---
_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'
...