@article{5920, abstract = {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.}, author = {Hillar, Christopher J. and Martin del Campo Sanchez, Abraham}, issn = {0747-7171}, journal = {Journal of Symbolic Computation}, pages = {314--334}, publisher = {Elsevier}, title = {{Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals}}, doi = {10.1016/j.jsc.2012.06.006}, volume = {50}, year = {2013}, } @article{591, abstract = {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 = {Schmid, David and Huang, Ting-Yu and Hazrat, Shiraz and Dirks, Radhika and Onur Hosten and Quint, Stephan and Thian, Dickson and Kwiat, Paul G}, journal = {Optics Express}, number = {13}, pages = {15538 -- 15552}, publisher = {Optical Society of America}, title = {{Adjustable and robust methods for polarization-dependent focusing}}, doi = {10.1364/OE.21.015538}, volume = {21}, year = {2013}, } @article{595, author = {Bernecky, Carrie A and Cramer, Patrick}, journal = {EMBO Journal}, number = {6}, pages = {771 -- 772}, publisher = {Wiley-Blackwell}, title = {{Struggling to let go: A non-coding RNA directs its own extension and destruction}}, doi = {10.1038/emboj.2013.36}, volume = {32}, year = {2013}, } @article{6128, abstract = {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.}, author = {Kodama-Namba, Eiji and Fenk, Lorenz A. and Bretscher, Andrew J. and Gross, Einav and Busch, K. Emanuel and de Bono, Mario}, issn = {1553-7404}, journal = {PLoS Genetics}, number = {12}, publisher = {Public Library of Science (PLoS)}, title = {{Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans}}, doi = {10.1371/journal.pgen.1004011}, volume = {9}, year = {2013}, } @article{6130, abstract = {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.}, author = {Chen, Changchun and Fenk, Lorenz A. and de Bono, Mario}, issn = {1362-4962}, journal = {Nucleic Acids Research}, number = {20}, publisher = {Oxford University Press}, title = {{Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination}}, doi = {10.1093/nar/gkt805}, volume = {41}, year = {2013}, }