---
_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
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
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'
...