and auxin-mediated sequential initiation of apical-basal
axis of plant embryo. The model relies on two precisely localized auxin sources
and a feedback between auxin and the polar, subcellular PIN transporter localization.
Simulations reproduced PIN polarity and auxin distribution, as well as previously
unknown polarization events during early embryogenesis. The spectrum of validated
model predictions suggests that our model corresponds to a minimal mechanistic
framework for initiation and orientation of the apical-basal axis to guide both
embryonic and postembryonic plant development.
author:
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Richard
full_name: Smith, Richard
last_name: Smith
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Wabnik KT, Robert H, Smith R, Friml J. Modeling framework for the establishment
of the apical-basal embryonic axis in plants. Current Biology. 2013;23(24):2513-2518.
doi:10.1016/j.cub.2013.10.038
apa: Wabnik, K. T., Robert, H., Smith, R., & Friml, J. (2013). Modeling framework
for the establishment of the apical-basal embryonic axis in plants. Current
Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.10.038
chicago: Wabnik, Krzysztof T, Hélène Robert, Richard Smith, and Jiří Friml. “Modeling
Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.”
Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.10.038.
ieee: K. T. Wabnik, H. Robert, R. Smith, and J. Friml, “Modeling framework for the
establishment of the apical-basal embryonic axis in plants,” Current Biology,
vol. 23, no. 24. Cell Press, pp. 2513–2518, 2013.
ista: Wabnik KT, Robert H, Smith R, Friml J. 2013. Modeling framework for the establishment
of the apical-basal embryonic axis in plants. Current Biology. 23(24), 2513–2518.
mla: Wabnik, Krzysztof T., et al. “Modeling Framework for the Establishment of the
Apical-Basal Embryonic Axis in Plants.” Current Biology, vol. 23, no. 24,
Cell Press, 2013, pp. 2513–18, doi:10.1016/j.cub.2013.10.038.
short: K.T. Wabnik, H. Robert, R. Smith, J. Friml, Current Biology 23 (2013) 2513–2518.
date_created: 2018-12-11T11:46:58Z
date_published: 2013-12-16T00:00:00Z
date_updated: 2021-01-12T08:01:24Z
day: '16'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1016/j.cub.2013.10.038
ec_funded: 1
intvolume: ' 23'
issue: '24'
language:
- iso: eng
month: '12'
oa_version: None
page: 2513 - 2518
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '7292'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modeling framework for the establishment of the apical-basal embryonic axis
in plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2013'
...
---
_id: '5399'
abstract:
- lang: eng
text: In this work we present a flexible tool for tumor progression, which simulates
the evolutionary dynamics of cancer. Tumor progression implements a multi-type
branching process where the key parameters are the fitness landscape, the mutation
rate, and the average time of cell division. The fitness of a cancer cell depends
on the mutations it has accumulated. The input to our tool could be any fitness
landscape, mutation rate, and cell division time, and the tool produces the growth
dynamics and all relevant statistics.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Ivana
full_name: Bozic, Ivana
last_name: Bozic
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: 'Reiter J, Bozic I, Chatterjee K, Nowak M. TTP: Tool for Tumor Progression.
IST Austria; 2013. doi:10.15479/AT:IST-2013-104-v1-1'
apa: 'Reiter, J., Bozic, I., Chatterjee, K., & Nowak, M. (2013). TTP: Tool
for Tumor Progression. IST Austria. https://doi.org/10.15479/AT:IST-2013-104-v1-1'
chicago: 'Reiter, Johannes, Ivana Bozic, Krishnendu Chatterjee, and Martin Nowak.
TTP: Tool for Tumor Progression. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-104-v1-1.'
ieee: 'J. Reiter, I. Bozic, K. Chatterjee, and M. Nowak, TTP: Tool for Tumor
Progression. IST Austria, 2013.'
ista: 'Reiter J, Bozic I, Chatterjee K, Nowak M. 2013. TTP: Tool for Tumor Progression,
IST Austria, 17p.'
mla: 'Reiter, Johannes, et al. TTP: Tool for Tumor Progression. IST Austria,
2013, doi:10.15479/AT:IST-2013-104-v1-1.'
short: 'J. Reiter, I. Bozic, K. Chatterjee, M. Nowak, TTP: Tool for Tumor Progression,
IST Austria, 2013.'
date_created: 2018-12-12T11:39:07Z
date_published: 2013-01-11T00:00:00Z
date_updated: 2023-02-23T10:23:57Z
day: '11'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-104-v1-1
file:
- access_level: open_access
checksum: 2cc8c6e157eca1271128db80bb3dec80
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:20Z
date_updated: 2020-07-14T12:46:44Z
file_id: '5542'
file_name: IST-2013-104-v1+1_tumortool.pdf
file_size: 1471954
relation: main_file
file_date_updated: 2020-07-14T12:46:44Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '17'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '104'
related_material:
record:
- id: '2000'
relation: later_version
status: public
status: public
title: 'TTP: Tool for Tumor Progression'
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2295'
abstract:
- lang: eng
text: We consider partially observable Markov decision processes (POMDPs) with ω-regular
conditions specified as parity objectives. The qualitative analysis problem given
a POMDP and a parity objective asks whether there is a strategy to ensure that
the objective is satisfied with probability 1 (resp. positive probability). While
the qualitative analysis problems are known to be undecidable even for very special
cases of parity objectives, we establish decidability (with optimal EXPTIME-complete
complexity) of the qualitative analysis problems for POMDPs with all parity objectives
under finite-memory strategies. We also establish asymptotically optimal (exponential)
memory bounds.
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: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Mathieu
full_name: Tracol, Mathieu
id: 3F54FA38-F248-11E8-B48F-1D18A9856A87
last_name: Tracol
citation:
ama: Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable
Markov decision processes with omega-regular objectives. 2013;23:165-180. doi:10.4230/LIPIcs.CSL.2013.165
apa: 'Chatterjee, K., Chmelik, M., & Tracol, M. (2013). What is decidable about
partially observable Markov decision processes with omega-regular objectives.
Presented at the CSL: Computer Science Logic, Torino, Italy: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2013.165'
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable
about Partially Observable Markov Decision Processes with Omega-Regular Objectives.”
Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2013. https://doi.org/10.4230/LIPIcs.CSL.2013.165.
ieee: K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially
observable Markov decision processes with omega-regular objectives,” vol. 23.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 165–180, 2013.
ista: Chatterjee K, Chmelik M, Tracol M. 2013. What is decidable about partially
observable Markov decision processes with omega-regular objectives. 23, 165–180.
mla: Chatterjee, Krishnendu, et al. What Is Decidable about Partially Observable
Markov Decision Processes with Omega-Regular Objectives. Vol. 23, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 165–80, doi:10.4230/LIPIcs.CSL.2013.165.
short: K. Chatterjee, M. Chmelik, M. Tracol, 23 (2013) 165–180.
conference:
end_date: 2013-09-05
location: Torino, Italy
name: 'CSL: Computer Science Logic'
start_date: 2013-09-02
date_created: 2018-12-11T11:56:50Z
date_published: 2013-08-27T00:00:00Z
date_updated: 2023-02-23T12:24:38Z
day: '27'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.CSL.2013.165
ec_funded: 1
file:
- access_level: open_access
checksum: ba2828322955574d9283bea0e17a37a6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:42Z
date_updated: 2020-07-14T12:45:37Z
file_id: '4766'
file_name: IST-2017-756-v1+1_2.pdf
file_size: 345171
relation: main_file
file_date_updated: 2020-07-14T12:45:37Z
has_accepted_license: '1'
intvolume: ' 23'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 165 - 180
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '4633'
pubrep_id: '756'
quality_controlled: '1'
related_material:
record:
- id: '1477'
relation: later_version
status: public
- id: '5400'
relation: earlier_version
status: public
scopus_import: 1
series_title: Leibniz International Proceedings in Informatics
status: public
title: What is decidable about partially observable Markov decision processes with
omega-regular objectives
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2013'
...
---
_id: '5403'
abstract:
- lang: eng
text: 'We consider concurrent games played by two-players on a finite state graph,
where in every round the players simultaneously choose a move, and the current
state along with the joint moves determine the successor state. We study the most
fundamental objective for concurrent games, namely, mean-payoff or limit-average
objective, where a reward is associated to every transition, and the goal of player
1 is to maximize the long-run average of the rewards, and the objective of player
2 is strictly the opposite (i.e., the games are zero-sum). The path constraint
for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward,
or arbitrarily close to it; or quantitative, i.e., a given threshold between the
minimal and maximal reward. We consider the computation of the almost-sure (resp.
positive) winning sets, where player 1 can ensure that the path constraint is
satisfied with probability 1 (resp. positive probability). Almost-sure winning
with qualitative constraint exactly corresponds to the question whether there
exists a strategy to ensure that the payoff is the maximal reward of the game.
Our main results for qualitative path constraints are as follows: (1) we establish
qualitative determinacy results that show for every state either player 1 has
a strategy to ensure almost-sure (resp. positive) winning against all player-2
strategies or player 2 has a spoiling strategy to falsify almost-sure (resp. positive)
winning against all player-1 strategies; (2) we present optimal strategy complexity
results that precisely characterize the classes of strategies required for almost-sure
and positive winning for both players; and (3) we present quadratic time algorithms
to compute the almost-sure and the positive winning sets, matching the best known
bound of the algorithms for much simpler problems (such as reachability objectives).
For quantitative constraints we show that a polynomial time solution for the almost-sure
or the positive winning set would imply a solution to a long-standing open problem
(of solving the value problem of mean-payoff games) that is not known to be in
polynomial time.'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: Chatterjee K, Ibsen-Jensen R. Qualitative Analysis of Concurrent Mean-Payoff
Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-126-v1-1
apa: Chatterjee, K., & Ibsen-Jensen, R. (2013). Qualitative analysis of concurrent
mean-payoff games. IST Austria. https://doi.org/10.15479/AT:IST-2013-126-v1-1
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. Qualitative Analysis
of Concurrent Mean-Payoff Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-126-v1-1.
ieee: K. Chatterjee and R. Ibsen-Jensen, Qualitative analysis of concurrent mean-payoff
games. IST Austria, 2013.
ista: Chatterjee K, Ibsen-Jensen R. 2013. Qualitative analysis of concurrent mean-payoff
games, IST Austria, 33p.
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. Qualitative Analysis of
Concurrent Mean-Payoff Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-126-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, Qualitative Analysis of Concurrent Mean-Payoff
Games, IST Austria, 2013.
date_created: 2018-12-12T11:39:08Z
date_published: 2013-07-03T00:00:00Z
date_updated: 2023-02-23T12:22:53Z
day: '03'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-126-v1-1
file:
- access_level: open_access
checksum: 063868c665beec37bf28160e2a695746
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:49Z
date_updated: 2020-07-14T12:46:45Z
file_id: '5510'
file_name: IST-2013-126-v1+1_soda_full.pdf
file_size: 434523
relation: main_file
file_date_updated: 2020-07-14T12:46:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '33'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '126'
related_material:
record:
- id: '524'
relation: later_version
status: public
status: public
title: Qualitative analysis of concurrent mean-payoff games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5402'
abstract:
- lang: eng
text: "Linearizability requires that the outcome of calls by competing threads to
a concurrent data structure is the same as some sequential execution where each
thread has exclusive access to the data structure. In an ordered data structure,
such as a queue or a stack, linearizability is ensured by requiring threads commit
in the order dictated by the sequential semantics of the data structure; e.g.,
in a concurrent queue implementation a dequeue can only remove the oldest element.
\r\nIn this paper, we investigate the impact of this strict ordering, by comparing
what linearizability allows to what existing implementations do. We first give
an operational definition for linearizability which allows us to build the most
general linearizable implementation as a transition system for any given sequential
specification. We then use this operational definition to categorize linearizable
implementations based on whether they are bound or free. In a bound implementation,
whenever all threads observe the same logical state, the updates to the logical
state and the temporal order of commits coincide. All existing queue implementations
we know of are bound. We then proceed to present, to the best of our knowledge,
the first ever free queue implementation. Our experiments show that free implementations
have the potential for better performance by suffering less from contention."
alternative_title:
- IST Austria Technical Report
author:
- 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: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: Henzinger TA, Sezgin A. How Free Is Your Linearizable Concurrent Data Structure?
IST Austria; 2013. doi:10.15479/AT:IST-2013-123-v1-1
apa: Henzinger, T. A., & Sezgin, A. (2013). How free is your linearizable
concurrent data structure? IST Austria. https://doi.org/10.15479/AT:IST-2013-123-v1-1
chicago: Henzinger, Thomas A, and Ali Sezgin. How Free Is Your Linearizable Concurrent
Data Structure? IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-123-v1-1.
ieee: T. A. Henzinger and A. Sezgin, How free is your linearizable concurrent
data structure? IST Austria, 2013.
ista: Henzinger TA, Sezgin A. 2013. How free is your linearizable concurrent data
structure?, IST Austria, 16p.
mla: Henzinger, Thomas A., and Ali Sezgin. How Free Is Your Linearizable Concurrent
Data Structure? IST Austria, 2013, doi:10.15479/AT:IST-2013-123-v1-1.
short: T.A. Henzinger, A. Sezgin, How Free Is Your Linearizable Concurrent Data
Structure?, IST Austria, 2013.
date_created: 2018-12-12T11:39:07Z
date_published: 2013-06-12T00:00:00Z
date_updated: 2020-07-14T23:04:47Z
day: '12'
ddc:
- '000'
- '004'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2013-123-v1-1
file:
- access_level: open_access
checksum: ce580605ae9756a8c99d7b403ebb8eed
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:19Z
date_updated: 2020-07-14T12:46:45Z
file_id: '5480'
file_name: IST-2013-123-v1+1_main-concur2013.pdf
file_size: 249790
relation: main_file
file_date_updated: 2020-07-14T12:46:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '16'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '123'
status: public
title: How free is your linearizable concurrent data structure?
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5400'
abstract:
- lang: eng
text: We consider partially observable Markov decision processes (POMDPs) with ω-regular
conditions specified as parity objectives. The class of ω-regular languages extends
regular languages to infinite strings and provides a robust specification language
to express all properties used in verification, and parity objectives are canonical
forms to express ω-regular conditions. The qualitative analysis problem given
a POMDP and a parity objective asks whether there is a strategy to ensure that
the objective is satis- fied with probability 1 (resp. positive probability).
While the qualitative analysis problems are known to be undecidable even for very
special cases of parity objectives, we establish decidability (with optimal complexity)
of the qualitative analysis problems for POMDPs with all parity objectives under
finite- memory strategies. We establish asymptotically optimal (exponential) memory
bounds and EXPTIME- completeness of the qualitative analysis problems under finite-memory
strategies for POMDPs with parity objectives.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Mathieu
full_name: Tracol, Mathieu
id: 3F54FA38-F248-11E8-B48F-1D18A9856A87
last_name: Tracol
citation:
ama: Chatterjee K, Chmelik M, Tracol M. What Is Decidable about Partially Observable
Markov Decision Processes with ω-Regular Objectives. IST Austria; 2013. doi:10.15479/AT:IST-2013-109-v1-1
apa: Chatterjee, K., Chmelik, M., & Tracol, M. (2013). What is decidable
about partially observable Markov decision processes with ω-regular objectives.
IST Austria. https://doi.org/10.15479/AT:IST-2013-109-v1-1
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. What Is
Decidable about Partially Observable Markov Decision Processes with ω-Regular
Objectives. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-109-v1-1.
ieee: K. Chatterjee, M. Chmelik, and M. Tracol, What is decidable about partially
observable Markov decision processes with ω-regular objectives. IST Austria,
2013.
ista: Chatterjee K, Chmelik M, Tracol M. 2013. What is decidable about partially
observable Markov decision processes with ω-regular objectives, IST Austria, 41p.
mla: Chatterjee, Krishnendu, et al. What Is Decidable about Partially Observable
Markov Decision Processes with ω-Regular Objectives. IST Austria, 2013, doi:10.15479/AT:IST-2013-109-v1-1.
short: K. Chatterjee, M. Chmelik, M. Tracol, What Is Decidable about Partially Observable
Markov Decision Processes with ω-Regular Objectives, IST Austria, 2013.
date_created: 2018-12-12T11:39:07Z
date_published: 2013-02-20T00:00:00Z
date_updated: 2023-02-23T10:36:45Z
day: '20'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-109-v1-1
file:
- access_level: open_access
checksum: cbba40210788a1b22c6cf06433b5ed6f
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:06Z
date_updated: 2020-07-14T12:46:44Z
file_id: '5467'
file_name: IST-2013-109-v1+1_What_is_Decidable_about_Partially_Observable_Markov_Decision_Processes_with_ω-Regular_Objectives.pdf
file_size: 483407
relation: main_file
file_date_updated: 2020-07-14T12:46:44Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '41'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '109'
related_material:
record:
- id: '1477'
relation: later_version
status: public
- id: '2295'
relation: later_version
status: public
status: public
title: What is decidable about partially observable Markov decision processes with
ω-regular objectives
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5404'
abstract:
- lang: eng
text: 'We study finite-state two-player (zero-sum) concurrent mean-payoff games
played on a graph. We focus on the important sub-class of ergodic games where
all states are visited infinitely often with probability 1. The algorithmic study
of ergodic games was initiated in a seminal work of Hoffman and Karp in 1966,
but all basic complexity questions have remained unresolved. Our main results
for ergodic games are as follows: We establish (1) an optimal exponential bound
on the patience of stationary strategies (where patience of a distribution is
the inverse of the smallest positive probability and represents a complexity measure
of a stationary strategy); (2) the approximation problem lie in FNP; (3) the approximation
problem is at least as hard as the decision problem for simple stochastic games
(for which NP and coNP is the long-standing best known bound). We show that the
exact value can be expressed in the existential theory of the reals, and also
establish square-root sum hardness for a related class of games.'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: Chatterjee K, Ibsen-Jensen R. The Complexity of Ergodic Games. IST Austria;
2013. doi:10.15479/AT:IST-2013-127-v1-1
apa: Chatterjee, K., & Ibsen-Jensen, R. (2013). The complexity of ergodic
games. IST Austria. https://doi.org/10.15479/AT:IST-2013-127-v1-1
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Ergodic
Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-127-v1-1.
ieee: K. Chatterjee and R. Ibsen-Jensen, The complexity of ergodic games.
IST Austria, 2013.
ista: Chatterjee K, Ibsen-Jensen R. 2013. The complexity of ergodic games, IST Austria,
29p.
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Ergodic
Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-127-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, The Complexity of Ergodic Games, IST Austria,
2013.
date_created: 2018-12-12T11:39:08Z
date_published: 2013-07-03T00:00:00Z
date_updated: 2023-02-23T10:30:55Z
day: '03'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-127-v1-1
file:
- access_level: open_access
checksum: 79ee5e677a82611ce06e0360c69d494a
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:35Z
date_updated: 2020-07-14T12:46:45Z
file_id: '5496'
file_name: IST-2013-127-v1+1_ergodic.pdf
file_size: 517275
relation: main_file
file_date_updated: 2020-07-14T12:46:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '29'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '127'
related_material:
record:
- id: '2162'
relation: later_version
status: public
status: public
title: The complexity of ergodic games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5401'
abstract:
- lang: eng
text: This document is created as a part of the project “Repository for Research
Data at IST Austria”. It summarises the actual initiatives, projects and standards
related to the project. It supports the preparation of standards and specifications
for the project, which should be considered and followed to ensure interoperability
and visibility of the uploaded data.
author:
- first_name: Jana
full_name: Porsche, Jana
id: 3252EDC2-F248-11E8-B48F-1D18A9856A87
last_name: Porsche
citation:
ama: Porsche J. Initiatives and Projects Related to RD. IST Austria; 2013.
apa: Porsche, J. (2013). Initiatives and projects related to RD. IST Austria.
chicago: Porsche, Jana. Initiatives and Projects Related to RD. IST Austria,
2013.
ieee: J. Porsche, Initiatives and projects related to RD. IST Austria, 2013.
ista: Porsche J. 2013. Initiatives and projects related to RD, IST Austria,p.
mla: Porsche, Jana. Initiatives and Projects Related to RD. IST Austria,
2013.
short: J. Porsche, Initiatives and Projects Related to RD, IST Austria, 2013.
date_created: 2018-12-12T11:39:07Z
date_published: 2013-03-20T00:00:00Z
date_updated: 2020-07-14T23:04:47Z
day: '20'
ddc:
- '020'
department:
- _id: E-Lib
file:
- access_level: open_access
checksum: d68712db838432ecdacf9ffb1de8f8a6
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:14Z
date_updated: 2020-07-14T12:46:45Z
file_id: '5536'
file_name: IST-2013-113-v1+1_Initiatives_and_projects_related_to_RD.pdf
file_size: 151208
relation: main_file
file_date_updated: 2020-07-14T12:46:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication_status: published
publisher: IST Austria
pubrep_id: '113'
status: public
title: Initiatives and projects related to RD
type: report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5405'
abstract:
- lang: eng
text: "The theory of graph games is the foundation for modeling and synthesizing
reactive processes. In the synthesis of stochastic processes, we use 2-1/2-player
games where some transitions of the game graph are controlled by two adversarial
players, the System and the Environment, and the other transitions are determined
probabilistically. We consider 2-1/2-player games where the objective of the System
is the conjunction of a qualitative objective (specified as a parity condition)
and a quantitative objective (specified as a mean-payoff condition). We establish
that the problem of deciding whether the System can ensure that the probability
to satisfy the mean-payoff parity objective is at least a given threshold is in
NP ∩ coNP, matching the best known bound in the special case of 2-player games
(where all transitions are deterministic) with only parity objectives, or with
only mean-payoff objectives. We present an algorithm running\r\nin time O(d ·
n^{2d}·MeanGame) to compute the set of almost-sure winning states from which the
objective\r\ncan be ensured with probability 1, where n is the number of states
of the game, d the number of priorities\r\nof the parity objective, and MeanGame
is the complexity to compute the set of almost-sure winning states\r\nin 2-1/2-player
mean-payoff games. Our results are useful in the synthesis of stochastic reactive
systems\r\nwith both functional requirement (given as a qualitative objective)
and performance requirement (given\r\nas a quantitative objective)."
alternative_title:
- IST Austria Technical Report
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: Hugo
full_name: Gimbert, Hugo
last_name: Gimbert
- first_name: Youssouf
full_name: Oualhadj, Youssouf
last_name: Oualhadj
citation:
ama: Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. Perfect-Information Stochastic
Mean-Payoff Parity Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-128-v1-1
apa: Chatterjee, K., Doyen, L., Gimbert, H., & Oualhadj, Y. (2013). Perfect-information
stochastic mean-payoff parity games. IST Austria. https://doi.org/10.15479/AT:IST-2013-128-v1-1
chicago: Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj.
Perfect-Information Stochastic Mean-Payoff Parity Games. IST Austria, 2013.
https://doi.org/10.15479/AT:IST-2013-128-v1-1.
ieee: K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, Perfect-information
stochastic mean-payoff parity games. IST Austria, 2013.
ista: Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2013. Perfect-information stochastic
mean-payoff parity games, IST Austria, 22p.
mla: Chatterjee, Krishnendu, et al. Perfect-Information Stochastic Mean-Payoff
Parity Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-128-v1-1.
short: K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, Perfect-Information Stochastic
Mean-Payoff Parity Games, IST Austria, 2013.
date_created: 2018-12-12T11:39:09Z
date_published: 2013-07-08T00:00:00Z
date_updated: 2023-02-23T10:33:08Z
day: '08'
ddc:
- '000'
- '005'
- '510'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-128-v1-1
file:
- access_level: open_access
checksum: ede787a10e74e4f7db302fab8f12f3ca
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:54Z
date_updated: 2020-07-14T12:46:45Z
file_id: '5516'
file_name: IST-2013-128-v1+1_full_stoch_mpp.pdf
file_size: 387467
relation: main_file
file_date_updated: 2020-07-14T12:46:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '22'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '128'
related_material:
record:
- id: '2212'
relation: later_version
status: public
status: public
title: Perfect-information stochastic mean-payoff parity games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5409'
abstract:
- lang: eng
text: "The edit distance between two (untimed) traces is the minimum cost of a sequence
of edit operations (insertion, deletion, or substitution) needed to transform
one trace to the other. Edit distances have been extensively studied in the untimed
setting, and form the basis for approximate matching of sequences in different
domains such as coding theory, parsing, and speech recognition. \r\nIn this paper,
we lift the study of edit distances from untimed languages to the timed setting.
We define an edit distance between timed words which incorporates both the edit
distance between the untimed words and the absolute difference in timestamps.
Our edit distance between two timed words is computable in polynomial time. Further,
we show that the edit distance between a timed word and a timed language generated
by a timed automaton, defined as the edit distance between the word and the closest
word in the language, is PSPACE-complete. While computing the edit distance between
two timed automata is undecidable, we show that the approximate version, where
we decide if the edit distance between two timed automata is either less than
a given parameter or more than delta away from the parameter, for delta>0, can
be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques
can be generalized to the setting of hybrid systems, and we show analogous decidability
results for rectangular automata."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
citation:
ama: Chatterjee K, Ibsen-Jensen R, Majumdar R. Edit Distance for Timed Automata.
IST Austria; 2013. doi:10.15479/AT:IST-2013-144-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Majumdar, R. (2013). Edit distance
for timed automata. IST Austria. https://doi.org/10.15479/AT:IST-2013-144-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Rupak Majumdar. Edit
Distance for Timed Automata. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-144-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, Edit distance for timed
automata. IST Austria, 2013.
ista: Chatterjee K, Ibsen-Jensen R, Majumdar R. 2013. Edit distance for timed automata,
IST Austria, 12p.
mla: Chatterjee, Krishnendu, et al. Edit Distance for Timed Automata. IST
Austria, 2013, doi:10.15479/AT:IST-2013-144-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, Edit Distance for Timed Automata,
IST Austria, 2013.
date_created: 2018-12-12T11:39:10Z
date_published: 2013-10-30T00:00:00Z
date_updated: 2023-02-23T10:33:18Z
day: '30'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-144-v1-1
file:
- access_level: open_access
checksum: 0f7633081ba8299c543322f0ad08571f
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:08Z
date_updated: 2020-07-14T12:46:46Z
file_id: '5469'
file_name: IST-2013-144-v1+1_main.pdf
file_size: 336377
relation: main_file
file_date_updated: 2020-07-14T12:46:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '12'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '144'
related_material:
record:
- id: '2216'
relation: later_version
status: public
status: public
title: Edit distance for timed automata
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '1376'
abstract:
- lang: eng
text: 'We consider the distributed synthesis problem for temporal logic specifications.
Traditionally, the problem has been studied for LTL, and the previous results
show that the problem is decidable iff there is no information fork in the architecture.
We consider the problem for fragments of LTL and our main results are as follows:
(1) We show that the problem is undecidable for architectures with information
forks even for the fragment of LTL with temporal operators restricted to next
and eventually. (2) For specifications restricted to globally along with non-nested
next operators, we establish decidability (in EXPSPACE) for star architectures
where the processes receive disjoint inputs, whereas we establish undecidability
for architectures containing an information fork-meet structure. (3) Finally,
we consider LTL without the next operator, and establish decidability (NEXPTIME-complete)
for all architectures for a fragment that consists of a set of safety assumptions,
and a set of guarantees where each guarantee is a safety, reachability, or liveness
condition.'
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
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed synthesis
for LTL fragments. In: 13th International Conference on Formal Methods in Computer-Aided
Design. IEEE; 2013:18-25. doi:10.1109/FMCAD.2013.6679386'
apa: 'Chatterjee, K., Henzinger, T. A., Otop, J., & Pavlogiannis, A. (2013).
Distributed synthesis for LTL fragments. In 13th International Conference on
Formal Methods in Computer-Aided Design (pp. 18–25). Portland, OR, United
States: IEEE. https://doi.org/10.1109/FMCAD.2013.6679386'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis.
“Distributed Synthesis for LTL Fragments.” In 13th International Conference
on Formal Methods in Computer-Aided Design, 18–25. IEEE, 2013. https://doi.org/10.1109/FMCAD.2013.6679386.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed
synthesis for LTL fragments,” in 13th International Conference on Formal Methods
in Computer-Aided Design, Portland, OR, United States, 2013, pp. 18–25.
ista: 'Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis
for LTL fragments. 13th International Conference on Formal Methods in Computer-Aided
Design. FMCAD: Formal Methods in Computer-Aided Design, 18–25.'
mla: Chatterjee, Krishnendu, et al. “Distributed Synthesis for LTL Fragments.” 13th
International Conference on Formal Methods in Computer-Aided Design, IEEE,
2013, pp. 18–25, doi:10.1109/FMCAD.2013.6679386.
short: K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, in:, 13th International
Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25.
conference:
end_date: 2013-10-23
location: Portland, OR, United States
name: 'FMCAD: Formal Methods in Computer-Aided Design'
start_date: 2013-10-20
date_created: 2018-12-11T11:51:40Z
date_published: 2013-12-11T00:00:00Z
date_updated: 2023-02-23T12:24:53Z
day: '11'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1109/FMCAD.2013.6679386
ec_funded: 1
language:
- iso: eng
month: '12'
oa_version: None
page: 18 - 25
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: 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: 13th International Conference on Formal Methods in Computer-Aided Design
publication_status: published
publisher: IEEE
publist_id: '5835'
quality_controlled: '1'
related_material:
record:
- id: '5406'
relation: earlier_version
status: public
status: public
title: Distributed synthesis for LTL fragments
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5406'
abstract:
- lang: eng
text: 'We consider the distributed synthesis problem fortemporal logic specifications.
Traditionally, the problem has been studied for LTL, and the previous results
show that the problem is decidable iff there is no information fork in the architecture.
We consider the problem for fragments of LTLand our main results are as follows:
(1) We show that the problem is undecidable for architectures with information
forks even for the fragment of LTL with temporal operators restricted to next
and eventually. (2) For specifications restricted to globally along with non-nested
next operators, we establish decidability (in EXPSPACE) for star architectures
where the processes receive disjoint inputs, whereas we establish undecidability
for architectures containing an information fork-meet structure. (3)Finally, we
consider LTL without the next operator, and establish decidability (NEXPTIME-complete)
for all architectures for a fragment that consists of a set of safety assumptions,
and a set of guarantees where each guarantee is a safety, reachability, or liveness
condition.'
alternative_title:
- IST Austria Technical Report
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
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed Synthesis
for LTL Fragments. IST Austria; 2013. doi:10.15479/AT:IST-2013-130-v1-1
apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Pavlogiannis, A. (2013).
Distributed synthesis for LTL Fragments. IST Austria. https://doi.org/10.15479/AT:IST-2013-130-v1-1
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis.
Distributed Synthesis for LTL Fragments. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-130-v1-1.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, Distributed
synthesis for LTL Fragments. IST Austria, 2013.
ista: Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis
for LTL Fragments, IST Austria, 11p.
mla: Chatterjee, Krishnendu, et al. Distributed Synthesis for LTL Fragments.
IST Austria, 2013, doi:10.15479/AT:IST-2013-130-v1-1.
short: K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, Distributed Synthesis
for LTL Fragments, IST Austria, 2013.
date_created: 2018-12-12T11:39:09Z
date_published: 2013-07-08T00:00:00Z
date_updated: 2023-02-21T17:01:26Z
day: '08'
ddc:
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2013-130-v1-1
file:
- access_level: open_access
checksum: 855513ebaf6f72228800c5fdb522f93c
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:18Z
date_updated: 2020-07-14T12:46:45Z
file_id: '5540'
file_name: IST-2013-130-v1+1_Distributed_Synthesis.pdf
file_size: 467895
relation: main_file
file_date_updated: 2020-07-14T12:46:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '11'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '130'
related_material:
record:
- id: '1376'
relation: later_version
status: public
status: public
title: Distributed synthesis for LTL Fragments
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5408'
abstract:
- lang: eng
text: "We consider two-player partial-observation stochastic games where player
1 has partial observation and player 2 has perfect observation. The winning condition
we study are omega-regular conditions specified as parity objectives. The qualitative
analysis problem given a partial-observation stochastic game and a parity objective
asks whether there is a strategy to ensure that the objective is satisfied with
probability 1 (resp. positive probability). While the qualitative analysis problems
are known to be undecidable even for very special cases of parity objectives,
they were shown to be decidable in 2EXPTIME under finite-memory strategies. We
improve the complexity and show that the qualitative analysis problems for partial-observation
stochastic parity games under finite-memory strategies are \r\nEXPTIME-complete;
and also establish optimal (exponential) memory bounds for finite-memory strategies
required for qualitative analysis. "
alternative_title:
- IST Austria Technical Report
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: Sumit
full_name: Nain, Sumit
last_name: Nain
- first_name: Moshe
full_name: Vardi, Moshe
last_name: Vardi
citation:
ama: Chatterjee K, Doyen L, Nain S, Vardi M. The Complexity of Partial-Observation
Stochastic Parity Games with Finite-Memory Strategies. IST Austria; 2013.
doi:10.15479/AT:IST-2013-141-v1-1
apa: Chatterjee, K., Doyen, L., Nain, S., & Vardi, M. (2013). The complexity
of partial-observation stochastic parity games with finite-memory strategies.
IST Austria. https://doi.org/10.15479/AT:IST-2013-141-v1-1
chicago: Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. The
Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies.
IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-141-v1-1.
ieee: K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, The complexity of partial-observation
stochastic parity games with finite-memory strategies. IST Austria, 2013.
ista: Chatterjee K, Doyen L, Nain S, Vardi M. 2013. The complexity of partial-observation
stochastic parity games with finite-memory strategies, IST Austria, 17p.
mla: Chatterjee, Krishnendu, et al. The Complexity of Partial-Observation Stochastic
Parity Games with Finite-Memory Strategies. IST Austria, 2013, doi:10.15479/AT:IST-2013-141-v1-1.
short: K. Chatterjee, L. Doyen, S. Nain, M. Vardi, The Complexity of Partial-Observation
Stochastic Parity Games with Finite-Memory Strategies, IST Austria, 2013.
date_created: 2018-12-12T11:39:10Z
date_published: 2013-09-12T00:00:00Z
date_updated: 2023-02-23T10:33:11Z
day: '12'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-141-v1-1
file:
- access_level: open_access
checksum: 226bc791124f8d3138379778ce834e86
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:16Z
date_updated: 2020-07-14T12:46:46Z
file_id: '5477'
file_name: IST-2013-141-v1+1_main-tech-rpt.pdf
file_size: 300481
relation: main_file
file_date_updated: 2020-07-14T12:46:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '17'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '141'
related_material:
record:
- id: '2213'
relation: later_version
status: public
status: public
title: The complexity of partial-observation stochastic parity games with finite-memory
strategies
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5407'
abstract:
- lang: eng
text: This document is created as a part of the project “Repository for Research
Data at IST Austria”. It summarises the mandatory features, which need to be fulfilled
to provide an institutional repository as a platform and also a service to the
scientists at the institute. It also includes optional features, which would be
of strong benefit for the scientists and would increase the usage of the repository,
and hence the visibility of research at IST Austria.
author:
- first_name: Jana
full_name: Porsche, Jana
id: 3252EDC2-F248-11E8-B48F-1D18A9856A87
last_name: Porsche
citation:
ama: Porsche J. Technical Requirements and Features. IST Austria; 2013.
apa: Porsche, J. (2013). Technical requirements and features. IST Austria.
chicago: Porsche, Jana. Technical Requirements and Features. IST Austria,
2013.
ieee: J. Porsche, Technical requirements and features. IST Austria, 2013.
ista: Porsche J. 2013. Technical requirements and features, IST Austria,p.
mla: Porsche, Jana. Technical Requirements and Features. IST Austria, 2013.
short: J. Porsche, Technical Requirements and Features, IST Austria, 2013.
date_created: 2018-12-12T11:39:09Z
date_published: 2013-07-13T00:00:00Z
date_updated: 2020-07-14T23:07:51Z
day: '13'
ddc:
- '020'
department:
- _id: E-Lib
file:
- access_level: open_access
checksum: 9e4f9abf79a56f651f0012a34909880f
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:02Z
date_updated: 2020-07-14T12:46:46Z
file_id: '5463'
file_name: IST-2013-135-v1+1_Features.pdf
file_size: 90311
relation: main_file
file_date_updated: 2020-07-14T12:46:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication_status: published
publisher: IST Austria
pubrep_id: '135'
status: public
title: Technical requirements and features
type: report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5410'
abstract:
- lang: eng
text: "Board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only
in development of mathematical and logical skills, but also in emotional and social
development. In this paper, we address the problem of generating targeted starting
positions for such games. This can facilitate new approaches for bringing novice
players to mastery, and also leads to discovery of interesting game variants.
\r\nOur approach generates starting states of varying hardness levels for player
1 in a two-player board game, given rules of the board game, the desired number
of steps required for player 1 to win, and the expertise levels of the two players.
Our approach leverages symbolic methods and iterative simulation to efficiently
search the extremely large state space. We present experimental results that include
discovery of states of varying hardness levels for several simple grid-based board
games. Also, the presence of such states for standard game variants like Tic-Tac-Toe
on board size 4x4 opens up new games to be played that have not been played for
ages since the default start state is heavily biased. "
alternative_title:
- IST Austria Technical Report
author:
- first_name: Umair
full_name: Ahmed, Umair
last_name: Ahmed
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Sumit
full_name: Gulwani, Sumit
last_name: Gulwani
citation:
ama: Ahmed U, Chatterjee K, Gulwani S. Automatic Generation of Alternative Starting
Positions for Traditional Board Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-146-v1-1
apa: Ahmed, U., Chatterjee, K., & Gulwani, S. (2013). Automatic generation
of alternative starting positions for traditional board games. IST Austria.
https://doi.org/10.15479/AT:IST-2013-146-v1-1
chicago: Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. Automatic Generation
of Alternative Starting Positions for Traditional Board Games. IST Austria,
2013. https://doi.org/10.15479/AT:IST-2013-146-v1-1.
ieee: U. Ahmed, K. Chatterjee, and S. Gulwani, Automatic generation of alternative
starting positions for traditional board games. IST Austria, 2013.
ista: Ahmed U, Chatterjee K, Gulwani S. 2013. Automatic generation of alternative
starting positions for traditional board games, IST Austria, 13p.
mla: Ahmed, Umair, et al. Automatic Generation of Alternative Starting Positions
for Traditional Board Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-146-v1-1.
short: U. Ahmed, K. Chatterjee, S. Gulwani, Automatic Generation of Alternative
Starting Positions for Traditional Board Games, IST Austria, 2013.
date_created: 2018-12-12T11:39:10Z
date_published: 2013-12-03T00:00:00Z
date_updated: 2023-02-23T10:00:50Z
day: '03'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-146-v1-1
file:
- access_level: open_access
checksum: 409f3aaaf1184e4057b89cbb449dac80
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:06Z
date_updated: 2020-07-14T12:46:46Z
file_id: '5528'
file_name: IST-2013-146-v1+1_main.pdf
file_size: 818189
relation: main_file
file_date_updated: 2020-07-14T12:46:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '13'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '146'
related_material:
record:
- id: '1481'
relation: later_version
status: public
status: public
title: Automatic generation of alternative starting positions for traditional board
games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2327'
abstract:
- lang: eng
text: 'We define the model-measuring problem: given a model M and specification
φ, what is the maximal distance ρ such that all models M′ within distance ρ from
M satisfy (or violate) φ. The model measuring problem presupposes a distance function
on models. We concentrate on automatic distance functions, which are defined by
weighted automata. The model-measuring problem subsumes several generalizations
of the classical model-checking problem, in particular, quantitative model-checking
problems that measure the degree of satisfaction of a specification, and robustness
problems that measure how much a model can be perturbed without violating the
specification. We show that for automatic distance functions, and ω-regular linear-time
and branching-time specifications, the model-measuring problem can be solved.
We use automata-theoretic model-checking methods for model measuring, replacing
the emptiness question for standard word and tree automata by the optimal-weight
question for the weighted versions of these automata. We consider weighted automata
that accumulate weights by maximizing, summing, discounting, and limit averaging.
We give several examples of using the model-measuring problem to compute various
notions of robustness and quantitative satisfaction for temporal specifications.'
alternative_title:
- LNCS
author:
- 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: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Henzinger TA, Otop J. From model checking to model measuring. 2013;8052:273-287.
doi:10.1007/978-3-642-40184-8_20
apa: 'Henzinger, T. A., & Otop, J. (2013). From model checking to model measuring.
Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Springer.
https://doi.org/10.1007/978-3-642-40184-8_20'
chicago: Henzinger, Thomas A, and Jan Otop. “From Model Checking to Model Measuring.”
Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40184-8_20.
ieee: T. A. Henzinger and J. Otop, “From model checking to model measuring,” vol.
8052. Springer, pp. 273–287, 2013.
ista: Henzinger TA, Otop J. 2013. From model checking to model measuring. 8052,
273–287.
mla: Henzinger, Thomas A., and Jan Otop. From Model Checking to Model Measuring.
Vol. 8052, Springer, 2013, pp. 273–87, doi:10.1007/978-3-642-40184-8_20.
short: T.A. Henzinger, J. Otop, 8052 (2013) 273–287.
conference:
end_date: 2013-08-30
location: Buenos Aires, Argentina
name: 'CONCUR: Concurrency Theory'
start_date: 2013-08-27
date_created: 2018-12-11T11:57:00Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2023-02-23T12:25:26Z
day: '01'
ddc:
- '005'
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-40184-8_20
file:
- access_level: open_access
checksum: 4c04695c4bfdf2119cd4f5d1babc3e8a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:45Z
date_updated: 2020-07-14T12:45:38Z
file_id: '5301'
file_name: IST-2013-129-v1+1_concur.pdf
file_size: 378587
relation: main_file
file_date_updated: 2020-07-14T12:45:38Z
has_accepted_license: '1'
intvolume: ' 8052'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 273 - 287
publication_status: published
publisher: Springer
publist_id: '4599'
pubrep_id: '129'
quality_controlled: '1'
related_material:
record:
- id: '5417'
relation: earlier_version
status: public
series_title: Lecture Notes in Computer Science
status: public
title: From model checking to model measuring
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8052
year: '2013'
...
---
_id: '590'
abstract:
- lang: eng
text: We present two methods of creating two orthogonally-polarized focal points
at customizable relative locations. These schemes may be critical for enhancing
entanglement sources and other applications.
alternative_title:
- Optics InfoBase Conference Papers
author:
- first_name: David
full_name: Schmid, David
last_name: Schmid
- first_name: Ting
full_name: Huang, Ting-Yu
last_name: Huang
- first_name: Radhika
full_name: Dirks, Radhika
last_name: Dirks
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Paul
full_name: Kwiat, Paul G
last_name: Kwiat
citation:
ama: 'Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. Polarization dependent focusing.
In: OSA; 2013. doi:10.1364/QIM.2013.W6.23'
apa: 'Schmid, D., Huang, T., Dirks, R., Hosten, O., & Kwiat, P. (2013). Polarization
dependent focusing. Presented at the QIM: Quantum Information and Measurement,
OSA. https://doi.org/10.1364/QIM.2013.W6.23'
chicago: Schmid, David, Ting Huang, Radhika Dirks, Onur Hosten, and Paul Kwiat.
“Polarization Dependent Focusing.” OSA, 2013. https://doi.org/10.1364/QIM.2013.W6.23.
ieee: 'D. Schmid, T. Huang, R. Dirks, O. Hosten, and P. Kwiat, “Polarization dependent
focusing,” presented at the QIM: Quantum Information and Measurement, 2013.'
ista: 'Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. 2013. Polarization dependent
focusing. QIM: Quantum Information and Measurement, Optics InfoBase Conference
Papers, .'
mla: Schmid, David, et al. Polarization Dependent Focusing. OSA, 2013, doi:10.1364/QIM.2013.W6.23.
short: D. Schmid, T. Huang, R. Dirks, O. Hosten, P. Kwiat, in:, OSA, 2013.
conference:
name: 'QIM: Quantum Information and Measurement'
date_created: 2018-12-11T11:47:22Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:05:10Z
day: '01'
doi: 10.1364/QIM.2013.W6.23
extern: 1
month: '01'
publication_status: published
publisher: OSA
publist_id: '7217'
quality_controlled: 0
status: public
title: Polarization dependent focusing
type: conference
year: '2013'
...