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