[{"type":"journal_article","day":"07","date_updated":"2021-12-14T08:26:44Z","date_created":"2021-06-07T07:31:02Z","status":"public","page":"7934-7939","pmid":1,"publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.1306164110","external_id":{"pmid":["23613580"]},"volume":110,"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"title":"Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm","_id":"9481","quality_controlled":"1","intvolume":"       110","department":[{"_id":"DaZi"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1306164110"}],"extern":"1","oa":1,"month":"05","citation":{"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.","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.","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>","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.","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>."},"issue":"19","author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"full_name":"Ruan, Randy","last_name":"Ruan","first_name":"Randy"},{"first_name":"Toshiro","last_name":"Nishimura","full_name":"Nishimura, Toshiro"},{"full_name":"Sharma, Manoj K.","first_name":"Manoj K.","last_name":"Sharma"},{"last_name":"Sharma","first_name":"Rita","full_name":"Sharma, Rita"},{"full_name":"Ronald, Pamela C","last_name":"Ronald","first_name":"Pamela C"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"keyword":["Multidisciplinary"],"article_type":"original","year":"2013","oa_version":"Published Version","publication_status":"published","date_published":"2013-05-07T00:00:00Z"},{"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2013.01.014"}],"oa":1,"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"title":"A conversation across generations: Soma-germ cell crosstalk in plants","_id":"9520","quality_controlled":"1","intvolume":"        24","article_type":"review","year":"2013","publication_status":"published","oa_version":"Published Version","date_published":"2013-02-11T00:00:00Z","month":"02","issue":"3","citation":{"ista":"Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.","short":"X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 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>.","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>","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>.","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.","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>"},"author":[{"orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"full_name":"Dickinson, Hugh","first_name":"Hugh","last_name":"Dickinson"}],"page":"215-225","pmid":1,"publisher":"Elsevier","publication":"Developmental Cell","type":"journal_article","day":"11","date_updated":"2023-05-08T11:00:59Z","status":"public","date_created":"2021-06-08T06:14:50Z","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"doi":"10.1016/j.devcel.2013.01.014","external_id":{"pmid":["23410937"]},"volume":24},{"pmid":1,"publisher":"AIP Publishing","publication":"The Journal of Chemical Physics","date_updated":"2021-08-09T12:35:34Z","type":"journal_article","day":"28","date_created":"2021-07-15T09:27:58Z","status":"public","language":[{"iso":"eng"}],"article_number":"164314","scopus_import":"1","article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.1063/1.4802025","external_id":{"pmid":["23635145"]},"volume":138,"main_file_link":[{"url":"https://pubmed.ncbi.nlm.nih.gov/23635145/","open_access":"1"}],"extern":"1","oa":1,"title":"Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion","_id":"9663","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"intvolume":"       138","quality_controlled":"1","article_type":"original","date_published":"2013-04-28T00:00:00Z","year":"2013","oa_version":"Submitted Version","publication_status":"published","month":"04","issue":"16","citation":{"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>","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.","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>.","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>","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>.","short":"B. Cheng, A.H.W. Ngan, The Journal of Chemical Physics 138 (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."},"author":[{"last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"full_name":"Ngan, Alfonso H. W.","last_name":"Ngan","first_name":"Alfonso H. W."}]},{"publisher":"Elsevier","publication":"International Journal of Plasticity","extern":"1","page":"65-79","date_created":"2021-07-15T14:27:44Z","intvolume":"        47","status":"public","quality_controlled":"1","title":"The crystal structures of sintered copper nanoparticles: A molecular dynamics study","date_updated":"2023-02-23T14:04:30Z","_id":"9674","publication_identifier":{"issn":["0749-6419"]},"type":"journal_article","day":"01","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The coalescence of nano-crystals during sintering is often found to result in interesting crystalline structures such as multi-fold twins, and yet the plasticity mechanism accompanying their formation is unclear. In this work, the sintering behavior of two unsupported copper nanoparticles initially at room temperature is investigated by molecular dynamics simulations under the constant-energy ensemble. The results reveal that once the two nanoparticles are brought into contact, they often go through drastic structural changes with the inter-particle grain boundary quickly eliminated, and single- and multi-fold twinning occurs frequently in the coalesced product. Whereas the formation of single twins is found to be via the more usual mechanism of emission of Shockley partials on {1 1 1} planes, the formation of fivefold twins, however, takes place via a novel dislocation-free mechanism involving a series of shear and rigid-body rotation processes caused by elastic waves with amplitudes not corresponding to any allowable Burgers vector in the fcc lattice. Such a lattice-wave, dislocation-free twinning mechanism has never been reported before."}],"date_published":"2013-08-01T00:00:00Z","year":"2013","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publication_status":"published","oa_version":"None","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","author":[{"first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"full_name":"Ngan, Alfonso H.W.","last_name":"Ngan","first_name":"Alfonso H.W."}],"volume":47,"month":"08","citation":{"ista":"Cheng B, Ngan AHW. 2013. The crystal structures of sintered copper nanoparticles: A molecular dynamics study. International Journal of Plasticity. 47, 65–79.","short":"B. Cheng, A.H.W. Ngan, International Journal of Plasticity 47 (2013) 65–79.","chicago":"Cheng, Bingqing, and Alfonso H.W. Ngan. “The Crystal Structures of Sintered Copper Nanoparticles: A Molecular Dynamics Study.” <i>International Journal of Plasticity</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.ijplas.2013.01.006\">https://doi.org/10.1016/j.ijplas.2013.01.006</a>.","mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “The Crystal Structures of Sintered Copper Nanoparticles: A Molecular Dynamics Study.” <i>International Journal of Plasticity</i>, vol. 47, Elsevier, 2013, pp. 65–79, doi:<a href=\"https://doi.org/10.1016/j.ijplas.2013.01.006\">10.1016/j.ijplas.2013.01.006</a>.","apa":"Cheng, B., &#38; Ngan, A. H. W. (2013). The crystal structures of sintered copper nanoparticles: A molecular dynamics study. <i>International Journal of Plasticity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijplas.2013.01.006\">https://doi.org/10.1016/j.ijplas.2013.01.006</a>","ieee":"B. Cheng and A. H. W. Ngan, “The crystal structures of sintered copper nanoparticles: A molecular dynamics study,” <i>International Journal of Plasticity</i>, vol. 47. Elsevier, pp. 65–79, 2013.","ama":"Cheng B, Ngan AHW. The crystal structures of sintered copper nanoparticles: A molecular dynamics study. <i>International Journal of Plasticity</i>. 2013;47:65-79. doi:<a href=\"https://doi.org/10.1016/j.ijplas.2013.01.006\">10.1016/j.ijplas.2013.01.006</a>"},"doi":"10.1016/j.ijplas.2013.01.006"},{"doi":"10.1016/j.commatsci.2013.03.014","month":"06","citation":{"ista":"Cheng B, Ngan AHW. 2013. The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. Computational Materials Science. 74, 1–11.","chicago":"Cheng, Bingqing, and Alfonso H.W. Ngan. “The Sintering and Densification Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” <i>Computational Materials Science</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.commatsci.2013.03.014\">https://doi.org/10.1016/j.commatsci.2013.03.014</a>.","short":"B. Cheng, A.H.W. Ngan, Computational Materials Science 74 (2013) 1–11.","ama":"Cheng B, Ngan AHW. The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. <i>Computational Materials Science</i>. 2013;74:1-11. doi:<a href=\"https://doi.org/10.1016/j.commatsci.2013.03.014\">10.1016/j.commatsci.2013.03.014</a>","mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “The Sintering and Densification Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” <i>Computational Materials Science</i>, vol. 74, Elsevier, 2013, pp. 1–11, doi:<a href=\"https://doi.org/10.1016/j.commatsci.2013.03.014\">10.1016/j.commatsci.2013.03.014</a>.","apa":"Cheng, B., &#38; Ngan, A. H. W. (2013). The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. <i>Computational Materials Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.commatsci.2013.03.014\">https://doi.org/10.1016/j.commatsci.2013.03.014</a>","ieee":"B. Cheng and A. H. W. Ngan, “The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study,” <i>Computational Materials Science</i>, vol. 74. Elsevier, pp. 1–11, 2013."},"author":[{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"first_name":"Alfonso H.W.","last_name":"Ngan","full_name":"Ngan, Alfonso H.W."}],"volume":74,"article_type":"original","scopus_import":"1","language":[{"iso":"eng"}],"year":"2013","publication_status":"published","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"None","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Despite its relevance to a range of technological applications including nanocrystalline material fabrication, the sintering mechanisms of nanoparticles have not been well understood. It has been recognized that extrapolation from understanding of macro-particle sintering is unreliable for the nano-particle size regime. In this work, the sintering behaviour of copper nanoparticles under periodic boundary conditions at different temperatures and pressures was investigated by Molecular Dynamics simulations. It was found that smaller particle sizes, higher temperature and higher external pressure facilitate densification. Through a comparison with a two-sphere model, the governing mechanisms for many nanoparticles sintered at low temperature (T⩽900K) were identified to be a variety of plasticity processes including dislocation, twinning and even amorphization at the contact neck regions, due to the presence of high stresses."}],"date_published":"2013-06-01T00:00:00Z","publication_identifier":{"issn":["0927-0256"]},"type":"journal_article","day":"01","title":"The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study","date_updated":"2023-02-23T14:04:35Z","_id":"9676","quality_controlled":"1","status":"public","date_created":"2021-07-16T06:46:38Z","intvolume":"        74","page":"1-11","extern":"1","publisher":"Elsevier","publication":"Computational Materials Science"},{"doi":"10.1016/j.msea.2013.07.065","month":"11","citation":{"ista":"Cheng B, Ngan AHW. 2013. Crystal plasticity of Cu nanocrystals during collision. Materials Science and Engineering: A. 585, 326–334.","short":"B. Cheng, A.H.W. Ngan, Materials Science and Engineering: A 585 (2013) 326–334.","chicago":"Cheng, Bingqing, and Alfonso H.W. Ngan. “Crystal Plasticity of Cu Nanocrystals during Collision.” <i>Materials Science and Engineering: A</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.msea.2013.07.065\">https://doi.org/10.1016/j.msea.2013.07.065</a>.","mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “Crystal Plasticity of Cu Nanocrystals during Collision.” <i>Materials Science and Engineering: A</i>, vol. 585, Elsevier, 2013, pp. 326–34, doi:<a href=\"https://doi.org/10.1016/j.msea.2013.07.065\">10.1016/j.msea.2013.07.065</a>.","ieee":"B. Cheng and A. H. W. Ngan, “Crystal plasticity of Cu nanocrystals during collision,” <i>Materials Science and Engineering: A</i>, vol. 585. Elsevier, pp. 326–334, 2013.","apa":"Cheng, B., &#38; Ngan, A. H. W. (2013). Crystal plasticity of Cu nanocrystals during collision. <i>Materials Science and Engineering: A</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.msea.2013.07.065\">https://doi.org/10.1016/j.msea.2013.07.065</a>","ama":"Cheng B, Ngan AHW. Crystal plasticity of Cu nanocrystals during collision. <i>Materials Science and Engineering: A</i>. 2013;585:326-334. doi:<a href=\"https://doi.org/10.1016/j.msea.2013.07.065\">10.1016/j.msea.2013.07.065</a>"},"author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing"},{"full_name":"Ngan, Alfonso H.W.","last_name":"Ngan","first_name":"Alfonso H.W."}],"volume":585,"article_type":"original","scopus_import":"1","language":[{"iso":"eng"}],"year":"2013","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publication_status":"published","oa_version":"None","article_processing_charge":"No","abstract":[{"text":"In this work, we simulate the response of two Cu nanoparticles colliding at different approaching rates at room temperature by MD. For small nanospheres, the formation of single twins is favored at high approach rates, whereas larger nanospheres mainly deform by dislocation slip. For small nanocubes with large {100} flat surfaces, however, a dislocation-free direct geometrical conversion process that leads to five-fold twinning dominates except at highly retarded approaching rates. For larger nanocubes, single twin formation is the governing plasticity mechanism. The probability for plastic deformation by dislocation slip or twinning is attributed to the abundance of surface steps, which act as sites for dislocation nucleation.","lang":"eng"}],"date_published":"2013-11-15T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0921-5093"]},"day":"15","date_updated":"2023-02-23T14:04:51Z","title":"Crystal plasticity of Cu nanocrystals during collision","_id":"9682","quality_controlled":"1","intvolume":"       585","date_created":"2021-07-19T09:04:36Z","status":"public","page":"326-334","extern":"1","publisher":"Elsevier","publication":"Materials Science and Engineering: A"},{"volume":87,"author":[{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Maksym Serbyn","first_name":"Maksym","last_name":"Serbyn"},{"last_name":"Abanin","first_name":"Dmitry","full_name":"Abanin, Dmitry A"}],"citation":{"mla":"Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau Level Crossings in Biased Trilayer Graphene.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 87, no. 11, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevB.87.115422\">10.1103/PhysRevB.87.115422</a>.","ieee":"M. Serbyn and D. Abanin, “New Dirac points and multiple Landau level crossings in biased trilayer graphene,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 87, no. 11. American Physical Society, 2013.","apa":"Serbyn, M., &#38; Abanin, D. (2013). New Dirac points and multiple Landau level crossings in biased trilayer graphene. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.87.115422\">https://doi.org/10.1103/PhysRevB.87.115422</a>","ama":"Serbyn M, Abanin D. New Dirac points and multiple Landau level crossings in biased trilayer graphene. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2013;87(11). doi:<a href=\"https://doi.org/10.1103/PhysRevB.87.115422\">10.1103/PhysRevB.87.115422</a>","ista":"Serbyn M, Abanin D. 2013. New Dirac points and multiple Landau level crossings in biased trilayer graphene. Physical Review B - Condensed Matter and Materials Physics. 87(11).","chicago":"Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau Level Crossings in Biased Trilayer Graphene.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevB.87.115422\">https://doi.org/10.1103/PhysRevB.87.115422</a>.","short":"M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 87 (2013)."},"issue":"11","month":"03","doi":"10.1103/PhysRevB.87.115422","date_published":"2013-03-18T00:00:00Z","abstract":[{"text":"Recently a new high-mobility Dirac material, trilayer graphene, was realized experimentally. The band structure of ABA-stacked trilayer graphene consists of a monolayer-like and a bilayer-like pair of bands. Here we study electronic properties of ABA-stacked trilayer graphene biased by a perpendicular electric field. We find that the combination of the bias and trigonal warping gives rise to a set of new Dirac points: In each valley, seven species of Dirac fermions with small masses of order of a few meV emerge. The positions and masses of the emergent Dirac fermions are tunable by bias, and one group of Dirac fermions becomes massless at a certain bias value. Therefore, in contrast to bilayer graphene, the conductivity at the neutrality point is expected to show nonmonotonic behavior, becoming of the order of a few e2/h when some Dirac masses vanish. Further, we analyze the evolution of the Landau level spectrum as a function of bias. The emergence of new Dirac points in the band structure translates into new threefold-degenerate groups of Landau levels. This leads to an anomalous quantum Hall effect, in which some quantum Hall steps have a height of 3e2/h. At an intermediate bias, the degeneracies of all Landau levels get lifted, and in this regime all quantum Hall plateaus are spaced by e2/h. Finally, we show that the pattern of Landau level crossings is very sensitive to certain band structure parameters, and can therefore provide a useful tool for determining their precise values.","lang":"eng"}],"publication_status":"published","year":"2013","status":"public","intvolume":"        87","date_created":"2018-12-11T11:49:28Z","quality_controlled":0,"_id":"970","title":"New Dirac points and multiple Landau level crossings in biased trilayer graphene","date_updated":"2021-01-12T08:22:20Z","day":"18","type":"journal_article","publication":"Physical Review B - Condensed Matter and Materials Physics","oa":1,"publisher":"American Physical Society","acknowledgement":"We thank Pablo Jarillo-Herrero, Leonardo Campos, and Thiti Taychatanapat for attracting our attention to the problem of biased trilayer graphene, and for many helpful discussions.","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1212.6251"}],"extern":1,"publist_id":"6428"},{"author":[{"full_name":"Maksym Serbyn","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"full_name":"Skvortsov, Mikhail A","first_name":"Mikhail","last_name":"Skvortsov"}],"volume":87,"month":"01","issue":"2","citation":{"mla":"Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a Voltage-Biased Normal-Superconducting-Normal Microbridge.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 87, no. 2, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevB.87.020501\">10.1103/PhysRevB.87.020501</a>.","apa":"Serbyn, M., &#38; Skvortsov, M. (2013). Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.87.020501\">https://doi.org/10.1103/PhysRevB.87.020501</a>","ieee":"M. Serbyn and M. Skvortsov, “Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 87, no. 2. American Physical Society, 2013.","ama":"Serbyn M, Skvortsov M. Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2013;87(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.87.020501\">10.1103/PhysRevB.87.020501</a>","ista":"Serbyn M, Skvortsov M. 2013. Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. Physical Review B - Condensed Matter and Materials Physics. 87(2).","short":"M. Serbyn, M. Skvortsov, Physical Review B - Condensed Matter and Materials Physics 87 (2013).","chicago":"Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a Voltage-Biased Normal-Superconducting-Normal Microbridge.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevB.87.020501\">https://doi.org/10.1103/PhysRevB.87.020501</a>."},"doi":"10.1103/PhysRevB.87.020501","date_published":"2013-01-02T00:00:00Z","abstract":[{"lang":"eng","text":"We study the stability of the normal state in a mesoscopic NSN junction biased by a constant voltage V with respect to the formation of the superconducting order. Using the linearized time-dependent Ginzburg-Landau equation, we obtain the temperature dependence of the instability line, V inst(T), where nucleation of superconductivity takes place. For sufficiently low biases, a stationary symmetric superconducting state emerges below the instability line. For higher biases, the normal phase is destroyed by the formation of a nonstationary bimodal state with two superconducting nuclei localized near the opposite terminals. The low-temperature and large-voltage behavior of the instability line is highly sensitive to the details of the inelastic relaxation mechanism in the wire. Therefore, experimental studies of Vinst(T) in NSN junctions may be used as an effective tool to access the parameters of the inelastic relaxation in the normal state."}],"year":"2013","publication_status":"published","status":"public","intvolume":"        87","date_created":"2018-12-11T11:49:28Z","quality_controlled":0,"date_updated":"2021-01-12T08:22:20Z","title":"Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge","_id":"971","type":"journal_article","day":"02","publisher":"American Physical Society","oa":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","extern":1,"main_file_link":[{"url":"https://arxiv.org/abs/1208.6004","open_access":"1"}],"acknowledgement":"We are grateful to M. V. Feigel'man, A. Kamenev, T. M. Klapwijk, J. P. Pekola, V. V. Ryazanov, J. C. W. Song, and D. Y. Vodolazov for discussions.","publist_id":"6429"},{"author":[{"full_name":"Okada, Yoshinori","last_name":"Okada","first_name":"Yoshinori"},{"first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lin, Hsin","last_name":"Lin","first_name":"Hsin"},{"full_name":"Walkup, Daniel","first_name":"Daniel","last_name":"Walkup"},{"full_name":"Zhou, Wenwen","last_name":"Zhou","first_name":"Wenwen"},{"last_name":"Dhital","first_name":"Chetan","full_name":"Dhital, Chetan"},{"first_name":"Madhab","last_name":"Neupane","full_name":"Neupane, Madhab"},{"last_name":"Xu","first_name":"Suyang","full_name":"Xu, Suyang"},{"full_name":"Wang, Yungjui","last_name":"Wang","first_name":"Yungjui"},{"last_name":"Sankar","first_name":"Raman","full_name":"Sankar, Raman"},{"full_name":"Chou, Fangcheng","first_name":"Fangcheng","last_name":"Chou"},{"first_name":"Arun","last_name":"Bansil","full_name":"Bansil, Arun"},{"last_name":"Hasan","first_name":"Md","full_name":"Hasan, Md"},{"full_name":"Wilson, Stephen","last_name":"Wilson","first_name":"Stephen"},{"last_name":"Fu","first_name":"Liang","full_name":"Fu, Liang"},{"full_name":"Madhavan, Vidya","last_name":"Madhavan","first_name":"Vidya"}],"issue":"6153","citation":{"ama":"Okada Y, Serbyn M, Lin H, et al. Observation of dirac node formation and mass acquisition in a topological crystalline insulator. <i>Science</i>. 2013;341(6153):1496-1499. doi:<a href=\"https://doi.org/10.1126/science.1239451\">10.1126/science.1239451</a>","mla":"Okada, Yoshinori, et al. “Observation of Dirac Node Formation and Mass Acquisition in a Topological Crystalline Insulator.” <i>Science</i>, vol. 341, no. 6153, American Association for the Advancement of Science, 2013, pp. 1496–99, doi:<a href=\"https://doi.org/10.1126/science.1239451\">10.1126/science.1239451</a>.","apa":"Okada, Y., Serbyn, M., Lin, H., Walkup, D., Zhou, W., Dhital, C., … Madhavan, V. (2013). Observation of dirac node formation and mass acquisition in a topological crystalline insulator. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1239451\">https://doi.org/10.1126/science.1239451</a>","ieee":"Y. Okada <i>et al.</i>, “Observation of dirac node formation and mass acquisition in a topological crystalline insulator,” <i>Science</i>, vol. 341, no. 6153. American Association for the Advancement of Science, pp. 1496–1499, 2013.","ista":"Okada Y, Serbyn M, Lin H, Walkup D, Zhou W, Dhital C, Neupane M, Xu S, Wang Y, Sankar R, Chou F, Bansil A, Hasan M, Wilson S, Fu L, Madhavan V. 2013. Observation of dirac node formation and mass acquisition in a topological crystalline insulator. Science. 341(6153), 1496–1499.","chicago":"Okada, Yoshinori, Maksym Serbyn, Hsin Lin, Daniel Walkup, Wenwen Zhou, Chetan Dhital, Madhab Neupane, et al. “Observation of Dirac Node Formation and Mass Acquisition in a Topological Crystalline Insulator.” <i>Science</i>. American Association for the Advancement of Science, 2013. <a href=\"https://doi.org/10.1126/science.1239451\">https://doi.org/10.1126/science.1239451</a>.","short":"Y. Okada, M. Serbyn, H. Lin, D. Walkup, W. Zhou, C. Dhital, M. Neupane, S. Xu, Y. Wang, R. Sankar, F. Chou, A. Bansil, M. Hasan, S. Wilson, L. Fu, V. Madhavan, Science 341 (2013) 1496–1499."},"month":"01","date_published":"2013-01-01T00:00:00Z","publication_status":"published","oa_version":"Preprint","year":"2013","intvolume":"       341","quality_controlled":"1","_id":"972","title":"Observation of dirac node formation and mass acquisition in a topological crystalline insulator","oa":1,"extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1305.2823","open_access":"1"}],"publist_id":"6430","volume":341,"external_id":{"arxiv":["1305.2823"]},"doi":"10.1126/science.1239451","abstract":[{"lang":"eng","text":"In topological crystalline insulators (TCIs), topology and crystal symmetry intertwine to create surface states with distinct characteristics. The breaking of crystal symmetry in TCIs is predicted to impart mass to the massless Dirac fermions. Here, we report high-resolution scanning tunneling microscopy studies of a TCI, Pb1-xSnxSe that reveal the coexistence of zero-mass Dirac fermions protected by crystal symmetry with massive Dirac fermions consistent with crystal symmetry breaking. In addition, we show two distinct regimes of the Fermi surface topology separated by a Van-Hove singularity at the Lifshitz transition point. Our work paves the way for engineering the Dirac band gap and realizing interaction-driven topological quantum phenomena in TCIs."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"status":"public","date_created":"2018-12-11T11:49:29Z","date_updated":"2021-01-12T08:22:20Z","arxiv":1,"day":"01","type":"journal_article","publication":"Science","publisher":"American Association for the Advancement of Science","page":"1496 - 1499"},{"publisher":"American Physical Society","oa":1,"publication":"Physical Review Letters","publist_id":"6424","main_file_link":[{"url":"https://arxiv.org/abs/1305.5554","open_access":"1"}],"acknowledgement":"We thank J. Moore for useful discussions. Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. Z. P. was supported by DOE Grant No. DE-SC0002140. M. S. was supported by the National Science Foundation under Grant No. DMR-1104498. The simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University.","extern":1,"quality_controlled":0,"intvolume":"       111","status":"public","date_created":"2018-12-11T11:49:29Z","type":"journal_article","day":"17","date_updated":"2021-01-12T08:22:21Z","title":"Local conservation laws and the structure of the many body localized states","_id":"973","year":"2013","publication_status":"published","abstract":[{"text":"We construct a complete set of local integrals of motion that characterize the many-body localized (MBL) phase. Our approach relies on the assumption that local perturbations act locally on the eigenstates in the MBL phase, which is supported by numerical simulations of the random-field XXZ spin chain. We describe the structure of the eigenstates in the MBL phase and discuss the implications of local conservation laws for its nonequilibrium quantum dynamics. We argue that the many-body localization can be used to protect coherence in the system by suppressing relaxation between eigenstates with different local integrals of motion.","lang":"eng"}],"date_published":"2013-09-17T00:00:00Z","author":[{"full_name":"Maksym Serbyn","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry A"}],"volume":111,"doi":"10.1103/PhysRevLett.111.127201","month":"09","issue":"12","citation":{"ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Local conservation laws and the structure of the many body localized states,” <i>Physical Review Letters</i>, vol. 111, no. 12. American Physical Society, 2013.","apa":"Serbyn, M., Papić, Z., &#38; Abanin, D. (2013). Local conservation laws and the structure of the many body localized states. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.111.127201\">https://doi.org/10.1103/PhysRevLett.111.127201</a>","mla":"Serbyn, Maksym, et al. “Local Conservation Laws and the Structure of the Many Body Localized States.” <i>Physical Review Letters</i>, vol. 111, no. 12, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.111.127201\">10.1103/PhysRevLett.111.127201</a>.","ama":"Serbyn M, Papić Z, Abanin D. Local conservation laws and the structure of the many body localized states. <i>Physical Review Letters</i>. 2013;111(12). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.111.127201\">10.1103/PhysRevLett.111.127201</a>","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Local Conservation Laws and the Structure of the Many Body Localized States.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.111.127201\">https://doi.org/10.1103/PhysRevLett.111.127201</a>.","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 111 (2013).","ista":"Serbyn M, Papić Z, Abanin D. 2013. Local conservation laws and the structure of the many body localized states. Physical Review Letters. 111(12)."}},{"language":[{"iso":"eng"}],"date_published":"2013-07-19T00:00:00Z","abstract":[{"lang":"eng","text":"We propose a possible realization of the overscreened Kondo impurity problem by a magnetic s=1/2 impurity embedded in a two-dimensional S=1 U(1) spin liquid with a Fermi surface. This problem contains an interesting interplay between non-Fermi-liquid behavior induced by a U(1) gauge field coupled to fermions and a non-Fermi-liquid fixed point in the overscreened Kondo problem. Using a large-N expansion together with an expansion in the dynamical exponent of the gauge field, we find that the coupling to the gauge field leads to weak but observable changes in the physical properties of the system at the overscreened Kondo fixed point. We discuss the extrapolation of this result to a physical case and argue that the realization of overscreened Kondo physics could lead to observations of effects due to gauge fields."}],"year":"2013","publication_status":"published","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","issue":"2","citation":{"mla":"Serbyn, Maksym, et al. “Overscreened Kondo Fixed Point in S=1 Spin Liquid.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 88, no. 2, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevB.88.024419\">10.1103/PhysRevB.88.024419</a>.","ieee":"M. Serbyn, T. Senthil, and P. Lee, “Overscreened Kondo fixed point in S=1 spin liquid,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 88, no. 2. American Physical Society, 2013.","apa":"Serbyn, M., Senthil, T., &#38; Lee, P. (2013). Overscreened Kondo fixed point in S=1 spin liquid. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.88.024419\">https://doi.org/10.1103/PhysRevB.88.024419</a>","ama":"Serbyn M, Senthil T, Lee P. Overscreened Kondo fixed point in S=1 spin liquid. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2013;88(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.88.024419\">10.1103/PhysRevB.88.024419</a>","ista":"Serbyn M, Senthil T, Lee P. 2013. Overscreened Kondo fixed point in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics. 88(2).","short":"M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 88 (2013).","chicago":"Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Overscreened Kondo Fixed Point in S=1 Spin Liquid.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevB.88.024419\">https://doi.org/10.1103/PhysRevB.88.024419</a>."},"doi":"10.1103/PhysRevB.88.024419","external_id":{"arxiv":["1212.5179"]},"author":[{"full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"first_name":"Todadri","last_name":"Senthil","full_name":"Senthil, Todadri"},{"first_name":"Patrick","last_name":"Lee","full_name":"Lee, Patrick"}],"volume":88,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1212.5179"}],"extern":"1","publist_id":"6425","publisher":"American Physical Society","oa":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","date_updated":"2021-01-12T08:22:21Z","arxiv":1,"title":"Overscreened Kondo fixed point in S=1 spin liquid","_id":"974","type":"journal_article","day":"19","date_created":"2018-12-11T11:49:29Z","status":"public","intvolume":"        88","quality_controlled":"1"},{"publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"status":"public","date_created":"2021-07-28T15:45:07Z","title":"Forgiver triumphs in alternating prisoner's dilemma ","date_updated":"2025-09-29T14:30:03Z","_id":"9749","type":"research_data_reference","day":"12","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise."}],"date_published":"2013-12-12T00:00:00Z","year":"2013","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","author":[{"last_name":"Zagorsky","first_name":"Benjamin","full_name":"Zagorsky, Benjamin"},{"first_name":"Johannes","last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"month":"12","citation":{"short":"B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013).","chicago":"Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">https://doi.org/10.1371/journal.pone.0080814.s001</a>.","ista":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma , Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>.","ieee":"B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma .” Public Library of Science, 2013.","apa":"Zagorsky, B., Reiter, J., Chatterjee, K., &#38; Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">https://doi.org/10.1371/journal.pone.0080814.s001</a>","mla":"Zagorsky, Benjamin, et al. <i>Forgiver Triumphs in Alternating Prisoner’s Dilemma </i>. Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>.","ama":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . 2013. doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>"},"doi":"10.1371/journal.pone.0080814.s001","related_material":{"record":[{"id":"2247","status":"public","relation":"used_in_publication"}]}},{"publisher":"American Physical Society","publication":"Physical Review Letters","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1304.4605","open_access":"1"}],"acknowledgement":"We would like to thank E. Altman and J. Moore for useful comments on the manuscript. This research was supported in part by Perimeter Institute for Theoretical Physics. Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. Z. P. was supported by DOE Grant No. DE-SC0002140. The simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University.","extern":1,"publist_id":"6426","status":"public","intvolume":"       110","date_created":"2018-12-11T11:49:29Z","quality_controlled":0,"title":"Universal slow growth of entanglement in interacting strongly disordered systems","date_updated":"2021-01-12T08:22:22Z","_id":"975","type":"journal_article","day":"28","abstract":[{"text":"Recent numerical work by Bardarson, Pollmann, and Moore revealed a slow, logarithmic in time, growth of the entanglement entropy for initial product states in a putative many-body localized phase. We show that this surprising phenomenon results from the dephasing due to exponentially small interaction-induced corrections to the eigenenergies of different states. For weak interactions, we find that the entanglement entropy grows as ξln (Vt/), where V is the interaction strength, and ξ is the single-particle localization length. The saturated value of the entanglement entropy at long times is determined by the participation ratios of the initial state over the eigenstates of the subsystem. Our work shows that the logarithmic entanglement growth is a universal phenomenon characteristic of the many-body localized phase in any number of spatial dimensions, and reveals a broad hierarchy of dephasing time scales present in such a phase.","lang":"eng"}],"date_published":"2013-06-28T00:00:00Z","year":"2013","publication_status":"published","author":[{"last_name":"Serbyn","first_name":"Maksym","full_name":"Maksym Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry A"}],"volume":110,"month":"06","citation":{"mla":"Serbyn, Maksym, et al. “Universal Slow Growth of Entanglement in Interacting Strongly Disordered Systems.” <i>Physical Review Letters</i>, vol. 110, no. 26, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.260601\">10.1103/PhysRevLett.110.260601</a>.","apa":"Serbyn, M., Papić, Z., &#38; Abanin, D. (2013). Universal slow growth of entanglement in interacting strongly disordered systems. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.260601\">https://doi.org/10.1103/PhysRevLett.110.260601</a>","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Universal slow growth of entanglement in interacting strongly disordered systems,” <i>Physical Review Letters</i>, vol. 110, no. 26. American Physical Society, 2013.","ama":"Serbyn M, Papić Z, Abanin D. Universal slow growth of entanglement in interacting strongly disordered systems. <i>Physical Review Letters</i>. 2013;110(26). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.260601\">10.1103/PhysRevLett.110.260601</a>","ista":"Serbyn M, Papić Z, Abanin D. 2013. Universal slow growth of entanglement in interacting strongly disordered systems. Physical Review Letters. 110(26).","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Universal Slow Growth of Entanglement in Interacting Strongly Disordered Systems.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.260601\">https://doi.org/10.1103/PhysRevLett.110.260601</a>.","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 110 (2013)."},"issue":"26","doi":"10.1103/PhysRevLett.110.260601"},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2853"}]},"doi":"10.5061/dryad.b1q2n","month":"03","citation":{"ista":"Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection, Dryad, <a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>.","chicago":"Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” Dryad, 2013. <a href=\"https://doi.org/10.5061/dryad.b1q2n\">https://doi.org/10.5061/dryad.b1q2n</a>.","short":"D. Refardt, T. Bergmiller, R. Kümmerli, (2013).","mla":"Refardt, Dominik, et al. <i>Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection</i>. Dryad, 2013, doi:<a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>.","apa":"Refardt, D., Bergmiller, T., &#38; Kümmerli, R. (2013). Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. Dryad. <a href=\"https://doi.org/10.5061/dryad.b1q2n\">https://doi.org/10.5061/dryad.b1q2n</a>","ieee":"D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection.” Dryad, 2013.","ama":"Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. 2013. doi:<a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>"},"author":[{"first_name":"Dominik","last_name":"Refardt","full_name":"Refardt, Dominik"},{"orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias"},{"full_name":"Kümmerli, Rolf","first_name":"Rolf","last_name":"Kümmerli"}],"year":"2013","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","date_published":"2013-03-21T00:00:00Z","abstract":[{"lang":"eng","text":"High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation."}],"type":"research_data_reference","day":"21","title":"Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection","date_updated":"2025-09-29T13:41:12Z","_id":"9751","status":"public","date_created":"2021-07-30T08:08:09Z","department":[{"_id":"CaGu"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.b1q2n","open_access":"1"}],"publisher":"Dryad","oa":1},{"publisher":"Dryad","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.r3r60","open_access":"1"}],"department":[{"_id":"NiBa"}],"status":"public","date_created":"2021-07-30T08:31:22Z","date_updated":"2025-09-29T11:38:51Z","title":"Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies","_id":"9754","type":"research_data_reference","day":"01","article_processing_charge":"No","date_published":"2013-10-01T00:00:00Z","abstract":[{"text":"Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.","lang":"eng"}],"year":"2013","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","author":[{"last_name":"Hearn","first_name":"Jack","full_name":"Hearn, Jack"},{"full_name":"Stone, Graham","last_name":"Stone","first_name":"Graham"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"last_name":"Bunnefeld","first_name":"Lynsey","full_name":"Bunnefeld, Lynsey"}],"month":"10","citation":{"chicago":"Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies.” Dryad, 2013. <a href=\"https://doi.org/10.5061/dryad.r3r60\">https://doi.org/10.5061/dryad.r3r60</a>.","short":"J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).","ista":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies, Dryad, <a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>.","apa":"Hearn, J., Stone, G., Barton, N. H., Lohse, K., &#38; Bunnefeld, L. (2013). Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. Dryad. <a href=\"https://doi.org/10.5061/dryad.r3r60\">https://doi.org/10.5061/dryad.r3r60</a>","ieee":"J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013.","mla":"Hearn, Jack, et al. <i>Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies</i>. Dryad, 2013, doi:<a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>.","ama":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. 2013. doi:<a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>"},"related_material":{"record":[{"id":"2170","status":"public","relation":"used_in_publication"}]},"doi":"10.5061/dryad.r3r60"},{"year":"2013","publication_status":"published","date_published":"2013-05-22T00:00:00Z","abstract":[{"lang":"eng","text":"Motivated by a search for experimental probes to access the physics of fractionalized excitations called spinons in spin liquids, we study the interaction of spinons with lattice vibrations. We consider the case of algebraic spin liquid, when spinons have fermionic statistics and a Dirac-like dispersion. We establish the general procedure for deriving spinon-phonon interactions, which is based on symmetry considerations. The procedure is illustrated for four different algebraic spin liquids: π-flux and staggered-flux phases on a square lattice, π-flux phase on a kagome lattice, and zero-flux phase on a honeycomb lattice. Although the low-energy description is similar for all these phases, different underlying symmetry groups lead to a distinct form of spinon-phonon interaction Hamiltonian. The explicit form of the spinon-phonon interaction is used to estimate the attenuation of ultrasound in an algebraic spin liquid. The prospects of the sound attenuation as a probe of spinons are discussed."}],"author":[{"full_name":"Maksym Serbyn","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"last_name":"Lee","first_name":"Patrick","full_name":"Lee, Patrick"}],"volume":87,"doi":"10.1103/PhysRevB.87.174424","month":"05","issue":"17","citation":{"ista":"Serbyn M, Lee P. 2013. Spinon-phonon interaction in algebraic spin liquids. Physical Review B - Condensed Matter and Materials Physics. 87(17).","short":"M. Serbyn, P. Lee, Physical Review B - Condensed Matter and Materials Physics 87 (2013).","chicago":"Serbyn, Maksym, and Patrick Lee. “Spinon-Phonon Interaction in Algebraic Spin Liquids.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevB.87.174424\">https://doi.org/10.1103/PhysRevB.87.174424</a>.","ama":"Serbyn M, Lee P. Spinon-phonon interaction in algebraic spin liquids. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2013;87(17). doi:<a href=\"https://doi.org/10.1103/PhysRevB.87.174424\">10.1103/PhysRevB.87.174424</a>","mla":"Serbyn, Maksym, and Patrick Lee. “Spinon-Phonon Interaction in Algebraic Spin Liquids.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 87, no. 17, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevB.87.174424\">10.1103/PhysRevB.87.174424</a>.","ieee":"M. Serbyn and P. Lee, “Spinon-phonon interaction in algebraic spin liquids,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 87, no. 17. American Physical Society, 2013.","apa":"Serbyn, M., &#38; Lee, P. (2013). Spinon-phonon interaction in algebraic spin liquids. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.87.174424\">https://doi.org/10.1103/PhysRevB.87.174424</a>"},"publisher":"American Physical Society","oa":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","publist_id":"6427","acknowledgement":"M. S. is grateful to X.-G. Wen, L. Levitov, M. Metlitski, K. Michaeli, K.-T. Chen, and A. Potter for many useful discussions. We acknowledge support by Grant No. NSF DMR 1104498. We acknowledge the hospitality of KITP, where final stages of this project were completed.","main_file_link":[{"url":"https://arxiv.org/abs/1303.0772","open_access":"1"}],"extern":1,"quality_controlled":0,"date_created":"2018-12-11T11:49:30Z","intvolume":"        87","status":"public","type":"journal_article","day":"22","date_updated":"2021-01-12T08:22:22Z","title":"Spinon-phonon interaction in algebraic spin liquids","_id":"976"},{"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"Maternal exposure to infection occurring mid-gestation produces a three-fold increase in the risk of schizophrenia in the offspring. The critical initiating factor appears to be the maternal immune activation (MIA) that follows infection. This process can be induced in rodents by exposure of pregnant dams to the viral mimic Poly I:C, which triggers an immune response that results in structural, functional, behavioral, and electrophysiological phenotypes in the adult offspring that model those seen in schizophrenia. We used this model to explore the role of synchronization in brain neural networks, a process thought to be dysfunctional in schizophrenia and previously associated with positive, negative, and cognitive symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced an impairment in long-range neural synchrony in adult offspring between two regions implicated in schizophrenia pathology; the hippocampus and the medial prefrontal cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the antipsychotic clozapine. MIA animals have previously been shown to have impaired pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits in animal models. Our data showed that deficits in synchrony were positively correlated with the impairments in PPI. Subsequent analysis of LFP activity during the PPI response also showed that reduced coupling between the mPFC and the hippocampus following processing of the pre-pulse was associated with reduced PPI. The ability of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology provides a useful platform from which to investigate the ontogeny of aberrant synchronous processes. Further, the way in which the model expresses translatable deficits such as aberrant synchrony and reduced PPI will allow researchers to explore novel intervention strategies targeted to these changes. "}],"article_processing_charge":"No","external_id":{"isi":["000329175600001"]},"doi":"10.3389/fnbeh.2013.00217","pubrep_id":"953","volume":7,"isi":1,"file_date_updated":"2020-07-14T12:46:35Z","publication":"Frontiers in Behavioral Neuroscience","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Frontiers Research Foundation","day":"27","type":"journal_article","date_updated":"2025-09-30T07:30:04Z","status":"public","date_created":"2018-12-11T11:46:41Z","publication_status":"published","oa_version":"Published Version","year":"2013","date_published":"2013-12-27T00:00:00Z","issue":"DEC","citation":{"mla":"Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” <i>Frontiers in Behavioral Neuroscience</i>, vol. 7, no. DEC, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">10.3389/fnbeh.2013.00217</a>.","apa":"Dickerson, D., &#38; Bilkey, D. (2013). Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. <i>Frontiers in Behavioral Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">https://doi.org/10.3389/fnbeh.2013.00217</a>","ieee":"D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions,” <i>Frontiers in Behavioral Neuroscience</i>, vol. 7, no. DEC. Frontiers Research Foundation, 2013.","ama":"Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. <i>Frontiers in Behavioral Neuroscience</i>. 2013;7(DEC). doi:<a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">10.3389/fnbeh.2013.00217</a>","ista":"Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. 7(DEC).","short":"D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013).","chicago":"Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” <i>Frontiers in Behavioral Neuroscience</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">https://doi.org/10.3389/fnbeh.2013.00217</a>."},"month":"12","author":[{"id":"444EB89E-F248-11E8-B48F-1D18A9856A87","first_name":"Desiree","last_name":"Dickerson","full_name":"Dickerson, Desiree"},{"first_name":"David","last_name":"Bilkey","full_name":"Bilkey, David"}],"department":[{"_id":"JoCs"}],"publist_id":"7346","ddc":["571"],"has_accepted_license":"1","oa":1,"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:46:35Z","creator":"system","file_id":"5128","date_created":"2018-12-12T10:15:10Z","file_size":530134,"file_name":"IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf","checksum":"cd7183121e56251176100ccac165c95c","content_type":"application/pdf","relation":"main_file"}],"_id":"476","title":"Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions","quality_controlled":"1","intvolume":"         7"},{"volume":339,"doi":"10.1126/science.1229858","external_id":{"isi":["000312985800059"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","abstract":[{"text":"Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to infrequently dividing or nondividing &quot;persisters.&quot; Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although persistence in these studies was characterized by stable numbers of cells, this apparent stability was actually a dynamic state of balanced division and death. Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic pulses that were negatively correlated with cell survival. These behaviors may reflect epigenetic effects, because KatG pulsing and death were correlated between sibling cells. Selection of lineages characterized by infrequent KatG pulsing could allow nonresponsive adaptation during prolonged drug exposure.","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:46:48Z","status":"public","type":"journal_article","day":"04","date_updated":"2025-09-30T07:29:30Z","isi":1,"publisher":"American Association for the Advancement of Science","publication":"Science","page":"91 - 95","author":[{"full_name":"Wakamoto, Yurichi","first_name":"Yurichi","last_name":"Wakamoto"},{"full_name":"Dhar, Neraaj","last_name":"Dhar","first_name":"Neraaj"},{"full_name":"Chait, Remy P","last_name":"Chait","first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187"},{"first_name":"Katrin","last_name":"Schneider","full_name":"Schneider, Katrin"},{"first_name":"François","last_name":"Signorino Gelo","full_name":"Signorino Gelo, François"},{"full_name":"Leibler, Stanislas","last_name":"Leibler","first_name":"Stanislas"},{"first_name":"John","last_name":"Mckinney","full_name":"Mckinney, John"}],"month":"01","issue":"6115","citation":{"ista":"Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115), 91–95.","chicago":"Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” <i>Science</i>. American Association for the Advancement of Science, 2013. <a href=\"https://doi.org/10.1126/science.1229858\">https://doi.org/10.1126/science.1229858</a>.","short":"Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.","ama":"Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed mycobacteria. <i>Science</i>. 2013;339(6115):91-95. doi:<a href=\"https://doi.org/10.1126/science.1229858\">10.1126/science.1229858</a>","mla":"Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” <i>Science</i>, vol. 339, no. 6115, American Association for the Advancement of Science, 2013, pp. 91–95, doi:<a href=\"https://doi.org/10.1126/science.1229858\">10.1126/science.1229858</a>.","apa":"Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler, S., &#38; Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1229858\">https://doi.org/10.1126/science.1229858</a>","ieee":"Y. Wakamoto <i>et al.</i>, “Dynamic persistence of antibiotic-stressed mycobacteria,” <i>Science</i>, vol. 339, no. 6115. American Association for the Advancement of Science, pp. 91–95, 2013."},"year":"2013","publication_status":"published","oa_version":"None","date_published":"2013-01-04T00:00:00Z","quality_controlled":"1","intvolume":"       339","title":"Dynamic persistence of antibiotic-stressed mycobacteria","_id":"499","publist_id":"7321","department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"month":"10","issue":"1","citation":{"chicago":"Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-222\">https://doi.org/10.1186/1471-2148-13-222</a>.","short":"M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013).","ista":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 13(1), 222.","ieee":"M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, 2013.","apa":"Ward, M., Lycett, S., Avila, D., Bollback, J. P., &#38; Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-222\">https://doi.org/10.1186/1471-2148-13-222</a>","mla":"Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, 222, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-222\">10.1186/1471-2148-13-222</a>.","ama":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. <i>BMC Evolutionary Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-13-222\">10.1186/1471-2148-13-222</a>"},"author":[{"full_name":"Ward, Melissa","first_name":"Melissa","last_name":"Ward"},{"first_name":"Samantha","last_name":"Lycett","full_name":"Lycett, Samantha"},{"full_name":"Avila, Dorita","last_name":"Avila","first_name":"Dorita"},{"first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Leigh Brown","first_name":"Andrew","full_name":"Leigh Brown, Andrew"}],"date_published":"2013-10-09T00:00:00Z","year":"2013","publication_status":"published","oa_version":"Published Version","title":"Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza","_id":"500","file":[{"date_updated":"2020-07-14T12:46:36Z","access_level":"open_access","file_id":"4722","file_size":1150052,"date_created":"2018-12-12T10:08:59Z","creator":"system","file_name":"IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf","checksum":"52cf48a7c1794676ae8b0029573a84a9","relation":"main_file","content_type":"application/pdf"}],"intvolume":"        13","quality_controlled":"1","publist_id":"7320","department":[{"_id":"JoBo"}],"oa":1,"has_accepted_license":"1","ddc":["576"],"pubrep_id":"941","doi":"10.1186/1471-2148-13-222","external_id":{"isi":["000326620200001"]},"volume":13,"language":[{"iso":"eng"}],"article_number":"222","scopus_import":"1","article_processing_charge":"No","abstract":[{"text":"Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-30T07:28:51Z","type":"journal_article","day":"09","date_created":"2018-12-11T11:46:49Z","status":"public","acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council, the Government of the Republic of Panama, the Interdisciplinary Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC BY 2.0\r\n","publisher":"BioMed Central","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"BMC Evolutionary Biology","file_date_updated":"2020-07-14T12:46:36Z","isi":1},{"date_published":"2013-12-01T00:00:00Z","year":"2013","oa_version":"Published Version","publication_status":"published","author":[{"last_name":"Cozzuol","first_name":"Mario","full_name":"Cozzuol, Mario"},{"full_name":"Clozato, Camila","last_name":"Clozato","first_name":"Camila"},{"full_name":"Holanda, Elizete","first_name":"Elizete","last_name":"Holanda"},{"full_name":"Rodrigues, Flávio","first_name":"Flávio","last_name":"Rodrigues"},{"full_name":"Nienow, Samuel","last_name":"Nienow","first_name":"Samuel"},{"first_name":"Benoit","last_name":"De Thoisy","full_name":"De Thoisy, Benoit"},{"orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A"},{"full_name":"Santos, Fabrício","first_name":"Fabrício","last_name":"Santos"}],"month":"12","issue":"6","citation":{"ista":"Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of Mammalogy. 94(6), 1331–1345.","chicago":"Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A New Species of Tapir from the Amazon.” <i>Journal of Mammalogy</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">https://doi.org/10.1644/12-MAMM-A-169.1</a>.","short":"M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy, R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.","mla":"Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” <i>Journal of Mammalogy</i>, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45, doi:<a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">10.1644/12-MAMM-A-169.1</a>.","ieee":"M. Cozzuol <i>et al.</i>, “A new species of tapir from the Amazon,” <i>Journal of Mammalogy</i>, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.","apa":"Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy, B., … Santos, F. (2013). A new species of tapir from the Amazon. <i>Journal of Mammalogy</i>. Oxford University Press. <a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">https://doi.org/10.1644/12-MAMM-A-169.1</a>","ama":"Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon. <i>Journal of Mammalogy</i>. 2013;94(6):1331-1345. doi:<a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">10.1644/12-MAMM-A-169.1</a>"},"oa":1,"has_accepted_license":"1","ddc":["570"],"publist_id":"7319","department":[{"_id":"JoBo"}],"intvolume":"        94","quality_controlled":"1","title":"A new species of tapir from the Amazon","_id":"501","file":[{"creator":"system","file_size":1040765,"date_created":"2018-12-12T10:12:59Z","file_id":"4980","access_level":"open_access","date_updated":"2020-07-14T12:46:36Z","content_type":"application/pdf","relation":"main_file","checksum":"8007815078dccac21ecd1cf73a269dc6","file_name":"IST-2018-940-v1+1_2013_Redondo_A_new.pdf"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"scopus_import":"1","volume":94,"pubrep_id":"940","doi":"10.1644/12-MAMM-A-169.1","external_id":{"isi":["000329010200015"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"publisher":"Oxford University Press","publication":"Journal of Mammalogy","isi":1,"file_date_updated":"2020-07-14T12:46:36Z","page":"1331 - 1345","date_created":"2018-12-11T11:46:49Z","status":"public","date_updated":"2025-09-30T07:28:20Z","type":"journal_article","day":"01"}]