[{"status":"public","type":"journal_article","author":[{"first_name":"Łukasz","full_name":"Łangowski, Łukasz","last_name":"Łangowski"},{"first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560"},{"full_name":"Li, Hongjiang","first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0001-5039-9660"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"last_name":"Naramoto","full_name":"Naramoto, Satoshi","first_name":"Satoshi"},{"last_name":"Tanaka","full_name":"Tanaka, Hirokazu","first_name":"Hirokazu"},{"first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"month":"07","file":[{"file_name":"IST-2017-757-v1+1_celldisc201618.pdf","file_id":"5017","date_updated":"2018-12-12T10:13:33Z","date_created":"2018-12-12T10:13:33Z","creator":"system","content_type":"application/pdf","relation":"main_file","file_size":5261671,"access_level":"open_access"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"19","oa_version":"Published Version","language":[{"iso":"eng"}],"publication":"Cell Discovery","date_updated":"2021-01-12T06:48:08Z","oa":1,"pubrep_id":"757","title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","has_accepted_license":"1","scopus_import":1,"intvolume":"         2","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"license":"https://creativecommons.org/licenses/by/4.0/","date_published":"2016-07-19T00:00:00Z","publisher":"Nature Publishing Group","quality_controlled":"1","volume":2,"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["580"],"abstract":[{"text":"The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells.","lang":"eng"}],"_id":"1081","file_date_updated":"2018-12-12T10:13:33Z","doi":"10.1038/celldisc.2016.18","year":"2016","acknowledgement":"We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP); Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN.","citation":{"ista":"Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2, 16018.","mla":"Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>, vol. 2, 16018, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>.","chicago":"Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste, Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>.","ama":"Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. 2016;2. doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>","ieee":"Ł. Łangowski <i>et al.</i>, “Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells,” <i>Cell Discovery</i>, vol. 2. Nature Publishing Group, 2016.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016).","apa":"Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., &#38; Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>"},"date_created":"2018-12-11T11:50:02Z","publist_id":"6299","article_number":"16018","ec_funded":1},{"date_created":"2022-03-03T10:43:10Z","citation":{"apa":"Rubel, P., Pani, D., Schlögl, A., Fayn, J., Badilini, F., Macfarlane, P., &#38; Varri, A. (2016). SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In <i>2016 Computing in Cardiology Conference</i> (Vol. 43, pp. 309–312). Vancouver, Canada: Computing in Cardiology. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>","mla":"Rubel, Paul, et al. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” <i>2016 Computing in Cardiology Conference</i>, vol. 43, Computing in Cardiology, 2016, pp. 309–12, doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>.","chicago":"Rubel, Paul, Danilo Pani, Alois Schlögl, Jocelyne Fayn, Fabio Badilini, Peter Macfarlane, and Alpo Varri. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” In <i>2016 Computing in Cardiology Conference</i>, 43:309–12. Computing in Cardiology, 2016. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>.","ista":"Rubel P, Pani D, Schlögl A, Fayn J, Badilini F, Macfarlane P, Varri A. 2016. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. 2016 Computing in Cardiology Conference. CinC: Computing in Cardiology vol. 43, 309–312.","ama":"Rubel P, Pani D, Schlögl A, et al. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In: <i>2016 Computing in Cardiology Conference</i>. Vol 43. Computing in Cardiology; 2016:309-312. doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>","ieee":"P. Rubel <i>et al.</i>, “SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography,” in <i>2016 Computing in Cardiology Conference</i>, Vancouver, Canada, 2016, vol. 43, pp. 309–312.","short":"P. Rubel, D. Pani, A. Schlögl, J. Fayn, F. Badilini, P. Macfarlane, A. Varri, in:, 2016 Computing in Cardiology Conference, Computing in Cardiology, 2016, pp. 309–312."},"acknowledgement":"The authors are thankful to Drs. Roger Abaecherli, Nikus Kjell, Paul Kligfield, Jay Mason, Patrice Nony, Vito Starc, Anders Thurin and the late Galen Wagner for their in depth review and constructive comments.","year":"2016","_id":"10810","doi":"10.22489/cinc.2016.090-500","publication_status":"published","abstract":[{"text":"The main goal of the SCP-ECG standard is to address ECG data and related metadata structuring, semantics and syntax, with the objective of facilitating interoperability and thus supporting and promoting the exchange of the relevant information for unary and serial ECG diagnosis. Starting with version V3.0, the standard now also provides support for the storage of continuous, long-term ECG recordings and affords a repository for selected ECG sequences and the related metadata to accommodate stress tests, drug trials and protocol-based ECG recordings. The global and per-lead measurements sections have been extended and three new sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements\r\nand annotations. The used terminology and the provided measurements and annotations have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis has also been put on harmonizing the Universal Statement Codes with the CDISC and the categorized AHA statement codes and similarly the drug and implanted devices codes with the ATC and NASPE/BPEG codes. ","lang":"eng"}],"department":[{"_id":"CampIT"}],"page":"309-312","volume":43,"quality_controlled":"1","publisher":"Computing in Cardiology","date_published":"2016-03-01T00:00:00Z","title":"SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography","date_updated":"2022-03-04T07:34:45Z","oa":1,"article_processing_charge":"No","intvolume":"        43","scopus_import":"1","language":[{"iso":"eng"}],"publication":"2016 Computing in Cardiology Conference","author":[{"last_name":"Rubel","full_name":"Rubel, Paul","first_name":"Paul"},{"last_name":"Pani","first_name":"Danilo","full_name":"Pani, Danilo"},{"last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","first_name":"Alois","full_name":"Schlögl, Alois"},{"last_name":"Fayn","full_name":"Fayn, Jocelyne","first_name":"Jocelyne"},{"full_name":"Badilini, Fabio","first_name":"Fabio","last_name":"Badilini"},{"first_name":"Peter","full_name":"Macfarlane, Peter","last_name":"Macfarlane"},{"last_name":"Varri","full_name":"Varri, Alpo","first_name":"Alpo"}],"oa_version":"Published Version","day":"01","main_file_link":[{"url":"https://doi.org/10.22489/cinc.2016.090-500","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"CinC: Computing in Cardiology","start_date":"2016-09-11","location":"Vancouver, Canada","end_date":"2016-09-14"},"month":"03","publication_identifier":{"issn":["2325-887X"]},"type":"conference","status":"public"},{"intvolume":"       538","scopus_import":"1","title":"Mechanism for DNA transposons to generate introns on genomic scales","issue":"7626","article_processing_charge":"No","date_updated":"2021-12-14T07:55:30Z","oa":1,"publication":"Nature","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/"}],"day":"27","oa_version":"Submitted Version","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"month":"10","author":[{"full_name":"Huff, Jason T.","first_name":"Jason T.","last_name":"Huff"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel"},{"first_name":"Scott W.","full_name":"Roy, Scott W.","last_name":"Roy"}],"type":"journal_article","status":"public","pmid":1,"date_created":"2021-06-04T11:34:55Z","citation":{"apa":"Huff, J. T., Zilberman, D., &#38; Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. Springer Nature . <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>","chicago":"Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>. Springer Nature , 2016. <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>.","ista":"Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 538(7626), 533–536.","mla":"Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>, vol. 538, no. 7626, Springer Nature , 2016, pp. 533–36, doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>.","ama":"Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. 2016;538(7626):533-536. doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>","ieee":"J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” <i>Nature</i>, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016.","short":"J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536."},"year":"2016","doi":"10.1038/nature20110","article_type":"letter_note","_id":"9456","abstract":[{"text":"The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution.","lang":"eng"}],"external_id":{"pmid":["27760113"]},"publication_status":"published","quality_controlled":"1","volume":538,"extern":"1","page":"533-536","department":[{"_id":"DaZi"}],"date_published":"2016-10-27T00:00:00Z","publisher":"Springer Nature "},{"publisher":"National Academy of Sciences","date_published":"2016-12-27T00:00:00Z","page":"15132-15137","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"extern":"1","volume":113,"quality_controlled":"1","publication_status":"published","external_id":{"pmid":["27956643"]},"abstract":[{"lang":"eng","text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations."}],"_id":"9473","article_type":"original","doi":"10.1073/pnas.1619074114","year":"2016","date_created":"2021-06-07T06:21:39Z","citation":{"ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15132-15137. doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>","ieee":"P.-H. Hsieh <i>et al.</i>, “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016.","short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>.","ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137.","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>.","apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>"},"pmid":1,"type":"journal_article","status":"public","author":[{"full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung","last_name":"Hsieh"},{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"full_name":"Buttress, Toby","first_name":"Toby","last_name":"Buttress"},{"last_name":"Gao","full_name":"Gao, Hongbo","first_name":"Hongbo"},{"full_name":"Couchman, Matthew","first_name":"Matthew","last_name":"Couchman"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel"},{"first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"}],"month":"12","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619074114","open_access":"1"}],"day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","date_updated":"2023-05-08T11:00:40Z","oa":1,"article_processing_charge":"No","issue":"52","title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","intvolume":"       113","scopus_import":"1"},{"author":[{"last_name":"Park","first_name":"Kyunghyuk","full_name":"Park, Kyunghyuk"},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"full_name":"Park, Jin-Sup","first_name":"Jin-Sup","last_name":"Park"},{"last_name":"Hyun","full_name":"Hyun, Youbong","first_name":"Youbong"},{"full_name":"Okamoto, Takashi","first_name":"Takashi","last_name":"Okamoto"},{"first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"},{"first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"},{"last_name":"Choi","first_name":"Yeonhee","full_name":"Choi, Yeonhee"},{"first_name":"Stefan","full_name":"Scholten, Stefan","last_name":"Scholten"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619047114","open_access":"1"}],"day":"27","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"12","pmid":1,"status":"public","type":"journal_article","title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","oa":1,"date_updated":"2023-05-08T11:00:07Z","article_processing_charge":"No","issue":"52","intvolume":"       113","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","publication_status":"published","external_id":{"pmid":["27956642"]},"abstract":[{"lang":"eng","text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm."}],"page":"15138-15143","extern":"1","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"quality_controlled":"1","volume":113,"publisher":"National Academy of Sciences","date_published":"2016-12-27T00:00:00Z","date_created":"2021-06-07T07:10:59Z","citation":{"ieee":"K. Park <i>et al.</i>, “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.","ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15138-15143. doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>","short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143.","chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>.","mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>.","apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>"},"keyword":["Multidisciplinary"],"year":"2016","_id":"9477","article_type":"original","doi":"10.1073/pnas.1619047114"},{"_id":"948","date_created":"2018-12-11T11:49:21Z","publist_id":"6469","citation":{"apa":"Monk, T., Savin, C., &#38; Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems.","short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems; 2016:4285-4293.","ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.","mla":"Monk, Travis, et al. <i>Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics</i>. Vol. 29, Neural Information Processing Systems, 2016, pp. 4285–93.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293.","chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems, 2016."},"year":"2016","acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and  LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","ec_funded":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","volume":29,"department":[{"_id":"GaTk"}],"page":"4285 - 4293","date_published":"2016-01-01T00:00:00Z","publisher":"Neural Information Processing Systems","publication_status":"published","abstract":[{"text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations.","lang":"eng"}],"language":[{"iso":"eng"}],"title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","date_updated":"2021-01-12T08:22:08Z","scopus_import":1,"intvolume":"        29","type":"conference","status":"public","alternative_title":["Advances in Neural Information Processing Systems"],"author":[{"first_name":"Travis","full_name":"Monk, Travis","last_name":"Monk"},{"full_name":"Savin, Cristina","first_name":"Cristina","last_name":"Savin","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lücke","full_name":"Lücke, Jörg","first_name":"Jörg"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics"}],"oa_version":"None","day":"01","month":"01","conference":{"location":"Barcelona, Spaine","end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems","start_date":"2016-12-05"}},{"language":[{"iso":"eng"}],"publication":"Combinatorics, Probability and Computing","date_updated":"2023-02-23T14:02:07Z","oa":1,"article_processing_charge":"No","issue":"6","title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","scopus_import":"1","intvolume":"        25","status":"public","type":"journal_article","author":[{"last_name":"Krivelevich","first_name":"Michael","full_name":"Krivelevich, Michael"},{"orcid":"0000-0002-4003-7567","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan"},{"first_name":"Benny","full_name":"Sudakov, Benny","last_name":"Sudakov"}],"arxiv":1,"publication_identifier":{"issn":["0963-5483"],"eissn":["1469-2163"]},"month":"11","oa_version":"Preprint","day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.04816"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9591","article_type":"original","doi":"10.1017/s0963548316000079","year":"2016","citation":{"ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” <i>Combinatorics, Probability and Computing</i>, vol. 25, no. 6. Cambridge University Press, pp. 909–927, 2016.","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Combinatorics, Probability and Computing</i>. 2016;25(6):909-927. doi:<a href=\"https://doi.org/10.1017/s0963548316000079\">10.1017/s0963548316000079</a>","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Combinatorics, Probability and Computing 25 (2016) 909–927.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2016. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Combinatorics, Probability and Computing. 25(6), 909–927.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Combinatorics, Probability and Computing</i>, vol. 25, no. 6, Cambridge University Press, 2016, pp. 909–27, doi:<a href=\"https://doi.org/10.1017/s0963548316000079\">10.1017/s0963548316000079</a>.","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Combinatorics, Probability and Computing</i>. Cambridge University Press, 2016. <a href=\"https://doi.org/10.1017/s0963548316000079\">https://doi.org/10.1017/s0963548316000079</a>.","apa":"Krivelevich, M., Kwan, M. A., &#38; Sudakov, B. (2016). Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Combinatorics, Probability and Computing</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/s0963548316000079\">https://doi.org/10.1017/s0963548316000079</a>"},"date_created":"2021-06-22T12:35:13Z","publisher":"Cambridge University Press","date_published":"2016-11-01T00:00:00Z","page":"909-927","extern":"1","volume":25,"quality_controlled":"1","publication_status":"published","external_id":{"arxiv":["1501.04816"]},"abstract":[{"text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.","lang":"eng"}]},{"pmid":1,"status":"public","type":"journal_article","author":[{"full_name":"Neyer, Simon","first_name":"Simon","last_name":"Neyer"},{"last_name":"Kunz","full_name":"Kunz, Michael","first_name":"Michael"},{"full_name":"Geiss, Christian","first_name":"Christian","last_name":"Geiss"},{"last_name":"Hantsche","full_name":"Hantsche, Merle","first_name":"Merle"},{"first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau"},{"last_name":"Seybert","full_name":"Seybert, Anja","first_name":"Anja"},{"last_name":"Engel","full_name":"Engel, Christoph","first_name":"Christoph"},{"last_name":"Scheffer","first_name":"Margot P.","full_name":"Scheffer, Margot P."},{"last_name":"Cramer","first_name":"Patrick","full_name":"Cramer, Patrick"},{"last_name":"Frangakis","first_name":"Achilleas S.","full_name":"Frangakis, Achilleas S."}],"month":"12","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"oa_version":"None","day":"22","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","language":[{"iso":"eng"}],"publication":"Nature","date_updated":"2021-07-22T09:22:20Z","article_processing_charge":"No","issue":"7634","title":"Structure of RNA polymerase I transcribing ribosomal DNA genes","scopus_import":"1","intvolume":"       540","publisher":"Springer Nature","date_published":"2016-12-22T00:00:00Z","page":"607-610","extern":"1","volume":540,"quality_controlled":"1","publication_status":"published","external_id":{"pmid":["27842382"]},"abstract":[{"lang":"eng","text":"RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation. The central bridge helix was unfolded and a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The structure of Pol I in its active transcribing conformation has yet to be determined, whereas structures of Pol II and Pol III have been solved with bound DNA template and RNA transcript. Here we report structures of active transcribing Pol I from yeast solved by two different cryo-electron microscopy approaches. A single-particle structure at 3.8 Å resolution reveals a contracted active centre cleft with bound DNA and RNA, and a narrowed pore beneath the active site that no longer holds the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution that was determined from cryo-electron tomograms of Pol I enzymes transcribing cellular rDNA confirms contraction of the cleft and reveals that incoming and exiting rDNA enclose an angle of around 150°. The structures suggest a model for the regulation of transcription elongation in which contracted and expanded polymerase conformations are associated with active and inactive states, respectively."}],"article_type":"letter_note","_id":"9654","doi":"10.1038/nature20561","year":"2016","date_created":"2021-07-14T09:04:24Z","citation":{"apa":"Neyer, S., Kunz, M., Geiss, C., Hantsche, M., Hodirnau, V.-V., Seybert, A., … Frangakis, A. S. (2016). Structure of RNA polymerase I transcribing ribosomal DNA genes. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature20561\">https://doi.org/10.1038/nature20561</a>","mla":"Neyer, Simon, et al. “Structure of RNA Polymerase I Transcribing Ribosomal DNA Genes.” <i>Nature</i>, vol. 540, no. 7634, Springer Nature, 2016, pp. 607–10, doi:<a href=\"https://doi.org/10.1038/nature20561\">10.1038/nature20561</a>.","chicago":"Neyer, Simon, Michael Kunz, Christian Geiss, Merle Hantsche, Victor-Valentin Hodirnau, Anja Seybert, Christoph Engel, Margot P. Scheffer, Patrick Cramer, and Achilleas S. Frangakis. “Structure of RNA Polymerase I Transcribing Ribosomal DNA Genes.” <i>Nature</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/nature20561\">https://doi.org/10.1038/nature20561</a>.","ista":"Neyer S, Kunz M, Geiss C, Hantsche M, Hodirnau V-V, Seybert A, Engel C, Scheffer MP, Cramer P, Frangakis AS. 2016. Structure of RNA polymerase I transcribing ribosomal DNA genes. Nature. 540(7634), 607–610.","ieee":"S. Neyer <i>et al.</i>, “Structure of RNA polymerase I transcribing ribosomal DNA genes,” <i>Nature</i>, vol. 540, no. 7634. Springer Nature, pp. 607–610, 2016.","ama":"Neyer S, Kunz M, Geiss C, et al. Structure of RNA polymerase I transcribing ribosomal DNA genes. <i>Nature</i>. 2016;540(7634):607-610. doi:<a href=\"https://doi.org/10.1038/nature20561\">10.1038/nature20561</a>","short":"S. Neyer, M. Kunz, C. Geiss, M. Hantsche, V.-V. Hodirnau, A. Seybert, C. Engel, M.P. Scheffer, P. Cramer, A.S. Frangakis, Nature 540 (2016) 607–610."}},{"external_id":{"pmid":["27203358"]},"abstract":[{"text":"One of the most prominent consequences of the quantum nature of light atomic nuclei is that their kinetic energy does not follow a Maxwell–Boltzmann distribution. Deep inelastic neutron scattering (DINS) experiments can measure this effect. Thus, the nuclear quantum kinetic energy can be probed directly in both ordered and disordered samples. However, the relation between the quantum kinetic energy and the atomic environment is a very indirect one, and cross-validation with theoretical modeling is therefore urgently needed. Here, we use state of the art path integral molecular dynamics techniques to compute the kinetic energy of hydrogen and oxygen nuclei in liquid, solid, and gas-phase water close to the triple point, comparing three different interatomic potentials and validating our results against equilibrium isotope fractionation measurements. We will then show how accurate simulations can draw a link between extremely precise fractionation experiments and DINS, therefore establishing a reliable benchmark for future measurements and providing key insights to increase further the accuracy of interatomic potentials for water.","lang":"eng"}],"publication_status":"published","extern":"1","page":"2210-2215","volume":7,"quality_controlled":"1","publisher":"American Chemical Society","date_published":"2016-06-16T00:00:00Z","date_created":"2021-07-19T08:57:32Z","citation":{"short":"B. Cheng, J. Behler, M. Ceriotti, The Journal of Physical Chemistry Letters 7 (2016) 2210–2215.","ieee":"B. Cheng, J. Behler, and M. Ceriotti, “Nuclear quantum effects in water at the triple point: Using theory as a link between experiments,” <i>The Journal of Physical Chemistry Letters</i>, vol. 7, no. 12. American Chemical Society, pp. 2210–2215, 2016.","ama":"Cheng B, Behler J, Ceriotti M. Nuclear quantum effects in water at the triple point: Using theory as a link between experiments. <i>The Journal of Physical Chemistry Letters</i>. 2016;7(12):2210-2215. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.6b00729\">10.1021/acs.jpclett.6b00729</a>","ista":"Cheng B, Behler J, Ceriotti M. 2016. Nuclear quantum effects in water at the triple point: Using theory as a link between experiments. The Journal of Physical Chemistry Letters. 7(12), 2210–2215.","chicago":"Cheng, Bingqing, Jörg Behler, and Michele Ceriotti. “Nuclear Quantum Effects in Water at the Triple Point: Using Theory as a Link between Experiments.” <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acs.jpclett.6b00729\">https://doi.org/10.1021/acs.jpclett.6b00729</a>.","mla":"Cheng, Bingqing, et al. “Nuclear Quantum Effects in Water at the Triple Point: Using Theory as a Link between Experiments.” <i>The Journal of Physical Chemistry Letters</i>, vol. 7, no. 12, American Chemical Society, 2016, pp. 2210–15, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.6b00729\">10.1021/acs.jpclett.6b00729</a>.","apa":"Cheng, B., Behler, J., &#38; Ceriotti, M. (2016). Nuclear quantum effects in water at the triple point: Using theory as a link between experiments. <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.6b00729\">https://doi.org/10.1021/acs.jpclett.6b00729</a>"},"year":"2016","doi":"10.1021/acs.jpclett.6b00729","_id":"9681","article_type":"letter_note","day":"16","oa_version":"None","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"06","publication_identifier":{"eissn":["1948-7185"]},"author":[{"first_name":"Bingqing","full_name":"Cheng, Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"full_name":"Behler, Jörg","first_name":"Jörg","last_name":"Behler"},{"last_name":"Ceriotti","full_name":"Ceriotti, Michele","first_name":"Michele"}],"pmid":1,"status":"public","type":"journal_article","intvolume":"         7","scopus_import":"1","title":"Nuclear quantum effects in water at the triple point: Using theory as a link between experiments","date_updated":"2023-02-23T14:04:49Z","issue":"12","article_processing_charge":"No","publication":"The Journal of Physical Chemistry Letters","language":[{"iso":"eng"}]},{"doi":"10.5061/dryad.cq7t1","_id":"9704","related_material":{"record":[{"status":"public","id":"1262","relation":"used_in_publication"}]},"citation":{"apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Dryad. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>.","mla":"Mcmahon, Dino, et al. <i>Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss, Dryad, <a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>","ieee":"D. Mcmahon <i>et al.</i>, “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016)."},"date_created":"2021-07-23T08:30:38Z","title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","article_processing_charge":"No","year":"2016","oa":1,"date_updated":"2023-02-21T16:54:31Z","department":[{"_id":"SyCr"}],"date_published":"2016-05-06T00:00:00Z","status":"public","type":"research_data_reference","publisher":"Dryad","abstract":[{"text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"06","main_file_link":[{"url":"https://doi.org/10.5061/dryad.cq7t1","open_access":"1"}],"oa_version":"Published Version","month":"05","author":[{"full_name":"Mcmahon, Dino","first_name":"Dino","last_name":"Mcmahon"},{"full_name":"Natsopoulou, Myrsini","first_name":"Myrsini","last_name":"Natsopoulou"},{"full_name":"Doublet, Vincent","first_name":"Vincent","last_name":"Doublet"},{"id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","orcid":"0000-0002-3712-925X","first_name":"Matthias","full_name":"Fürst, Matthias"},{"first_name":"Silvio","full_name":"Weging, Silvio","last_name":"Weging"},{"last_name":"Brown","first_name":"Mark","full_name":"Brown, Mark"},{"last_name":"Gogol Döring","full_name":"Gogol Döring, Andreas","first_name":"Andreas"},{"last_name":"Paxton","first_name":"Robert","full_name":"Paxton, Robert"}]},{"date_updated":"2025-05-28T11:57:03Z","oa":1,"article_processing_charge":"No","year":"2016","title":"Data from: How does epistasis influence the response to selection?","date_created":"2021-07-23T11:45:47Z","citation":{"chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>.","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, <a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","mla":"Barton, Nicholas H. <i>Data from: How Does Epistasis Influence the Response to Selection?</i> Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","short":"N.H. Barton, (2016).","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>"},"related_material":{"record":[{"id":"1199","relation":"used_in_publication","status":"public"}]},"_id":"9710","doi":"10.5061/dryad.s5s7r","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"month":"09","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.s5s7r","open_access":"1"}],"day":"23","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.","lang":"eng"}],"publisher":"Dryad","type":"research_data_reference","status":"public","date_published":"2016-09-23T00:00:00Z","department":[{"_id":"NiBa"}]},{"author":[{"last_name":"Mcmahon","full_name":"Mcmahon, Dino","first_name":"Dino"},{"last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","first_name":"Matthias"},{"first_name":"Jesicca","full_name":"Caspar, Jesicca","last_name":"Caspar"},{"first_name":"Panagiotis","full_name":"Theodorou, Panagiotis","last_name":"Theodorou"},{"last_name":"Brown","first_name":"Mark","full_name":"Brown, Mark"},{"last_name":"Paxton","full_name":"Paxton, Robert","first_name":"Robert"}],"month":"01","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.4b565"}],"day":"22","abstract":[{"lang":"eng","text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","status":"public","date_published":"2016-01-22T00:00:00Z","type":"research_data_reference","department":[{"_id":"SyCr"}],"oa":1,"date_updated":"2023-02-23T10:17:25Z","year":"2016","article_processing_charge":"No","title":"Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees","citation":{"chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>.","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees, Dryad, <a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","mla":"Mcmahon, Dino, et al. <i>Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees.” Dryad, 2016.","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., &#38; Paxton, R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. Dryad. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>"},"date_created":"2021-07-26T09:14:19Z","related_material":{"record":[{"id":"1855","relation":"used_in_publication","status":"public"}]},"_id":"9720","doi":"10.5061/dryad.4b565"},{"abstract":[{"text":"The half-filled Landau level is expected to be approximately particle-hole symmetric, which requires an extension of the Halperin-Lee-Read (HLR) theory of the compressible state observed at this filling. Recent work indicates that, when particle-hole symmetry is preserved, the composite fermions experience a quantized π-Berry phase upon winding around the composite Fermi surface, analogous to Dirac fermions at the surface of a 3D topological insulator. In contrast, the effective low-energy theory of the composite fermion liquid originally proposed by HLR lacks particle-hole symmetry and has vanishing Berry phase. In this paper, we explain how thermoelectric transport measurements can be used to test the Dirac nature of the composite fermions by quantitatively extracting this Berry phase. First, we point out that longitudinal thermopower (Seebeck effect) is nonvanishing because of the unusual nature of particle-hole symmetry in this context and is not sensitive to the Berry phase. In contrast, we find that off-diagonal thermopower (Nernst effect) is directly related to the topological structure of the composite Fermi surface, vanishing for zero Berry phase and taking its maximal value for π Berry phase. In contrast, in purely electrical transport signatures, the Berry phase contributions appear as small corrections to a large background signal, making the Nernst effect a promising diagnostic of the Dirac nature of composite fermions.","lang":"eng"}],"day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1512.06852","open_access":"1"}],"month":"01","author":[{"full_name":"Potter, Andrew C","first_name":"Andrew","last_name":"Potter"},{"first_name":"Maksym","full_name":"Maksym Serbyn","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"last_name":"Vishwanath","full_name":"Vishwanath, Ashvin K","first_name":"Ashvin"}],"publication_status":"published","volume":6,"quality_controlled":0,"extern":1,"date_published":"2016-01-01T00:00:00Z","status":"public","type":"journal_article","publisher":"American Physical Society","intvolume":"         6","date_created":"2018-12-11T11:49:32Z","citation":{"chicago":"Potter, Andrew, Maksym Serbyn, and Ashvin Vishwanath. “Thermoelectric Transport Signatures of Dirac Composite Fermions in the Half-Filled Landau Level.” <i>Physical Review X</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevX.6.031026\">https://doi.org/10.1103/PhysRevX.6.031026</a>.","ista":"Potter A, Serbyn M, Vishwanath A. 2016. Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level. Physical Review X. 6(3).","mla":"Potter, Andrew, et al. “Thermoelectric Transport Signatures of Dirac Composite Fermions in the Half-Filled Landau Level.” <i>Physical Review X</i>, vol. 6, no. 3, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031026\">10.1103/PhysRevX.6.031026</a>.","short":"A. Potter, M. Serbyn, A. Vishwanath, Physical Review X 6 (2016).","ieee":"A. Potter, M. Serbyn, and A. Vishwanath, “Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level,” <i>Physical Review X</i>, vol. 6, no. 3. American Physical Society, 2016.","ama":"Potter A, Serbyn M, Vishwanath A. Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level. <i>Physical Review X</i>. 2016;6(3). doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031026\">10.1103/PhysRevX.6.031026</a>","apa":"Potter, A., Serbyn, M., &#38; Vishwanath, A. (2016). Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.6.031026\">https://doi.org/10.1103/PhysRevX.6.031026</a>"},"title":"Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level","publist_id":"6417","year":"2016","issue":"3","acknowledgement":"We thank B. I. Halperin, N. Cooper, C. Wang, J. Alicea, and M. Zaletel for insightful conversations. A. C. P. and M. S. were supported by the Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant No. GBMF4307. A. V. was supported by a Simons Investigator grant.","date_updated":"2021-01-12T08:22:25Z","oa":1,"doi":"10.1103/PhysRevX.6.031026","publication":"Physical Review X","_id":"983"},{"issue":"16","year":"2016","oa":1,"acknowledgement":"We thank M. Stoudenmire and C. Turner for useful discussions. M. S. was supported by Gordon and Betty Moore Foundation's EPiQS Initiative through Grant No. GBMF4307. This research was supported in part by the National Science Foundation under Grant No. NSF PHY11-25915, and by the Swiss National Science Foundation and Alfred Sloan Foundation (D. A.). This work made use of the facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities of Leeds and Manchester.","date_updated":"2021-01-12T08:22:25Z","citation":{"chicago":"Serbyn, Maksym, Alexios Michailidis, Dmitry Abanin, and Zlatko Papić. “Power-Law Entanglement Spectrum in Many-Body Localized Phases.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevLett.117.160601\">https://doi.org/10.1103/PhysRevLett.117.160601</a>.","ista":"Serbyn M, Michailidis A, Abanin D, Papić Z. 2016. Power-law entanglement spectrum in many-body localized phases. Physical Review Letters. 117(16).","mla":"Serbyn, Maksym, et al. “Power-Law Entanglement Spectrum in Many-Body Localized Phases.” <i>Physical Review Letters</i>, vol. 117, no. 16, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.117.160601\">10.1103/PhysRevLett.117.160601</a>.","short":"M. Serbyn, A. Michailidis, D. Abanin, Z. Papić, Physical Review Letters 117 (2016).","ama":"Serbyn M, Michailidis A, Abanin D, Papić Z. Power-law entanglement spectrum in many-body localized phases. <i>Physical Review Letters</i>. 2016;117(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.117.160601\">10.1103/PhysRevLett.117.160601</a>","ieee":"M. Serbyn, A. Michailidis, D. Abanin, and Z. Papić, “Power-law entanglement spectrum in many-body localized phases,” <i>Physical Review Letters</i>, vol. 117, no. 16. American Physical Society, 2016.","apa":"Serbyn, M., Michailidis, A., Abanin, D., &#38; Papić, Z. (2016). Power-law entanglement spectrum in many-body localized phases. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.117.160601\">https://doi.org/10.1103/PhysRevLett.117.160601</a>"},"date_created":"2018-12-11T11:49:32Z","publist_id":"6414","title":"Power-law entanglement spectrum in many-body localized phases","intvolume":"       117","_id":"984","publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.117.160601","author":[{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Maksym Serbyn"},{"first_name":"Alexios","full_name":"Alexios Michailidis","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Abanin","first_name":"Dmitry","full_name":"Abanin, Dmitry A"},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"}],"publication_status":"published","month":"10","abstract":[{"text":"The entanglement spectrum of the reduced density matrix contains information beyond the von Neumann entropy and provides unique insights into exotic orders or critical behavior of quantum systems. Here, we show that strongly disordered systems in the many-body localized phase have power-law entanglement spectra, arising from the presence of extensively many local integrals of motion. The power-law entanglement spectrum distinguishes many-body localized systems from ergodic systems, as well as from ground states of gapped integrable models or free systems in the vicinity of scale-invariant critical points. We confirm our results using large-scale exact diagonalization. In addition, we develop a matrix-product state algorithm which allows us to access the eigenstates of large systems close to the localization transition, and discuss general implications of our results for variational studies of highly excited eigenstates in many-body localized systems.","lang":"eng"}],"day":"16","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.05737"}],"date_published":"2016-10-16T00:00:00Z","type":"journal_article","status":"public","publisher":"American Physical Society","volume":117,"quality_controlled":0,"extern":1},{"citation":{"short":"L. Campos, T. Taychatanapat, M. Serbyn, K. Surakitbovorn, K. Watanabe, T. Taniguchi, D. Abanin, P. Jarillo Herrero, Physical Review Letters 117 (2016).","ama":"Campos L, Taychatanapat T, Serbyn M, et al. Landau Level Splittings, Phase Transitions, and Nonuniform Charge Distribution in Trilayer Graphene. <i>Physical Review Letters</i>. 2016;117(6). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.117.066601\">10.1103/PhysRevLett.117.066601</a>","ieee":"L. Campos <i>et al.</i>, “Landau Level Splittings, Phase Transitions, and Nonuniform Charge Distribution in Trilayer Graphene,” <i>Physical Review Letters</i>, vol. 117, no. 6. American Physical Society, 2016.","chicago":"Campos, Leonardo, Thiti Taychatanapat, Maksym Serbyn, Kawin Surakitbovorn, Kenji Watanabe, Takashi Taniguchi, Dmitry Abanin, and Pablo Jarillo Herrero. “Landau Level Splittings, Phase Transitions, and Nonuniform Charge Distribution in Trilayer Graphene.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevLett.117.066601\">https://doi.org/10.1103/PhysRevLett.117.066601</a>.","mla":"Campos, Leonardo, et al. “Landau Level Splittings, Phase Transitions, and Nonuniform Charge Distribution in Trilayer Graphene.” <i>Physical Review Letters</i>, vol. 117, no. 6, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.117.066601\">10.1103/PhysRevLett.117.066601</a>.","ista":"Campos L, Taychatanapat T, Serbyn M, Surakitbovorn K, Watanabe K, Taniguchi T, Abanin D, Jarillo Herrero P. 2016. Landau Level Splittings, Phase Transitions, and Nonuniform Charge Distribution in Trilayer Graphene. Physical Review Letters. 117(6).","apa":"Campos, L., Taychatanapat, T., Serbyn, M., Surakitbovorn, K., Watanabe, K., Taniguchi, T., … Jarillo Herrero, P. (2016). Landau Level Splittings, Phase Transitions, and Nonuniform Charge Distribution in Trilayer Graphene. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.117.066601\">https://doi.org/10.1103/PhysRevLett.117.066601</a>"},"publist_id":"6415","date_created":"2018-12-11T11:49:33Z","title":"Landau Level Splittings, Phase Transitions, and Nonuniform Charge Distribution in Trilayer Graphene","year":"2016","issue":"6","oa":1,"date_updated":"2021-01-12T08:22:26Z","acknowledgement":"This work has been primarily supported by the National Science Foundation (DMR-1405221) for device fabrication and transport, and partly by ONR Young Investigator Award N00014-13-1-0610 for data analysis.","intvolume":"       117","_id":"985","doi":"10.1103/PhysRevLett.117.066601","publication":"Physical Review Letters","publication_status":"published","author":[{"full_name":"Campos, Leonardo C","first_name":"Leonardo","last_name":"Campos"},{"last_name":"Taychatanapat","full_name":"Taychatanapat, Thiti","first_name":"Thiti"},{"orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Maksym Serbyn"},{"last_name":"Surakitbovorn","full_name":"Surakitbovorn, Kawin N","first_name":"Kawin"},{"first_name":"Kenji","full_name":"Watanabe, Kenji","last_name":"Watanabe"},{"first_name":"Takashi","full_name":"Taniguchi, Takashi","last_name":"Taniguchi"},{"last_name":"Abanin","first_name":"Dmitry","full_name":"Abanin, Dmitry A"},{"first_name":"Pablo","full_name":"Jarillo-Herrero, Pablo","last_name":"Jarillo Herrero"}],"abstract":[{"lang":"eng","text":"We report on magnetotransport studies of dual-gated, Bernal-stacked trilayer graphene (TLG) encapsulated in boron nitride crystals. We observe a quantum Hall effect staircase which indicates a complete lifting of the 12-fold degeneracy of the zeroth Landau level. As a function of perpendicular electric field, our data exhibit a sequence of phase transitions between all integer quantum Hall states in the filling factor interval -8&lt;ν&lt;0. We develop a theoretical model and argue that, in contrast to monolayer and bilayer graphene, the observed Landau level splittings and quantum Hall phase transitions can be understood within a single-particle picture, but imply the presence of a charge density imbalance between the inner and outer layers of TLG, even at charge neutrality and zero transverse electric field. Our results indicate the importance of a previously unaccounted band structure parameter which, together with a more accurate estimate of the other tight-binding parameters, results in a significantly improved determination of the electronic and Landau level structure of TLG."}],"day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00784"}],"month":"04","volume":117,"quality_controlled":0,"extern":1,"type":"journal_article","status":"public","date_published":"2016-04-01T00:00:00Z","publisher":"American Physical Society"},{"doi":"10.1103/PhysRevB.93.041424","publication":"Physical Review B - Condensed Matter and Materials Physics","_id":"986","intvolume":"        93","title":"Spectral statistics across the many-body localization transition","publist_id":"6416","citation":{"mla":"Serbyn, Maksym, and Joel Moore. “Spectral Statistics across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 93, no. 4, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.93.041424\">10.1103/PhysRevB.93.041424</a>.","ista":"Serbyn M, Moore J. 2016. Spectral statistics across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 93(4).","chicago":"Serbyn, Maksym, and Joel Moore. “Spectral Statistics across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevB.93.041424\">https://doi.org/10.1103/PhysRevB.93.041424</a>.","ieee":"M. Serbyn and J. Moore, “Spectral statistics across the many-body localization transition,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 93, no. 4. American Physical Society, 2016.","ama":"Serbyn M, Moore J. Spectral statistics across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2016;93(4). doi:<a href=\"https://doi.org/10.1103/PhysRevB.93.041424\">10.1103/PhysRevB.93.041424</a>","short":"M. Serbyn, J. Moore, Physical Review B - Condensed Matter and Materials Physics 93 (2016).","apa":"Serbyn, M., &#38; Moore, J. (2016). Spectral statistics across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.93.041424\">https://doi.org/10.1103/PhysRevB.93.041424</a>"},"date_created":"2018-12-11T11:49:33Z","oa":1,"date_updated":"2021-01-12T08:22:26Z","issue":"4","year":"2016","extern":1,"volume":93,"quality_controlled":0,"publisher":"American Physical Society","date_published":"2016-01-29T00:00:00Z","status":"public","type":"journal_article","day":"29","main_file_link":[{"url":"https://arxiv.org/abs/1508.07293","open_access":"1"}],"abstract":[{"lang":"eng","text":"The many-body localization transition (MBLT) between ergodic and many-body localized phases in disordered interacting systems is a subject of much recent interest. The statistics of eigenenergies is known to be a powerful probe of crossovers between ergodic and integrable systems in simpler examples of quantum chaos. We consider the evolution of the spectral statistics across the MBLT, starting with mapping to a Brownian motion process that analytically relates the spectral properties to the statistics of matrix elements. We demonstrate that the flow from Wigner-Dyson to Poisson statistics is a two-stage process. First, a fractal enhancement of matrix elements upon approaching the MBLT from the delocalized side produces an effective power-law interaction between energy levels, and leads to a plasma model for level statistics. At the second stage, the gas of eigenvalues has local interactions and the level statistics belongs to a semi-Poisson universality class. We verify our findings numerically on the XXZ spin chain. We provide a microscopic understanding of the level statistics across the MBLT and discuss implications for the transition that are strong constraints on possible theories."}],"month":"01","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn","first_name":"Maksym"},{"last_name":"Moore","full_name":"Moore, Joel E","first_name":"Joel"}],"publication_status":"published"},{"title":"Simulation study to test the robustness of ABC in face of recent times of divergence","date_created":"2021-08-10T08:20:17Z","citation":{"apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>","mla":"Roux, Camille, et al. <i>Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016)."},"year":"2016","article_processing_charge":"No","date_updated":"2023-02-21T16:21:20Z","related_material":{"record":[{"status":"public","id":"1158","relation":"used_in_publication"}]},"_id":"9862","doi":"10.1371/journal.pbio.2000234.s016","author":[{"last_name":"Roux","full_name":"Roux, Camille","first_name":"Camille"},{"full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"first_name":"Youann","full_name":"Anciaux, Youann","last_name":"Anciaux"},{"first_name":"Nicolas","full_name":"Galtier, Nicolas","last_name":"Galtier"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"27","oa_version":"Published Version","month":"12","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"type":"research_data_reference","status":"public","publisher":"Public Library of Science"},{"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"type":"research_data_reference","status":"public","publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","day":"27","month":"12","author":[{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"last_name":"Anciaux","full_name":"Anciaux, Youann","first_name":"Youann"},{"first_name":"Nicolas","full_name":"Galtier, Nicolas","last_name":"Galtier"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"}],"doi":"10.1371/journal.pbio.2000234.s017","_id":"9863","related_material":{"record":[{"relation":"used_in_publication","id":"1158","status":"public"}]},"citation":{"apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>.","mla":"Roux, Camille, et al. <i>Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016)."},"title":"Accessions of surveyed individuals, geographic locations and summary statistics","date_created":"2021-08-10T08:22:52Z","article_processing_charge":"No","year":"2016","date_updated":"2023-02-21T16:21:20Z"},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1077"}]},"date_created":"2021-08-10T08:29:47Z","citation":{"apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","mla":"Fernandes Redondo, Rodrigo A., et al. <i>Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family</i>. The Royal Society, 2016, doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>."},"title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","date_updated":"2025-05-28T11:57:06Z","oa":1,"year":"2016","article_processing_charge":"No","doi":"10.6084/m9.figshare.4315652.v1","_id":"9864","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.4315652.v1"}],"oa_version":"Published Version","day":"14","abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"12","author":[{"first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793"},{"orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"de Vladar","first_name":"Harold","full_name":"de Vladar, Harold"},{"last_name":"Włodarski","full_name":"Włodarski, Tomasz","first_name":"Tomasz"},{"orcid":"0000-0002-4624-4612","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","first_name":"Jonathan P"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"The Royal Society","type":"research_data_reference","status":"public","date_published":"2016-12-14T00:00:00Z"},{"doi":"10.1371/journal.pcbi.1005218.s009","_id":"9866","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1167"}]},"date_created":"2021-08-10T08:37:20Z","title":"ZIP-archived directory containing all data and computer programs","citation":{"short":"M.P. Zagórski, Z. Burda, B. Wacław, (2016).","ama":"Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data and computer programs. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing all data and computer programs.” Public Library of Science, 2016.","mla":"Zagórski, Marcin P., et al. <i>ZIP-Archived Directory Containing All Data and Computer Programs</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>.","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived Directory Containing All Data and Computer Programs.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>.","ista":"Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all data and computer programs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>.","apa":"Zagórski, M. P., Burda, Z., &#38; Wacław, B. (2016). ZIP-archived directory containing all data and computer programs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>"},"date_updated":"2023-02-21T16:24:29Z","year":"2016","article_processing_charge":"No","department":[{"_id":"AnKi"}],"publisher":"Public Library of Science","status":"public","date_published":"2016-12-09T00:00:00Z","type":"research_data_reference","day":"09","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"12","author":[{"first_name":"Marcin P","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski"},{"full_name":"Burda, Zdzisław","first_name":"Zdzisław","last_name":"Burda"},{"full_name":"Wacław, Bartłomiej","first_name":"Bartłomiej","last_name":"Wacław"}]}]