--- _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' ...