---
_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'
...
---
_id: '5920'
abstract:
- lang: eng
text: We study chains of lattice ideals that are invariant under a symmetric group
action. In our setting, the ambient rings for these ideals are polynomial rings
which are increasing in (Krull) dimension. Thus, these chains will fail to stabilize
in the traditional commutative algebra sense. However, we prove a theorem which
says that “up to the action of the group”, these chains locally stabilize. We
also give an algorithm, which we have implemented in software, for explicitly
constructing these stabilization generators for a family of Laurent toric ideals
involved in applications to algebraic statistics. We close with several open problems
and conjectures arising from our theoretical and computational investigations.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher J.
full_name: Hillar, Christopher J.
last_name: Hillar
- first_name: Abraham
full_name: Martin del Campo Sanchez, Abraham
id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87
last_name: Martin del Campo Sanchez
citation:
ama: Hillar CJ, Martin del Campo Sanchez A. Finiteness theorems and algorithms for
permutation invariant chains of Laurent lattice ideals. Journal of Symbolic
Computation. 2013;50:314-334. doi:10.1016/j.jsc.2012.06.006
apa: Hillar, C. J., & Martin del Campo Sanchez, A. (2013). Finiteness theorems
and algorithms for permutation invariant chains of Laurent lattice ideals. Journal
of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2012.06.006
chicago: Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness
Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.”
Journal of Symbolic Computation. Elsevier, 2013. https://doi.org/10.1016/j.jsc.2012.06.006.
ieee: C. J. Hillar and A. Martin del Campo Sanchez, “Finiteness theorems and algorithms
for permutation invariant chains of Laurent lattice ideals,” Journal of Symbolic
Computation, vol. 50. Elsevier, pp. 314–334, 2013.
ista: Hillar CJ, Martin del Campo Sanchez A. 2013. Finiteness theorems and algorithms
for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic
Computation. 50, 314–334.
mla: Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems
and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” Journal
of Symbolic Computation, vol. 50, Elsevier, 2013, pp. 314–34, doi:10.1016/j.jsc.2012.06.006.
short: C.J. Hillar, A. Martin del Campo Sanchez, Journal of Symbolic Computation
50 (2013) 314–334.
date_created: 2019-02-05T08:48:24Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2021-01-12T08:05:15Z
day: '01'
doi: 10.1016/j.jsc.2012.06.006
extern: '1'
intvolume: ' 50'
language:
- iso: eng
month: '03'
oa_version: None
page: 314-334
publication: Journal of Symbolic Computation
publication_identifier:
issn:
- 0747-7171
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1016/j.jsc.2015.09.002
status: public
title: Finiteness theorems and algorithms for permutation invariant chains of Laurent
lattice ideals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2013'
...
---
_id: '591'
abstract:
- lang: eng
text: We present two methods for the precise independent focusing of orthogonal
linear polarizations of light at arbitrary relative locations. Our first scheme
uses a displaced lens in a polarization Sagnac interferometer to provide adjustable
longitudinal and lateral focal displacements via simple geometry; the second uses
uniaxial crystals to achieve the same effect in a compact collinear setup. We
develop the theoretical applications and limitations of our schemes, and provide
experimental confirmation of our calculations.
author:
- first_name: David
full_name: Schmid, David
last_name: Schmid
- first_name: Ting
full_name: Huang, Ting-Yu
last_name: Huang
- first_name: Shiraz
full_name: Hazrat, Shiraz
last_name: Hazrat
- 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: Stephan
full_name: Quint, Stephan
last_name: Quint
- first_name: Dickson
full_name: Thian, Dickson
last_name: Thian
- first_name: Paul
full_name: Kwiat, Paul G
last_name: Kwiat
citation:
ama: Schmid D, Huang T, Hazrat S, et al. Adjustable and robust methods for polarization-dependent
focusing. Optics Express. 2013;21(13):15538-15552. doi:10.1364/OE.21.015538
apa: Schmid, D., Huang, T., Hazrat, S., Dirks, R., Hosten, O., Quint, S., … Kwiat,
P. (2013). Adjustable and robust methods for polarization-dependent focusing.
Optics Express. Optical Society of America. https://doi.org/10.1364/OE.21.015538
chicago: Schmid, David, Ting Huang, Shiraz Hazrat, Radhika Dirks, Onur Hosten, Stephan
Quint, Dickson Thian, and Paul Kwiat. “Adjustable and Robust Methods for Polarization-Dependent
Focusing.” Optics Express. Optical Society of America, 2013. https://doi.org/10.1364/OE.21.015538.
ieee: D. Schmid et al., “Adjustable and robust methods for polarization-dependent
focusing,” Optics Express, vol. 21, no. 13. Optical Society of America,
pp. 15538–15552, 2013.
ista: Schmid D, Huang T, Hazrat S, Dirks R, Hosten O, Quint S, Thian D, Kwiat P.
2013. Adjustable and robust methods for polarization-dependent focusing. Optics
Express. 21(13), 15538–15552.
mla: Schmid, David, et al. “Adjustable and Robust Methods for Polarization-Dependent
Focusing.” Optics Express, vol. 21, no. 13, Optical Society of America,
2013, pp. 15538–52, doi:10.1364/OE.21.015538.
short: D. Schmid, T. Huang, S. Hazrat, R. Dirks, O. Hosten, S. Quint, D. Thian,
P. Kwiat, Optics Express 21 (2013) 15538–15552.
date_created: 2018-12-11T11:47:22Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T08:05:12Z
day: '01'
doi: 10.1364/OE.21.015538
extern: 1
intvolume: ' 21'
issue: '13'
month: '07'
page: 15538 - 15552
publication: Optics Express
publication_status: published
publisher: Optical Society of America
publist_id: '7218'
quality_controlled: 0
status: public
title: Adjustable and robust methods for polarization-dependent focusing
type: journal_article
volume: 21
year: '2013'
...
---
_id: '595'
article_processing_charge: No
author:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: 'Bernecky C, Cramer P. Struggling to let go: A non-coding RNA directs its own
extension and destruction. EMBO Journal. 2013;32(6):771-772. doi:10.1038/emboj.2013.36'
apa: 'Bernecky, C., & Cramer, P. (2013). Struggling to let go: A non-coding
RNA directs its own extension and destruction. EMBO Journal. Wiley-Blackwell.
https://doi.org/10.1038/emboj.2013.36'
chicago: 'Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding
RNA Directs Its Own Extension and Destruction.” EMBO Journal. Wiley-Blackwell,
2013. https://doi.org/10.1038/emboj.2013.36.'
ieee: 'C. Bernecky and P. Cramer, “Struggling to let go: A non-coding RNA directs
its own extension and destruction,” EMBO Journal, vol. 32, no. 6. Wiley-Blackwell,
pp. 771–772, 2013.'
ista: 'Bernecky C, Cramer P. 2013. Struggling to let go: A non-coding RNA directs
its own extension and destruction. EMBO Journal. 32(6), 771–772.'
mla: 'Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding
RNA Directs Its Own Extension and Destruction.” EMBO Journal, vol. 32,
no. 6, Wiley-Blackwell, 2013, pp. 771–72, doi:10.1038/emboj.2013.36.'
short: C. Bernecky, P. Cramer, EMBO Journal 32 (2013) 771–772.
date_created: 2018-12-11T11:47:23Z
date_published: 2013-03-20T00:00:00Z
date_updated: 2021-01-12T08:05:20Z
day: '20'
doi: 10.1038/emboj.2013.36
extern: '1'
intvolume: ' 32'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604726/
month: '03'
oa: 1
oa_version: None
page: 771 - 772
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7207'
status: public
title: 'Struggling to let go: A non-coding RNA directs its own extension and destruction'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '6128'
abstract:
- lang: eng
text: Different interoceptive systems must be integrated to ensure that multiple
homeostatic insults evoke appropriate behavioral and physiological responses.
Little is known about how this is achieved. Using C. elegans, we dissect cross-modulation
between systems that monitor temperature, O2 and CO2. CO2 is less aversive to
animals acclimated to 15°C than those grown at 22°C. This difference requires
the AFD neurons, which respond to both temperature and CO2 changes. CO2 evokes
distinct AFD Ca2+ responses in animals acclimated at 15°C or 22°C. Mutants defective
in synaptic transmission can reprogram AFD CO2 responses according to temperature
experience, suggesting reprogramming occurs cell autonomously. AFD is exquisitely
sensitive to CO2. Surprisingly, gradients of 0.01% CO2/second evoke very different
Ca2+ responses from gradients of 0.04% CO2/second. Ambient O2 provides further
contextual modulation of CO2 avoidance. At 21% O2 tonic signalling from the O2-sensing
neuron URX inhibits CO2 avoidance. This inhibition can be graded according to
O2 levels. In a natural wild isolate, a switch from 21% to 19% O2 is sufficient
to convert CO2 from a neutral to an aversive cue. This sharp tuning is conferred
partly by the neuroglobin GLB-5. The modulatory effects of O2 on CO2 avoidance
involve the RIA interneurons, which are post-synaptic to URX and exhibit CO2-evoked
Ca2+ responses. Ambient O2 and acclimation temperature act combinatorially to
modulate CO2 responsiveness. Our work highlights the integrated architecture of
homeostatic responses in C. elegans.
article_number: e1004011
author:
- first_name: Eiji
full_name: Kodama-Namba, Eiji
last_name: Kodama-Namba
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Andrew J.
full_name: Bretscher, Andrew J.
last_name: Bretscher
- first_name: Einav
full_name: Gross, Einav
last_name: Gross
- first_name: K. Emanuel
full_name: Busch, K. Emanuel
last_name: Busch
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. Cross-modulation
of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans.
PLoS Genetics. 2013;9(12). doi:10.1371/journal.pgen.1004011
apa: Kodama-Namba, E., Fenk, L. A., Bretscher, A. J., Gross, E., Busch, K. E., &
de Bono, M. (2013). Cross-modulation of homeostatic responses to temperature,
oxygen and carbon dioxide in C. elegans. PLoS Genetics. Public Library
of Science (PLoS). https://doi.org/10.1371/journal.pgen.1004011
chicago: Kodama-Namba, Eiji, Lorenz A. Fenk, Andrew J. Bretscher, Einav Gross, K.
Emanuel Busch, and Mario de Bono. “Cross-Modulation of Homeostatic Responses to
Temperature, Oxygen and Carbon Dioxide in C. Elegans.” PLoS Genetics. Public
Library of Science (PLoS), 2013. https://doi.org/10.1371/journal.pgen.1004011.
ieee: E. Kodama-Namba, L. A. Fenk, A. J. Bretscher, E. Gross, K. E. Busch, and M.
de Bono, “Cross-modulation of homeostatic responses to temperature, oxygen and
carbon dioxide in C. elegans,” PLoS Genetics, vol. 9, no. 12. Public Library
of Science (PLoS), 2013.
ista: Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. 2013.
Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide
in C. elegans. PLoS Genetics. 9(12), e1004011.
mla: Kodama-Namba, Eiji, et al. “Cross-Modulation of Homeostatic Responses to Temperature,
Oxygen and Carbon Dioxide in C. Elegans.” PLoS Genetics, vol. 9, no. 12,
e1004011, Public Library of Science (PLoS), 2013, doi:10.1371/journal.pgen.1004011.
short: E. Kodama-Namba, L.A. Fenk, A.J. Bretscher, E. Gross, K.E. Busch, M. de Bono,
PLoS Genetics 9 (2013).
date_created: 2019-03-19T14:58:51Z
date_published: 2013-12-19T00:00:00Z
date_updated: 2021-01-12T08:06:15Z
day: '19'
ddc:
- '570'
doi: 10.1371/journal.pgen.1004011
extern: '1'
external_id:
pmid:
- '24385919'
file:
- access_level: open_access
checksum: 299b6321be79931c7c17c5db6e69c711
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T15:14:51Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6129'
file_name: 2013_PLOS_Kodama-Namba.PDF
file_size: 4499039
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science (PLoS)
quality_controlled: '1'
status: public
title: Cross-modulation of homeostatic responses to temperature, oxygen and carbon
dioxide in C. elegans
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: 9
year: '2013'
...
---
_id: '6130'
abstract:
- lang: eng
text: 'Cas9 is an RNA-guided double-stranded DNA nuclease that participates in clustered
regularly interspaced short palindromic repeats (CRISPR)-mediated adaptive immunity
in prokaryotes. CRISPR–Cas9 has recently been used to generate insertion and deletion
mutations in Caenorhabditis elegans, but not to create tailored changes (knock-ins).
We show that the CRISPR–CRISPR-associated (Cas) system can be adapted for efficient
and precise editing of the C. elegans genome. The targeted double-strand breaks
generated by CRISPR are substrates for transgene-instructed gene conversion. This
allows customized changes in the C. elegans genome by homologous recombination:
sequences contained in the repair template (the transgene) are copied by gene
conversion into the genome. The possibility to edit the C. elegans genome at selected
locations will facilitate the systematic study of gene function in this widely
used model organism.'
article_number: e193
author:
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Chen C, Fenk LA, de Bono M. Efficient genome editing in Caenorhabditis elegans
by CRISPR-targeted homologous recombination. Nucleic Acids Research. 2013;41(20).
doi:10.1093/nar/gkt805
apa: Chen, C., Fenk, L. A., & de Bono, M. (2013). Efficient genome editing in
Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic
Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkt805
chicago: Chen, Changchun, Lorenz A. Fenk, and Mario de Bono. “Efficient Genome Editing
in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” Nucleic
Acids Research. Oxford University Press, 2013. https://doi.org/10.1093/nar/gkt805.
ieee: C. Chen, L. A. Fenk, and M. de Bono, “Efficient genome editing in Caenorhabditis
elegans by CRISPR-targeted homologous recombination,” Nucleic Acids Research,
vol. 41, no. 20. Oxford University Press, 2013.
ista: Chen C, Fenk LA, de Bono M. 2013. Efficient genome editing in Caenorhabditis
elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. 41(20),
e193.
mla: Chen, Changchun, et al. “Efficient Genome Editing in Caenorhabditis Elegans
by CRISPR-Targeted Homologous Recombination.” Nucleic Acids Research, vol.
41, no. 20, e193, Oxford University Press, 2013, doi:10.1093/nar/gkt805.
short: C. Chen, L.A. Fenk, M. de Bono, Nucleic Acids Research 41 (2013).
date_created: 2019-03-19T15:17:40Z
date_published: 2013-11-01T00:00:00Z
date_updated: 2021-01-12T08:06:16Z
day: '01'
ddc:
- '570'
doi: 10.1093/nar/gkt805
extern: '1'
external_id:
pmid:
- '24013562'
file:
- access_level: open_access
checksum: 0f1f127cefd043cb922b292e1cd16f02
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T15:25:42Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6131'
file_name: 2013_OUP_Chen.pdf
file_size: 340225
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 41'
issue: '20'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nucleic Acids Research
publication_identifier:
issn:
- 1362-4962
- 0305-1048
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous
recombination
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: 41
year: '2013'
...
---
_id: '6133'
abstract:
- lang: eng
text: cGMP signaling is widespread in the nervous system. However, it has proved
difficult to visualize and genetically probe endogenously evoked cGMP dynamics
in neurons in vivo. Here, we combine cGMP and Ca2+ biosensors to image and dissect
a cGMP signaling network in a Caenorhabditis elegans oxygen-sensing neuron. We
show that a rise in O2 can evoke a tonic increase in cGMP that requires an atypical
O2-binding soluble guanylate cyclase and that is sustained until oxygen levels
fall. Increased cGMP leads to a sustained Ca2+ response in the neuron that depends
on cGMP-gated ion channels. Elevated levels of cGMP and Ca2+ stimulate competing
negative feedback loops that shape cGMP dynamics. Ca2+-dependent negative feedback
loops, including activation of phosphodiesterase-1 (PDE-1), dampen the rise of
cGMP. A different negative feedback loop, mediated by phosphodiesterase-2 (PDE-2)
and stimulated by cGMP-dependent kinase (PKG), unexpectedly promotes cGMP accumulation
following a rise in O2, apparently by keeping in check gating of cGMP channels
and limiting activation of Ca2+-dependent negative feedback loops. Simultaneous
imaging of Ca2+ and cGMP suggests that cGMP levels can rise close to cGMP channels
while falling elsewhere. O2-evoked cGMP and Ca2+ responses are highly reproducible
when the same neuron in an individual animal is stimulated repeatedly, suggesting
that cGMP transduction has high intrinsic reliability. However, responses vary
substantially across individuals, despite animals being genetically identical
and similarly reared. This variability may reflect stochastic differences in expression
of cGMP signaling components. Our work provides in vivo insights into the architecture
of neuronal cGMP signaling.
author:
- first_name: A.
full_name: Couto, A.
last_name: Couto
- first_name: S.
full_name: Oda, S.
last_name: Oda
- first_name: V. O.
full_name: Nikolaev, V. O.
last_name: Nikolaev
- first_name: Z.
full_name: Soltesz, Z.
last_name: Soltesz
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. In vivo genetic dissection
of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings
of the National Academy of Sciences. 2013;110(35):E3301-E3310. doi:10.1073/pnas.1217428110
apa: Couto, A., Oda, S., Nikolaev, V. O., Soltesz, Z., & de Bono, M. (2013).
In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans
gas sensor. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1217428110
chicago: Couto, A., S. Oda, V. O. Nikolaev, Z. Soltesz, and Mario de Bono. “In Vivo
Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas
Sensor.” Proceedings of the National Academy of Sciences. Proceedings of
the National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1217428110.
ieee: A. Couto, S. Oda, V. O. Nikolaev, Z. Soltesz, and M. de Bono, “In vivo genetic
dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor,”
Proceedings of the National Academy of Sciences, vol. 110, no. 35. Proceedings
of the National Academy of Sciences, pp. E3301–E3310, 2013.
ista: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. 2013. In vivo genetic dissection
of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings
of the National Academy of Sciences. 110(35), E3301–E3310.
mla: Couto, A., et al. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in
a Caenorhabditis Elegans Gas Sensor.” Proceedings of the National Academy of
Sciences, vol. 110, no. 35, Proceedings of the National Academy of Sciences,
2013, pp. E3301–10, doi:10.1073/pnas.1217428110.
short: A. Couto, S. Oda, V.O. Nikolaev, Z. Soltesz, M. de Bono, Proceedings of the
National Academy of Sciences 110 (2013) E3301–E3310.
date_created: 2019-03-20T14:05:06Z
date_published: 2013-08-27T00:00:00Z
date_updated: 2021-01-12T08:06:16Z
day: '27'
ddc:
- '570'
doi: 10.1073/pnas.1217428110
extern: '1'
external_id:
pmid:
- '23940325'
file:
- access_level: open_access
checksum: 3ee28a694f74a49f0d098970ae391a91
content_type: application/pdf
creator: kschuh
date_created: 2019-03-20T14:07:53Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6134'
file_name: 2013_PNAS_Couto.pdf
file_size: 2198763
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 110'
issue: '35'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: E3301-E3310
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans
gas sensor
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '6135'
abstract:
- lang: eng
text: Many organisms have stress response pathways, components of which share homology
with players in complex human disease pathways. Research on stress response in
the nematode worm Caenorhabditis elegans has provided detailed insights into the
genetic and molecular mechanisms underlying complex human diseases. In this review
we focus on four different types of environmental stress responses – heat shock,
oxidative stress, hypoxia, and osmotic stress – and on how these can be used to
study the genetics of complex human diseases. All four types of responses involve
the genetic machineries that underlie a number of complex human diseases such
as cancer and neurodegenerative diseases, including Alzheimer's and Parkinson's.
We highlight the types of stress response experiments required to detect the genes
and pathways underlying human disease and suggest that studying stress biology
in worms can be translated to understanding human disease and provide potential
targets for drug discovery.
author:
- first_name: Miriam
full_name: Rodriguez, Miriam
last_name: Rodriguez
- first_name: L. Basten
full_name: Snoek, L. Basten
last_name: Snoek
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: Jan E.
full_name: Kammenga, Jan E.
last_name: Kammenga
citation:
ama: 'Rodriguez M, Snoek LB, de Bono M, Kammenga JE. Worms under stress: C. elegans
stress response and its relevance to complex human disease and aging. Trends
in Genetics. 2013;29(6):367-374. doi:10.1016/j.tig.2013.01.010'
apa: 'Rodriguez, M., Snoek, L. B., de Bono, M., & Kammenga, J. E. (2013). Worms
under stress: C. elegans stress response and its relevance to complex human disease
and aging. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2013.01.010'
chicago: 'Rodriguez, Miriam, L. Basten Snoek, Mario de Bono, and Jan E. Kammenga.
“Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human
Disease and Aging.” Trends in Genetics. Elsevier, 2013. https://doi.org/10.1016/j.tig.2013.01.010.'
ieee: 'M. Rodriguez, L. B. Snoek, M. de Bono, and J. E. Kammenga, “Worms under stress:
C. elegans stress response and its relevance to complex human disease and aging,”
Trends in Genetics, vol. 29, no. 6. Elsevier, pp. 367–374, 2013.'
ista: 'Rodriguez M, Snoek LB, de Bono M, Kammenga JE. 2013. Worms under stress:
C. elegans stress response and its relevance to complex human disease and aging.
Trends in Genetics. 29(6), 367–374.'
mla: 'Rodriguez, Miriam, et al. “Worms under Stress: C. Elegans Stress Response
and Its Relevance to Complex Human Disease and Aging.” Trends in Genetics,
vol. 29, no. 6, Elsevier, 2013, pp. 367–74, doi:10.1016/j.tig.2013.01.010.'
short: M. Rodriguez, L.B. Snoek, M. de Bono, J.E. Kammenga, Trends in Genetics 29
(2013) 367–374.
date_created: 2019-03-20T14:17:42Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2021-01-12T08:06:17Z
day: '01'
doi: 10.1016/j.tig.2013.01.010
extern: '1'
intvolume: ' 29'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 367-374
publication: Trends in Genetics
publication_identifier:
issn:
- 0168-9525
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Worms under stress: C. elegans stress response and its relevance to complex
human disease and aging'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2013'
...
---
_id: '6132'
author:
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: W.R.
full_name: Schafer, W.R.
last_name: Schafer
- first_name: A.
full_name: Gottschalk, A.
last_name: Gottschalk
citation:
ama: 'de Bono M, Schafer WR, Gottschalk A. Optogenetic actuation, inhibition, modulation
and readout for neuronal networks generating behavior in the nematode Caenorhabditis
elegans. In: Hegemann P, Sigrist S, eds. Optogenetics. Walter de Gruyter;
2013:61-78.'
apa: de Bono, M., Schafer, W. R., & Gottschalk, A. (2013). Optogenetic actuation,
inhibition, modulation and readout for neuronal networks generating behavior in
the nematode Caenorhabditis elegans. In P. Hegemann & S. Sigrist (Eds.), Optogenetics
(pp. 61–78). Walter de Gruyter.
chicago: Bono, Mario de, W.R. Schafer, and A. Gottschalk. “Optogenetic Actuation,
Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in
the Nematode Caenorhabditis Elegans.” In Optogenetics, edited by Peter
Hegemann and Stephan Sigrist, 61–78. Walter de Gruyter, 2013.
ieee: M. de Bono, W. R. Schafer, and A. Gottschalk, “Optogenetic actuation, inhibition,
modulation and readout for neuronal networks generating behavior in the nematode
Caenorhabditis elegans,” in Optogenetics, P. Hegemann and S. Sigrist, Eds.
Walter de Gruyter, 2013, pp. 61–78.
ista: 'de Bono M, Schafer WR, Gottschalk A. 2013.Optogenetic actuation, inhibition,
modulation and readout for neuronal networks generating behavior in the nematode
Caenorhabditis elegans. In: Optogenetics. , 61–78.'
mla: de Bono, Mario, et al. “Optogenetic Actuation, Inhibition, Modulation and Readout
for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.”
Optogenetics, edited by Peter Hegemann and Stephan Sigrist, Walter de Gruyter,
2013, pp. 61–78.
short: M. de Bono, W.R. Schafer, A. Gottschalk, in:, P. Hegemann, S. Sigrist (Eds.),
Optogenetics, Walter de Gruyter, 2013, pp. 61–78.
date_created: 2019-03-20T13:54:05Z
date_published: 2013-08-28T00:00:00Z
date_updated: 2021-01-12T08:06:16Z
day: '28'
editor:
- first_name: Peter
full_name: Hegemann, Peter
last_name: Hegemann
- first_name: Stephan
full_name: Sigrist, Stephan
last_name: Sigrist
extern: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 61-78
publication: Optogenetics
publication_identifier:
isbn:
- 9783110270723; 9783110270716
publication_status: published
publisher: Walter de Gruyter
quality_controlled: '1'
status: public
title: Optogenetic actuation, inhibition, modulation and readout for neuronal networks
generating behavior in the nematode Caenorhabditis elegans
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '6370'
abstract:
- lang: eng
text: 'The molecular and supramolecular origins of the superior nonlinear optical
(NLO) properties observed in the organic phenolic triene material, OH1 (2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene)malononitrile),
are presented. The molecular charge-transfer distribution is topographically mapped,
demonstrating that a uniformly delocalized passive electronic medium facilitates
the charge-transfer between the phenolic electron donor and the cyano electron
acceptors which lie at opposite ends of the molecule. Its ability to act as a
“push–pull” π-conjugated molecule is quantified, relative to similar materials,
by supporting empirical calculations; these include bond-length alternation and
harmonic-oscillator stabilization energy (HOSE) tests. Such tests, together with
frontier molecular orbital considerations, reveal that OH1 can exist readily in
its aromatic (neutral) or quinoidal (charge-separated) state, thereby overcoming
the “nonlinearity-thermal stability trade-off”. The HOSE calculation also reveals
a correlation between the quinoidal resonance contribution to the overall structure
of OH1 and the UV–vis absorption peak wavelength in the wider family of configurationally
locked polyene framework materials. Solid-state tensorial coefficients of the
molecular dipole, polarizability, and the first hyperpolarizability for OH1 are
derived from the first-, second-, and third-order electronic moments of the experimental
charge-density distribution. The overall solid-state molecular dipole moment is
compared with those from gas-phase calculations, revealing that crystal field
effects are very significant in OH1. The solid-state hyperpolarizability derived
from this charge-density study affords good agreement with gas-phase calculations
as well as optical measurements based on hyper-Rayleigh scattering (HRS) and electric-field-induced
second harmonic (EFISH) generation. This lends support to the further use of charge-density
studies to calculate solid-state hyperpolarizability coefficients in other organic
NLO materials. Finally, this charge-density study is also employed to provide
an advanced classification of hydrogen bonds in OH1, which requires more stringent
criteria than those from conventional structure analysis. As a result, only the
strongest OH···NC interaction is so classified as a true hydrogen bond. Indeed,
it is this electrostatic interaction that influences the molecular charge transfer:
the other four, weaker, nonbonded contacts nonetheless affect the crystal packing.
Overall, the establishment of these structure–property relationships lays a blueprint
for designing further, more NLO efficient, materials in this industrially leading
organic family of compounds.'
author:
- first_name: Tze-Chia
full_name: Lin, Tze-Chia
last_name: Lin
- first_name: Jacqueline M.
full_name: Cole, Jacqueline M.
last_name: Cole
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Alison J.
full_name: Edwards, Alison J.
last_name: Edwards
- first_name: Ross O.
full_name: Piltz, Ross O.
last_name: Piltz
- first_name: Javier
full_name: Pérez-Moreno, Javier
last_name: Pérez-Moreno
- first_name: Ji-Youn
full_name: Seo, Ji-Youn
last_name: Seo
- first_name: Seung-Chul
full_name: Lee, Seung-Chul
last_name: Lee
- first_name: Koen
full_name: Clays, Koen
last_name: Clays
- first_name: O-Pil
full_name: Kwon, O-Pil
last_name: Kwon
citation:
ama: 'Lin T-C, Cole JM, Higginbotham AP, et al. Molecular origins of the high-performance
nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density
distributions, hydrogen bonding, and ab initio calculations. The Journal of
Physical Chemistry C. 2013;117(18):9416-9430. doi:10.1021/jp400648q'
apa: 'Lin, T.-C., Cole, J. M., Higginbotham, A. P., Edwards, A. J., Piltz, R. O.,
Pérez-Moreno, J., … Kwon, O.-P. (2013). Molecular origins of the high-performance
nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density
distributions, hydrogen bonding, and ab initio calculations. The Journal of
Physical Chemistry C. American Chemical Society (ACS). https://doi.org/10.1021/jp400648q'
chicago: 'Lin, Tze-Chia, Jacqueline M. Cole, Andrew P Higginbotham, Alison J. Edwards,
Ross O. Piltz, Javier Pérez-Moreno, Ji-Youn Seo, Seung-Chul Lee, Koen Clays, and
O-Pil Kwon. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility
in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding,
and Ab Initio Calculations.” The Journal of Physical Chemistry C. American
Chemical Society (ACS), 2013. https://doi.org/10.1021/jp400648q.'
ieee: 'T.-C. Lin et al., “Molecular origins of the high-performance nonlinear
optical susceptibility in a phenolic polyene chromophore: Electron density distributions,
hydrogen bonding, and ab initio calculations,” The Journal of Physical Chemistry
C, vol. 117, no. 18. American Chemical Society (ACS), pp. 9416–9430, 2013.'
ista: 'Lin T-C, Cole JM, Higginbotham AP, Edwards AJ, Piltz RO, Pérez-Moreno J,
Seo J-Y, Lee S-C, Clays K, Kwon O-P. 2013. Molecular origins of the high-performance
nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density
distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical
Chemistry C. 117(18), 9416–9430.'
mla: 'Lin, Tze-Chia, et al. “Molecular Origins of the High-Performance Nonlinear
Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions,
Hydrogen Bonding, and Ab Initio Calculations.” The Journal of Physical Chemistry
C, vol. 117, no. 18, American Chemical Society (ACS), 2013, pp. 9416–30, doi:10.1021/jp400648q.'
short: T.-C. Lin, J.M. Cole, A.P. Higginbotham, A.J. Edwards, R.O. Piltz, J. Pérez-Moreno,
J.-Y. Seo, S.-C. Lee, K. Clays, O.-P. Kwon, The Journal of Physical Chemistry
C 117 (2013) 9416–9430.
date_created: 2019-05-03T09:40:31Z
date_published: 2013-05-09T00:00:00Z
date_updated: 2021-01-12T08:07:17Z
day: '09'
doi: 10.1021/jp400648q
extern: '1'
intvolume: ' 117'
issue: '18'
language:
- iso: eng
month: '05'
oa_version: None
page: 9416-9430
publication: The Journal of Physical Chemistry C
publication_identifier:
issn:
- 1932-7447
- 1932-7455
publication_status: published
publisher: American Chemical Society (ACS)
quality_controlled: '1'
status: public
title: 'Molecular origins of the high-performance nonlinear optical susceptibility
in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding,
and ab initio calculations'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2013'
...
---
_id: '6440'
abstract:
- lang: eng
text: In order to guarantee that each method of a data structure updates the logical
state exactly once, al-most all non-blocking implementations employ Compare-And-Swap
(CAS) based synchronization. For FIFO queue implementations this translates into concurrent enqueue or dequeue methods
competing among themselves to update the same variable, the tail or the head,
respectively, leading to high contention and poor scalability. Recent non-blocking
queue implementations try to alleviate high contentionby increasing the number
of contention points, all the while using CAS-based synchronization. Furthermore,
obtaining a wait-free implementation with competition is achieved by additional
synchronization which leads to further degradation of performance.In this paper
we formalize the notion of competitiveness of a synchronizing statement which
can beused as a measure for the scalability of concurrent implementations. We
present a new queue implementation, the Speculative Pairing (SP) queue, which,
as we show, decreases competitiveness by using Fetch-And-Increment (FAI) instead
of CAS. We prove that the SP queue is linearizable and lock-free.We also show
that replacing CAS with FAI leads to wait-freedom for dequeue methods without
an adverse effect on performance. In fact, our experiments suggest that the SP
queue can perform and scale better than the state-of-the-art queue implementations.
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: Hannes
full_name: Payer, Hannes
last_name: Payer
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: Henzinger TA, Payer H, Sezgin A. Replacing Competition with Cooperation
to Achieve Scalable Lock-Free FIFO Queues . IST Austria; 2013. doi:10.15479/AT:IST-2013-124-v1-1
apa: Henzinger, T. A., Payer, H., & Sezgin, A. (2013). Replacing competition
with cooperation to achieve scalable lock-free FIFO queues . IST Austria.
https://doi.org/10.15479/AT:IST-2013-124-v1-1
chicago: Henzinger, Thomas A, Hannes Payer, and Ali Sezgin. Replacing Competition
with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria,
2013. https://doi.org/10.15479/AT:IST-2013-124-v1-1.
ieee: T. A. Henzinger, H. Payer, and A. Sezgin, Replacing competition with cooperation
to achieve scalable lock-free FIFO queues . IST Austria, 2013.
ista: Henzinger TA, Payer H, Sezgin A. 2013. Replacing competition with cooperation
to achieve scalable lock-free FIFO queues , IST Austria, 23p.
mla: Henzinger, Thomas A., et al. Replacing Competition with Cooperation to Achieve
Scalable Lock-Free FIFO Queues . IST Austria, 2013, doi:10.15479/AT:IST-2013-124-v1-1.
short: T.A. Henzinger, H. Payer, A. Sezgin, Replacing Competition with Cooperation
to Achieve Scalable Lock-Free FIFO Queues , IST Austria, 2013.
date_created: 2019-05-13T14:13:27Z
date_published: 2013-06-13T00:00:00Z
date_updated: 2020-07-14T23:06:19Z
day: '13'
ddc:
- '000'
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2013-124-v1-1
file:
- access_level: open_access
checksum: a219ba4eada6cd62befed52262ee15d4
content_type: application/pdf
creator: dernst
date_created: 2019-05-13T14:11:39Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6441'
file_name: 2013_TechRep_Henzinger.pdf
file_size: 549684
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '23'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '124'
status: public
title: 'Replacing competition with cooperation to achieve scalable lock-free FIFO
queues '
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '6768'
abstract:
- lang: eng
text: The paper presents an algorithm that applies a stack filter simulating the
Mean Curvature Motion equation via a finite difference scheme.
article_type: original
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: Mondelli M. A finite difference scheme for the stack filter simulating the
MCM. Image Processing On Line. 2013;3:68-111. doi:10.5201/ipol.2013.53
apa: Mondelli, M. (2013). A finite difference scheme for the stack filter simulating
the MCM. Image Processing On Line. Image Processing On Line. https://doi.org/10.5201/ipol.2013.53
chicago: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating
the MCM.” Image Processing On Line. Image Processing On Line, 2013. https://doi.org/10.5201/ipol.2013.53.
ieee: M. Mondelli, “A finite difference scheme for the stack filter simulating the
MCM,” Image Processing On Line, vol. 3. Image Processing On Line, pp. 68–111,
2013.
ista: Mondelli M. 2013. A finite difference scheme for the stack filter simulating
the MCM. Image Processing On Line. 3, 68–111.
mla: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating
the MCM.” Image Processing On Line, vol. 3, Image Processing On Line, 2013,
pp. 68–111, doi:10.5201/ipol.2013.53.
short: M. Mondelli, Image Processing On Line 3 (2013) 68–111.
date_created: 2019-08-05T12:30:38Z
date_published: 2013-07-11T00:00:00Z
date_updated: 2021-01-12T08:08:56Z
day: '11'
ddc:
- '510'
doi: 10.5201/ipol.2013.53
extern: '1'
file:
- access_level: open_access
checksum: 83b7d429bc248c6c461229d3504fb139
content_type: application/pdf
creator: dernst
date_created: 2019-08-05T12:33:40Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6769'
file_name: 2013_IPOL_Mondelli.pdf
file_size: 4306158
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 68-111
publication: Image Processing On Line
publication_identifier:
issn:
- 2105-1232
publication_status: published
publisher: Image Processing On Line
quality_controlled: '1'
status: public
title: A finite difference scheme for the stack filter simulating the MCM
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2013'
...
---
_id: '2329'
abstract:
- lang: eng
text: 'Two-player games on graphs are central in many problems in formal verification
and program analysis such as synthesis and verification of open systems. In this
work, we consider both finite-state game graphs, and recursive game graphs (or
pushdown game graphs) that model the control flow of sequential programs with
recursion. The objectives we study are multidimensional mean-payoff objectives,
where the goal of player 1 is to ensure that the mean-payoff is non-negative in
all dimensions. In pushdown games two types of strategies are relevant: (1) global
strategies, that depend on the entire global history; and (2) modular strategies,
that have only local memory and thus do not depend on the context of invocation.
Our main contributions are as follows: (1) We show that finite-state multidimensional
mean-payoff games can be solved in polynomial time if the number of dimensions
and the maximal absolute value of the weights are fixed; whereas if the number
of dimensions is arbitrary, then the problem is known to be coNP-complete. (2)
We show that pushdown graphs with multidimensional mean-payoff objectives can
be solved in polynomial time. For both (1) and (2) our algorithms are based on
hyperplane separation technique. (3) For pushdown games under global strategies
both one and multidimensional mean-payoff objectives problems are known to be
undecidable, and we show that under modular strategies the multidimensional problem
is also undecidable; under modular strategies the one-dimensional problem is NP-complete.
We show that if the number of modules, the number of exits, and the maximal absolute
value of the weights are fixed, then pushdown games under modular strategies with
one-dimensional mean-payoff objectives can be solved in polynomial time, and if
either the number of exits or the number of modules is unbounded, then the problem
is NP-hard. (4) Finally we show that a fixed parameter tractable algorithm for
finite-state multidimensional mean-payoff games or pushdown games under modular
strategies with one-dimensional mean-payoff objectives would imply the fixed parameter
tractability of parity games.'
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: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional
mean-payoff games. 2013;8052:500-515. doi:10.1007/978-3-642-40184-8_35
apa: 'Chatterjee, K., & Velner, Y. (2013). Hyperplane separation technique for
multidimensional mean-payoff games. Presented at the CONCUR: Concurrency Theory,
Buenos Aires, Argentinia: Springer. https://doi.org/10.1007/978-3-642-40184-8_35'
chicago: Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique
for Multidimensional Mean-Payoff Games.” Lecture Notes in Computer Science. Springer,
2013. https://doi.org/10.1007/978-3-642-40184-8_35.
ieee: K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional
mean-payoff games,” vol. 8052. Springer, pp. 500–515, 2013.
ista: Chatterjee K, Velner Y. 2013. Hyperplane separation technique for multidimensional
mean-payoff games. 8052, 500–515.
mla: Chatterjee, Krishnendu, and Yaron Velner. Hyperplane Separation Technique
for Multidimensional Mean-Payoff Games. Vol. 8052, Springer, 2013, pp. 500–15,
doi:10.1007/978-3-642-40184-8_35.
short: K. Chatterjee, Y. Velner, 8052 (2013) 500–515.
conference:
end_date: 2013-08-30
location: Buenos Aires, Argentinia
name: 'CONCUR: Concurrency Theory'
start_date: 2013-08-27
date_created: 2018-12-11T11:57:01Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2023-02-23T13:00:42Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-40184-8_35
ec_funded: 1
external_id:
arxiv:
- '1210.3141'
intvolume: ' 8052'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1210.3141
month: '08'
oa: 1
oa_version: Preprint
page: 500 - 515
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: '4597'
quality_controlled: '1'
related_material:
record:
- id: '717'
relation: later_version
status: public
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Hyperplane separation technique for multidimensional mean-payoff games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8052
year: '2013'
...
---
_id: '7306'
abstract:
- lang: eng
text: Rechargeable lithium–air (O2) batteries are receiving intense interest because
their high theoretical specific energy exceeds that of lithium-ion batteries.
If the Li–O2 battery is ever to succeed, highly reversible formation/decomposition
of Li2O2 must take place at the cathode on cycling. However, carbon, used ubiquitously
as the basis of the cathode, decomposes during Li2O2 oxidation on charge and actively
promotes electrolyte decomposition on cycling. Replacing carbon with a nanoporous
gold cathode, when in contact with a dimethyl sulphoxide-based electrolyte, does
seem to demonstrate better stability. However, nanoporous gold is not a suitable
cathode; its high mass destroys the key advantage of Li–O2 over Li ion (specific
energy), it is too expensive and too difficult to fabricate. Identifying a suitable
cathode material for the Li–O2 cell is one of the greatest challenges at present.
Here we show that a TiC-based cathode reduces greatly side reactions (arising
from the electrolyte and electrode degradation) compared with carbon and exhibits
better reversible formation/decomposition of Li2O2 even than nanoporous gold (>98%
capacity retention after 100 cycles, compared with 95% for nanoporous gold); it
is also four times lighter, of lower cost and easier to fabricate. The stability
may originate from the presence of TiO2 (along with some TiOC) on the surface
of TiC. In contrast to carbon or nanoporous gold, TiC seems to represent a more
viable, stable, cathode for aprotic Li–O2 cells.
article_processing_charge: No
article_type: original
author:
- first_name: Muhammed M.
full_name: Ottakam Thotiyl, Muhammed M.
last_name: Ottakam Thotiyl
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Zhangquan
full_name: Peng, Zhangquan
last_name: Peng
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
- first_name: Zheng
full_name: Liu, Zheng
last_name: Liu
- first_name: Peter G.
full_name: Bruce, Peter G.
last_name: Bruce
citation:
ama: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. A stable
cathode for the aprotic Li–O2 battery. Nature Materials. 2013;12(11):1050-1056.
doi:10.1038/nmat3737
apa: Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., Chen, Y., Liu, Z., &
Bruce, P. G. (2013). A stable cathode for the aprotic Li–O2 battery. Nature
Materials. Springer Nature. https://doi.org/10.1038/nmat3737
chicago: Ottakam Thotiyl, Muhammed M., Stefan Alexander Freunberger, Zhangquan Peng,
Yuhui Chen, Zheng Liu, and Peter G. Bruce. “A Stable Cathode for the Aprotic Li–O2 Battery.”
Nature Materials. Springer Nature, 2013. https://doi.org/10.1038/nmat3737.
ieee: M. M. Ottakam Thotiyl, S. A. Freunberger, Z. Peng, Y. Chen, Z. Liu, and P.
G. Bruce, “A stable cathode for the aprotic Li–O2 battery,” Nature Materials,
vol. 12, no. 11. Springer Nature, pp. 1050–1056, 2013.
ista: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. 2013.
A stable cathode for the aprotic Li–O2 battery. Nature Materials. 12(11), 1050–1056.
mla: Ottakam Thotiyl, Muhammed M., et al. “A Stable Cathode for the Aprotic Li–O2 Battery.”
Nature Materials, vol. 12, no. 11, Springer Nature, 2013, pp. 1050–56,
doi:10.1038/nmat3737.
short: M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, Y. Chen, Z. Liu, P.G. Bruce,
Nature Materials 12 (2013) 1050–1056.
date_created: 2020-01-15T12:18:29Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T08:12:55Z
day: '01'
doi: 10.1038/nmat3737
extern: '1'
intvolume: ' 12'
issue: '11'
language:
- iso: eng
month: '09'
oa_version: None
page: 1050-1056
publication: Nature Materials
publication_identifier:
issn:
- 1476-1122
- 1476-4660
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: A stable cathode for the aprotic Li–O2 battery
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2013'
...
---
_id: '7307'
abstract:
- lang: eng
text: The non-aqueous Li–air (O2) battery is receiving intense interest because
its theoretical specific energy exceeds that of Li-ion batteries. Recharging the
Li–O2 battery depends on oxidizing solid lithium peroxide (Li2O2), which is formed
on discharge within the porous cathode. However, transporting charge between Li2O2
particles and the solid electrode surface is at best very difficult and leads
to voltage polarization on charging, even at modest rates. This is a significant
problem facing the non-aqueous Li–O2 battery. Here we show that incorporation
of a redox mediator, tetrathiafulvalene (TTF), enables recharging at rates that
are impossible for the cell in the absence of the mediator. On charging, TTF is
oxidized to TTF+ at the cathode surface; TTF+ in turn oxidizes the solid Li2O2,
which results in the regeneration of TTF. The mediator acts as an electron–hole
transfer agent that permits efficient oxidation of solid Li2O2. The cell with
the mediator demonstrated 100 charge/discharge cycles.
article_processing_charge: No
article_type: original
author:
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Zhangquan
full_name: Peng, Zhangquan
last_name: Peng
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
- first_name: Peter G.
full_name: Bruce, Peter G.
last_name: Bruce
citation:
ama: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. Charging a Li–O2 battery
using a redox mediator. Nature Chemistry. 2013;5(6):489-494. doi:10.1038/nchem.1646
apa: Chen, Y., Freunberger, S. A., Peng, Z., Fontaine, O., & Bruce, P. G. (2013).
Charging a Li–O2 battery using a redox mediator. Nature Chemistry. Springer
Nature. https://doi.org/10.1038/nchem.1646
chicago: Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Olivier Fontaine,
and Peter G. Bruce. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature
Chemistry. Springer Nature, 2013. https://doi.org/10.1038/nchem.1646.
ieee: Y. Chen, S. A. Freunberger, Z. Peng, O. Fontaine, and P. G. Bruce, “Charging
a Li–O2 battery using a redox mediator,” Nature Chemistry, vol. 5, no.
6. Springer Nature, pp. 489–494, 2013.
ista: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. 2013. Charging a Li–O2
battery using a redox mediator. Nature Chemistry. 5(6), 489–494.
mla: Chen, Yuhui, et al. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature
Chemistry, vol. 5, no. 6, Springer Nature, 2013, pp. 489–94, doi:10.1038/nchem.1646.
short: Y. Chen, S.A. Freunberger, Z. Peng, O. Fontaine, P.G. Bruce, Nature Chemistry
5 (2013) 489–494.
date_created: 2020-01-15T12:18:43Z
date_published: 2013-05-12T00:00:00Z
date_updated: 2021-01-12T08:12:56Z
day: '12'
doi: 10.1038/nchem.1646
extern: '1'
intvolume: ' 5'
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 489-494
publication: Nature Chemistry
publication_identifier:
issn:
- 1755-4330
- 1755-4349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Charging a Li–O2 battery using a redox mediator
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2013'
...
---
_id: '7596'
abstract:
- lang: eng
text: Casein kinase1 (CK1) plays crucial roles in regulating growth and development
via phosphorylating various substrates throughout the eukaryote kingdom. Blue
light is crucial for normal growth of both plants and animals, and blue light
receptor cryptochrome2 (CRY2) undergoes blue light–dependent phosphorylation and
degradation in planta. To study the function of plant CK1s, systematic genetic
analysis showed that deficiency of two paralogous Arabidopsis thaliana CK1s, CK1.3
and CK1.4, caused shortened hypocotyls, especially under blue light, while overexpression
of either CK1.3 or CK1.4 resulted in the insensitive response to blue light and
delayed flowering under long-day conditions. CK1.3 or CK1.4 act dependently on
CRY2, and overexpression of CK1.3 or CK1.4 significantly suppresses the hypersensitive
response to blue light by CRY2 overexpression. Biochemical studies showed that
CK1.3 and CK1.4 directly phosphorylate CRY2 at Ser-587 and Thr-603 in vitro and
negatively regulate CRY2 stability in planta, which are stimulated by blue light,
further confirming the crucial roles of CK1.3 and CK1.4 in blue light responses
through phosphorylating CRY2. Interestingly, expression of CK1.3 and CK1.4 is
stimulated by blue light and feedback regulated by CRY2-mediated signaling. These
results provide direct evidence for CRY2 phosphorylation and informative clues
on the mechanisms of CRY2-mediated light responses.
article_processing_charge: No
article_type: original
author:
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: C.
full_name: Dai, C.
last_name: Dai
- first_name: H.-T.
full_name: Liu, H.-T.
last_name: Liu
- first_name: H.-W.
full_name: Xue, H.-W.
last_name: Xue
citation:
ama: Tan S, Dai C, Liu H-T, Xue H-W. Arabidopsis casein kinase1 proteins CK1.3 and
CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant
Cell. 2013;25(7):2618-2632. doi:10.1105/tpc.113.114322
apa: Tan, S., Dai, C., Liu, H.-T., & Xue, H.-W. (2013). Arabidopsis casein kinase1
proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling.
The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114322
chicago: Tan, Shutang, C. Dai, H.-T. Liu, and H.-W. Xue. “Arabidopsis Casein Kinase1
Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.”
The Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114322.
ieee: S. Tan, C. Dai, H.-T. Liu, and H.-W. Xue, “Arabidopsis casein kinase1 proteins
CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling,”
The Plant Cell, vol. 25, no. 7. American Society of Plant Biologists, pp.
2618–2632, 2013.
ista: Tan S, Dai C, Liu H-T, Xue H-W. 2013. Arabidopsis casein kinase1 proteins
CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling.
The Plant Cell. 25(7), 2618–2632.
mla: Tan, Shutang, et al. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate
Cryptochrome2 to Regulate Blue Light Signaling.” The Plant Cell, vol. 25,
no. 7, American Society of Plant Biologists, 2013, pp. 2618–32, doi:10.1105/tpc.113.114322.
short: S. Tan, C. Dai, H.-T. Liu, H.-W. Xue, The Plant Cell 25 (2013) 2618–2632.
date_created: 2020-03-21T16:06:55Z
date_published: 2013-08-26T00:00:00Z
date_updated: 2021-01-12T08:14:24Z
day: '26'
doi: 10.1105/tpc.113.114322
extern: '1'
external_id:
pmid:
- '23897926'
intvolume: ' 25'
issue: '7'
language:
- iso: eng
month: '08'
oa_version: None
page: 2618-2632
pmid: 1
publication: The Plant Cell
publication_identifier:
issn:
- 1040-4651
- 1532-298X
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
status: public
title: Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2
to regulate blue light signaling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '7595'
abstract:
- lang: eng
text: Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK) phosphorylates inositol 1,3,4-trisphosphate
to form inositol 1,3,4,5-tetrakisphosphate and inositol 1,3,4,6-tetrakisphosphate
which can be finally transferred to inositol hexaphosphate (IP6) and play important
roles during plant growth and development. There are 4 putative ITPK members in
Arabidopsis. Expression pattern analysis showed that ITPK2 is constitutively expressed
in various tissues. A T-DNA knockout mutant of ITPK2 was identified and scanning
electron microscopy (SEM) analysis showed that the epidermis structure of seed
coat was irregularly formed in seeds of itpk2-1 mutant, resulting in the increased
permeability of seed coat to tetrazolium salts. Further analysis by gas chromatography
coupled with mass spectrometry of lipid polyester monomers in cell wall confirmed
a dramatic decrease in composition of suberin and cutin, which relate to the permeability
of seed coat and the formation of which is accompanied with seed coat development.
These results indicate that ITPK2 plays an essential role in seed coat development
and lipid polyester barrier formation.
article_processing_charge: No
article_type: original
author:
- first_name: Yong
full_name: Tang, Yong
last_name: Tang
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Hongwei
full_name: Xue, Hongwei
last_name: Xue
citation:
ama: Tang Y, Tan S, Xue H. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2
is required for seed coat development. Acta Biochimica et Biophysica Sinica.
2013;45(7):549-560. doi:10.1093/abbs/gmt039
apa: Tang, Y., Tan, S., & Xue, H. (2013). Arabidopsis inositol 1,3,4-trisphosphate
5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica
Sinica. Oxford University Press. https://doi.org/10.1093/abbs/gmt039
chicago: Tang, Yong, Shutang Tan, and Hongwei Xue. “Arabidopsis Inositol 1,3,4-Trisphosphate
5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica
Sinica. Oxford University Press, 2013. https://doi.org/10.1093/abbs/gmt039.
ieee: Y. Tang, S. Tan, and H. Xue, “Arabidopsis inositol 1,3,4-trisphosphate 5/6
kinase 2 is required for seed coat development,” Acta Biochimica et Biophysica
Sinica, vol. 45, no. 7. Oxford University Press, pp. 549–560, 2013.
ista: Tang Y, Tan S, Xue H. 2013. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase
2 is required for seed coat development. Acta Biochimica et Biophysica Sinica.
45(7), 549–560.
mla: Tang, Yong, et al. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is
Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica,
vol. 45, no. 7, Oxford University Press, 2013, pp. 549–60, doi:10.1093/abbs/gmt039.
short: Y. Tang, S. Tan, H. Xue, Acta Biochimica et Biophysica Sinica 45 (2013) 549–560.
date_created: 2020-03-21T16:06:36Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T08:14:23Z
day: '01'
doi: 10.1093/abbs/gmt039
extern: '1'
external_id:
pmid:
- '23595027'
intvolume: ' 45'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 549-560
pmid: 1
publication: Acta Biochimica et Biophysica Sinica
publication_identifier:
issn:
- 1745-7270
- 1672-9145
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed
coat development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2013'
...
---
_id: '765'
abstract:
- lang: eng
text: Renaming is a classic distributed coordination task in which a set of processes
must pick distinct identifiers from a small namespace. In this paper, we consider
the time complexity of this problem when the namespace is linear in the number
of participants, a variant known as loose renaming. We give a non-adaptive algorithm
with O(log log n) (individual) step complexity, where n is a known upper bound
on contention, and an adaptive algorithm with step complexity O((log log k)2),
where k is the actual contention in the execution. We also present a variant of
the adaptive algorithm which requires O(k log log k) total process steps. All
upper bounds hold with high probability against a strong adaptive adversary. We
complement the algorithms with an ω(log log n) expected time lower bound on the
complexity of randomized renaming using test-and-set operations and linear space.
The result is based on a new coupling technique, and is the first to apply to
non-adaptive randomized renaming. Since our algorithms use O(n) test-and-set objects,
our results provide matching bounds on the cost of loose renaming in this setting.
acknowledgement: "Dan Alistarh - This author was supported by the SNF Postdoctoral
Fellows Program, NSF grant CCF-1217921, DoE ASCR grant\r\nER26116/DE-SC0008923,
\ and by grants from the Oracle\r\nand Intel corporations.\r\nJames Aspnes
- Supported in part by NSF grant CCF-0916389.\r\nGeorge Giakkoupis - This work was
funded in part by INRIA Associate Team\r\nRADCON, and ERC Starting Grant GOSSPLE
204742.\r\nPhilipp Woelfel - This research was undertaken, in part, thanks to funding\r\nfrom
the Canada Research Chairs program and the HP Labs\r\nInnovation Research Program."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: George
full_name: Giakkoupis, George
last_name: Giakkoupis
- first_name: Philipp
full_name: Woelfel, Philipp
last_name: Woelfel
citation:
ama: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. Randomized loose renaming
in O(loglogn) time. In: ACM; 2013:200-209. doi:10.1145/2484239.2484240'
apa: 'Alistarh, D.-A., Aspnes, J., Giakkoupis, G., & Woelfel, P. (2013). Randomized
loose renaming in O(loglogn) time (pp. 200–209). Presented at the PODC: Principles
of Distributed Computing, ACM. https://doi.org/10.1145/2484239.2484240'
chicago: Alistarh, Dan-Adrian, James Aspnes, George Giakkoupis, and Philipp Woelfel.
“Randomized Loose Renaming in O(Loglogn) Time,” 200–209. ACM, 2013. https://doi.org/10.1145/2484239.2484240.
ieee: 'D.-A. Alistarh, J. Aspnes, G. Giakkoupis, and P. Woelfel, “Randomized loose
renaming in O(loglogn) time,” presented at the PODC: Principles of Distributed
Computing, 2013, pp. 200–209.'
ista: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. 2013. Randomized loose renaming
in O(loglogn) time. PODC: Principles of Distributed Computing, 200–209.'
mla: Alistarh, Dan-Adrian, et al. Randomized Loose Renaming in O(Loglogn) Time.
ACM, 2013, pp. 200–09, doi:10.1145/2484239.2484240.
short: D.-A. Alistarh, J. Aspnes, G. Giakkoupis, P. Woelfel, in:, ACM, 2013, pp.
200–209.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:23Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2023-02-23T13:13:14Z
day: '01'
doi: 10.1145/2484239.2484240
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 200 - 209
publication_status: published
publisher: ACM
publist_id: '6889'
status: public
title: Randomized loose renaming in O(loglogn) time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '7745'
abstract:
- lang: eng
text: The underlying basis of genetic variation in quantitative traits, in terms
of the number of causal variants and the size of their effects, is largely unknown
in natural populations. The expectation is that complex quantitative trait variation
is attributable to many, possibly interacting, causal variants, whose effects
may depend upon the sex, age and the environment in which they are expressed.
A recently developed methodology in animal breeding derives a value of relatedness
among individuals from high‐density genomic marker data, to estimate additive
genetic variance within livestock populations. Here, we adapt and test the effectiveness
of these methods to partition genetic variation for complex traits across genomic
regions within ecological study populations where individuals have varying degrees
of relatedness. We then apply this approach for the first time to a natural population
and demonstrate that genetic variation in wing length in the great tit (Parus
major) reflects contributions from multiple genomic regions. We show that a polygenic
additive mode of gene action best describes the patterns observed, and we find
no evidence of dosage compensation for the sex chromosome. Our results suggest
that most of the genomic regions that influence wing length have the same effects
in both sexes. We found a limited amount of genetic variance in males that is
attributed to regions that have no effects in females, which could facilitate
the sexual dimorphism observed for this trait. Although this exploratory work
focuses on one complex trait, the methodology is generally applicable to any trait
for any laboratory or wild population, paving the way for investigating sex‐,
age‐ and environment‐specific genetic effects and thus the underlying genetic
architecture of phenotype in biological study systems.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Anna W.
full_name: Santure, Anna W.
last_name: Santure
- first_name: Isabelle
full_name: DeCauwer, Isabelle
last_name: DeCauwer
- first_name: Ben C.
full_name: Sheldon, Ben C.
last_name: Sheldon
- first_name: Jon
full_name: Slate, Jon
last_name: Slate
citation:
ama: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. Partitioning of genetic
variation across the genome using multimarker methods in a wild bird population.
Molecular Ecology. 2013;22(15):3963-3980. doi:10.1111/mec.12375
apa: Robinson, M. R., Santure, A. W., DeCauwer, I., Sheldon, B. C., & Slate,
J. (2013). Partitioning of genetic variation across the genome using multimarker
methods in a wild bird population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12375
chicago: Robinson, Matthew Richard, Anna W. Santure, Isabelle DeCauwer, Ben C. Sheldon,
and Jon Slate. “Partitioning of Genetic Variation across the Genome Using Multimarker
Methods in a Wild Bird Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12375.
ieee: M. R. Robinson, A. W. Santure, I. DeCauwer, B. C. Sheldon, and J. Slate, “Partitioning
of genetic variation across the genome using multimarker methods in a wild bird
population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3963–3980,
2013.
ista: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. 2013. Partitioning
of genetic variation across the genome using multimarker methods in a wild bird
population. Molecular Ecology. 22(15), 3963–3980.
mla: Robinson, Matthew Richard, et al. “Partitioning of Genetic Variation across
the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular
Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3963–80, doi:10.1111/mec.12375.
short: M.R. Robinson, A.W. Santure, I. DeCauwer, B.C. Sheldon, J. Slate, Molecular
Ecology 22 (2013) 3963–3980.
date_created: 2020-04-30T11:00:15Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:15:14Z
day: '01'
doi: 10.1111/mec.12375
extern: '1'
intvolume: ' 22'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3963-3980
publication: Molecular Ecology
publication_identifier:
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Partitioning of genetic variation across the genome using multimarker methods
in a wild bird population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '7746'
abstract:
- lang: eng
text: Clutch size and egg mass are life history traits that have been extensively
studied in wild bird populations, as life history theory predicts a negative trade‐off
between them, either at the phenotypic or at the genetic level. Here, we analyse
the genomic architecture of these heritable traits in a wild great tit (Parus
major) population, using three marker‐based approaches – chromosome partitioning,
quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS).
The variance explained by each great tit chromosome scales with predicted chromosome
size, no location in the genome contains genome‐wide significant QTL, and no individual
SNPs are associated with a large proportion of phenotypic variation, all of which
may suggest that variation in both traits is due to many loci of small effect,
located across the genome. There is no evidence that any regions of the genome
contribute significantly to both traits, which combined with a small, nonsignificant
negative genetic covariance between the traits, suggests the absence of genetic
constraints on the independent evolution of these traits. Our findings support
the hypothesis that variation in life history traits in natural populations is
likely to be determined by many loci of small effect spread throughout the genome,
which are subject to continued input of variation by mutation and migration, although
we cannot exclude the possibility of an additional input of major effect genes
influencing either trait.
article_processing_charge: No
article_type: original
author:
- first_name: Anna W.
full_name: Santure, Anna W.
last_name: Santure
- first_name: Isabelle
full_name: De Cauwer, Isabelle
last_name: De Cauwer
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Jocelyn
full_name: Poissant, Jocelyn
last_name: Poissant
- first_name: Ben C.
full_name: Sheldon, Ben C.
last_name: Sheldon
- first_name: Jon
full_name: Slate, Jon
last_name: Slate
citation:
ama: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic
dissection of variation in clutch size and egg mass in a wild great tit (Parus
major) population. Molecular Ecology. 2013;22(15):3949-3962. doi:10.1111/mec.12376
apa: Santure, A. W., De Cauwer, I., Robinson, M. R., Poissant, J., Sheldon, B. C.,
& Slate, J. (2013). Genomic dissection of variation in clutch size and egg
mass in a wild great tit (Parus major) population. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.12376
chicago: Santure, Anna W., Isabelle De Cauwer, Matthew Richard Robinson, Jocelyn
Poissant, Ben C. Sheldon, and Jon Slate. “Genomic Dissection of Variation in Clutch
Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular
Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12376.
ieee: A. W. Santure, I. De Cauwer, M. R. Robinson, J. Poissant, B. C. Sheldon, and
J. Slate, “Genomic dissection of variation in clutch size and egg mass in a wild
great tit (Parus major) population,” Molecular Ecology, vol. 22, no. 15.
Wiley, pp. 3949–3962, 2013.
ista: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. 2013.
Genomic dissection of variation in clutch size and egg mass in a wild great tit
(Parus major) population. Molecular Ecology. 22(15), 3949–3962.
mla: Santure, Anna W., et al. “Genomic Dissection of Variation in Clutch Size and
Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology,
vol. 22, no. 15, Wiley, 2013, pp. 3949–62, doi:10.1111/mec.12376.
short: A.W. Santure, I. De Cauwer, M.R. Robinson, J. Poissant, B.C. Sheldon, J.
Slate, Molecular Ecology 22 (2013) 3949–3962.
date_created: 2020-04-30T11:00:32Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:15:14Z
day: '01'
doi: 10.1111/mec.12376
extern: '1'
intvolume: ' 22'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3949-3962
publication: Molecular Ecology
publication_identifier:
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Genomic dissection of variation in clutch size and egg mass in a wild great
tit (Parus major) population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '7747'
abstract:
- lang: eng
text: Acquisition and allocation of resources are central to life‐history theory.
However, empirical work typically focuses only on allocation despite the fact
that relationships between fitness components may be governed by differences in
the ability of individuals to acquire resources across environments. Here, we
outline a statistical framework to partition the genetic basis of multivariate
plasticity into independent axes of genetic variation, and quantify for the first
time, the extent to which specific traits drive multitrait genotype–environment
interactions. Our framework generalises to analyses of plasticity, growth and
ageing. We apply this approach to a unique, large‐scale, multivariate study of
acquisition, allocation and plasticity in the life history of the cricket, Gryllus
firmus. We demonstrate that resource acquisition and allocation are genetically
correlated, and that plasticity in trade‐offs between allocation to components
of fitness is 90% dependent on genetic variance for total resource acquisition.
These results suggest that genotype–environment effects for resource acquisition
can maintain variation in life‐history components that are typically observed
in the wild.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Andrew P.
full_name: Beckerman, Andrew P.
last_name: Beckerman
citation:
ama: 'Robinson MR, Beckerman AP. Quantifying multivariate plasticity: Genetic variation
in resource acquisition drives plasticity in resource allocation to components
of life history. Ecology Letters. 2013;16(3):281-290. doi:10.1111/ele.12047'
apa: 'Robinson, M. R., & Beckerman, A. P. (2013). Quantifying multivariate plasticity:
Genetic variation in resource acquisition drives plasticity in resource allocation
to components of life history. Ecology Letters. Wiley. https://doi.org/10.1111/ele.12047'
chicago: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate
Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource
Allocation to Components of Life History.” Ecology Letters. Wiley, 2013.
https://doi.org/10.1111/ele.12047.'
ieee: 'M. R. Robinson and A. P. Beckerman, “Quantifying multivariate plasticity:
Genetic variation in resource acquisition drives plasticity in resource allocation
to components of life history,” Ecology Letters, vol. 16, no. 3. Wiley,
pp. 281–290, 2013.'
ista: 'Robinson MR, Beckerman AP. 2013. Quantifying multivariate plasticity: Genetic
variation in resource acquisition drives plasticity in resource allocation to
components of life history. Ecology Letters. 16(3), 281–290.'
mla: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate
Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource
Allocation to Components of Life History.” Ecology Letters, vol. 16, no.
3, Wiley, 2013, pp. 281–90, doi:10.1111/ele.12047.'
short: M.R. Robinson, A.P. Beckerman, Ecology Letters 16 (2013) 281–290.
date_created: 2020-04-30T11:00:49Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2021-01-12T08:15:15Z
day: '01'
doi: 10.1111/ele.12047
extern: '1'
intvolume: ' 16'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 281-290
publication: Ecology Letters
publication_identifier:
issn:
- 1461-023X
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'Quantifying multivariate plasticity: Genetic variation in resource acquisition
drives plasticity in resource allocation to components of life history'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2013'
...
---
_id: '7775'
abstract:
- lang: eng
text: As a function of packing fraction at zero temperature and applied stress,
an amorphous packing of spheres exhibits a jamming transition where the system
is sensitive to boundary conditions even in the thermodynamic limit. Upon further
compression, the system should become insensitive to boundary conditions provided
it is sufficiently large. Here we explore the linear response to a large class
of boundary perturbations in 2 and 3 dimensions. We consider each finite packing
with periodic-boundary conditions as the basis of an infinite square or cubic
lattice and study properties of vibrational modes at arbitrary wave vector. We
find that the stability of such modes can be understood in terms of a competition
between plane waves and the anomalous vibrational modes associated with the jamming
transition; infinitesimal boundary perturbations become irrelevant for systems
that are larger than a length scale that characterizes the transverse excitations.
This previously identified length diverges at the jamming transition.
article_number: '11000'
article_processing_charge: No
article_type: original
author:
- first_name: Samuel S.
full_name: Schoenholz, Samuel S.
last_name: Schoenholz
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Oleg
full_name: Kogan, Oleg
last_name: Kogan
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed
packings II: The transverse length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51096d'
apa: 'Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., & Nagel, S.
R. (2013). Stability of jammed packings II: The transverse length scale. Soft
Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51096d'
chicago: 'Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu,
and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.”
Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51096d.'
ieee: 'S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability
of jammed packings II: The transverse length scale,” Soft Matter, vol.
9, no. 46. Royal Society of Chemistry, 2013.'
ista: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of
jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.'
mla: 'Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse
Length Scale.” Soft Matter, vol. 9, no. 46, 11000, Royal Society of Chemistry,
2013, doi:10.1039/c3sm51096d.'
short: S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter
9 (2013).
date_created: 2020-04-30T11:43:58Z
date_published: 2013-10-08T00:00:00Z
date_updated: 2021-01-12T08:15:27Z
day: '08'
doi: 10.1039/c3sm51096d
extern: '1'
intvolume: ' 9'
issue: '46'
language:
- iso: eng
month: '10'
oa_version: None
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Stability of jammed packings II: The transverse length scale'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '7774'
abstract:
- lang: eng
text: In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low
frequency vibrational properties of jammed amorphous sphere packings can be understood
in terms of a length scale, called l*, that diverges as the system becomes marginally
unstable. Despite the tremendous success of this theory, it has been difficult
to connect the counting argument that defines l* to other length scales that diverge
near the jamming transition. We present an alternate derivation of l* based on
the onset of rigidity. This phenomenological approach reveals the physical mechanism
underlying the length scale and is relevant to a range of systems for which the
original argument breaks down. It also allows us to present the first direct numerical
measurement of l*.
article_number: '10993'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Wouter G.
full_name: Ellenbroek, Wouter G.
last_name: Ellenbroek
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
citation:
ama: 'Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity
length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51095f'
apa: 'Goodrich, C. P., Ellenbroek, W. G., & Liu, A. J. (2013). Stability of
jammed packings I: The rigidity length scale. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c3sm51095f'
chicago: 'Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability
of Jammed Packings I: The Rigidity Length Scale.” Soft Matter. Royal Society
of Chemistry, 2013. https://doi.org/10.1039/c3sm51095f.'
ieee: 'C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings
I: The rigidity length scale,” Soft Matter, vol. 9, no. 46. Royal Society
of Chemistry, 2013.'
ista: 'Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I:
The rigidity length scale. Soft Matter. 9(46), 10993.'
mla: 'Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity
Length Scale.” Soft Matter, vol. 9, no. 46, 10993, Royal Society of Chemistry,
2013, doi:10.1039/c3sm51095f.'
short: C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013).
date_created: 2020-04-30T11:43:42Z
date_published: 2013-10-08T00:00:00Z
date_updated: 2021-01-12T08:15:27Z
day: '08'
doi: 10.1039/c3sm51095f
extern: '1'
intvolume: ' 9'
issue: '46'
language:
- iso: eng
month: '10'
oa_version: None
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Stability of jammed packings I: The rigidity length scale'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '8030'
abstract:
- lang: eng
text: While the plasticity of excitatory synaptic connections in the brain has been
widely studied, the plasticity of inhibitory connections is much less understood.
Here, we present recent experimental and theoretical findings concerning the rules
of spike timing-dependent inhibitory plasticity and their putative network function.
This is a summary of a workshop at the COSYNE conference 2012.
article_number: '119'
article_processing_charge: No
article_type: original
author:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: R. C.
full_name: Froemke, R. C.
last_name: Froemke
- first_name: N.
full_name: Doyon, N.
last_name: Doyon
- first_name: M.
full_name: Gilson, M.
last_name: Gilson
- first_name: J. S.
full_name: Haas, J. S.
last_name: Haas
- first_name: R.
full_name: Liu, R.
last_name: Liu
- first_name: A.
full_name: Maffei, A.
last_name: Maffei
- first_name: P.
full_name: Miller, P.
last_name: Miller
- first_name: C. J.
full_name: Wierenga, C. J.
last_name: Wierenga
- first_name: M. A.
full_name: Woodin, M. A.
last_name: Woodin
- first_name: F.
full_name: Zenke, F.
last_name: Zenke
- first_name: H.
full_name: Sprekeler, H.
last_name: Sprekeler
citation:
ama: 'Vogels TP, Froemke RC, Doyon N, et al. Inhibitory synaptic plasticity: Spike
timing-dependence and putative network function. Frontiers in Neural Circuits.
2013;7. doi:10.3389/fncir.2013.00119'
apa: 'Vogels, T. P., Froemke, R. C., Doyon, N., Gilson, M., Haas, J. S., Liu, R.,
… Sprekeler, H. (2013). Inhibitory synaptic plasticity: Spike timing-dependence
and putative network function. Frontiers in Neural Circuits. Frontiers
Media. https://doi.org/10.3389/fncir.2013.00119'
chicago: 'Vogels, Tim P, R. C. Froemke, N. Doyon, M. Gilson, J. S. Haas, R. Liu,
A. Maffei, et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and
Putative Network Function.” Frontiers in Neural Circuits. Frontiers Media,
2013. https://doi.org/10.3389/fncir.2013.00119.'
ieee: 'T. P. Vogels et al., “Inhibitory synaptic plasticity: Spike timing-dependence
and putative network function,” Frontiers in Neural Circuits, vol. 7. Frontiers
Media, 2013.'
ista: 'Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller
P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. 2013. Inhibitory synaptic plasticity:
Spike timing-dependence and putative network function. Frontiers in Neural Circuits.
7, 119.'
mla: 'Vogels, Tim P., et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence
and Putative Network Function.” Frontiers in Neural Circuits, vol. 7, 119,
Frontiers Media, 2013, doi:10.3389/fncir.2013.00119.'
short: T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei,
P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, Frontiers in Neural
Circuits 7 (2013).
date_created: 2020-06-25T13:23:50Z
date_published: 2013-07-18T00:00:00Z
date_updated: 2021-01-12T08:16:38Z
day: '18'
ddc:
- '570'
doi: 10.3389/fncir.2013.00119
extern: '1'
external_id:
pmid:
- '23882186'
file:
- access_level: open_access
checksum: 9c321cb12977d84048712eefa7f0c497
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T11:23:40Z
date_updated: 2020-07-16T11:23:40Z
file_id: '8123'
file_name: 2013_FrontNeurCirc_Vogels.pdf
file_size: 1530469
relation: main_file
success: 1
file_date_updated: 2020-07-16T11:23:40Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Neural Circuits
publication_identifier:
eissn:
- 1662-5110
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
status: public
title: 'Inhibitory synaptic plasticity: Spike timing-dependence and putative network
function'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2013'
...
---
_id: '811'
abstract:
- lang: eng
text: Cell migration is commonly accompanied by protrusion of membrane ruffles and
lamellipodia. In two-dimensional migration, protrusion of these thin sheets of
cytoplasm is considered relevant to both exploration of new space and initiation
of nascent adhesion to the substratum. Lamellipodium formation can be potently
stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here
we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack
detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent
lamellipodia, but these structures were restored by expression of either Rac subfamily
member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction
in wound closure and random cell migration and a notable loss of sensitivity to
a chemotactic gradient. Despite these defects, Rac-deficient cells were able to
spread, formed filopodia and established focal adhesions. Spreading in these cells
was achieved by the extension of filopodia followed by the advancement of cytoplasmic
veils between them. The number and size of focal adhesions as well as their intensity
were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased
the mobility of different components in focal adhesions, potentially explaining
how Rac - although not essential - can contribute to focal adhesion assembly.
Together, our data demonstrate that Rac signaling is essential for lamellipodium
protrusion and for efficient cell migration, but not for spreading or filopodium
formation. Our findings also suggest that Rac GTPases are crucial to the establishment
or maintenance of polarity in chemotactic migration.
acknowledgement: |-
This work was supported in part by the Deutsche Forschungsgemeinschaft [grants within programs SFB621 to K.R., and FOR629 and SFB629 to T.E.B.S.]. Deposited in PMC for immediate release.
We thank Brigitte Denker and Gerd Landsberg for excellent technical assistance. We are grateful to Robert Geffers (HZI Braunschweig, Germany) for microarray analyses and to Mirko Himmel (UKE Hamburg, Germany) for valuable advice on FRAP analysis.
author:
- first_name: Anika
full_name: Steffen, Anika
last_name: Steffen
- first_name: Markus
full_name: Ladwein, Markus
last_name: Ladwein
- first_name: Georgi A
full_name: Georgi Dimchev
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
- first_name: Anke
full_name: Hein, Anke
last_name: Hein
- first_name: Lisa
full_name: Schwenkmezger, Lisa
last_name: Schwenkmezger
- first_name: Stefan
full_name: Arens, Stefan
last_name: Arens
- first_name: Kathrin
full_name: Ladwein, Kathrin I
last_name: Ladwein
- first_name: J.
full_name: Holleboom, J. Margit
last_name: Holleboom
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: John
full_name: Small, John V
last_name: Small
- first_name: Janett
full_name: Schwarz, Janett
last_name: Schwarz
- first_name: Ralf
full_name: Gerhard, Ralf
last_name: Gerhard
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Theresia
full_name: Stradal, Theresia E
last_name: Stradal
- first_name: Cord
full_name: Brakebusch, Cord H
last_name: Brakebusch
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
citation:
ama: Steffen A, Ladwein M, Dimchev GA, et al. Rac function is crucial for cell migration
but is not required for spreading and focal adhesion formation. Journal of
Cell Science. 2013;126(20):4572-4588. doi:10.1242/jcs.118232
apa: Steffen, A., Ladwein, M., Dimchev, G. A., Hein, A., Schwenkmezger, L., Arens,
S., … Rottner, K. (2013). Rac function is crucial for cell migration but is not
required for spreading and focal adhesion formation. Journal of Cell Science.
Company of Biologists. https://doi.org/10.1242/jcs.118232
chicago: Steffen, Anika, Markus Ladwein, Georgi A Dimchev, Anke Hein, Lisa Schwenkmezger,
Stefan Arens, Kathrin Ladwein, et al. “Rac Function Is Crucial for Cell Migration
but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of
Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.118232.
ieee: A. Steffen et al., “Rac function is crucial for cell migration but
is not required for spreading and focal adhesion formation,” Journal of Cell
Science, vol. 126, no. 20. Company of Biologists, pp. 4572–4588, 2013.
ista: Steffen A, Ladwein M, Dimchev GA, Hein A, Schwenkmezger L, Arens S, Ladwein
K, Holleboom J, Schur FK, Small J, Schwarz J, Gerhard R, Faix J, Stradal T, Brakebusch
C, Rottner K. 2013. Rac function is crucial for cell migration but is not required
for spreading and focal adhesion formation. Journal of Cell Science. 126(20),
4572–4588.
mla: Steffen, Anika, et al. “Rac Function Is Crucial for Cell Migration but Is Not
Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science,
vol. 126, no. 20, Company of Biologists, 2013, pp. 4572–88, doi:10.1242/jcs.118232.
short: A. Steffen, M. Ladwein, G.A. Dimchev, A. Hein, L. Schwenkmezger, S. Arens,
K. Ladwein, J. Holleboom, F.K. Schur, J. Small, J. Schwarz, R. Gerhard, J. Faix,
T. Stradal, C. Brakebusch, K. Rottner, Journal of Cell Science 126 (2013) 4572–4588.
date_created: 2018-12-11T11:48:38Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:16:57Z
day: '01'
doi: 10.1242/jcs.118232
extern: 1
intvolume: ' 126'
issue: '20'
month: '01'
page: 4572 - 4588
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '6840'
quality_controlled: 0
status: public
title: Rac function is crucial for cell migration but is not required for spreading
and focal adhesion formation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 126
year: '2013'
...
---
_id: '812'
abstract:
- lang: eng
text: Lamellipodia are sheet-like protrusions formed during migration or phagocytosis
and comprise a network of actin filaments. Filament formation in this network
is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3)
complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin
homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching
versus actin filament elongation is unknown. Here we use instantaneous interference
with Arp2/3 complex function in live fibroblasts with established lamellipodia.
This allows direct examination of both the fate of elongating filaments upon instantaneous
suppression of Arp2/3 complex activity and the consequences of this treatment
on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex
is an essential organizer of treadmilling actin filament arrays but has little
effect on the net rate of actin filament turnover at the cell periphery. In addition,
Arp2/3 complex serves as key upstream factor for the recruitment of modulators
of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is
thus decisive for filament organization and geometry within the network not only
by generating branches and novel filament ends, but also by directing capping
or severing activities to the lamellipodium. Arp2/3 complex is also crucial to
lamellipodia-based migration of keratocytes.
acknowledgement: "This work was supported in part by Deutsche Forschungsgemeinschaft
Grants RO2414/3-1 (to K.R.) and FA330/6-1 (to J.F.), Austrian \nScience Fund Projects
FWF 1516-B09 and FWF P21292-B09 (to J.V.S.), the Vienna Science and Technology
\ Fund (WWTF, to \nJ.V.S. and C.S.), and Australian National Health and
\ Medical \nResearch Council Grant APP1004175 (to P.W.G.). We thank J. Adams, \nR.
Chisholm, A. Hall, L. Machesky, H. G. Mannherz, D. Schafer, and \nR. Wedlich-Söldner
\ for expression constructs and B. Denker, \nP. Hagendorff, and G. Landsberg
for technical assistance."
author:
- first_name: Stefan
full_name: Koestler, Stefan A
last_name: Koestler
- first_name: Anika
full_name: Steffen, Anika
last_name: Steffen
- first_name: Maria
full_name: Maria Nemethova
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Moritz
full_name: Winterhoff, Moritz
last_name: Winterhoff
- first_name: Ningning
full_name: Luo, Ningning
last_name: Luo
- first_name: J.
full_name: Holleboom, J. Margit
last_name: Holleboom
- first_name: Jessica
full_name: Krupp, Jessica
last_name: Krupp
- first_name: Sonja
full_name: Jacob, Sonja
last_name: Jacob
- first_name: Marlene
full_name: Vinzenz, Marlene
last_name: Vinzenz
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Kai
full_name: Schlüter, Kai
last_name: Schlüter
- first_name: Peter
full_name: Gunning, Peter W
last_name: Gunning
- first_name: Christoph
full_name: Winkler, Christoph
last_name: Winkler
- first_name: Christian
full_name: Schmeiser, Christian
last_name: Schmeiser
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Theresia
full_name: Stradal, Theresia E
last_name: Stradal
- first_name: John
full_name: Small, John V
last_name: Small
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
citation:
ama: Koestler S, Steffen A, Nemethova M, et al. Arp2/3 complex is essential for
actin network treadmilling as well as for targeting of capping protein and cofilin.
Molecular Biology of the Cell. 2013;24(18):2861-2875. doi:10.1091/mbc.E12-12-0857
apa: Koestler, S., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom,
J., … Rottner, K. (2013). Arp2/3 complex is essential for actin network treadmilling
as well as for targeting of capping protein and cofilin. Molecular Biology
of the Cell. American Society for Biology. https://doi.org/10.1091/mbc.E12-12-0857
chicago: Koestler, Stefan, Anika Steffen, Maria Nemethova, Moritz Winterhoff, Ningning
Luo, J. Holleboom, Jessica Krupp, et al. “Arp2/3 Complex Is Essential for Actin
Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.”
Molecular Biology of the Cell. American Society for Biology, 2013. https://doi.org/10.1091/mbc.E12-12-0857.
ieee: S. Koestler et al., “Arp2/3 complex is essential for actin network
treadmilling as well as for targeting of capping protein and cofilin,” Molecular
Biology of the Cell, vol. 24, no. 18. American Society for Biology, pp. 2861–2875,
2013.
ista: Koestler S, Steffen A, Nemethova M, Winterhoff M, Luo N, Holleboom J, Krupp
J, Jacob S, Vinzenz M, Schur FK, Schlüter K, Gunning P, Winkler C, Schmeiser C,
Faix J, Stradal T, Small J, Rottner K. 2013. Arp2/3 complex is essential for actin
network treadmilling as well as for targeting of capping protein and cofilin.
Molecular Biology of the Cell. 24(18), 2861–2875.
mla: Koestler, Stefan, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling
as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology
of the Cell, vol. 24, no. 18, American Society for Biology, 2013, pp. 2861–75,
doi:10.1091/mbc.E12-12-0857.
short: S. Koestler, A. Steffen, M. Nemethova, M. Winterhoff, N. Luo, J. Holleboom,
J. Krupp, S. Jacob, M. Vinzenz, F.K. Schur, K. Schlüter, P. Gunning, C. Winkler,
C. Schmeiser, J. Faix, T. Stradal, J. Small, K. Rottner, Molecular Biology of
the Cell 24 (2013) 2861–2875.
date_created: 2018-12-11T11:48:38Z
date_published: 2013-09-15T00:00:00Z
date_updated: 2021-01-12T08:17:00Z
day: '15'
doi: 10.1091/mbc.E12-12-0857
extern: 1
intvolume: ' 24'
issue: '18'
month: '09'
page: 2861 - 2875
publication: Molecular Biology of the Cell
publication_status: published
publisher: American Society for Biology
publist_id: '6841'
quality_controlled: 0
status: public
title: Arp2/3 complex is essential for actin network treadmilling as well as for targeting
of capping protein and cofilin
type: journal_article
volume: 24
year: '2013'
...
---
_id: '810'
abstract:
- lang: eng
text: Cryo-electron tomography combined with image processing by sub-tomogram averaging
is unique in its power to resolve the structures of proteins and macromolecular
complexes in situ. Limitations of the method, including the low signal to noise
ratio within individual images from cryo-tomographic datasets and difficulties
in determining the defocus at which the data was collected, mean that to date
the very best structures obtained by sub-tomogram averaging are limited to a resolution
of approximately 15. Å. Here, by optimizing data collection and defocus determination
steps, we have determined the structure of assembled Mason-Pfizer monkey virus
Gag protein using sub-tomogram averaging to a resolution of 8.5. Å. At this resolution
alpha-helices can be directly and clearly visualized. These data demonstrate for
the first time that high-resolution structural information can be obtained from
cryo-electron tomograms using sub-tomogram averaging. Sub-tomogram averaging has
the potential to allow detailed studies of unsolved and biologically relevant
structures under biologically relevant conditions.
acknowledgement: The M-PMV ΔPro CANC tubes imaged in this study were a kind gift from
Pavel Ulbrich and Tomas Ruml, Institute of Chemical Technology, Prague. The cryo-EM
grids were prepared by Tanmay Bharat. This study was technically supported by EMBL’s
IT services unit and by Frank Thommen. We thank Martin Schorb and Svetlana Dodonova
for discussions and advice; Khanh Huy Bui for advice and scripts to streamline tomogram
reconstruction; and Giulia Zanetti, Tanmay Bharat, and Martin Beck for comments
on the manuscript. This study was supported by Deutsche Forschungsgemeinschaft grant
BR 3635/2-1 to JAGB.
author:
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Wim
full_name: Hagen, Wim J
last_name: Hagen
- first_name: Alex
full_name: De Marco, Alex
last_name: De Marco
- first_name: John
full_name: Briggs, John A
last_name: Briggs
citation:
ama: Schur FK, Hagen W, De Marco A, Briggs J. Determination of protein structure
at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging.
Journal of Structural Biology. 2013;184(3):394-400. doi:10.1016/j.jsb.2013.10.015
apa: Schur, F. K., Hagen, W., De Marco, A., & Briggs, J. (2013). Determination
of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram
averaging. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2013.10.015
chicago: Schur, Florian KM, Wim Hagen, Alex De Marco, and John Briggs. “Determination
of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram
Averaging.” Journal of Structural Biology. Academic Press, 2013. https://doi.org/10.1016/j.jsb.2013.10.015.
ieee: F. K. Schur, W. Hagen, A. De Marco, and J. Briggs, “Determination of protein
structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging,”
Journal of Structural Biology, vol. 184, no. 3. Academic Press, pp. 394–400,
2013.
ista: Schur FK, Hagen W, De Marco A, Briggs J. 2013. Determination of protein structure
at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging.
Journal of Structural Biology. 184(3), 394–400.
mla: Schur, Florian KM, et al. “Determination of Protein Structure at 8.5Å Resolution
Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” Journal of Structural
Biology, vol. 184, no. 3, Academic Press, 2013, pp. 394–400, doi:10.1016/j.jsb.2013.10.015.
short: F.K. Schur, W. Hagen, A. De Marco, J. Briggs, Journal of Structural Biology
184 (2013) 394–400.
date_created: 2018-12-11T11:48:37Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:54Z
day: '01'
doi: 10.1016/j.jsb.2013.10.015
extern: 1
intvolume: ' 184'
issue: '3'
month: '12'
page: 394 - 400
publication: Journal of Structural Biology
publication_status: published
publisher: Academic Press
publist_id: '6839'
quality_controlled: 0
status: public
title: Determination of protein structure at 8.5Å resolution using cryo-electron tomography
and sub-tomogram averaging
type: journal_article
volume: 184
year: '2013'
...
---
_id: '8245'
abstract:
- lang: eng
text: "Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable
addition to breast cancer therapy.\r\nData obtained from neoadjuvant settings
revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a\r\nmajor
mechanism of action for the mAb trastuzumab. Conflicting results still call into
question whether disease\r\nprogression, prolonged treatment or concomitant chemotherapy
influences ADCC and related immunological\r\nphenomena.\r\nMethods: We analyzed
the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP)
of\r\nperipheral blood mononuclear cells (PBMCs) from human epidermal growth factor
receptor 2 (HER2/neu) positive\r\nbreast cancer patients receiving trastuzumab
therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as\r\nwell
as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n =
15). PBMCs from healthy volunteers\r\n(n = 24) were used as controls. ADCC and
ADCP activity was correlated with the expression of antibody binding\r\nFc-gamma
receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes)
and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells
and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients,
markers were correlated with progression-free survival (PFS).\r\nResults: ADCC
activity was significantly down regulated in metastatic, adjuvant and t-naive
patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely
correlated with the expression of CD107a on CD56+\r\ncells in adjuvant patients.
ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment
duration\r\nor additional chemotherapy. PFS in metastatic patients inversely correlated
with the number of peripheral Treg cells.\r\nConclusion: The reduction of ADCC
in patients as compared to healthy controls calls for adjuvant strategies, such
as\r\nimmune-enhancing agents, to improve the activity of trastuzumab. However,
efficacy of trastuzumab-specific ADCC\r\nand ADCP appears not to be affected by
treatment duration, disease progression or concomitant chemotherapy. This\r\nfinding
supports the application of trastuzumab at any stage of the disease."
article_number: '307'
article_processing_charge: No
author:
- first_name: Branka
full_name: Petricevic, Branka
last_name: Petricevic
- first_name: Johannes
full_name: Laengle, Johannes
last_name: Laengle
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Monika
full_name: Sachet, Monika
last_name: Sachet
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Guenther
full_name: Steger, Guenther
last_name: Steger
- first_name: Rupert
full_name: Bartsch, Rupert
last_name: Bartsch
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Michael
full_name: Bergmann, Michael
last_name: Bergmann
citation:
ama: Petricevic B, Laengle J, Singer J, et al. Trastuzumab mediates antibody-dependent
cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant
and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine.
2013;11. doi:10.1186/1479-5876-11-307
apa: Petricevic, B., Laengle, J., Singer, J., Sachet, M., Singer, J., Steger, G.,
… Bergmann, M. (2013). Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity
and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast
cancer patients. Journal of Translational Medicine. Springer Nature. https://doi.org/10.1186/1479-5876-11-307
chicago: Petricevic, Branka, Johannes Laengle, Josef Singer, Monika Sachet, Judit
Singer, Guenther Steger, Rupert Bartsch, Erika Jensen-Jarolim, and Michael Bergmann.
“Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis
to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.”
Journal of Translational Medicine. Springer Nature, 2013. https://doi.org/10.1186/1479-5876-11-307.
ieee: B. Petricevic et al., “Trastuzumab mediates antibody-dependent cell-mediated
cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic
HER2/neu breast cancer patients,” Journal of Translational Medicine, vol.
11. Springer Nature, 2013.
ista: Petricevic B, Laengle J, Singer J, Sachet M, Singer J, Steger G, Bartsch R,
Jensen-Jarolim E, Bergmann M. 2013. Trastuzumab mediates antibody-dependent cell-mediated
cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic
HER2/neu breast cancer patients. Journal of Translational Medicine. 11, 307.
mla: Petricevic, Branka, et al. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated
Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic
HER2/Neu Breast Cancer Patients.” Journal of Translational Medicine, vol.
11, 307, Springer Nature, 2013, doi:10.1186/1479-5876-11-307.
short: B. Petricevic, J. Laengle, J. Singer, M. Sachet, J. Singer, G. Steger, R.
Bartsch, E. Jensen-Jarolim, M. Bergmann, Journal of Translational Medicine 11
(2013).
date_created: 2020-08-10T11:54:34Z
date_published: 2013-12-12T00:00:00Z
date_updated: 2022-08-25T14:52:39Z
day: '12'
ddc:
- '570'
doi: 10.1186/1479-5876-11-307
extern: '1'
external_id:
pmid:
- '24330813'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-10T13:45:19Z
date_updated: 2020-08-10T13:45:19Z
file_id: '8247'
file_name: 2013_JoTM_Petricevic.pdf
file_size: 777311
relation: main_file
success: 1
file_date_updated: 2020-08-10T13:45:19Z
has_accepted_license: '1'
intvolume: ' 11'
language:
- iso: eng
month: '12'
oa: 1
oa_version: None
pmid: 1
publication: Journal of Translational Medicine
publication_identifier:
issn:
- 1479-5876
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis
to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2013'
...
---
_id: '827'
abstract:
- lang: eng
text: As sessile organisms, plants have to be able to adapt to a continuously changing
environment. Plants that perceive some of these changes as stress signals activate
signaling pathways to modulate their development and to enable them to survive.
The complex responses to environmental cues are to a large extent mediated by
plant hormones that together orchestrate the final plant response. The phytohormone
cytokinin is involved in many plant developmental processes. Recently, it has
been established that cytokinin plays an important role in stress responses, but
does not act alone. Indeed, the hormonal control of plant development and stress
adaptation is the outcome of a complex network of multiple synergistic and antagonistic
interactions between various hormones. Here, we review the recent findings on
the cytokinin function as part of this hormonal network. We focus on the importance
of the crosstalk between cytokinin and other hormones, such as abscisic acid,
jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development
and stress adaptation. Finally, the impact of the current research in the biotechnological
industry will be discussed.
article_number: '451'
author:
- first_name: José
full_name: O'Brien, José
last_name: O'Brien
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress
responses. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00451
apa: O’Brien, J., & Benková, E. (2013). Cytokinin cross talking during biotic
and abiotic stress responses. Frontiers in Plant Science. Frontiers Research
Foundation. https://doi.org/10.3389/fpls.2013.00451
chicago: O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic
and Abiotic Stress Responses.” Frontiers in Plant Science. Frontiers Research
Foundation, 2013. https://doi.org/10.3389/fpls.2013.00451.
ieee: J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic
stress responses,” Frontiers in Plant Science, vol. 4. Frontiers Research
Foundation, 2013.
ista: O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic
stress responses. Frontiers in Plant Science. 4, 451.
mla: O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and
Abiotic Stress Responses.” Frontiers in Plant Science, vol. 4, 451, Frontiers
Research Foundation, 2013, doi:10.3389/fpls.2013.00451.
short: J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).
date_created: 2018-12-11T11:48:43Z
date_published: 2013-11-19T00:00:00Z
date_updated: 2021-01-12T08:17:50Z
day: '19'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.3389/fpls.2013.00451
ec_funded: 1
file:
- access_level: open_access
checksum: fdc25ddd1bf9a99b99f662cdbafeddd4
content_type: application/pdf
creator: dernst
date_created: 2019-01-31T10:40:38Z
date_updated: 2020-07-14T12:48:11Z
file_id: '5903'
file_name: 2013_FrontiersPlant_OBrien.pdf
file_size: 953299
relation: main_file
file_date_updated: 2020-07-14T12:48:11Z
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '6821'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinin cross talking during biotic and abiotic stress responses
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: 4
year: '2013'
...
---
_id: '828'
abstract:
- lang: eng
text: The plant root system is essential for providing anchorage to the soil, supplying
minerals and water, and synthesizing metabolites. It is a dynamic organ modulated
by external cues such as environmental signals, water and nutrients availability,
salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically,
after which they progress through discrete developmental stages which can be independently
controlled, providing a high level of plasticity during root system formation.
Within this review, main contributions are presented, from the classical forward
genetic screens to the more recent high-throughput approaches, combined with computer
model predictions, dissecting how LRs and thereby root system architecture is
established and developed.
article_number: '537'
author:
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- 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: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture
dynamics. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00537
apa: Cuesta, C., Wabnik, K. T., & Benková, E. (2013). Systems approaches to
study root architecture dynamics. Frontiers in Plant Science. Frontiers
Research Foundation. https://doi.org/10.3389/fpls.2013.00537
chicago: Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches
to Study Root Architecture Dynamics.” Frontiers in Plant Science. Frontiers
Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00537.
ieee: C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root
architecture dynamics,” Frontiers in Plant Science, vol. 4. Frontiers Research
Foundation, 2013.
ista: Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture
dynamics. Frontiers in Plant Science. 4, 537.
mla: Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.”
Frontiers in Plant Science, vol. 4, 537, Frontiers Research Foundation,
2013, doi:10.3389/fpls.2013.00537.
short: C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013).
date_created: 2018-12-11T11:48:43Z
date_published: 2013-12-26T00:00:00Z
date_updated: 2021-01-12T08:17:52Z
day: '26'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.3389/fpls.2013.00537
ec_funded: 1
file:
- access_level: open_access
checksum: 0185b3c4d7df9a94bd3ce5a66d213506
content_type: application/pdf
creator: dernst
date_created: 2019-01-31T10:36:43Z
date_updated: 2020-07-14T12:48:11Z
file_id: '5902'
file_name: 2013_FrontiersPlant_Cuesta.pdf
file_size: 710835
relation: main_file
file_date_updated: 2020-07-14T12:48:11Z
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '6820'
quality_controlled: '1'
scopus_import: 1
status: public
title: Systems approaches to study root architecture dynamics
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: 4
year: '2013'
...
---
_id: '830'
abstract:
- lang: eng
text: Upon hormonal signaling, ovules develop as lateral organs from the placenta.
Ovule numbers ultimately determine the number of seeds that develop, and thereby
contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED
COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule
primordia formation. We show that expression of the CUC1 and CUC2 genes is required
to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required
for ovule primordia formation. Furthermore, our results suggest that the auxin
response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and
promote their transcription. Based on our findings, we propose an integrative
model to describe the molecular mechanisms of the early stages of ovule development.
acknowledgement: The project and F.G. were supported by the CARIPLO Foundation (project
2009-2990) and COST (European Cooperation in Science and Technology) action HAPRECI
(Harnessing Plant Reproduction for Crop Improvement). E.B. and C.C. were supported
by the European Research Council through a ‘Starting Independent Research’ grant
(ERC-2007-Stg-207362-HCPO). We thank A.P. MacCabe (Consejo Superior de Investigaciones
Científicas, Valencia, Spain) for critical reading of the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Galbiati, Francesca
last_name: Galbiati
- first_name: Dola
full_name: Sinha Roy, Dola
last_name: Sinha Roy
- first_name: Sara
full_name: Simonini, Sara
last_name: Simonini
- first_name: Mara
full_name: Cucinotta, Mara
last_name: Cucinotta
- first_name: Luca
full_name: Ceccato, Luca
last_name: Ceccato
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Mária
full_name: Šimášková, Mária
last_name: Šimášková
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Yuri
full_name: Kamiuchi, Yuri
last_name: Kamiuchi
- first_name: Mitsuhiro
full_name: Aida, Mitsuhiro
last_name: Aida
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Rüdiger
full_name: Simon, Rüdiger
last_name: Simon
- first_name: Simona
full_name: Masiero, Simona
last_name: Masiero
- first_name: Lucia
full_name: Colombo, Lucia
last_name: Colombo
citation:
ama: Galbiati F, Sinha Roy D, Simonini S, et al. An integrative model of the control
of ovule primordia formation. The Plant journal for cell and molecular biology.
2013;76(3):446-455. doi:10.1111/tpj.12309
apa: Galbiati, F., Sinha Roy, D., Simonini, S., Cucinotta, M., Ceccato, L., Cuesta,
C., … Colombo, L. (2013). An integrative model of the control of ovule primordia
formation. The Plant Journal for Cell and Molecular Biology. Wiley-Blackwell.
https://doi.org/10.1111/tpj.12309
chicago: Galbiati, Francesca, Dola Sinha Roy, Sara Simonini, Mara Cucinotta, Luca
Ceccato, Candela Cuesta, Mária Šimášková, et al. “An Integrative Model of the
Control of Ovule Primordia Formation.” The Plant Journal for Cell and Molecular
Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/tpj.12309.
ieee: F. Galbiati et al., “An integrative model of the control of ovule primordia
formation,” The Plant journal for cell and molecular biology, vol. 76,
no. 3. Wiley-Blackwell, pp. 446–455, 2013.
ista: Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L, Cuesta C, Šimášková
M, Benková E, Kamiuchi Y, Aida M, Weijers D, Simon R, Masiero S, Colombo L. 2013.
An integrative model of the control of ovule primordia formation. The Plant journal
for cell and molecular biology. 76(3), 446–455.
mla: Galbiati, Francesca, et al. “An Integrative Model of the Control of Ovule Primordia
Formation.” The Plant Journal for Cell and Molecular Biology, vol. 76,
no. 3, Wiley-Blackwell, 2013, pp. 446–55, doi:10.1111/tpj.12309.
short: F. Galbiati, D. Sinha Roy, S. Simonini, M. Cucinotta, L. Ceccato, C. Cuesta,
M. Šimášková, E. Benková, Y. Kamiuchi, M. Aida, D. Weijers, R. Simon, S. Masiero,
L. Colombo, The Plant Journal for Cell and Molecular Biology 76 (2013) 446–455.
date_created: 2018-12-11T11:48:44Z
date_published: 2013-09-19T00:00:00Z
date_updated: 2022-03-21T07:17:26Z
day: '19'
doi: 10.1111/tpj.12309
extern: '1'
external_id:
pmid:
- '23941199'
intvolume: ' 76'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 446 - 455
pmid: 1
publication: The Plant journal for cell and molecular biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6818'
quality_controlled: '1'
scopus_import: '1'
status: public
title: An integrative model of the control of ovule primordia formation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2013'
...
---
_id: '831'
abstract:
- lang: eng
text: In Arabidopsis, lateral roots originate from pericycle cells deep within the
primary root. New lateral root primordia (LRP) have to emerge through several
overlaying tissues. Here, we report that auxin produced in new LRP is transported
towards the outer tissues where it triggers cell separation by inducing both the
auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two
cell files overlaying new LRP. To understand how this striking pattern of LAX3
expression is regulated, we developed a mathematical model that captures the network
regulating its expression and auxin transport within realistic three-dimensional
cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression
to be robust to natural variations in root tissue geometry, an efflux carrier
is required--later identified to be PIN3. To prevent LAX3 from being transiently
expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively,
which we later demonstrated to be the case. Our study exemplifies how mathematical
models can be used to direct experiments to elucidate complex developmental processes.
acknowledgement: This work was supported by an FEBS Long‐Term Fellowship (BP), an
Intra‐European Fellowship for Career Development under the 7th framework of the
European Commission (IEF‐2008‐220506 to BP), an EMBO Long‐Term Fellowship (BP),
an European Reintegration Grant under the 7th framework of the European Commission
(ERG‐2010‐276662 to BP) and the Swedish Research Council (VR 621‐2010‐5720 to IS,
GS and KL). AMM, APF, AL, LRB, SP, NM, DMW, MO, JRK and MJB acknowledge the support
of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering
and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative
Biology (CPIB); BBSRC Professorial Research Fellowship funding to DMW and MJB; Belgian
Scientific policy (BELSPO contract MARS) to TB and MJB. We thank Bert de Rybel for
his help in Multisite Gateway cloning.
author:
- first_name: Benjamin
full_name: Péret, Benjamin
last_name: Péret
- first_name: Alistair
full_name: Middleton, Alistair M
last_name: Middleton
- first_name: Andrew
full_name: French, Andrew P
last_name: French
- first_name: Antoine
full_name: Larrieu, Antoine
last_name: Larrieu
- first_name: Anthony
full_name: Bishopp, Anthony
last_name: Bishopp
- first_name: Maria
full_name: Njo, Maria
last_name: Njo
- first_name: Darren
full_name: Wells, Darren M
last_name: Wells
- first_name: Silvana
full_name: Porco, Silvana
last_name: Porco
- first_name: Nathan
full_name: Mellor, Nathan
last_name: Mellor
- first_name: Leah
full_name: Band, Leah R
last_name: Band
- first_name: Ilda
full_name: Casimiro, Ilda
last_name: Casimiro
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Ilkka
full_name: Sairanen, Ilkka
last_name: Sairanen
- first_name: Romain
full_name: Mallet, Romain
last_name: Mallet
- first_name: Göran
full_name: Sandberg, Göran
last_name: Sandberg
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- 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: Eric
full_name: Kramer, Eric
last_name: Kramer
- first_name: John
full_name: King, John R
last_name: King
- first_name: Ive
full_name: De Smet, Ive
last_name: De Smet
- first_name: Tony
full_name: Pridmore, Tony
last_name: Pridmore
- first_name: Markus
full_name: Owen, Markus
last_name: Owen
- first_name: Malcolm
full_name: Bennett, Malcolm J
last_name: Bennett
citation:
ama: Péret B, Middleton A, French A, et al. Sequential induction of auxin efflux
and influx carriers regulates lateral root emergence. Molecular Systems Biology.
2013;9. doi:10.1038/msb.2013.43
apa: Péret, B., Middleton, A., French, A., Larrieu, A., Bishopp, A., Njo, M., …
Bennett, M. (2013). Sequential induction of auxin efflux and influx carriers regulates
lateral root emergence. Molecular Systems Biology. Nature Publishing Group.
https://doi.org/10.1038/msb.2013.43
chicago: Péret, Benjamin, Alistair Middleton, Andrew French, Antoine Larrieu, Anthony
Bishopp, Maria Njo, Darren Wells, et al. “Sequential Induction of Auxin Efflux
and Influx Carriers Regulates Lateral Root Emergence.” Molecular Systems Biology.
Nature Publishing Group, 2013. https://doi.org/10.1038/msb.2013.43.
ieee: B. Péret et al., “Sequential induction of auxin efflux and influx carriers
regulates lateral root emergence,” Molecular Systems Biology, vol. 9. Nature
Publishing Group, 2013.
ista: Péret B, Middleton A, French A, Larrieu A, Bishopp A, Njo M, Wells D, Porco
S, Mellor N, Band L, Casimiro I, Kleine Vehn J, Vanneste S, Sairanen I, Mallet
R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King J, De Smet
I, Pridmore T, Owen M, Bennett M. 2013. Sequential induction of auxin efflux and
influx carriers regulates lateral root emergence. Molecular Systems Biology. 9.
mla: Péret, Benjamin, et al. “Sequential Induction of Auxin Efflux and Influx Carriers
Regulates Lateral Root Emergence.” Molecular Systems Biology, vol. 9, Nature
Publishing Group, 2013, doi:10.1038/msb.2013.43.
short: B. Péret, A. Middleton, A. French, A. Larrieu, A. Bishopp, M. Njo, D. Wells,
S. Porco, N. Mellor, L. Band, I. Casimiro, J. Kleine Vehn, S. Vanneste, I. Sairanen,
R. Mallet, G. Sandberg, K. Ljung, T. Beeckman, E. Benková, J. Friml, E. Kramer,
J. King, I. De Smet, T. Pridmore, M. Owen, M. Bennett, Molecular Systems Biology
9 (2013).
date_created: 2018-12-11T11:48:44Z
date_published: 2013-10-22T00:00:00Z
date_updated: 2021-01-12T08:18:03Z
day: '22'
doi: 10.1038/msb.2013.43
extern: 1
intvolume: ' 9'
month: '10'
publication: Molecular Systems Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '6817'
quality_controlled: 0
status: public
title: Sequential induction of auxin efflux and influx carriers regulates lateral
root emergence
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
volume: 9
year: '2013'
...
---
_id: '8461'
abstract:
- lang: eng
text: Solid-state NMR provides insight into protein motion over time scales ranging
from picoseconds to seconds. While in solution state the methodology to measure
protein dynamics is well established, there is currently no such consensus protocol
for measuring dynamics in solids. In this article, we perform a detailed investigation
of measurement protocols for fast motions, i.e. motions ranging from picoseconds
to a few microseconds, which is the range covered by dipolar coupling and relaxation
experiments. We perform a detailed theoretical investigation how dipolar couplings
and relaxation data can provide information about amplitudes and time scales of
local motion. We show that the measurement of dipolar couplings is crucial for
obtaining accurate motional parameters, while systematic errors are found when
only relaxation data are used. Based on this realization, we investigate how the
REDOR experiment can provide such data in a very accurate manner. We identify
that with accurate rf calibration, and explicit consideration of rf field inhomogeneities,
one can obtain highly accurate absolute order parameters. We then perform joint
model-free analyses of 6 relaxation data sets and dipolar couplings, based on
previously existing, as well as new data sets on microcrystalline ubiquitin. We
show that nanosecond motion can be detected primarily in loop regions, and compare
solid-state data to solution-state relaxation and RDC analyses. The protocols
investigated here will serve as a useful basis towards the establishment of a
routine protocol for the characterization of ps–μs motions in proteins by solid-state
NMR.
article_processing_charge: No
article_type: original
author:
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin. Journal of Biomolecular
NMR. 2013;57(3):263-280. doi:10.1007/s10858-013-9787-x'
apa: 'Haller, J. D., & Schanda, P. (2013). Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin. Journal of Biomolecular
NMR. Springer Nature. https://doi.org/10.1007/s10858-013-9787-x'
chicago: 'Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond
Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental
Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular
NMR. Springer Nature, 2013. https://doi.org/10.1007/s10858-013-9787-x.'
ieee: 'J. D. Haller and P. Schanda, “Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin,” Journal of Biomolecular
NMR, vol. 57, no. 3. Springer Nature, pp. 263–280, 2013.'
ista: 'Haller JD, Schanda P. 2013. Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR.
57(3), 263–280.'
mla: 'Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond
Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental
Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular
NMR, vol. 57, no. 3, Springer Nature, 2013, pp. 263–80, doi:10.1007/s10858-013-9787-x.'
short: J.D. Haller, P. Schanda, Journal of Biomolecular NMR 57 (2013) 263–280.
date_created: 2020-09-18T10:09:05Z
date_published: 2013-10-09T00:00:00Z
date_updated: 2021-01-12T08:19:26Z
day: '09'
doi: 10.1007/s10858-013-9787-x
extern: '1'
intvolume: ' 57'
issue: '3'
keyword:
- Spectroscopy
- Biochemistry
language:
- iso: eng
month: '10'
oa_version: None
page: 263-280
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Amplitudes and time scales of picosecond-to-microsecond motion in proteins
studied by solid-state NMR: a critical evaluation of experimental approaches and
application to crystalline ubiquitin'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2013'
...
---
_id: '8462'
abstract:
- lang: eng
text: The transition of proteins from their soluble functional state to amyloid
fibrils and aggregates is associated with the onset of several human diseases.
Protein aggregation often requires some structural reshaping and the subsequent
formation of intermolecular contacts. Therefore, the study of the conformation
of excited protein states and their ability to form oligomers is of primary importance
for understanding the molecular basis of amyloid fibril formation. Here, we investigated
the oligomerization processes that occur along the folding of the amyloidogenic
human protein β2-microglobulin. The combination of real-time two-dimensional NMR
data with real-time small-angle X-ray scattering measurements allowed us to derive
thermodynamic and kinetic information on protein oligomerization of different
conformational states populated along the folding pathways. In particular, we
could demonstrate that a long-lived folding intermediate (I-state) has a higher
propensity to oligomerize compared to the native state. Our data agree well with
a simple five-state kinetic model that involves only monomeric and dimeric species.
The dimers have an elongated shape with the dimerization interface located at
the apical side of β2-microglobulin close to Pro32, the residue that has a trans
conformation in the I-state and a cis conformation in the native (N) state. Our
experimental data suggest that partial unfolding in the apical half of the protein
close to Pro32 leads to an excited state conformation with enhanced propensity
for oligomerization. This excited state becomes more populated in the transient
I-state due to the destabilization of the native conformation by the trans-Pro32
configuration.
article_processing_charge: No
article_type: original
author:
- first_name: E.
full_name: Rennella, E.
last_name: Rennella
- first_name: T.
full_name: Cutuil, T.
last_name: Cutuil
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: I.
full_name: Ayala, I.
last_name: Ayala
- first_name: F.
full_name: Gabel, F.
last_name: Gabel
- first_name: V.
full_name: Forge, V.
last_name: Forge
- first_name: A.
full_name: Corazza, A.
last_name: Corazza
- first_name: G.
full_name: Esposito, G.
last_name: Esposito
- first_name: B.
full_name: Brutscher, B.
last_name: Brutscher
citation:
ama: 'Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding
pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal
of Molecular Biology. 2013;425(15):2722-2736. doi:10.1016/j.jmb.2013.04.028'
apa: 'Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., …
Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin:
Kinetics, thermodynamics, and structure. Journal of Molecular Biology.
Elsevier. https://doi.org/10.1016/j.jmb.2013.04.028'
chicago: 'Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A.
Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways
of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” Journal of Molecular
Biology. Elsevier, 2013. https://doi.org/10.1016/j.jmb.2013.04.028.'
ieee: 'E. Rennella et al., “Oligomeric states along the folding pathways
of β2-microglobulin: Kinetics, thermodynamics, and structure,” Journal of Molecular
Biology, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.'
ista: 'Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito
G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin:
Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15),
2722–2736.'
mla: 'Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin:
Kinetics, Thermodynamics, and Structure.” Journal of Molecular Biology,
vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:10.1016/j.jmb.2013.04.028.'
short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza,
G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736.
date_created: 2020-09-18T10:09:12Z
date_published: 2013-08-09T00:00:00Z
date_updated: 2022-08-25T14:56:24Z
day: '09'
doi: 10.1016/j.jmb.2013.04.028
extern: '1'
intvolume: ' 425'
issue: '15'
keyword:
- Molecular Biology
language:
- iso: eng
month: '08'
oa_version: None
page: 2722-2736
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Oligomeric states along the folding pathways of β2-microglobulin: Kinetics,
thermodynamics, and structure'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 425
year: '2013'
...
---
_id: '899'
abstract:
- lang: eng
text: Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype
relationship, is crucial to many areas of biology. Two aspects of fitness landscapes
are the focus of contemporary studies of molecular evolution. First, the local
shape of the fitness landscape defined by the contribution of individual alleles
to fitness that is independent of all genetic interactions. Second, the global,
multidimensional fitness landscape shape determined by how interactions between
alleles at different loci change each other’s fitness impact, or epistasis. In
explaining the high amino-acid usage (u), we focused on the global shape of the
fitness landscape, ignoring the perturbations at individual sites.
author:
- first_name: Michael
full_name: Breen, Michael S
last_name: Breen
- first_name: Carsten
full_name: Kemena, Carsten
last_name: Kemena
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Cédric
full_name: Notredame, Cédric
last_name: Notredame
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Breen et al. reply.
Nature. 2013;497(7451):E2-E3. doi:10.1038/nature12220
apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2013).
Breen et al. reply. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12220
chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor
Kondrashov. “Breen et Al. Reply.” Nature. Nature Publishing Group, 2013.
https://doi.org/10.1038/nature12220.
ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et
al. reply,” Nature, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3,
2013.
ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al.
reply. Nature. 497(7451), E2–E3.
mla: Breen, Michael, et al. “Breen et Al. Reply.” Nature, vol. 497, no. 7451,
Nature Publishing Group, 2013, pp. E2–3, doi:10.1038/nature12220.
short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013)
E2–E3.
date_created: 2018-12-11T11:49:05Z
date_published: 2013-05-30T00:00:00Z
date_updated: 2021-01-12T08:21:40Z
day: '30'
doi: 10.1038/nature12220
extern: 1
intvolume: ' 497'
issue: '7451'
month: '05'
page: E2 - E3
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6747'
quality_controlled: 0
status: public
title: Breen et al. reply
type: journal_article
volume: 497
year: '2013'
...
---
_id: '9674'
abstract:
- lang: eng
text: The coalescence of nano-crystals during sintering is often found to result
in interesting crystalline structures such as multi-fold twins, and yet the plasticity
mechanism accompanying their formation is unclear. In this work, the sintering
behavior of two unsupported copper nanoparticles initially at room temperature
is investigated by molecular dynamics simulations under the constant-energy ensemble.
The results reveal that once the two nanoparticles are brought into contact, they
often go through drastic structural changes with the inter-particle grain boundary
quickly eliminated, and single- and multi-fold twinning occurs frequently in the
coalesced product. Whereas the formation of single twins is found to be via the
more usual mechanism of emission of Shockley partials on {1 1 1} planes, the formation
of fivefold twins, however, takes place via a novel dislocation-free mechanism
involving a series of shear and rigid-body rotation processes caused by elastic
waves with amplitudes not corresponding to any allowable Burgers vector in the
fcc lattice. Such a lattice-wave, dislocation-free twinning mechanism has never
been reported before.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alfonso H.W.
full_name: Ngan, Alfonso H.W.
last_name: Ngan
citation:
ama: 'Cheng B, Ngan AHW. The crystal structures of sintered copper nanoparticles:
A molecular dynamics study. International Journal of Plasticity. 2013;47:65-79.
doi:10.1016/j.ijplas.2013.01.006'
apa: 'Cheng, B., & Ngan, A. H. W. (2013). The crystal structures of sintered
copper nanoparticles: A molecular dynamics study. International Journal of
Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2013.01.006'
chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “The Crystal Structures of Sintered
Copper Nanoparticles: A Molecular Dynamics Study.” International Journal of
Plasticity. Elsevier, 2013. https://doi.org/10.1016/j.ijplas.2013.01.006.'
ieee: 'B. Cheng and A. H. W. Ngan, “The crystal structures of sintered copper nanoparticles:
A molecular dynamics study,” International Journal of Plasticity, vol.
47. Elsevier, pp. 65–79, 2013.'
ista: 'Cheng B, Ngan AHW. 2013. The crystal structures of sintered copper nanoparticles:
A molecular dynamics study. International Journal of Plasticity. 47, 65–79.'
mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “The Crystal Structures of Sintered
Copper Nanoparticles: A Molecular Dynamics Study.” International Journal of
Plasticity, vol. 47, Elsevier, 2013, pp. 65–79, doi:10.1016/j.ijplas.2013.01.006.'
short: B. Cheng, A.H.W. Ngan, International Journal of Plasticity 47 (2013) 65–79.
date_created: 2021-07-15T14:27:44Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2023-02-23T14:04:30Z
day: '01'
doi: 10.1016/j.ijplas.2013.01.006
extern: '1'
intvolume: ' 47'
language:
- iso: eng
month: '08'
oa_version: None
page: 65-79
publication: International Journal of Plasticity
publication_identifier:
issn:
- 0749-6419
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The crystal structures of sintered copper nanoparticles: A molecular dynamics
study'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 47
year: '2013'
...
---
_id: '9676'
abstract:
- lang: eng
text: Despite its relevance to a range of technological applications including nanocrystalline
material fabrication, the sintering mechanisms of nanoparticles have not been
well understood. It has been recognized that extrapolation from understanding
of macro-particle sintering is unreliable for the nano-particle size regime. In
this work, the sintering behaviour of copper nanoparticles under periodic boundary
conditions at different temperatures and pressures was investigated by Molecular
Dynamics simulations. It was found that smaller particle sizes, higher temperature
and higher external pressure facilitate densification. Through a comparison with
a two-sphere model, the governing mechanisms for many nanoparticles sintered at
low temperature (T⩽900K) were identified to be a variety of plasticity processes
including dislocation, twinning and even amorphization at the contact neck regions,
due to the presence of high stresses.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alfonso H.W.
full_name: Ngan, Alfonso H.W.
last_name: Ngan
citation:
ama: 'Cheng B, Ngan AHW. The sintering and densification behaviour of many copper
nanoparticles: A molecular dynamics study. Computational Materials Science.
2013;74:1-11. doi:10.1016/j.commatsci.2013.03.014'
apa: 'Cheng, B., & Ngan, A. H. W. (2013). The sintering and densification behaviour
of many copper nanoparticles: A molecular dynamics study. Computational Materials
Science. Elsevier. https://doi.org/10.1016/j.commatsci.2013.03.014'
chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “The Sintering and Densification
Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” Computational
Materials Science. Elsevier, 2013. https://doi.org/10.1016/j.commatsci.2013.03.014.'
ieee: 'B. Cheng and A. H. W. Ngan, “The sintering and densification behaviour of
many copper nanoparticles: A molecular dynamics study,” Computational Materials
Science, vol. 74. Elsevier, pp. 1–11, 2013.'
ista: 'Cheng B, Ngan AHW. 2013. The sintering and densification behaviour of many
copper nanoparticles: A molecular dynamics study. Computational Materials Science.
74, 1–11.'
mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “The Sintering and Densification
Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” Computational
Materials Science, vol. 74, Elsevier, 2013, pp. 1–11, doi:10.1016/j.commatsci.2013.03.014.'
short: B. Cheng, A.H.W. Ngan, Computational Materials Science 74 (2013) 1–11.
date_created: 2021-07-16T06:46:38Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2023-02-23T14:04:35Z
day: '01'
doi: 10.1016/j.commatsci.2013.03.014
extern: '1'
intvolume: ' 74'
language:
- iso: eng
month: '06'
oa_version: None
page: 1-11
publication: Computational Materials Science
publication_identifier:
issn:
- 0927-0256
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The sintering and densification behaviour of many copper nanoparticles: A
molecular dynamics study'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 74
year: '2013'
...
---
_id: '971'
abstract:
- lang: eng
text: We study the stability of the normal state in a mesoscopic NSN junction biased
by a constant voltage V with respect to the formation of the superconducting order.
Using the linearized time-dependent Ginzburg-Landau equation, we obtain the temperature
dependence of the instability line, V inst(T), where nucleation of superconductivity
takes place. For sufficiently low biases, a stationary symmetric superconducting
state emerges below the instability line. For higher biases, the normal phase
is destroyed by the formation of a nonstationary bimodal state with two superconducting
nuclei localized near the opposite terminals. The low-temperature and large-voltage
behavior of the instability line is highly sensitive to the details of the inelastic
relaxation mechanism in the wire. Therefore, experimental studies of Vinst(T)
in NSN junctions may be used as an effective tool to access the parameters of
the inelastic relaxation in the normal state.
acknowledgement: We are grateful to M. V. Feigel'man, A. Kamenev, T. M. Klapwijk,
J. P. Pekola, V. V. Ryazanov, J. C. W. Song, and D. Y. Vodolazov for discussions.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Mikhail
full_name: Skvortsov, Mikhail A
last_name: Skvortsov
citation:
ama: Serbyn M, Skvortsov M. Onset of superconductivity in a voltage-biased normal-superconducting-normal
microbridge. Physical Review B - Condensed Matter and Materials Physics.
2013;87(2). doi:10.1103/PhysRevB.87.020501
apa: Serbyn, M., & Skvortsov, M. (2013). Onset of superconductivity in a voltage-biased
normal-superconducting-normal microbridge. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.020501
chicago: Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a
Voltage-Biased Normal-Superconducting-Normal Microbridge.” Physical Review
B - Condensed Matter and Materials Physics. American Physical Society, 2013.
https://doi.org/10.1103/PhysRevB.87.020501.
ieee: M. Serbyn and M. Skvortsov, “Onset of superconductivity in a voltage-biased
normal-superconducting-normal microbridge,” Physical Review B - Condensed Matter
and Materials Physics, vol. 87, no. 2. American Physical Society, 2013.
ista: Serbyn M, Skvortsov M. 2013. Onset of superconductivity in a voltage-biased
normal-superconducting-normal microbridge. Physical Review B - Condensed Matter
and Materials Physics. 87(2).
mla: Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a Voltage-Biased
Normal-Superconducting-Normal Microbridge.” Physical Review B - Condensed Matter
and Materials Physics, vol. 87, no. 2, American Physical Society, 2013, doi:10.1103/PhysRevB.87.020501.
short: M. Serbyn, M. Skvortsov, Physical Review B - Condensed Matter and Materials
Physics 87 (2013).
date_created: 2018-12-11T11:49:28Z
date_published: 2013-01-02T00:00:00Z
date_updated: 2021-01-12T08:22:20Z
day: '02'
doi: 10.1103/PhysRevB.87.020501
extern: 1
intvolume: ' 87'
issue: '2'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1208.6004
month: '01'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6429'
quality_controlled: 0
status: public
title: Onset of superconductivity in a voltage-biased normal-superconducting-normal
microbridge
type: journal_article
volume: 87
year: '2013'
...
---
_id: '972'
abstract:
- lang: eng
text: In topological crystalline insulators (TCIs), topology and crystal symmetry
intertwine to create surface states with distinct characteristics. The breaking
of crystal symmetry in TCIs is predicted to impart mass to the massless Dirac
fermions. Here, we report high-resolution scanning tunneling microscopy studies
of a TCI, Pb1-xSnxSe that reveal the coexistence of zero-mass Dirac fermions protected
by crystal symmetry with massive Dirac fermions consistent with crystal symmetry
breaking. In addition, we show two distinct regimes of the Fermi surface topology
separated by a Van-Hove singularity at the Lifshitz transition point. Our work
paves the way for engineering the Dirac band gap and realizing interaction-driven
topological quantum phenomena in TCIs.
author:
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Chetan
full_name: Dhital, Chetan
last_name: Dhital
- first_name: Madhab
full_name: Neupane, Madhab
last_name: Neupane
- first_name: Suyang
full_name: Xu, Suyang
last_name: Xu
- first_name: Yungjui
full_name: Wang, Yungjui
last_name: Wang
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Md
full_name: Hasan, Md
last_name: Hasan
- first_name: Stephen
full_name: Wilson, Stephen
last_name: Wilson
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Okada Y, Serbyn M, Lin H, et al. Observation of dirac node formation and mass
acquisition in a topological crystalline insulator. Science. 2013;341(6153):1496-1499.
doi:10.1126/science.1239451
apa: Okada, Y., Serbyn, M., Lin, H., Walkup, D., Zhou, W., Dhital, C., … Madhavan,
V. (2013). Observation of dirac node formation and mass acquisition in a topological
crystalline insulator. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1239451
chicago: Okada, Yoshinori, Maksym Serbyn, Hsin Lin, Daniel Walkup, Wenwen Zhou,
Chetan Dhital, Madhab Neupane, et al. “Observation of Dirac Node Formation and
Mass Acquisition in a Topological Crystalline Insulator.” Science. American
Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1239451.
ieee: Y. Okada et al., “Observation of dirac node formation and mass acquisition
in a topological crystalline insulator,” Science, vol. 341, no. 6153. American
Association for the Advancement of Science, pp. 1496–1499, 2013.
ista: Okada Y, Serbyn M, Lin H, Walkup D, Zhou W, Dhital C, Neupane M, Xu S, Wang
Y, Sankar R, Chou F, Bansil A, Hasan M, Wilson S, Fu L, Madhavan V. 2013. Observation
of dirac node formation and mass acquisition in a topological crystalline insulator.
Science. 341(6153), 1496–1499.
mla: Okada, Yoshinori, et al. “Observation of Dirac Node Formation and Mass Acquisition
in a Topological Crystalline Insulator.” Science, vol. 341, no. 6153, American
Association for the Advancement of Science, 2013, pp. 1496–99, doi:10.1126/science.1239451.
short: Y. Okada, M. Serbyn, H. Lin, D. Walkup, W. Zhou, C. Dhital, M. Neupane, S.
Xu, Y. Wang, R. Sankar, F. Chou, A. Bansil, M. Hasan, S. Wilson, L. Fu, V. Madhavan,
Science 341 (2013) 1496–1499.
date_created: 2018-12-11T11:49:29Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:20Z
day: '01'
doi: 10.1126/science.1239451
extern: '1'
external_id:
arxiv:
- '1305.2823'
intvolume: ' 341'
issue: '6153'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1305.2823
month: '01'
oa: 1
oa_version: Preprint
page: 1496 - 1499
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6430'
quality_controlled: '1'
status: public
title: Observation of dirac node formation and mass acquisition in a topological crystalline
insulator
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 341
year: '2013'
...
---
_id: '975'
abstract:
- lang: eng
text: Recent numerical work by Bardarson, Pollmann, and Moore revealed a slow, logarithmic
in time, growth of the entanglement entropy for initial product states in a putative
many-body localized phase. We show that this surprising phenomenon results from
the dephasing due to exponentially small interaction-induced corrections to the
eigenenergies of different states. For weak interactions, we find that the entanglement
entropy grows as ξln (Vt/), where V is the interaction strength, and ξ is the
single-particle localization length. The saturated value of the entanglement entropy
at long times is determined by the participation ratios of the initial state over
the eigenstates of the subsystem. Our work shows that the logarithmic entanglement
growth is a universal phenomenon characteristic of the many-body localized phase
in any number of spatial dimensions, and reveals a broad hierarchy of dephasing
time scales present in such a phase.
acknowledgement: We would like to thank E. Altman and J. Moore for useful comments
on the manuscript. This research was supported in part by Perimeter Institute for
Theoretical Physics. Research at Perimeter Institute is supported by the Government
of Canada through Industry Canada and by the Province of Ontario through the Ministry
of Economic Development & Innovation. Z. P. was supported by DOE Grant No. DE-SC0002140.
The simulations presented in this article were performed on computational resources
supported by the High Performance Computing Center (PICSciE) at Princeton University.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Universal slow growth of entanglement in interacting
strongly disordered systems. Physical Review Letters. 2013;110(26). doi:10.1103/PhysRevLett.110.260601
apa: Serbyn, M., Papić, Z., & Abanin, D. (2013). Universal slow growth of entanglement
in interacting strongly disordered systems. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.110.260601
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Universal Slow Growth
of Entanglement in Interacting Strongly Disordered Systems.” Physical Review
Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.260601.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Universal slow growth of entanglement
in interacting strongly disordered systems,” Physical Review Letters, vol.
110, no. 26. American Physical Society, 2013.
ista: Serbyn M, Papić Z, Abanin D. 2013. Universal slow growth of entanglement in
interacting strongly disordered systems. Physical Review Letters. 110(26).
mla: Serbyn, Maksym, et al. “Universal Slow Growth of Entanglement in Interacting
Strongly Disordered Systems.” Physical Review Letters, vol. 110, no. 26,
American Physical Society, 2013, doi:10.1103/PhysRevLett.110.260601.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 110 (2013).
date_created: 2018-12-11T11:49:29Z
date_published: 2013-06-28T00:00:00Z
date_updated: 2021-01-12T08:22:22Z
day: '28'
doi: 10.1103/PhysRevLett.110.260601
extern: 1
intvolume: ' 110'
issue: '26'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1304.4605
month: '06'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6426'
quality_controlled: 0
status: public
title: Universal slow growth of entanglement in interacting strongly disordered systems
type: journal_article
volume: 110
year: '2013'
...
---
_id: '9749'
abstract:
- lang: eng
text: Cooperative behavior, where one individual incurs a cost to help another,
is a wide spread phenomenon. Here we study direct reciprocity in the context of
the alternating Prisoner's Dilemma. We consider all strategies that can be implemented
by one and two-state automata. We calculate the payoff matrix of all pairwise
encounters in the presence of noise. We explore deterministic selection dynamics
with and without mutation. Using different error rates and payoff values, we observe
convergence to a small number of distinct equilibria. Two of them are uncooperative
strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium
is mixed and represents a cooperative alliance of several strategies, dominated
by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent
has cooperated; it defects once when the opponent has defected, but subsequently
Forgiver attempts to re-establish cooperation even if the opponent has defected
again. Forgiver is not an evolutionarily stable strategy, but the alliance, which
it rules, is asymptotically stable. For a wide range of parameter values the most
commonly observed outcome is convergence to the mixed equilibrium, dominated by
Forgiver. Our results show that although forgiving might incur a short-term loss
it can lead to a long-term gain. Forgiveness facilitates stable cooperation in
the presence of exploitation and noise.
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Zagorsky, Benjamin
last_name: Zagorsky
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- 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: Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating
prisoner’s dilemma . 2013. doi:10.1371/journal.pone.0080814.s001
apa: Zagorsky, B., Reiter, J., Chatterjee, K., & Nowak, M. (2013). Forgiver
triumphs in alternating prisoner’s dilemma . Public Library of Science. https://doi.org/10.1371/journal.pone.0080814.s001
chicago: Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin
Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library
of Science, 2013. https://doi.org/10.1371/journal.pone.0080814.s001.
ieee: B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in
alternating prisoner’s dilemma .” Public Library of Science, 2013.
ista: Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating
prisoner’s dilemma , Public Library of Science, 10.1371/journal.pone.0080814.s001.
mla: Zagorsky, Benjamin, et al. Forgiver Triumphs in Alternating Prisoner’s Dilemma
. Public Library of Science, 2013, doi:10.1371/journal.pone.0080814.s001.
short: B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013).
date_created: 2021-07-28T15:45:07Z
date_published: 2013-12-12T00:00:00Z
date_updated: 2023-02-23T10:34:39Z
day: '12'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0080814.s001
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2247'
relation: used_in_publication
status: public
status: public
title: 'Forgiver triumphs in alternating prisoner''s dilemma '
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '2944'
abstract:
- lang: eng
text: 'We propose a two-step procedure for estimating multiple migration rates in
an approximate Bayesian computation (ABC) framework, accounting for global nuisance
parameters. The approach is not limited to migration, but generally of interest
for inference problems with multiple parameters and a modular structure (e.g.
independent sets of demes or loci). We condition on a known, but complex demographic
model of a spatially subdivided population, motivated by the reintroduction of
Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters
ancestral mutation rate and male mating skew have been estimated for the whole
population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step,
we estimate in this study the migration rates independently for clusters of demes
putatively connected by migration. For large clusters (many migration rates),
ABC faces the problem of too many summary statistics. We therefore assess by simulation
if estimation per pair of demes is a valid alternative. We find that the trade-off
between reduced dimensionality for the pairwise estimation on the one hand and
lower accuracy due to the assumption of pairwise independence on the other depends
on the number of migration rates to be inferred: the accuracy of the pairwise
approach increases with the number of parameters, relative to the joint estimation
approach. To distinguish between low and zero migration, we perform ABC-type model
comparison between a model with migration and one without. Applying the approach
to microsatellite data from Alpine ibex, we find no evidence for substantial gene
flow via migration, except for one pair of demes in one direction.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: This study has made use of the computational resources provided by
IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk).
The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk).
S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation,
St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in
the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
citation:
ama: 'Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for
modular inference problems with many parameters: the example of migration rates.
. Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165'
apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165'
chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate
Bayesian Computation for Modular Inference Problems with Many Parameters: The
Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013.
https://doi.org/10.1111/mec.12165.'
ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002,
2013.'
ista: 'Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. . Molecular Ecology. 22(4), 987–1002.'
mla: 'Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference
Problems with Many Parameters: The Example of Migration Rates. .” Molecular
Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.'
short: S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.
date_created: 2018-12-11T12:00:28Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2023-02-23T14:07:19Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/mec.12165
intvolume: ' 22'
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 987 - 1002
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3788'
quality_controlled: '1'
related_material:
record:
- id: '9758'
relation: research_data
status: public
scopus_import: 1
status: public
title: 'Approximate Bayesian computation for modular inference problems with many
parameters: the example of migration rates. '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '894'
abstract:
- lang: eng
text: 'Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene
is correlated with melanin color variation in many birds. Feral pigeons (Columba
livia) show two major melanin-based colorations: a red coloration due to pheomelanic
pigment and a black coloration due to eumelanic pigment. Furthermore, within each
color type, feral pigeons display continuous variation in the amount of melanin
pigment present in the feathers, with individuals varying from pure white to a
full dark melanic color. Coloration is highly heritable and it has been suggested
that it is under natural or sexual selection, or both. Our objective was to investigate
whether MC1R allelic variants are associated with plumage color in feral pigeons.
Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying
both in the type, eumelanin or pheomelanin, and the amount of melanin in their
feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution
but none of them were associated with a plumage type. It remains possible that
non-synonymous substitutions that influence coloration are present in the short
MC1R fragment that we did not sequence but this seems unlikely because we analyzed
the entire functionally important region of the gene. Conclusions: Our results
show that color differences among feral pigeons are probably not attributable
to amino acid variation at the MC1R locus. Therefore, variation in regulatory
regions of MC1R or variation in other genes may be responsible for the color polymorphism
of feral pigeons.'
acknowledgement: Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329.
Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute)
003803 and EMBO 003691 EUI-EURYIP-2011-4320.
author:
- first_name: Romain
full_name: Derelle, Romain
last_name: Derelle
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir
full_name: Arkhipov, Vladimir
last_name: Arkhipov
- first_name: Hélène
full_name: Corbel, Hélène
last_name: Corbel
- first_name: Adrien
full_name: Frantz, Adrien
last_name: Frantz
- first_name: Julien
full_name: Gasparini, Julien
last_name: Gasparini
- first_name: Lisa
full_name: Jacquin, Lisa
last_name: Jacquin
- first_name: Gwenaël
full_name: Jacob, Gwenaël
last_name: Jacob
- first_name: Sophie
full_name: Thibault, Sophie
last_name: Thibault
- first_name: Emmanuelle
full_name: Baudry, Emmanuelle
last_name: Baudry
citation:
ama: Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons
(Columba livia) are not attributable to sequence variation in the coding region
of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 2013;6(1).
doi:10.1186/1756-0500-6-310
apa: Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini,
J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia)
are not attributable to sequence variation in the coding region of the melanocortin-1
receptor gene MC1R. BMC Research Notes. BioMed Central. https://doi.org/10.1186/1756-0500-6-310
chicago: Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien
Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle
Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable
to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene
MC1R.” BMC Research Notes. BioMed Central, 2013. https://doi.org/10.1186/1756-0500-6-310.
ieee: R. Derelle et al., “Color differences among feral pigeons (Columba
livia) are not attributable to sequence variation in the coding region of the
melanocortin-1 receptor gene MC1R,” BMC Research Notes, vol. 6, no. 1.
BioMed Central, 2013.
ista: Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin
L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons
(Columba livia) are not attributable to sequence variation in the coding region
of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1).
mla: Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia)
Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1
Receptor Gene MC1R.” BMC Research Notes, vol. 6, no. 1, BioMed Central,
2013, doi:10.1186/1756-0500-6-310.
short: R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini,
L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013).
date_created: 2018-12-11T11:49:04Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:25Z
day: '01'
doi: 10.1186/1756-0500-6-310
extern: '1'
intvolume: ' 6'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: BMC Research Notes
publication_status: published
publisher: BioMed Central
publist_id: '6752'
status: public
title: Color differences among feral pigeons (Columba livia) are not attributable
to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2013'
...
---
_id: '9055'
abstract:
- lang: eng
text: Spontaneous formation of colonies of bacteria or flocks of birds are examples
of self-organization in active living matter. Here, we demonstrate a form of self-organization
from nonequilibrium driving forces in a suspension of synthetic photoactivated
colloidal particles. They lead to two-dimensional "living crystals," which form,
break, explode, and re-form elsewhere. The dynamic assembly results from a competition
between self-propulsion of particles and an attractive interaction induced respectively
by osmotic and phoretic effects and activated by light. We measured a transition
from normal to giant-number fluctuations. Our experiments are quantitatively described
by simple numerical simulations. We show that the existence of the living crystals
is intrinsically related to the out-of-equilibrium collisions of the self-propelled
particles.
article_processing_charge: No
article_type: original
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: S.
full_name: Sacanna, S.
last_name: Sacanna
- first_name: A. P.
full_name: Steinberg, A. P.
last_name: Steinberg
- first_name: D. J.
full_name: Pine, D. J.
last_name: Pine
- first_name: P. M.
full_name: Chaikin, P. M.
last_name: Chaikin
citation:
ama: Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. Living crystals of
light-activated colloidal surfers. Science. 2013;339(6122):936-940. doi:10.1126/science.1230020
apa: Palacci, J. A., Sacanna, S., Steinberg, A. P., Pine, D. J., & Chaikin,
P. M. (2013). Living crystals of light-activated colloidal surfers. Science.
American Association for the Advancement of Science . https://doi.org/10.1126/science.1230020
chicago: Palacci, Jérémie A, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M.
Chaikin. “Living Crystals of Light-Activated Colloidal Surfers.” Science.
American Association for the Advancement of Science , 2013. https://doi.org/10.1126/science.1230020.
ieee: J. A. Palacci, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin,
“Living crystals of light-activated colloidal surfers,” Science, vol. 339,
no. 6122. American Association for the Advancement of Science , pp. 936–940, 2013.
ista: Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. 2013. Living crystals
of light-activated colloidal surfers. Science. 339(6122), 936–940.
mla: Palacci, Jérémie A., et al. “Living Crystals of Light-Activated Colloidal Surfers.”
Science, vol. 339, no. 6122, American Association for the Advancement of
Science , 2013, pp. 936–40, doi:10.1126/science.1230020.
short: J.A. Palacci, S. Sacanna, A.P. Steinberg, D.J. Pine, P.M. Chaikin, Science
339 (2013) 936–940.
date_created: 2021-02-01T14:37:29Z
date_published: 2013-02-22T00:00:00Z
date_updated: 2022-08-25T14:57:43Z
day: '22'
doi: 10.1126/science.1230020
extern: '1'
external_id:
pmid:
- '23371555'
intvolume: ' 339'
issue: '6122'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '02'
oa_version: None
page: 936-940
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: 'American Association for the Advancement of Science '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Living crystals of light-activated colloidal surfers
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2013'
...
---
_id: '905'
abstract:
- lang: eng
text: A survey of avifauna was carried out in the Mys Shmidta area, north Chukotka,
Russia from 8 June to 12 July 2011. A total of 90 species was recorded in the
area, which together with literature data made a final list of 104 species. For
several species this area is beyond the northern, north-eastern or north-western
limits of their known distribution. We collected new data for 19 globally or locally
threatened species. Tundra Swan Cygnus columbianus, Emperor Goose Anser canagica,
American Golden Plover Pluvialis dominica, Western Sandpiper Calidris mauri, Semipalmated
Sandpiper C. pusilla, Northern House Martin Delichon urbica and Barn Swallow Hirundo
rustica were all confirmed to be breeding. Breeding of Brent Goose Branta bernicla
nigricans, Spectacled Eider Somateria fischeri and Steller's Eider Polysticta
stelleri was judged to be 'very likely'. There was no evidence for breeding of
Ross's Gull Rhodostethia rosea despite several records. Two Eurasian Dotterels
Eudromias morinellus were recorded displaying for the first time in the area,
but the status of the species is unclear. The area is important for Snowy Owl
Nyctea scandiaca, and as moulting grounds for Emperor Goose. Canada Goose Branta
canadensis, Baikal Teal Anas formosa, Bar-tailed Godwit Limosa lapponica, Slaty-backed
Gull Larus schistisagus, Thayer's Gull L. thayeri, Black-headed Gull L. ridibundus,
White-tailed Eagle Haliaeetus albicilla, Steller's Sea Eagle H. pelagicus, Osprey
Pandion haliaetus, Arctic Warbler Phylloscopus borealis and House Sparrow Passer
domesticus are more likely to be rare vagrants or migrants. An observation of
a Pine Siskin Carduelis pinus is the first record for Eurasia.
acknowledgement: We thank Natalya Kveten and Oksana Makarova, heads of administrations
of Mys Shmidta and Ryrkaypiy for hospitality and for help with organising our excursions.
Warm thanks too to Pavel Tomkovich for useful comments on local birds and ornithological
literature. We are very grateful to The David and Lucile Packard Foundation for
the support to Birds Russia’s Spoon-billed Sandpiper conservation programme in 2011
and to Evgeny Syroechkovsky Jr, the leader of the Spoon-billed Sandpiper conservation
team in Russia.
author:
- first_name: Vladimir
full_name: Arkhipov, Vladimir Y
last_name: Arkhipov
- first_name: T
full_name: Noah T
last_name: Noah
- first_name: Steffen
full_name: Koschkar, Steffen
last_name: Koschkar
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Arkhipov V, Noah T, Koschkar S, Kondrashov F. Birds of Mys Shmidta, north Chukotka,
Russia. Forktail. 2013;(29):25-30.
apa: Arkhipov, V., Noah, T., Koschkar, S., & Kondrashov, F. (2013). Birds of
Mys Shmidta, north Chukotka, Russia. Forktail. Oriental Bird Club.
chicago: Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds
of Mys Shmidta, North Chukotka, Russia.” Forktail. Oriental Bird Club,
2013.
ieee: V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta,
north Chukotka, Russia,” Forktail, no. 29. Oriental Bird Club, pp. 25–30,
2013.
ista: Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta,
north Chukotka, Russia. Forktail. (29), 25–30.
mla: Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.”
Forktail, no. 29, Oriental Bird Club, 2013, pp. 25–30.
short: V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30.
date_created: 2018-12-11T11:49:07Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T08:21:48Z
day: '01'
extern: 1
issue: '29'
main_file_link:
- open_access: '1'
url: http://orientalbirdclub.org/forktail29/
month: '09'
oa: 1
page: 25 - 30
publication: Forktail
publication_status: published
publisher: Oriental Bird Club
publist_id: '6741'
quality_controlled: 0
status: public
title: Birds of Mys Shmidta, north Chukotka, Russia
type: journal_article
year: '2013'
...
---
_id: '9153'
abstract:
- lang: eng
text: Internal tide driven mixing plays a key role in sustaining the deep ocean
stratification and meridional overturning circulation. Internal tides can be generated
by topographic horizontal scales ranging from hundreds of meters to tens of kilometers.
State of the art topographic products barely resolve scales smaller than ∼10 km
in the deep ocean. On these scales abyssal hills dominate ocean floor roughness.
The impact of abyssal hill roughness on internal‐tide generation is evaluated
in this study. The conversion of M2 barotropic to baroclinic tidal energy is calculated
based on linear wave theory both in real and spectral space using the Shuttle
Radar Topography Mission SRTM30_PLUS bathymetric product at 1/120° resolution
with and without the addition of synthetic abyssal hill roughness. Internal tide
generation by abyssal hills integrates to 0.1 TW globally or 0.03 TW when the
energy flux is empirically corrected for supercritical slope (i.e., ∼10% of the
energy flux due to larger topographic scales resolved in standard products in
both cases). The abyssal hill driven energy conversion is dominated by mid‐ocean
ridges, where abyssal hill roughness is large. Focusing on two regions located
over the Mid‐Atlantic Ridge and the East Pacific Rise, it is shown that regionally
linear theory predicts an increase of the energy flux due to abyssal hills of
up to 100% or 60% when an empirical correction for supercritical slopes is attempted.
Therefore, abyssal hills, unresolved in state of the art topographic products,
can have a strong impact on internal tide generation, especially over mid‐ocean
ridges.
article_processing_charge: No
article_type: original
author:
- first_name: Angélique
full_name: Melet, Angélique
last_name: Melet
- first_name: Maxim
full_name: Nikurashin, Maxim
last_name: Nikurashin
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: S.
full_name: Falahat, S.
last_name: Falahat
- first_name: Jonas
full_name: Nycander, Jonas
last_name: Nycander
- first_name: Patrick G.
full_name: Timko, Patrick G.
last_name: Timko
- first_name: Brian K.
full_name: Arbic, Brian K.
last_name: Arbic
- first_name: John A.
full_name: Goff, John A.
last_name: Goff
citation:
ama: 'Melet A, Nikurashin M, Muller CJ, et al. Internal tide generation by abyssal
hills using analytical theory. Journal of Geophysical Research: Oceans.
2013;118(11):6303-6318. doi:10.1002/2013jc009212'
apa: 'Melet, A., Nikurashin, M., Muller, C. J., Falahat, S., Nycander, J., Timko,
P. G., … Goff, J. A. (2013). Internal tide generation by abyssal hills using analytical
theory. Journal of Geophysical Research: Oceans. American Geophysical Union.
https://doi.org/10.1002/2013jc009212'
chicago: 'Melet, Angélique, Maxim Nikurashin, Caroline J Muller, S. Falahat, Jonas
Nycander, Patrick G. Timko, Brian K. Arbic, and John A. Goff. “Internal Tide Generation
by Abyssal Hills Using Analytical Theory.” Journal of Geophysical Research:
Oceans. American Geophysical Union, 2013. https://doi.org/10.1002/2013jc009212.'
ieee: 'A. Melet et al., “Internal tide generation by abyssal hills using
analytical theory,” Journal of Geophysical Research: Oceans, vol. 118,
no. 11. American Geophysical Union, pp. 6303–6318, 2013.'
ista: 'Melet A, Nikurashin M, Muller CJ, Falahat S, Nycander J, Timko PG, Arbic
BK, Goff JA. 2013. Internal tide generation by abyssal hills using analytical
theory. Journal of Geophysical Research: Oceans. 118(11), 6303–6318.'
mla: 'Melet, Angélique, et al. “Internal Tide Generation by Abyssal Hills Using
Analytical Theory.” Journal of Geophysical Research: Oceans, vol. 118,
no. 11, American Geophysical Union, 2013, pp. 6303–18, doi:10.1002/2013jc009212.'
short: 'A. Melet, M. Nikurashin, C.J. Muller, S. Falahat, J. Nycander, P.G. Timko,
B.K. Arbic, J.A. Goff, Journal of Geophysical Research: Oceans 118 (2013) 6303–6318.'
date_created: 2021-02-15T15:11:39Z
date_published: 2013-11-07T00:00:00Z
date_updated: 2022-01-24T13:46:15Z
day: '07'
doi: 10.1002/2013jc009212
extern: '1'
intvolume: ' 118'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2013JC009212
month: '11'
oa: 1
oa_version: Published Version
page: 6303-6318
publication: 'Journal of Geophysical Research: Oceans'
publication_identifier:
issn:
- 2169-9275
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
status: public
title: Internal tide generation by abyssal hills using analytical theory
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 118
year: '2013'
...
---
_id: '9154'
abstract:
- lang: eng
text: "In this study the response of tropical precipitation extremes to warming
in organized convection is examined using a cloud-resolving model. Vertical shear
is imposed to organize the convection into squall lines. Earlier studies show
that in disorganized convection, the fractional increase of precipitation extremes
is similar to that of surface water vapor, which is substantially smaller than
the increase in column water vapor. It has been suggested that organized convection
could lead to stronger amplifications.\r\nRegardless of the strength of the shear,
amplifications of precipitation extremes in the cloud-resolving simulations are
comparable to those of surface water vapor and are substantially less than increases
in column water vapor. The results without shear and with critical shear, for
which the squall lines are perpendicular to the shear, are surprisingly similar
with a fractional rate of increase of precipitation extremes slightly smaller
than that of surface water vapor. Interestingly, the dependence on shear is nonmonotonic,
and stronger supercritical shear yields larger rates, close to or slightly larger
than surface humidity.\r\nA scaling is used to evaluate the thermodynamic and
dynamic contributions to precipitation extreme changes. To first order, they are
dominated by the thermodynamic component, which has the same magnitude for all
shears, close to the change in surface water vapor. The dynamic contribution plays
a secondary role and tends to weaken extremes without shear and with critical
shear, while it strengthens extremes with supercritical shear. These different
dynamic contributions for different shears are due to different responses of convective
mass fluxes in individual updrafts to warming."
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: Muller CJ. Impact of convective organization on the response of tropical precipitation
extremes to warming. Journal of Climate. 2013;26(14):5028-5043. doi:10.1175/jcli-d-12-00655.1
apa: Muller, C. J. (2013). Impact of convective organization on the response of
tropical precipitation extremes to warming. Journal of Climate. American
Meteorological Society. https://doi.org/10.1175/jcli-d-12-00655.1
chicago: Muller, Caroline J. “Impact of Convective Organization on the Response
of Tropical Precipitation Extremes to Warming.” Journal of Climate. American
Meteorological Society, 2013. https://doi.org/10.1175/jcli-d-12-00655.1.
ieee: C. J. Muller, “Impact of convective organization on the response of tropical
precipitation extremes to warming,” Journal of Climate, vol. 26, no. 14.
American Meteorological Society, pp. 5028–5043, 2013.
ista: Muller CJ. 2013. Impact of convective organization on the response of tropical
precipitation extremes to warming. Journal of Climate. 26(14), 5028–5043.
mla: Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical
Precipitation Extremes to Warming.” Journal of Climate, vol. 26, no. 14,
American Meteorological Society, 2013, pp. 5028–43, doi:10.1175/jcli-d-12-00655.1.
short: C.J. Muller, Journal of Climate 26 (2013) 5028–5043.
date_created: 2021-02-15T15:26:39Z
date_published: 2013-07-15T00:00:00Z
date_updated: 2022-01-24T13:46:41Z
day: '15'
doi: 10.1175/jcli-d-12-00655.1
extern: '1'
intvolume: ' 26'
issue: '14'
keyword:
- Atmospheric Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1175/JCLI-D-12-00655.1
month: '07'
oa: 1
oa_version: Published Version
page: 5028-5043
publication: Journal of Climate
publication_identifier:
issn:
- 0894-8755
- 1520-0442
publication_status: published
publisher: American Meteorological Society
quality_controlled: '1'
status: public
title: Impact of convective organization on the response of tropical precipitation
extremes to warming
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 26
year: '2013'
...
---
_id: '9167'
abstract:
- lang: eng
text: We introduce a self-propelled colloidal hematite docker that can be steered
to a small particle cargo many times its size, dock, transport the cargo to a
remote location, and then release it. The self-propulsion and docking are reversible
and activated by visible light. The docker can be steered either by a weak uniform
magnetic field or by nanoscale tracks in a textured substrate. The light-activated
motion and docking originate from osmotic/phoretic particle transport in a concentration
gradient of fuel, hydrogen peroxide, induced by the photocatalytic activity of
the hematite. The docking mechanism is versatile and can be applied to various
materials and shapes. The hematite dockers are simple single-component particles
and are synthesized in bulk quantities. This system opens up new possibilities
for designing complex micrometer-size factories as well as new biomimetic systems.
article_processing_charge: No
article_type: original
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Stefano
full_name: Sacanna, Stefano
last_name: Sacanna
- first_name: Adrian
full_name: Vatchinsky, Adrian
last_name: Vatchinsky
- first_name: Paul M.
full_name: Chaikin, Paul M.
last_name: Chaikin
- first_name: David J.
full_name: Pine, David J.
last_name: Pine
citation:
ama: Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. Photoactivated colloidal
dockers for cargo transportation. Journal of the American Chemical Society.
2013;135(43):15978-15981. doi:10.1021/ja406090s
apa: Palacci, J. A., Sacanna, S., Vatchinsky, A., Chaikin, P. M., & Pine, D.
J. (2013). Photoactivated colloidal dockers for cargo transportation. Journal
of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja406090s
chicago: Palacci, Jérémie A, Stefano Sacanna, Adrian Vatchinsky, Paul M. Chaikin,
and David J. Pine. “Photoactivated Colloidal Dockers for Cargo Transportation.”
Journal of the American Chemical Society. American Chemical Society, 2013.
https://doi.org/10.1021/ja406090s.
ieee: J. A. Palacci, S. Sacanna, A. Vatchinsky, P. M. Chaikin, and D. J. Pine, “Photoactivated
colloidal dockers for cargo transportation,” Journal of the American Chemical
Society, vol. 135, no. 43. American Chemical Society, pp. 15978–15981, 2013.
ista: Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. 2013. Photoactivated
colloidal dockers for cargo transportation. Journal of the American Chemical Society.
135(43), 15978–15981.
mla: Palacci, Jérémie A., et al. “Photoactivated Colloidal Dockers for Cargo Transportation.”
Journal of the American Chemical Society, vol. 135, no. 43, American Chemical
Society, 2013, pp. 15978–81, doi:10.1021/ja406090s.
short: J.A. Palacci, S. Sacanna, A. Vatchinsky, P.M. Chaikin, D.J. Pine, Journal
of the American Chemical Society 135 (2013) 15978–15981.
date_created: 2021-02-18T14:31:26Z
date_published: 2013-10-30T00:00:00Z
date_updated: 2021-02-22T10:10:41Z
day: '30'
doi: 10.1021/ja406090s
extern: '1'
external_id:
arxiv:
- '1310.5724'
pmid:
- '24131488'
intvolume: ' 135'
issue: '43'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.5724
month: '10'
oa: 1
oa_version: Preprint
page: 15978-15981
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- '15205126'
issn:
- '00027863'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Photoactivated colloidal dockers for cargo transportation
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 135
year: '2013'
...
---
_id: '921'
abstract:
- lang: eng
text: Recent experiments have shown that spreading epithelial sheets exhibit a long-range
coordination of motility forces that leads to a buildup of tension in the tissue,
which may enhance cell division and the speed of wound healing. Furthermore, the
edges of these epithelial sheets commonly show finger-like protrusions whereas
the bulk often displays spontaneous swirls of motile cells. To explain these experimental
observations, we propose a simple flocking-type mechanism, in which cells tend
to align their motility forceswith their velocity. Implementing this idea in amechanical
tissue simulation, the proposed model gives rise to efficient spreading and can
explain the experimentally observed long-range alignment of motility forces in
highly disordered patterns, as well as the buildup of tensile stress throughout
the tissue. Our model also qualitatively reproduces the dependence of swirl size
and swirl velocity on cell density reported in experiments and exhibits an undulation
instability at the edge of the spreading tissue commonly observed in vivo. Finally,
we study the dependence of colony spreading speed on important physical and biological
parameters and derive simple scaling relations that show that coordination of
motility forces leads to an improvement of the wound healing process for realistic
tissue parameters.
acknowledgement: "This work was supported by National Science Foundation (NSF) Grant
DMS-1068869 and by the NSF Center for Theoretical Biological Physics (Grant NSF
PHY-0822283).\r\nWe acknowledge useful discussions with Eshel Ben-Jacob and Assaf
Zaritsky. "
article_processing_charge: No
author:
- first_name: Markus
full_name: Basan, Markus
last_name: Basan
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Wouter
full_name: Rappel, Wouter
last_name: Rappel
- first_name: Herbert
full_name: Levine, Herbert
last_name: Levine
citation:
ama: Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. Alignment of cellular motility
forces with tissue flow as a mechanism for efficient wound healing. PNAS.
2013;110(7):2452-2459. doi:10.1073/pnas.1219937110
apa: Basan, M., Elgeti, J., Hannezo, E. B., Rappel, W., & Levine, H. (2013).
Alignment of cellular motility forces with tissue flow as a mechanism for efficient
wound healing. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1219937110
chicago: Basan, Markus, Jens Elgeti, Edouard B Hannezo, Wouter Rappel, and Herbert
Levine. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism
for Efficient Wound Healing.” PNAS. National Academy of Sciences, 2013.
https://doi.org/10.1073/pnas.1219937110.
ieee: M. Basan, J. Elgeti, E. B. Hannezo, W. Rappel, and H. Levine, “Alignment of
cellular motility forces with tissue flow as a mechanism for efficient wound healing,”
PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2452–2459, 2013.
ista: Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. 2013. Alignment of cellular
motility forces with tissue flow as a mechanism for efficient wound healing. PNAS.
110(7), 2452–2459.
mla: Basan, Markus, et al. “Alignment of Cellular Motility Forces with Tissue Flow
as a Mechanism for Efficient Wound Healing.” PNAS, vol. 110, no. 7, National
Academy of Sciences, 2013, pp. 2452–59, doi:10.1073/pnas.1219937110.
short: M. Basan, J. Elgeti, E.B. Hannezo, W. Rappel, H. Levine, PNAS 110 (2013)
2452–2459.
date_created: 2018-12-11T11:49:12Z
date_published: 2013-02-12T00:00:00Z
date_updated: 2021-01-12T08:21:55Z
day: '12'
doi: 10.1073/pnas.1219937110
extern: '1'
intvolume: ' 110'
issue: '7'
language:
- iso: eng
month: '02'
oa_version: None
page: 2452 - 2459
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6518'
status: public
title: Alignment of cellular motility forces with tissue flow as a mechanism for efficient
wound healing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '9459'
abstract:
- lang: eng
text: Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation
of transposable elements, but the reason for this is unknown. How DDM1 interacts
with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM),
which is thought to mediate plant asymmetric methylation through DRM enzymes,
is also unclear. Here, we show that most asymmetric methylation is facilitated
by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find
that heterochromatic sequences preferentially require DDM1 for DNA methylation
and that this preference depends on linker histone H1. RdDM is instead inhibited
by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together,
DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress
transposition and regulate the methylation and expression of genes. Our results
indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin
to allow stable silencing of transposable elements in cooperation with the RdDM
pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Devin
full_name: Coleman-Derr, Devin
last_name: Coleman-Derr
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Ka
full_name: Thao, Ka
last_name: Thao
- first_name: Stacey L.
full_name: Harmer, Stacey L.
last_name: Harmer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1
allows DNA methyltransferases to access H1-containing heterochromatin. Cell.
2013;153(1):193-205. doi:10.1016/j.cell.2013.02.033
apa: Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L.,
Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows
DNA methyltransferases to access H1-containing heterochromatin. Cell. Elsevier.
https://doi.org/10.1016/j.cell.2013.02.033
chicago: Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor
Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis
Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing
Heterochromatin.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.02.033.
ieee: A. Zemach et al., “The Arabidopsis nucleosome remodeler DDM1 allows
DNA methyltransferases to access H1-containing heterochromatin,” Cell,
vol. 153, no. 1. Elsevier, pp. 193–205, 2013.
ista: Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer
SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases
to access H1-containing heterochromatin. Cell. 153(1), 193–205.
mla: Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA
Methyltransferases to Access H1-Containing Heterochromatin.” Cell, vol.
153, no. 1, Elsevier, 2013, pp. 193–205, doi:10.1016/j.cell.2013.02.033.
short: A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K.
Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.
date_created: 2021-06-04T12:23:28Z
date_published: 2013-03-28T00:00:00Z
date_updated: 2021-12-14T08:25:35Z
day: '28'
department:
- _id: DaZi
doi: 10.1016/j.cell.2013.02.033
extern: '1'
external_id:
pmid:
- '23540698'
intvolume: ' 153'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.02.033
month: '03'
oa: 1
oa_version: Published Version
page: 193-205
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to
access H1-containing heterochromatin
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 153
year: '2013'
...
---
_id: '9481'
abstract:
- lang: eng
text: Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo,
exhibits extensive localized DNA demethylation on maternally inherited chromosomes.
Demethylation mediates parent-of-origin–specific (imprinted) gene expression but
is apparently unnecessary for the extensive accumulation of maternally biased
small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related
monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation
is generally parent-of-origin specific is unknown. Imprinted expression of sRNA
also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing
of the Kitaake rice cultivar that enabled us to show that localized hypomethylation
in rice endosperm occurs solely on the maternal genome, preferring regions of
high DNA accessibility. Maternally expressed imprinted genes are enriched for
hypomethylation at putative promoter regions and transcriptional termini and paternally
expressed genes at promoters and gene bodies, mirroring our recent results in
A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are
dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are
expressed from both parental genomes and correlate with hypomethylation. Overlaps
between imprinted sRNA loci and imprinted genes expressed from opposite alleles
suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling
tissues primarily originate from small class II (cut-and-paste) transposable elements,
those in endosperm are more uniformly derived, including sequences from other
transposon classes, as well as genic and intergenic regions. Our data indicate
that the endosperm exhibits a unique pattern of sRNA expression and suggest that
localized hypomethylation of maternal endosperm DNA is conserved in flowering
plants.
article_processing_charge: No
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Randy
full_name: Ruan, Randy
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: Pamela C
full_name: Ronald, Pamela C
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and
small RNA is associated with localized hypomethylation of the maternal genome
in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939.
doi:10.1073/pnas.1306164110
apa: Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald,
P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is
associated with localized hypomethylation of the maternal genome in rice endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1306164110
chicago: Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma,
Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted
Expression of Genes and Small RNA Is Associated with Localized Hypomethylation
of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110.
ieee: J. A. Rodrigues et al., “Imprinted expression of genes and small RNA
is associated with localized hypomethylation of the maternal genome in rice endosperm,”
Proceedings of the National Academy of Sciences, vol. 110, no. 19. National
Academy of Sciences, pp. 7934–7939, 2013.
ista: Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer
RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated
with localized hypomethylation of the maternal genome in rice endosperm. Proceedings
of the National Academy of Sciences. 110(19), 7934–7939.
mla: Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA
Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 110, no. 19, National
Academy of Sciences, 2013, pp. 7934–39, doi:10.1073/pnas.1306164110.
short: J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald,
R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110
(2013) 7934–7939.
date_created: 2021-06-07T07:31:02Z
date_published: 2013-05-07T00:00:00Z
date_updated: 2021-12-14T08:26:44Z
day: '07'
department:
- _id: DaZi
doi: 10.1073/pnas.1306164110
extern: '1'
external_id:
pmid:
- '23613580'
intvolume: ' 110'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1306164110
month: '05'
oa: 1
oa_version: Published Version
page: 7934-7939
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Imprinted expression of genes and small RNA is associated with localized hypomethylation
of the maternal genome in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 110
year: '2013'
...
---
_id: '9663'
abstract:
- lang: eng
text: 'Molecular dynamics simulations of small Cu nanoparticles using three different
interatomic potentials at rising temperature indicate that small nanoparticles
can undergo solid-solid structural transitions through a direct geometrical conversion
route. The direct geometrical conversion can happen for cuboctahedral nanoparticles,
which turn into an icosahedra shape: one diagonal of the square faces contracts,
and the faces are folded along the diagonal to give rise to two equilateral triangles.
The transition is a kinetic process that cannot be fully explained through an
energetic point of view. It has low activation energy and fast reaction time in
the simulations. The transition mechanism is via the transmission of shear waves
initiated from the particle surface and does not involve dislocation activity.'
article_number: '164314'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alfonso H. W.
full_name: Ngan, Alfonso H. W.
last_name: Ngan
citation:
ama: Cheng B, Ngan AHW. Thermally induced solid-solid structural transition of copper
nanoparticles through direct geometrical conversion. The Journal of Chemical
Physics. 2013;138(16). doi:10.1063/1.4802025
apa: Cheng, B., & Ngan, A. H. W. (2013). Thermally induced solid-solid structural
transition of copper nanoparticles through direct geometrical conversion. The
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4802025
chicago: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid
Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.”
The Journal of Chemical Physics. AIP Publishing, 2013. https://doi.org/10.1063/1.4802025.
ieee: B. Cheng and A. H. W. Ngan, “Thermally induced solid-solid structural transition
of copper nanoparticles through direct geometrical conversion,” The Journal
of Chemical Physics, vol. 138, no. 16. AIP Publishing, 2013.
ista: Cheng B, Ngan AHW. 2013. Thermally induced solid-solid structural transition
of copper nanoparticles through direct geometrical conversion. The Journal of
Chemical Physics. 138(16), 164314.
mla: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural
Transition of Copper Nanoparticles through Direct Geometrical Conversion.” The
Journal of Chemical Physics, vol. 138, no. 16, 164314, AIP Publishing, 2013,
doi:10.1063/1.4802025.
short: B. Cheng, A.H.W. Ngan, The Journal of Chemical Physics 138 (2013).
date_created: 2021-07-15T09:27:58Z
date_published: 2013-04-28T00:00:00Z
date_updated: 2021-08-09T12:35:34Z
day: '28'
doi: 10.1063/1.4802025
extern: '1'
external_id:
pmid:
- '23635145'
intvolume: ' 138'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pubmed.ncbi.nlm.nih.gov/23635145/
month: '04'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermally induced solid-solid structural transition of copper nanoparticles
through direct geometrical conversion
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 138
year: '2013'
...
---
_id: '9682'
abstract:
- lang: eng
text: In this work, we simulate the response of two Cu nanoparticles colliding at
different approaching rates at room temperature by MD. For small nanospheres,
the formation of single twins is favored at high approach rates, whereas larger
nanospheres mainly deform by dislocation slip. For small nanocubes with large
{100} flat surfaces, however, a dislocation-free direct geometrical conversion
process that leads to five-fold twinning dominates except at highly retarded approaching
rates. For larger nanocubes, single twin formation is the governing plasticity
mechanism. The probability for plastic deformation by dislocation slip or twinning
is attributed to the abundance of surface steps, which act as sites for dislocation
nucleation.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alfonso H.W.
full_name: Ngan, Alfonso H.W.
last_name: Ngan
citation:
ama: 'Cheng B, Ngan AHW. Crystal plasticity of Cu nanocrystals during collision.
Materials Science and Engineering: A. 2013;585:326-334. doi:10.1016/j.msea.2013.07.065'
apa: 'Cheng, B., & Ngan, A. H. W. (2013). Crystal plasticity of Cu nanocrystals
during collision. Materials Science and Engineering: A. Elsevier. https://doi.org/10.1016/j.msea.2013.07.065'
chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “Crystal Plasticity of Cu Nanocrystals
during Collision.” Materials Science and Engineering: A. Elsevier, 2013.
https://doi.org/10.1016/j.msea.2013.07.065.'
ieee: 'B. Cheng and A. H. W. Ngan, “Crystal plasticity of Cu nanocrystals during
collision,” Materials Science and Engineering: A, vol. 585. Elsevier, pp.
326–334, 2013.'
ista: 'Cheng B, Ngan AHW. 2013. Crystal plasticity of Cu nanocrystals during collision.
Materials Science and Engineering: A. 585, 326–334.'
mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “Crystal Plasticity of Cu Nanocrystals
during Collision.” Materials Science and Engineering: A, vol. 585, Elsevier,
2013, pp. 326–34, doi:10.1016/j.msea.2013.07.065.'
short: 'B. Cheng, A.H.W. Ngan, Materials Science and Engineering: A 585 (2013) 326–334.'
date_created: 2021-07-19T09:04:36Z
date_published: 2013-11-15T00:00:00Z
date_updated: 2023-02-23T14:04:51Z
day: '15'
doi: 10.1016/j.msea.2013.07.065
extern: '1'
intvolume: ' 585'
language:
- iso: eng
month: '11'
oa_version: None
page: 326-334
publication: 'Materials Science and Engineering: A'
publication_identifier:
issn:
- 0921-5093
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crystal plasticity of Cu nanocrystals during collision
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 585
year: '2013'
...
---
_id: '970'
abstract:
- lang: eng
text: 'Recently a new high-mobility Dirac material, trilayer graphene, was realized
experimentally. The band structure of ABA-stacked trilayer graphene consists of
a monolayer-like and a bilayer-like pair of bands. Here we study electronic properties
of ABA-stacked trilayer graphene biased by a perpendicular electric field. We
find that the combination of the bias and trigonal warping gives rise to a set
of new Dirac points: In each valley, seven species of Dirac fermions with small
masses of order of a few meV emerge. The positions and masses of the emergent
Dirac fermions are tunable by bias, and one group of Dirac fermions becomes massless
at a certain bias value. Therefore, in contrast to bilayer graphene, the conductivity
at the neutrality point is expected to show nonmonotonic behavior, becoming of
the order of a few e2/h when some Dirac masses vanish. Further, we analyze the
evolution of the Landau level spectrum as a function of bias. The emergence of
new Dirac points in the band structure translates into new threefold-degenerate
groups of Landau levels. This leads to an anomalous quantum Hall effect, in which
some quantum Hall steps have a height of 3e2/h. At an intermediate bias, the degeneracies
of all Landau levels get lifted, and in this regime all quantum Hall plateaus
are spaced by e2/h. Finally, we show that the pattern of Landau level crossings
is very sensitive to certain band structure parameters, and can therefore provide
a useful tool for determining their precise values.'
acknowledgement: We thank Pablo Jarillo-Herrero, Leonardo Campos, and Thiti Taychatanapat
for attracting our attention to the problem of biased trilayer graphene, and for
many helpful discussions.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Abanin D. New Dirac points and multiple Landau level crossings in
biased trilayer graphene. Physical Review B - Condensed Matter and Materials
Physics. 2013;87(11). doi:10.1103/PhysRevB.87.115422
apa: Serbyn, M., & Abanin, D. (2013). New Dirac points and multiple Landau level
crossings in biased trilayer graphene. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.115422
chicago: Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau
Level Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.115422.
ieee: M. Serbyn and D. Abanin, “New Dirac points and multiple Landau level crossings
in biased trilayer graphene,” Physical Review B - Condensed Matter and Materials
Physics, vol. 87, no. 11. American Physical Society, 2013.
ista: Serbyn M, Abanin D. 2013. New Dirac points and multiple Landau level crossings
in biased trilayer graphene. Physical Review B - Condensed Matter and Materials
Physics. 87(11).
mla: Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau Level
Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed Matter
and Materials Physics, vol. 87, no. 11, American Physical Society, 2013, doi:10.1103/PhysRevB.87.115422.
short: M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials
Physics 87 (2013).
date_created: 2018-12-11T11:49:28Z
date_published: 2013-03-18T00:00:00Z
date_updated: 2021-01-12T08:22:20Z
day: '18'
doi: 10.1103/PhysRevB.87.115422
extern: 1
intvolume: ' 87'
issue: '11'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1212.6251
month: '03'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6428'
quality_controlled: 0
status: public
title: New Dirac points and multiple Landau level crossings in biased trilayer graphene
type: journal_article
volume: 87
year: '2013'
...
---
_id: '973'
abstract:
- lang: eng
text: We construct a complete set of local integrals of motion that characterize
the many-body localized (MBL) phase. Our approach relies on the assumption that
local perturbations act locally on the eigenstates in the MBL phase, which is
supported by numerical simulations of the random-field XXZ spin chain. We describe
the structure of the eigenstates in the MBL phase and discuss the implications
of local conservation laws for its nonequilibrium quantum dynamics. We argue that
the many-body localization can be used to protect coherence in the system by suppressing
relaxation between eigenstates with different local integrals of motion.
acknowledgement: We thank J. Moore for useful discussions. Research at Perimeter Institute
is supported by the Government of Canada through Industry Canada and by the Province
of Ontario through the Ministry of Economic Development & Innovation. Z. P. was
supported by DOE Grant No. DE-SC0002140. M. S. was supported by the National Science
Foundation under Grant No. DMR-1104498. The simulations presented in this article
were performed on computational resources supported by the High Performance Computing
Center (PICSciE) at Princeton University.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Local conservation laws and the structure of the
many body localized states. Physical Review Letters. 2013;111(12). doi:10.1103/PhysRevLett.111.127201
apa: Serbyn, M., Papić, Z., & Abanin, D. (2013). Local conservation laws and
the structure of the many body localized states. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.111.127201
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Local Conservation Laws
and the Structure of the Many Body Localized States.” Physical Review Letters.
American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.111.127201.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Local conservation laws and the structure
of the many body localized states,” Physical Review Letters, vol. 111,
no. 12. American Physical Society, 2013.
ista: Serbyn M, Papić Z, Abanin D. 2013. Local conservation laws and the structure
of the many body localized states. Physical Review Letters. 111(12).
mla: Serbyn, Maksym, et al. “Local Conservation Laws and the Structure of the Many
Body Localized States.” Physical Review Letters, vol. 111, no. 12, American
Physical Society, 2013, doi:10.1103/PhysRevLett.111.127201.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 111 (2013).
date_created: 2018-12-11T11:49:29Z
date_published: 2013-09-17T00:00:00Z
date_updated: 2021-01-12T08:22:21Z
day: '17'
doi: 10.1103/PhysRevLett.111.127201
extern: 1
intvolume: ' 111'
issue: '12'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1305.5554
month: '09'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6424'
quality_controlled: 0
status: public
title: Local conservation laws and the structure of the many body localized states
type: journal_article
volume: 111
year: '2013'
...
---
_id: '974'
abstract:
- lang: eng
text: We propose a possible realization of the overscreened Kondo impurity problem
by a magnetic s=1/2 impurity embedded in a two-dimensional S=1 U(1) spin liquid
with a Fermi surface. This problem contains an interesting interplay between non-Fermi-liquid
behavior induced by a U(1) gauge field coupled to fermions and a non-Fermi-liquid
fixed point in the overscreened Kondo problem. Using a large-N expansion together
with an expansion in the dynamical exponent of the gauge field, we find that the
coupling to the gauge field leads to weak but observable changes in the physical
properties of the system at the overscreened Kondo fixed point. We discuss the
extrapolation of this result to a physical case and argue that the realization
of overscreened Kondo physics could lead to observations of effects due to gauge
fields.
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Todadri
full_name: Senthil, Todadri
last_name: Senthil
- first_name: Patrick
full_name: Lee, Patrick
last_name: Lee
citation:
ama: Serbyn M, Senthil T, Lee P. Overscreened Kondo fixed point in S=1 spin liquid.
Physical Review B - Condensed Matter and Materials Physics. 2013;88(2).
doi:10.1103/PhysRevB.88.024419
apa: Serbyn, M., Senthil, T., & Lee, P. (2013). Overscreened Kondo fixed point
in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.88.024419
chicago: Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Overscreened Kondo Fixed
Point in S=1 Spin Liquid.” Physical Review B - Condensed Matter and Materials
Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.024419.
ieee: M. Serbyn, T. Senthil, and P. Lee, “Overscreened Kondo fixed point in S=1
spin liquid,” Physical Review B - Condensed Matter and Materials Physics,
vol. 88, no. 2. American Physical Society, 2013.
ista: Serbyn M, Senthil T, Lee P. 2013. Overscreened Kondo fixed point in S=1 spin
liquid. Physical Review B - Condensed Matter and Materials Physics. 88(2).
mla: Serbyn, Maksym, et al. “Overscreened Kondo Fixed Point in S=1 Spin Liquid.”
Physical Review B - Condensed Matter and Materials Physics, vol. 88, no.
2, American Physical Society, 2013, doi:10.1103/PhysRevB.88.024419.
short: M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials
Physics 88 (2013).
date_created: 2018-12-11T11:49:29Z
date_published: 2013-07-19T00:00:00Z
date_updated: 2021-01-12T08:22:21Z
day: '19'
doi: 10.1103/PhysRevB.88.024419
extern: '1'
external_id:
arxiv:
- '1212.5179'
intvolume: ' 88'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1212.5179
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6425'
quality_controlled: '1'
status: public
title: Overscreened Kondo fixed point in S=1 spin liquid
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 88
year: '2013'
...
---
_id: '2284'
abstract:
- lang: eng
text: 'Background: The brood of ants and other social insects is highly susceptible
to pathogens, particularly those that penetrate the soft larval and pupal cuticle.
We here test whether the presence of a pupal cocoon, which occurs in some ant
species but not in others, affects the sanitary brood care and fungal infection
patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We
use a) a comparative approach analysing four species with either naked or cocooned
pupae and b) a within-species analysis of a single ant species, in which both
pupal types co-exist in the same colony. Results: We found that the presence of
a cocoon did not compromise fungal pathogen detection by the ants and that species
with cocooned pupae increased brood grooming after pathogen exposure. All tested
ant species further removed brood from their nests, which was predominantly expressed
towards larvae and naked pupae treated with the live fungal pathogen. In contrast,
cocooned pupae exposed to live fungus were not removed at higher rates than cocooned
pupae exposed to dead fungus or a sham control. Consistent with this, exposure
to the live fungus caused high numbers of infections and fungal outgrowth in larvae
and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed
the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion:
Our study suggests that the pupal cocoon has a protective effect against fungal
infection, causing an adaptive change in sanitary behaviours by the ants. It further
demonstrates that brood removal-originally described for honeybees as "hygienic
behaviour"-is a widespread sanitary behaviour in ants, which likely has important
implications on disease dynamics in social insect colonies.'
acknowledgement: "The study was funded by the European Research Council (Marie Curie
ERG 036569) and Marie Curie IEF 302204 to LVU\r\nCC BY 2.0\r\n"
article_number: '225'
author:
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Michel
full_name: Chapuisat, Michel
last_name: Chapuisat
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Pupal cocoons affect
sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary
Biology. 2013;13(1). doi:10.1186/1471-2148-13-225
apa: Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., & Cremer, S. (2013).
Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies.
BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-225
chicago: Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia
Cremer. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections
in Ant Colonies.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-225.
ieee: S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Pupal
cocoons affect sanitary brood care and limit fungal infections in ant colonies,”
BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.
ista: Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2013. Pupal cocoons
affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary
Biology. 13(1), 225.
mla: Tragust, Simon, et al. “Pupal Cocoons Affect Sanitary Brood Care and Limit
Fungal Infections in Ant Colonies.” BMC Evolutionary Biology, vol. 13,
no. 1, 225, BioMed Central, 2013, doi:10.1186/1471-2148-13-225.
short: S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, BMC Evolutionary
Biology 13 (2013).
date_created: 2018-12-11T11:56:46Z
date_published: 2013-10-14T00:00:00Z
date_updated: 2023-02-23T14:07:06Z
day: '14'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1186/1471-2148-13-225
ec_funded: 1
file:
- access_level: open_access
checksum: c16ef36f2a10786a7885e19c4528d707
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:41Z
date_updated: 2020-07-14T12:45:37Z
file_id: '5026'
file_name: IST-2016-402-v1+1_1471-2148-13-225.pdf
file_size: 281736
relation: main_file
file_date_updated: 2020-07-14T12:45:37Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '4647'
pubrep_id: '402'
quality_controlled: '1'
related_material:
record:
- id: '9753'
relation: research_data
status: public
scopus_import: 1
status: public
title: Pupal cocoons affect sanitary brood care and limit fungal infections in ant
colonies
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: '2277'
abstract:
- lang: eng
text: Redundancies and correlations in the responses of sensory neurons may seem
to waste neural resources, but they can also carry cues about structured stimuli
and may help the brain to correct for response errors. To investigate the effect
of stimulus structure on redundancy in retina, we measured simultaneous responses
from populations of retinal ganglion cells presented with natural and artificial
stimuli that varied greatly in correlation structure; these stimuli and recordings
are publicly available online. Responding to spatio-temporally structured stimuli
such as natural movies, pairs of ganglion cells were modestly more correlated
than in response to white noise checkerboards, but they were much less correlated
than predicted by a non-adapting functional model of retinal response. Meanwhile,
responding to stimuli with purely spatial correlations, pairs of ganglion cells
showed increased correlations consistent with a static, non-adapting receptive
field and nonlinearity. We found that in response to spatio-temporally correlated
stimuli, ganglion cells had faster temporal kernels and tended to have stronger
surrounds. These properties of individual cells, along with gain changes that
opposed changes in effective contrast at the ganglion cell input, largely explained
the pattern of pairwise correlations across stimuli where receptive field measurements
were possible.
article_number: e1003344
author:
- first_name: Kristina
full_name: Simmons, Kristina
last_name: Simmons
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Jan
full_name: Homann, Jan
last_name: Homann
- first_name: Heather
full_name: Yee, Heather
last_name: Yee
- first_name: Stephanie
full_name: Palmer, Stephanie
last_name: Palmer
- first_name: Philip
full_name: Nelson, Philip
last_name: Nelson
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
citation:
ama: Simmons K, Prentice J, Tkačik G, et al. Transformation of stimulus correlations
by the retina. PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003344
apa: Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian,
V. (2013). Transformation of stimulus correlations by the retina. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003344
chicago: Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee,
Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Transformation of
Stimulus Correlations by the Retina.” PLoS Computational Biology. Public
Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1003344.
ieee: K. Simmons et al., “Transformation of stimulus correlations by the
retina,” PLoS Computational Biology, vol. 9, no. 12. Public Library of
Science, 2013.
ista: Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian
V. 2013. Transformation of stimulus correlations by the retina. PLoS Computational
Biology. 9(12), e1003344.
mla: Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.”
PLoS Computational Biology, vol. 9, no. 12, e1003344, Public Library of
Science, 2013, doi:10.1371/journal.pcbi.1003344.
short: K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson,
V. Balasubramanian, PLoS Computational Biology 9 (2013).
date_created: 2018-12-11T11:56:43Z
date_published: 2013-12-05T00:00:00Z
date_updated: 2023-02-23T14:07:04Z
day: '05'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1003344
file:
- access_level: open_access
checksum: 46722afc4f7eabb0831165d9c1b171ad
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:36Z
date_updated: 2020-07-14T12:45:36Z
file_id: '5089'
file_name: IST-2016-410-v1+1_journal.pcbi.1003344.pdf
file_size: 3115568
relation: main_file
file_date_updated: 2020-07-14T12:45:36Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '4667'
pubrep_id: '410'
quality_controlled: '1'
related_material:
record:
- id: '9752'
relation: research_data
status: public
scopus_import: 1
status: public
title: Transformation of stimulus correlations by the retina
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: 9
year: '2013'
...