[{"intvolume":"        21","publist_id":"7218","month":"07","date_created":"2018-12-11T11:47:22Z","status":"public","date_published":"2013-07-01T00:00:00Z","page":"15538 - 15552","issue":"13","volume":21,"publisher":"Optical Society of America","title":"Adjustable and robust methods for polarization-dependent focusing","publication":"Optics Express","_id":"591","doi":"10.1364/OE.21.015538","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."}],"publication_status":"published","citation":{"mla":"Schmid, David, et al. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” <i>Optics Express</i>, vol. 21, no. 13, Optical Society of America, 2013, pp. 15538–52, doi:<a href=\"https://doi.org/10.1364/OE.21.015538\">10.1364/OE.21.015538</a>.","apa":"Schmid, D., Huang, T., Hazrat, S., Dirks, R., Hosten, O., Quint, S., … Kwiat, P. (2013). Adjustable and robust methods for polarization-dependent focusing. <i>Optics Express</i>. Optical Society of America. <a href=\"https://doi.org/10.1364/OE.21.015538\">https://doi.org/10.1364/OE.21.015538</a>","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.","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.” <i>Optics Express</i>. Optical Society of America, 2013. <a href=\"https://doi.org/10.1364/OE.21.015538\">https://doi.org/10.1364/OE.21.015538</a>.","short":"D. Schmid, T. Huang, S. Hazrat, R. Dirks, O. Hosten, S. Quint, D. Thian, P. Kwiat, Optics Express 21 (2013) 15538–15552.","ieee":"D. Schmid <i>et al.</i>, “Adjustable and robust methods for polarization-dependent focusing,” <i>Optics Express</i>, vol. 21, no. 13. Optical Society of America, pp. 15538–15552, 2013.","ama":"Schmid D, Huang T, Hazrat S, et al. Adjustable and robust methods for polarization-dependent focusing. <i>Optics Express</i>. 2013;21(13):15538-15552. doi:<a href=\"https://doi.org/10.1364/OE.21.015538\">10.1364/OE.21.015538</a>"},"quality_controlled":0,"extern":1,"author":[{"first_name":"David","last_name":"Schmid","full_name":"Schmid, David"},{"full_name":"Huang, Ting-Yu","first_name":"Ting","last_name":"Huang"},{"full_name":"Hazrat, Shiraz","first_name":"Shiraz","last_name":"Hazrat"},{"first_name":"Radhika","last_name":"Dirks","full_name":"Dirks, Radhika"},{"first_name":"Onur","last_name":"Hosten","full_name":"Onur Hosten","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Quint, Stephan","last_name":"Quint","first_name":"Stephan"},{"first_name":"Dickson","last_name":"Thian","full_name":"Thian, Dickson"},{"full_name":"Kwiat, Paul G","last_name":"Kwiat","first_name":"Paul"}],"type":"journal_article","date_updated":"2021-01-12T08:05:12Z","year":"2013","day":"01"},{"publication_identifier":{"issn":["0747-7171"]},"intvolume":"        50","status":"public","month":"03","date_created":"2019-02-05T08:48:24Z","page":"314-334","volume":50,"date_published":"2013-03-01T00:00:00Z","article_type":"original","publisher":"Elsevier","_id":"5920","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1016/j.jsc.2015.09.002"}]},"doi":"10.1016/j.jsc.2012.06.006","publication":"Journal of Symbolic Computation","title":"Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals","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."}],"publication_status":"published","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","author":[{"last_name":"Hillar","first_name":"Christopher J.","full_name":"Hillar, Christopher J."},{"first_name":"Abraham","last_name":"Martin del Campo Sanchez","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","full_name":"Martin del Campo Sanchez, Abraham"}],"citation":{"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.","chicago":"Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” <i>Journal of Symbolic Computation</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">https://doi.org/10.1016/j.jsc.2012.06.006</a>.","short":"C.J. Hillar, A. Martin del Campo Sanchez, Journal of Symbolic Computation 50 (2013) 314–334.","ieee":"C. J. Hillar and A. Martin del Campo Sanchez, “Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals,” <i>Journal of Symbolic Computation</i>, vol. 50. Elsevier, pp. 314–334, 2013.","ama":"Hillar CJ, Martin del Campo Sanchez A. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. <i>Journal of Symbolic Computation</i>. 2013;50:314-334. doi:<a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">10.1016/j.jsc.2012.06.006</a>","mla":"Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” <i>Journal of Symbolic Computation</i>, vol. 50, Elsevier, 2013, pp. 314–34, doi:<a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">10.1016/j.jsc.2012.06.006</a>.","apa":"Hillar, C. J., &#38; Martin del Campo Sanchez, A. (2013). Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. <i>Journal of Symbolic Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">https://doi.org/10.1016/j.jsc.2012.06.006</a>"},"year":"2013","day":"01","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T08:05:15Z"},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604726/","open_access":"1"}],"citation":{"mla":"Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” <i>EMBO Journal</i>, vol. 32, no. 6, Wiley-Blackwell, 2013, pp. 771–72, doi:<a href=\"https://doi.org/10.1038/emboj.2013.36\">10.1038/emboj.2013.36</a>.","apa":"Bernecky, C., &#38; Cramer, P. (2013). Struggling to let go: A non-coding RNA directs its own extension and destruction. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2013.36\">https://doi.org/10.1038/emboj.2013.36</a>","ieee":"C. Bernecky and P. Cramer, “Struggling to let go: A non-coding RNA directs its own extension and destruction,” <i>EMBO Journal</i>, vol. 32, no. 6. Wiley-Blackwell, pp. 771–772, 2013.","ama":"Bernecky C, Cramer P. Struggling to let go: A non-coding RNA directs its own extension and destruction. <i>EMBO Journal</i>. 2013;32(6):771-772. doi:<a href=\"https://doi.org/10.1038/emboj.2013.36\">10.1038/emboj.2013.36</a>","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.","chicago":"Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2013.36\">https://doi.org/10.1038/emboj.2013.36</a>.","short":"C. Bernecky, P. Cramer, EMBO Journal 32 (2013) 771–772."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","first_name":"Carrie A"},{"full_name":"Cramer, Patrick","last_name":"Cramer","first_name":"Patrick"}],"oa_version":"None","date_updated":"2021-01-12T08:05:20Z","type":"journal_article","year":"2013","day":"20","publication":"EMBO Journal","title":"Struggling to let go: A non-coding RNA directs its own extension and destruction","_id":"595","doi":"10.1038/emboj.2013.36","language":[{"iso":"eng"}],"oa":1,"publication_status":"published","date_published":"2013-03-20T00:00:00Z","volume":32,"issue":"6","page":"771 - 772","publisher":"Wiley-Blackwell","intvolume":"        32","publist_id":"7207","month":"03","date_created":"2018-12-11T11:47:23Z","status":"public"},{"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."}],"publication_status":"published","pmid":1,"title":"Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans","publication":"PLoS Genetics","_id":"6128","ddc":["570"],"oa":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2013","citation":{"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.” <i>PLoS Genetics</i>. Public Library of Science (PLoS), 2013. <a href=\"https://doi.org/10.1371/journal.pgen.1004011\">https://doi.org/10.1371/journal.pgen.1004011</a>.","short":"E. Kodama-Namba, L.A. Fenk, A.J. Bretscher, E. Gross, K.E. Busch, M. de Bono, PLoS Genetics 9 (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.","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,” <i>PLoS Genetics</i>, vol. 9, no. 12. Public Library of Science (PLoS), 2013.","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. <i>PLoS Genetics</i>. 2013;9(12). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1004011\">10.1371/journal.pgen.1004011</a>","mla":"Kodama-Namba, Eiji, et al. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” <i>PLoS Genetics</i>, vol. 9, no. 12, e1004011, Public Library of Science (PLoS), 2013, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1004011\">10.1371/journal.pgen.1004011</a>.","apa":"Kodama-Namba, E., Fenk, L. A., Bretscher, A. J., Gross, E., Busch, K. E., &#38; de Bono, M. (2013). Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. <i>PLoS Genetics</i>. Public Library of Science (PLoS). <a href=\"https://doi.org/10.1371/journal.pgen.1004011\">https://doi.org/10.1371/journal.pgen.1004011</a>"},"extern":"1","quality_controlled":"1","author":[{"full_name":"Kodama-Namba, Eiji","last_name":"Kodama-Namba","first_name":"Eiji"},{"first_name":"Lorenz A.","last_name":"Fenk","full_name":"Fenk, Lorenz A."},{"last_name":"Bretscher","first_name":"Andrew J.","full_name":"Bretscher, Andrew J."},{"first_name":"Einav","last_name":"Gross","full_name":"Gross, Einav"},{"first_name":"K. Emanuel","last_name":"Busch","full_name":"Busch, K. Emanuel"},{"last_name":"de Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443"}],"month":"12","date_created":"2019-03-19T14:58:51Z","status":"public","article_number":"e1004011","intvolume":"         9","file_date_updated":"2020-07-14T12:47:20Z","publisher":"Public Library of Science (PLoS)","issue":"12","volume":9,"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1004011","oa_version":"Published Version","date_updated":"2021-01-12T08:06:15Z","type":"journal_article","day":"19","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1553-7404"]},"external_id":{"pmid":["24385919"]},"file":[{"access_level":"open_access","checksum":"299b6321be79931c7c17c5db6e69c711","file_name":"2013_PLOS_Kodama-Namba.PDF","file_id":"6129","date_updated":"2020-07-14T12:47:20Z","file_size":4499039,"creator":"kschuh","content_type":"application/pdf","date_created":"2019-03-19T15:14:51Z","relation":"main_file"}],"date_published":"2013-12-19T00:00:00Z"},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2013","citation":{"mla":"Chen, Changchun, et al. “Efficient Genome Editing in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” <i>Nucleic Acids Research</i>, vol. 41, no. 20, e193, Oxford University Press, 2013, doi:<a href=\"https://doi.org/10.1093/nar/gkt805\">10.1093/nar/gkt805</a>.","apa":"Chen, C., Fenk, L. A., &#38; de Bono, M. (2013). Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkt805\">https://doi.org/10.1093/nar/gkt805</a>","ieee":"C. Chen, L. A. Fenk, and M. de Bono, “Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination,” <i>Nucleic Acids Research</i>, vol. 41, no. 20. Oxford University Press, 2013.","ama":"Chen C, Fenk LA, de Bono M. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. <i>Nucleic Acids Research</i>. 2013;41(20). doi:<a href=\"https://doi.org/10.1093/nar/gkt805\">10.1093/nar/gkt805</a>","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.","short":"C. Chen, L.A. Fenk, M. de Bono, Nucleic Acids Research 41 (2013).","chicago":"Chen, Changchun, Lorenz A. Fenk, and Mario de Bono. “Efficient Genome Editing in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” <i>Nucleic Acids Research</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/nar/gkt805\">https://doi.org/10.1093/nar/gkt805</a>."},"quality_controlled":"1","author":[{"full_name":"Chen, Changchun","first_name":"Changchun","last_name":"Chen"},{"last_name":"Fenk","first_name":"Lorenz A.","full_name":"Fenk, Lorenz A."},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"de Bono"}],"extern":"1","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."}],"publication_status":"published","pmid":1,"publication":"Nucleic Acids Research","title":"Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination","_id":"6130","ddc":["570"],"oa":1,"file_date_updated":"2020-07-14T12:47:20Z","publisher":"Oxford University Press","volume":41,"issue":"20","month":"11","date_created":"2019-03-19T15:17:40Z","status":"public","article_number":"e193","intvolume":"        41","oa_version":"Published Version","type":"journal_article","date_updated":"2021-01-12T08:06:16Z","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","doi":"10.1093/nar/gkt805","language":[{"iso":"eng"}],"file":[{"file_id":"6131","date_updated":"2020-07-14T12:47:20Z","file_name":"2013_OUP_Chen.pdf","checksum":"0f1f127cefd043cb922b292e1cd16f02","access_level":"open_access","relation":"main_file","date_created":"2019-03-19T15:25:42Z","content_type":"application/pdf","creator":"kschuh","file_size":340225}],"external_id":{"pmid":["24013562"]},"date_published":"2013-11-01T00:00:00Z","publication_identifier":{"issn":["1362-4962","0305-1048"]}},{"_id":"6132","language":[{"iso":"eng"}],"publication":"Optogenetics","title":"Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans","publication_status":"published","author":[{"first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"},{"full_name":"Schafer, W.R.","first_name":"W.R.","last_name":"Schafer"},{"full_name":"Gottschalk, A.","first_name":"A.","last_name":"Gottschalk"}],"quality_controlled":"1","extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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 <i>Optogenetics</i>, P. Hegemann and S. Sigrist, Eds. Walter de Gruyter, 2013, pp. 61–78.","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. <i>Optogenetics</i>. Walter de Gruyter; 2013:61-78.","short":"M. de Bono, W.R. Schafer, A. Gottschalk, in:, P. Hegemann, S. Sigrist (Eds.), Optogenetics, Walter de Gruyter, 2013, pp. 61–78.","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 <i>Optogenetics</i>, edited by Peter Hegemann and Stephan Sigrist, 61–78. Walter de Gruyter, 2013.","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.","apa":"de Bono, M., Schafer, W. R., &#38; Gottschalk, A. (2013). Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In P. Hegemann &#38; S. Sigrist (Eds.), <i>Optogenetics</i> (pp. 61–78). Walter de Gruyter.","mla":"de Bono, Mario, et al. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” <i>Optogenetics</i>, edited by Peter Hegemann and Stephan Sigrist, Walter de Gruyter, 2013, pp. 61–78."},"year":"2013","day":"28","oa_version":"None","type":"book_chapter","date_updated":"2021-01-12T08:06:16Z","publication_identifier":{"isbn":["9783110270723; 9783110270716"]},"status":"public","month":"08","date_created":"2019-03-20T13:54:05Z","page":"61-78","date_published":"2013-08-28T00:00:00Z","editor":[{"first_name":"Peter","last_name":"Hegemann","full_name":"Hegemann, Peter"},{"full_name":"Sigrist, Stephan","first_name":"Stephan","last_name":"Sigrist"}],"publisher":"Walter de Gruyter"},{"publication_identifier":{"issn":["0027-8424","1091-6490"]},"page":"E3301-E3310","date_published":"2013-08-27T00:00:00Z","external_id":{"pmid":["23940325"]},"file":[{"file_size":2198763,"creator":"kschuh","content_type":"application/pdf","date_created":"2019-03-20T14:07:53Z","relation":"main_file","access_level":"open_access","file_name":"2013_PNAS_Couto.pdf","checksum":"3ee28a694f74a49f0d098970ae391a91","date_updated":"2020-07-14T12:47:20Z","file_id":"6134"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1217428110","has_accepted_license":"1","day":"27","date_updated":"2021-01-12T08:06:16Z","type":"journal_article","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","date_created":"2019-03-20T14:05:06Z","month":"08","intvolume":"       110","publisher":"Proceedings of the National Academy of Sciences","file_date_updated":"2020-07-14T12:47:20Z","volume":110,"issue":"35","publication_status":"published","abstract":[{"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.","lang":"eng"}],"ddc":["570"],"oa":1,"_id":"6133","title":"In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor","publication":"Proceedings of the National Academy of Sciences","pmid":1,"year":"2013","quality_controlled":"1","extern":"1","author":[{"last_name":"Couto","first_name":"A.","full_name":"Couto, A."},{"full_name":"Oda, S.","last_name":"Oda","first_name":"S."},{"full_name":"Nikolaev, V. O.","first_name":"V. O.","last_name":"Nikolaev"},{"full_name":"Soltesz, Z.","first_name":"Z.","last_name":"Soltesz"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario"}],"citation":{"short":"A. Couto, S. Oda, V.O. Nikolaev, Z. Soltesz, M. de Bono, Proceedings of the National Academy of Sciences 110 (2013) E3301–E3310.","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.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1217428110\">https://doi.org/10.1073/pnas.1217428110</a>.","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.","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. <i>Proceedings of the National Academy of Sciences</i>. 2013;110(35):E3301-E3310. doi:<a href=\"https://doi.org/10.1073/pnas.1217428110\">10.1073/pnas.1217428110</a>","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,” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 35. Proceedings of the National Academy of Sciences, pp. E3301–E3310, 2013.","mla":"Couto, A., et al. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 35, Proceedings of the National Academy of Sciences, 2013, pp. E3301–10, doi:<a href=\"https://doi.org/10.1073/pnas.1217428110\">10.1073/pnas.1217428110</a>.","apa":"Couto, A., Oda, S., Nikolaev, V. O., Soltesz, Z., &#38; de Bono, M. (2013). In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1217428110\">https://doi.org/10.1073/pnas.1217428110</a>"}},{"year":"2013","day":"01","oa_version":"None","date_updated":"2021-01-12T08:06:17Z","type":"journal_article","extern":"1","author":[{"first_name":"Miriam","last_name":"Rodriguez","full_name":"Rodriguez, Miriam"},{"full_name":"Snoek, L. Basten","first_name":"L. Basten","last_name":"Snoek"},{"last_name":"de Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kammenga, Jan E.","first_name":"Jan E.","last_name":"Kammenga"}],"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"M. Rodriguez, L.B. Snoek, M. de Bono, J.E. Kammenga, Trends in Genetics 29 (2013) 367–374.","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.” <i>Trends in Genetics</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">https://doi.org/10.1016/j.tig.2013.01.010</a>.","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. <i>Trends in Genetics</i>. 2013;29(6):367-374. doi:<a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">10.1016/j.tig.2013.01.010</a>","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,” <i>Trends in Genetics</i>, vol. 29, no. 6. Elsevier, pp. 367–374, 2013.","apa":"Rodriguez, M., Snoek, L. B., de Bono, M., &#38; Kammenga, J. E. (2013). Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">https://doi.org/10.1016/j.tig.2013.01.010</a>","mla":"Rodriguez, Miriam, et al. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” <i>Trends in Genetics</i>, vol. 29, no. 6, Elsevier, 2013, pp. 367–74, doi:<a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">10.1016/j.tig.2013.01.010</a>."},"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."}],"publication_status":"published","_id":"6135","language":[{"iso":"eng"}],"doi":"10.1016/j.tig.2013.01.010","title":"Worms under stress: C. elegans stress response and its relevance to complex human disease and aging","publication":"Trends in Genetics","publisher":"Elsevier","volume":29,"page":"367-374","issue":"6","date_published":"2013-06-01T00:00:00Z","status":"public","month":"06","date_created":"2019-03-20T14:17:42Z","publication_identifier":{"issn":["0168-9525"]},"intvolume":"        29"},{"publisher":"American Chemical Society (ACS)","page":"9416-9430","issue":"18","volume":117,"date_published":"2013-05-09T00:00:00Z","status":"public","month":"05","date_created":"2019-05-03T09:40:31Z","publication_identifier":{"issn":["1932-7447","1932-7455"]},"intvolume":"       117","year":"2013","day":"09","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T08:07:17Z","author":[{"first_name":"Tze-Chia","last_name":"Lin","full_name":"Lin, Tze-Chia"},{"first_name":"Jacqueline M.","last_name":"Cole","full_name":"Cole, Jacqueline M."},{"first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alison J.","last_name":"Edwards","full_name":"Edwards, Alison J."},{"full_name":"Piltz, Ross O.","first_name":"Ross O.","last_name":"Piltz"},{"full_name":"Pérez-Moreno, Javier","first_name":"Javier","last_name":"Pérez-Moreno"},{"full_name":"Seo, Ji-Youn","first_name":"Ji-Youn","last_name":"Seo"},{"full_name":"Lee, Seung-Chul","last_name":"Lee","first_name":"Seung-Chul"},{"last_name":"Clays","first_name":"Koen","full_name":"Clays, Koen"},{"last_name":"Kwon","first_name":"O-Pil","full_name":"Kwon, O-Pil"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","quality_controlled":"1","citation":{"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.” <i>The Journal of Physical Chemistry C</i>, vol. 117, no. 18, American Chemical Society (ACS), 2013, pp. 9416–30, doi:<a href=\"https://doi.org/10.1021/jp400648q\">10.1021/jp400648q</a>.","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. <i>The Journal of Physical Chemistry C</i>. American Chemical Society (ACS). <a href=\"https://doi.org/10.1021/jp400648q\">https://doi.org/10.1021/jp400648q</a>","ieee":"T.-C. Lin <i>et al.</i>, “Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations,” <i>The Journal of Physical Chemistry C</i>, vol. 117, no. 18. American Chemical Society (ACS), pp. 9416–9430, 2013.","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. <i>The Journal of Physical Chemistry C</i>. 2013;117(18):9416-9430. doi:<a href=\"https://doi.org/10.1021/jp400648q\">10.1021/jp400648q</a>","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.","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.” <i>The Journal of Physical Chemistry C</i>. American Chemical Society (ACS), 2013. <a href=\"https://doi.org/10.1021/jp400648q\">https://doi.org/10.1021/jp400648q</a>.","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."},"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."}],"publication_status":"published","_id":"6370","language":[{"iso":"eng"}],"doi":"10.1021/jp400648q","publication":"The Journal of Physical Chemistry C","title":"Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations"},{"date_published":"2013-06-13T00:00:00Z","file":[{"date_updated":"2020-07-14T12:47:30Z","file_id":"6441","file_name":"2013_TechRep_Henzinger.pdf","checksum":"a219ba4eada6cd62befed52262ee15d4","access_level":"open_access","relation":"main_file","date_created":"2019-05-13T14:11:39Z","content_type":"application/pdf","creator":"dernst","file_size":549684}],"page":"23","pubrep_id":"124","file_date_updated":"2020-07-14T12:47:30Z","publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"publication_identifier":{"issn":["2664-1690"]},"date_created":"2019-05-13T14:13:27Z","month":"06","status":"public","citation":{"ama":"Henzinger TA, Payer H, Sezgin A. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">10.15479/AT:IST-2013-124-v1-1</a>","ieee":"T. A. Henzinger, H. Payer, and A. Sezgin, <i>Replacing competition with cooperation to achieve scalable lock-free FIFO queues </i>. IST Austria, 2013.","chicago":"Henzinger, Thomas A, Hannes Payer, and Ali Sezgin. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">https://doi.org/10.15479/AT:IST-2013-124-v1-1</a>.","short":"T.A. Henzinger, H. Payer, 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. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">10.15479/AT:IST-2013-124-v1-1</a>.","apa":"Henzinger, T. A., Payer, H., &#38; Sezgin, A. (2013). <i>Replacing competition with cooperation to achieve scalable lock-free FIFO queues </i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">https://doi.org/10.15479/AT:IST-2013-124-v1-1</a>"},"author":[{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Payer, Hannes","first_name":"Hannes","last_name":"Payer"},{"first_name":"Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","full_name":"Sezgin, Ali"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"technical_report","date_updated":"2020-07-14T23:06:19Z","oa_version":"Published Version","day":"13","year":"2013","title":"Replacing competition with cooperation to achieve scalable lock-free FIFO queues ","oa":1,"ddc":["000","005"],"doi":"10.15479/AT:IST-2013-124-v1-1","language":[{"iso":"eng"}],"has_accepted_license":"1","_id":"6440","department":[{"_id":"ToHe"}],"publication_status":"published","abstract":[{"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.","lang":"eng"}]},{"oa_version":"Published Version","date_updated":"2021-01-12T08:08:56Z","type":"journal_article","day":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","doi":"10.5201/ipol.2013.53","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","language":[{"iso":"eng"}],"file":[{"relation":"main_file","date_created":"2019-08-05T12:33:40Z","creator":"dernst","content_type":"application/pdf","file_size":4306158,"file_id":"6769","date_updated":"2020-07-14T12:47:40Z","file_name":"2013_IPOL_Mondelli.pdf","checksum":"83b7d429bc248c6c461229d3504fb139","access_level":"open_access"}],"date_published":"2013-07-11T00:00:00Z","page":"68-111","publication_identifier":{"issn":["2105-1232"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"year":"2013","citation":{"ama":"Mondelli M. A finite difference scheme for the stack filter simulating the MCM. <i>Image Processing On Line</i>. 2013;3:68-111. doi:<a href=\"https://doi.org/10.5201/ipol.2013.53\">10.5201/ipol.2013.53</a>","ieee":"M. Mondelli, “A finite difference scheme for the stack filter simulating the MCM,” <i>Image Processing On Line</i>, 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.","short":"M. Mondelli, Image Processing On Line 3 (2013) 68–111.","chicago":"Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” <i>Image Processing On Line</i>. Image Processing On Line, 2013. <a href=\"https://doi.org/10.5201/ipol.2013.53\">https://doi.org/10.5201/ipol.2013.53</a>.","apa":"Mondelli, M. (2013). A finite difference scheme for the stack filter simulating the MCM. <i>Image Processing On Line</i>. Image Processing On Line. <a href=\"https://doi.org/10.5201/ipol.2013.53\">https://doi.org/10.5201/ipol.2013.53</a>","mla":"Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” <i>Image Processing On Line</i>, vol. 3, Image Processing On Line, 2013, pp. 68–111, doi:<a href=\"https://doi.org/10.5201/ipol.2013.53\">10.5201/ipol.2013.53</a>."},"extern":"1","quality_controlled":"1","author":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco"}],"abstract":[{"text":"The paper presents an algorithm that applies a stack filter simulating the Mean Curvature Motion equation via a finite difference scheme.","lang":"eng"}],"publication_status":"published","title":"A finite difference scheme for the stack filter simulating the MCM","publication":"Image Processing On Line","_id":"6768","ddc":["510"],"oa":1,"file_date_updated":"2020-07-14T12:47:40Z","publisher":"Image Processing On Line","article_type":"original","volume":3,"month":"07","date_created":"2019-08-05T12:30:38Z","status":"public","intvolume":"         3"},{"acknowledgement":"This work was supported by the ERC Advanced Grant 227758, the National Science Foundation under Career Grant No. DMR-0846426, the Wolfson Merit Award 2007/R3 of the Royal Society of London and the EPSRC Programme Grant EP/I001352/1. BMM acknowledge T. Curk and A. Ballard for useful discussions. C. V. acknowledges financial support from a Juan de la Cierva Fellowship, from the Marie Curie Integration Grant PCIG-GA-2011-303941 ANISOKINEQ, and from the National Project FIS2010- 16159. S. A-U acknowledges support from the Alexander von Humboldt Foundation.","language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.111.245702","day":"11","oa_version":"Preprint","type":"journal_article","date_updated":"2021-11-29T14:05:19Z","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","arxiv":1,"scopus_import":"1","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"keyword":["general physics and astronomy"],"external_id":{"pmid":["24483677"],"arxiv":["1311.4681"]},"date_published":"2013-12-11T00:00:00Z","abstract":[{"text":"Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.","lang":"eng"}],"publication_status":"published","_id":"10384","oa":1,"pmid":1,"publication":"Physical Review Letters","title":"Living clusters and crystals from low-density suspensions of active colloids","year":"2013","quality_controlled":"1","author":[{"full_name":"Mognetti, B. M.","first_name":"B. M.","last_name":"Mognetti"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Angioletti-Uberti, S.","first_name":"S.","last_name":"Angioletti-Uberti"},{"first_name":"A.","last_name":"Cacciuto","full_name":"Cacciuto, A."},{"first_name":"C.","last_name":"Valeriani","full_name":"Valeriani, C."},{"last_name":"Frenkel","first_name":"D.","full_name":"Frenkel, D."}],"extern":"1","citation":{"mla":"Mognetti, B. M., et al. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” <i>Physical Review Letters</i>, vol. 111, no. 24, 245702, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/physrevlett.111.245702\">10.1103/physrevlett.111.245702</a>.","apa":"Mognetti, B. M., Šarić, A., Angioletti-Uberti, S., Cacciuto, A., Valeriani, C., &#38; Frenkel, D. (2013). Living clusters and crystals from low-density suspensions of active colloids. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.111.245702\">https://doi.org/10.1103/physrevlett.111.245702</a>","ama":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. Living clusters and crystals from low-density suspensions of active colloids. <i>Physical Review Letters</i>. 2013;111(24). doi:<a href=\"https://doi.org/10.1103/physrevlett.111.245702\">10.1103/physrevlett.111.245702</a>","ieee":"B. M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel, “Living clusters and crystals from low-density suspensions of active colloids,” <i>Physical Review Letters</i>, vol. 111, no. 24. American Physical Society, 2013.","chicago":"Mognetti, B. M., Anđela Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/physrevlett.111.245702\">https://doi.org/10.1103/physrevlett.111.245702</a>.","short":"B.M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, D. Frenkel, Physical Review Letters 111 (2013).","ista":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. 2013. Living clusters and crystals from low-density suspensions of active colloids. Physical Review Letters. 111(24), 245702."},"main_file_link":[{"url":"https://arxiv.org/abs/1311.4681","open_access":"1"}],"status":"public","article_number":"245702","month":"12","date_created":"2021-11-29T13:29:31Z","intvolume":"       111","publisher":"American Physical Society","article_type":"original","issue":"24","volume":111},{"abstract":[{"lang":"eng","text":"We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials."}],"publication_status":"published","_id":"10385","title":"Collapsing nanoparticle-laden nanotubes","publication":"Soft Matter","year":"2013","quality_controlled":"1","author":[{"first_name":"Joseph A.","last_name":"Napoli","full_name":"Napoli, Joseph A."},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Cacciuto, Angelo","first_name":"Angelo","last_name":"Cacciuto"}],"extern":"1","citation":{"mla":"Napoli, Joseph A., et al. “Collapsing Nanoparticle-Laden Nanotubes.” <i>Soft Matter</i>, vol. 9, no. 37, Royal Society of Chemistry, 2013, pp. 8881–86, doi:<a href=\"https://doi.org/10.1039/c3sm51495a\">10.1039/c3sm51495a</a>.","apa":"Napoli, J. A., Šarić, A., &#38; Cacciuto, A. (2013). Collapsing nanoparticle-laden nanotubes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm51495a\">https://doi.org/10.1039/c3sm51495a</a>","short":"J.A. Napoli, A. Šarić, A. Cacciuto, Soft Matter 9 (2013) 8881–8886.","chicago":"Napoli, Joseph A., Anđela Šarić, and Angelo Cacciuto. “Collapsing Nanoparticle-Laden Nanotubes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm51495a\">https://doi.org/10.1039/c3sm51495a</a>.","ista":"Napoli JA, Šarić A, Cacciuto A. 2013. Collapsing nanoparticle-laden nanotubes. Soft Matter. 9(37), 8881–8886.","ieee":"J. A. Napoli, A. Šarić, and A. Cacciuto, “Collapsing nanoparticle-laden nanotubes,” <i>Soft Matter</i>, vol. 9, no. 37. Royal Society of Chemistry, pp. 8881–8886, 2013.","ama":"Napoli JA, Šarić A, Cacciuto A. Collapsing nanoparticle-laden nanotubes. <i>Soft Matter</i>. 2013;9(37):8881-8886. doi:<a href=\"https://doi.org/10.1039/c3sm51495a\">10.1039/c3sm51495a</a>"},"status":"public","month":"08","date_created":"2021-11-29T13:31:24Z","intvolume":"         9","article_type":"original","publisher":"Royal Society of Chemistry","issue":"37","volume":9,"acknowledgement":"This work was supported by the National Science Foundation under Career Grant no. DMR-0846426.","doi":"10.1039/c3sm51495a","language":[{"iso":"eng"}],"day":"08","oa_version":"None","date_updated":"2021-11-29T14:05:23Z","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","scopus_import":"1","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"page":"8881-8886","keyword":["condensed matter physics","general chemistry"],"date_published":"2013-08-08T00:00:00Z"},{"acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR 0846426. The authors thank J. C. Pàmies for many fruitful discussions on the subject.","doi":"10.1039/c3sm50188d","language":[{"iso":"eng"}],"day":"03","date_updated":"2021-11-29T14:29:31Z","type":"journal_article","oa_version":"None","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"scopus_import":"1","date_published":"2013-05-03T00:00:00Z","keyword":["condensed matter physics","general chemistry"],"publication_status":"published","abstract":[{"text":"In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface.","lang":"eng"}],"_id":"10386","title":"Self-assembly of nanoparticles adsorbed on fluid and elastic membranes","publication":"Soft Matter","year":"2013","quality_controlled":"1","author":[{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Cacciuto, Angelo","last_name":"Cacciuto","first_name":"Angelo"}],"extern":"1","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2013/sm/c3sm50188d"}],"citation":{"short":"A. Šarić, A. Cacciuto, Soft Matter 9 (2013).","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm50188d\">https://doi.org/10.1039/c3sm50188d</a>.","ista":"Šarić A, Cacciuto A. 2013. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 9(29), 6677.","ama":"Šarić A, Cacciuto A. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. <i>Soft Matter</i>. 2013;9(29). doi:<a href=\"https://doi.org/10.1039/c3sm50188d\">10.1039/c3sm50188d</a>","ieee":"A. Šarić and A. Cacciuto, “Self-assembly of nanoparticles adsorbed on fluid and elastic membranes,” <i>Soft Matter</i>, vol. 9, no. 29. Royal Society of Chemistry, 2013.","mla":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” <i>Soft Matter</i>, vol. 9, no. 29, 6677, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3sm50188d\">10.1039/c3sm50188d</a>.","apa":"Šarić, A., &#38; Cacciuto, A. (2013). Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm50188d\">https://doi.org/10.1039/c3sm50188d</a>"},"article_number":"6677","status":"public","date_created":"2021-11-29T14:06:32Z","month":"05","intvolume":"         9","article_type":"original","publisher":"Royal Society of Chemistry","volume":9,"issue":"29"},{"day":"01","date_updated":"2021-12-02T12:51:12Z","type":"journal_article","oa_version":"Submitted Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","doi":"10.1515/bmt-2013-4181","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"has_accepted_license":"1","date_published":"2013-08-01T00:00:00Z","file":[{"success":1,"date_updated":"2021-12-01T14:38:08Z","file_id":"10397","file_name":"Schloegl_Abstract-BMT2013.pdf","checksum":"cdfc5339b530a25d6079f7223f0b1f16","access_level":"open_access","relation":"main_file","date_created":"2021-12-01T14:38:08Z","file_size":149825,"content_type":"application/pdf","creator":"schloegl"}],"keyword":["biomedical engineering","data analysis","free software"],"external_id":{"pmid":["24042795"]},"publication_identifier":{"eissn":["1862-278X"],"issn":["0013-5585"]},"year":"2013","author":[{"last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas"},{"last_name":"Schmidt-Hieber","first_name":"C.","full_name":"Schmidt-Hieber, C."},{"last_name":"Guzman","first_name":"S. J.","full_name":"Guzman, S. J."}],"quality_controlled":"1","citation":{"mla":"Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>.","apa":"Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., &#38; Guzman, S. J. (2013). Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. Graz, Austria: De Gruyter. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>","ama":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. 2013;58(SI-1-Track-G). doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>","ieee":"A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A fast visualization and analysis environment for cellular neurophysiology,” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G. De Gruyter, 2013.","ista":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.","chicago":"Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>. De Gruyter, 2013. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>.","short":"A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013)."},"publication_status":"published","abstract":[{"text":"Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable.","lang":"eng"}],"oa":1,"ddc":["005","610"],"_id":"10396","publication":"Biomedical Engineering / Biomedizinische Technik","title":"Stimfit: A fast visualization and analysis environment for cellular neurophysiology","pmid":1,"publisher":"De Gruyter","article_type":"original","file_date_updated":"2021-12-01T14:38:08Z","issue":"SI-1-Track-G","volume":58,"status":"public","article_number":"000010151520134181","date_created":"2021-12-01T14:35:35Z","conference":{"location":"Graz, Austria","start_date":"2013-09-19","name":"BMT: Biomedizinische Technik ","end_date":"2013-09-21"},"month":"08","intvolume":"        58"},{"month":"03","conference":{"end_date":"2013-03-22","name":"APS: American Physical Society","location":"Baltimore, MD, United States","start_date":"2013-03-18"},"date_created":"2022-02-08T10:34:29Z","status":"public","article_number":"N36.00001","intvolume":"        58","publisher":"American Physical Society","volume":58,"issue":"1","abstract":[{"lang":"eng","text":"Fluxoid quantization provides a direct means to study phase coherence. In cuprate superconductors, there have been observations which suggest that phase coherent superconducting fluctuations may persist at temperatures significantly above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate superconducting samples to directly probe phase coherence over a wide range of temperatures. We present cantilever torque susceptometry measurements of micron and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique allowed observation of transitions between different fluxoid states of a single ring, and the discrete vortex states of micron size disks. The dependence of magnetic susceptibility on diameter and wall thickness of the ring was investigated. Measurements were made at different values of the in-plane magnetic field, and over a wide range of temperatures."}],"publication_status":"published","publication":"APS March Meeting 2013","title":"Cantilever micro-susceptometry of mesoscopic Bi2212 samples","_id":"10749","oa":1,"year":"2013","citation":{"ieee":"H. Polshyn, R. Budakian, and G. Gu, “Cantilever micro-susceptometry of mesoscopic Bi2212 samples,” in <i>APS March Meeting 2013</i>, Baltimore, MD, United States, 2013, vol. 58, no. 1.","ama":"Polshyn H, Budakian R, Gu G. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In: <i>APS March Meeting 2013</i>. Vol 58. American Physical Society; 2013.","chicago":"Polshyn, Hryhoriy, Raffi Budakian, and Genda Gu. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” In <i>APS March Meeting 2013</i>, Vol. 58. American Physical Society, 2013.","short":"H. Polshyn, R. Budakian, G. Gu, in:, APS March Meeting 2013, American Physical Society, 2013.","ista":"Polshyn H, Budakian R, Gu G. 2013. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. APS March Meeting 2013. APS: American Physical Society, Bulletin of the American Physical Society, vol. 58, N36.00001.","apa":"Polshyn, H., Budakian, R., &#38; Gu, G. (2013). Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In <i>APS March Meeting 2013</i> (Vol. 58). Baltimore, MD, United States: American Physical Society.","mla":"Polshyn, Hryhoriy, et al. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” <i>APS March Meeting 2013</i>, vol. 58, no. 1, N36.00001, American Physical Society, 2013."},"main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR13/Event/186873","open_access":"1"}],"extern":"1","quality_controlled":"1","author":[{"last_name":"Polshyn","first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896"},{"full_name":"Budakian, Raffi","first_name":"Raffi","last_name":"Budakian"},{"first_name":"Genda","last_name":"Gu","full_name":"Gu, Genda"}],"alternative_title":["Bulletin of the American Physical Society"],"publication_identifier":{"issn":["0003-0503"]},"date_published":"2013-03-01T00:00:00Z","acknowledgement":"This work was supported by the Center for Emergent Superconductivity, an Energy Frontier Research Center funded by the US DOE, Office of Science.","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"conference","date_updated":"2022-02-08T10:48:06Z","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No"},{"page":"193-205","date_published":"2013-03-28T00:00:00Z","external_id":{"pmid":["23540698"]},"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"scopus_import":"1","day":"28","date_updated":"2021-12-14T08:25:35Z","type":"journal_article","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","doi":"10.1016/j.cell.2013.02.033","language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"article_type":"original","publisher":"Elsevier","volume":153,"issue":"1","status":"public","date_created":"2021-06-04T12:23:28Z","month":"03","intvolume":"       153","year":"2013","quality_controlled":"1","extern":"1","author":[{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung","last_name":"Hsieh"},{"first_name":"Devin","last_name":"Coleman-Derr","full_name":"Coleman-Derr, Devin"},{"full_name":"Eshed-Williams, Leor","last_name":"Eshed-Williams","first_name":"Leor"},{"full_name":"Thao, Ka","first_name":"Ka","last_name":"Thao"},{"last_name":"Harmer","first_name":"Stacey L.","full_name":"Harmer, Stacey L."},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"}],"citation":{"apa":"Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>","mla":"Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>.","ama":"Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. 2013;153(1):193-205. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>","ieee":"A. Zemach <i>et al.</i>, “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” <i>Cell</i>, vol. 153, no. 1. Elsevier, pp. 193–205, 2013.","short":"A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.","chicago":"Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>.","ista":"Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205."},"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.02.033","open_access":"1"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway."}],"oa":1,"_id":"9459","publication":"Cell","title":"The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin","pmid":1},{"year":"2013","quality_controlled":"1","extern":"1","author":[{"first_name":"Jessica A.","last_name":"Rodrigues","full_name":"Rodrigues, Jessica A."},{"full_name":"Ruan, Randy","last_name":"Ruan","first_name":"Randy"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"last_name":"Sharma","first_name":"Manoj K.","full_name":"Sharma, Manoj K."},{"first_name":"Rita","last_name":"Sharma","full_name":"Sharma, Rita"},{"last_name":"Ronald","first_name":"Pamela C","full_name":"Ronald, Pamela C"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"}],"citation":{"apa":"Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>","mla":"Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7934–39, doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>.","ista":"Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 110(19), 7934–7939.","chicago":"Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>.","short":"J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939.","ieee":"J. A. Rodrigues <i>et al.</i>, “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013.","ama":"Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2013;110(19):7934-7939. doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1306164110"}],"publication_status":"published","abstract":[{"text":"Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants.","lang":"eng"}],"oa":1,"_id":"9481","title":"Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm","publication":"Proceedings of the National Academy of Sciences","pmid":1,"article_type":"original","publisher":"National Academy of Sciences","issue":"19","volume":110,"status":"public","date_created":"2021-06-07T07:31:02Z","month":"05","intvolume":"       110","day":"07","date_updated":"2021-12-14T08:26:44Z","type":"journal_article","oa_version":"Published Version","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1073/pnas.1306164110","language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"page":"7934-7939","date_published":"2013-05-07T00:00:00Z","external_id":{"pmid":["23613580"]},"keyword":["Multidisciplinary"],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1"},{"intvolume":"        24","date_created":"2021-06-08T06:14:50Z","month":"02","status":"public","volume":24,"issue":"3","publisher":"Elsevier","article_type":"review","title":"A conversation across generations: Soma-germ cell crosstalk in plants","publication":"Developmental Cell","pmid":1,"oa":1,"_id":"9520","publication_status":"published","abstract":[{"lang":"eng","text":"Plants undergo alternation of generation in which reproductive cells develop in the plant body (\"sporophytic generation\") and then differentiate into a multicellular gamete-forming \"gametophytic generation.\" Different populations of helper cells assist in this transgenerational journey, with somatic tissues supporting early development and single nurse cells supporting gametogenesis. New data reveal a two-way relationship between early reproductive cells and their helpers involving complex epigenetic and signaling networks determining cell number and fate. Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes."}],"citation":{"mla":"Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>, vol. 24, no. 3, Elsevier, 2013, pp. 215–25, doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>.","apa":"Feng, X., Zilberman, D., &#38; Dickinson, H. (2013). A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>","ista":"Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.","chicago":"Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>.","short":"X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.","ama":"Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. 2013;24(3):215-225. doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>","ieee":"X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” <i>Developmental Cell</i>, vol. 24, no. 3. Elsevier, pp. 215–225, 2013."},"main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2013.01.014","open_access":"1"}],"author":[{"last_name":"Feng","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"last_name":"Dickinson","first_name":"Hugh","full_name":"Dickinson, Hugh"}],"quality_controlled":"1","extern":"1","year":"2013","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"scopus_import":"1","date_published":"2013-02-11T00:00:00Z","external_id":{"pmid":["23410937"]},"page":"215-225","language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2013.01.014","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_updated":"2023-05-08T11:00:59Z","oa_version":"Published Version","day":"11"},{"intvolume":"       138","month":"04","date_created":"2021-07-15T09:27:58Z","status":"public","article_number":"164314","volume":138,"issue":"16","publisher":"AIP Publishing","article_type":"original","pmid":1,"title":"Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion","publication":"The Journal of Chemical Physics","_id":"9663","oa":1,"abstract":[{"text":"Molecular dynamics simulations of small Cu nanoparticles using three different interatomic potentials at rising temperature indicate that small nanoparticles can undergo solid-solid structural transitions through a direct geometrical conversion route. The direct geometrical conversion can happen for cuboctahedral nanoparticles, which turn into an icosahedra shape: one diagonal of the square faces contracts, and the faces are folded along the diagonal to give rise to two equilateral triangles. The transition is a kinetic process that cannot be fully explained through an energetic point of view. It has low activation energy and fast reaction time in the simulations. The transition mechanism is via the transmission of shear waves initiated from the particle surface and does not involve dislocation activity.","lang":"eng"}],"publication_status":"published","citation":{"ama":"Cheng B, Ngan AHW. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. <i>The Journal of Chemical Physics</i>. 2013;138(16). doi:<a href=\"https://doi.org/10.1063/1.4802025\">10.1063/1.4802025</a>","ieee":"B. Cheng and A. H. W. Ngan, “Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion,” <i>The Journal of Chemical Physics</i>, vol. 138, no. 16. AIP Publishing, 2013.","ista":"Cheng B, Ngan AHW. 2013. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. 138(16), 164314.","short":"B. Cheng, A.H.W. Ngan, The Journal of Chemical Physics 138 (2013).","chicago":"Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2013. <a href=\"https://doi.org/10.1063/1.4802025\">https://doi.org/10.1063/1.4802025</a>.","apa":"Cheng, B., &#38; Ngan, A. H. W. (2013). Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4802025\">https://doi.org/10.1063/1.4802025</a>","mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” <i>The Journal of Chemical Physics</i>, vol. 138, no. 16, 164314, AIP Publishing, 2013, doi:<a href=\"https://doi.org/10.1063/1.4802025\">10.1063/1.4802025</a>."},"main_file_link":[{"open_access":"1","url":"https://pubmed.ncbi.nlm.nih.gov/23635145/"}],"extern":"1","author":[{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing"},{"first_name":"Alfonso H. W.","last_name":"Ngan","full_name":"Ngan, Alfonso H. W."}],"quality_controlled":"1","year":"2013","scopus_import":"1","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"external_id":{"pmid":["23635145"]},"date_published":"2013-04-28T00:00:00Z","doi":"10.1063/1.4802025","language":[{"iso":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","oa_version":"Submitted Version","type":"journal_article","date_updated":"2021-08-09T12:35:34Z","day":"28"}]