[{"issue":"6","pmid":1,"extern":"1","type":"journal_article","article_processing_charge":"No","year":"2014","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.01.029","open_access":"1"}],"abstract":[{"text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.","lang":"eng"}],"intvolume":"       156","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","date_updated":"2021-12-14T08:22:36Z","month":"03","publication":"Cell","day":"13","date_created":"2021-06-04T12:00:16Z","oa_version":"Published Version","language":[{"iso":"eng"}],"scopus_import":"1","_id":"9458","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.1016/j.cell.2014.01.029","volume":156,"oa":1,"publication_status":"published","external_id":{"pmid":["24630728"]},"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"date_published":"2014-03-13T00:00:00Z","article_type":"original","department":[{"_id":"DaZi"}],"doi":"10.1016/j.cell.2014.01.029","page":"1286-1297","author":[{"last_name":"Huff","full_name":"Huff, Jason T.","first_name":"Jason T."},{"full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"citation":{"mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297."},"quality_controlled":"1","publisher":"Elsevier","status":"public"},{"date_created":"2021-06-07T07:23:43Z","day":"11","scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"9479","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.1073/pnas.1418564111","volume":111,"publication_status":"published","oa":1,"date_published":"2014-11-11T00:00:00Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"external_id":{"pmid":["25344531"]},"article_type":"original","doi":"10.1073/pnas.1418564111","department":[{"_id":"DaZi"}],"author":[{"first_name":"Zsuzsanna","full_name":"Mérai, Zsuzsanna","last_name":"Mérai"},{"first_name":"Nina","full_name":"Chumak, Nina","last_name":"Chumak"},{"first_name":"Marcelina","full_name":"García-Aguilar, Marcelina","last_name":"García-Aguilar"},{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"last_name":"Schoft","first_name":"Vera K.","full_name":"Schoft, Vera K."},{"last_name":"Bindics","first_name":"János","full_name":"Bindics, János"},{"last_name":"Ślusarz","first_name":"Lucyna","full_name":"Ślusarz, Lucyna"},{"last_name":"Arnoux","full_name":"Arnoux, Stéphanie","first_name":"Stéphanie"},{"last_name":"Opravil","full_name":"Opravil, Susanne","first_name":"Susanne"},{"last_name":"Mechtler","full_name":"Mechtler, Karl","first_name":"Karl"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"},{"last_name":"Tamaru","full_name":"Tamaru, Hisashi","first_name":"Hisashi"}],"page":"16166-16171","quality_controlled":"1","citation":{"mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171."},"publisher":"National Academy of Sciences","status":"public","issue":"45","pmid":1,"extern":"1","type":"journal_article","article_processing_charge":"No","year":"2014","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}],"abstract":[{"lang":"eng","text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction."}],"intvolume":"       111","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","month":"11","date_updated":"2021-12-14T08:23:26Z","publication":"Proceedings of the National Academy of Sciences"},{"date_created":"2021-06-07T14:38:09Z","day":"04","scopus_import":"1","language":[{"iso":"eng"}],"oa_version":"None","_id":"9519","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.1016/j.tplants.2014.01.014","volume":19,"publication_status":"published","date_published":"2014-05-04T00:00:00Z","publication_identifier":{"issn":["1360-1385"],"eissn":["1878-4372"]},"external_id":{"pmid":["24618094 "]},"article_type":"review","doi":"10.1016/j.tplants.2014.01.014","department":[{"_id":"DaZi"}],"page":"320-326","author":[{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel"}],"quality_controlled":"1","citation":{"ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326.","mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>.","ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. 2014;19(5):320-326. doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>","apa":"Kim, M. Y., &#38; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>.","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.","ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” <i>Trends in Plant Science</i>, vol. 19, no. 5. Elsevier, pp. 320–326, 2014."},"publisher":"Elsevier","status":"public","issue":"5","pmid":1,"extern":"1","type":"journal_article","article_processing_charge":"No","year":"2014","abstract":[{"lang":"eng","text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression."}],"intvolume":"        19","title":"DNA methylation as a system of plant genomic immunity","month":"05","date_updated":"2021-12-14T08:24:48Z","publication":"Trends in Plant Science"},{"month":"02","arxiv":1,"date_updated":"2023-02-23T14:02:12Z","publication":"The Electronic Journal of Combinatorics","intvolume":"        21","title":"On the number of spanning trees in random regular graphs","year":"2014","abstract":[{"text":"Let d≥3 be a fixed integer. We give an asympotic formula for the expected number of spanning trees in a uniformly random d-regular graph with n vertices. (The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain the asymptotic distribution of the number of spanning trees in a uniformly random cubic graph, and conjecture that the corresponding result holds for arbitrary (fixed) d. Numerical evidence is presented which supports our conjecture.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.37236/3752"}],"article_processing_charge":"No","extern":"1","type":"journal_article","article_number":"P1.45","issue":"1","publisher":"The Electronic Journal of Combinatorics","status":"public","author":[{"last_name":"Greenhill","first_name":"Catherine","full_name":"Greenhill, Catherine"},{"last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan"},{"last_name":"Wind","full_name":"Wind, David","first_name":"David"}],"quality_controlled":"1","citation":{"ama":"Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular graphs. <i>The Electronic Journal of Combinatorics</i>. 2014;21(1). doi:<a href=\"https://doi.org/10.37236/3752\">10.37236/3752</a>","ista":"Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.","mla":"Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular Graphs.” <i>The Electronic Journal of Combinatorics</i>, vol. 21, no. 1, P1.45, The Electronic Journal of Combinatorics, 2014, doi:<a href=\"https://doi.org/10.37236/3752\">10.37236/3752</a>.","short":"C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics 21 (2014).","ieee":"C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in random regular graphs,” <i>The Electronic Journal of Combinatorics</i>, vol. 21, no. 1. The Electronic Journal of Combinatorics, 2014.","apa":"Greenhill, C., Kwan, M. A., &#38; Wind, D. (2014). On the number of spanning trees in random regular graphs. <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/3752\">https://doi.org/10.37236/3752</a>","chicago":"Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number of Spanning Trees in Random Regular Graphs.” <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics, 2014. <a href=\"https://doi.org/10.37236/3752\">https://doi.org/10.37236/3752</a>."},"doi":"10.37236/3752","date_published":"2014-02-28T00:00:00Z","publication_identifier":{"eissn":["1077-8926"]},"external_id":{"arxiv":["1309.6710"]},"article_type":"original","volume":21,"oa":1,"publication_status":"published","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","fulldoi":"https://doi.org/10.37236/3752","scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"9594","date_created":"2021-06-23T06:29:35Z","day":"28"},{"language":[{"iso":"eng"}],"oa_version":"Preprint","_id":"96","day":"14","date_created":"2018-12-11T11:44:36Z","volume":112,"publication_status":"published","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1103/PhysRevLett.112.026801","doi":"10.1103/PhysRevLett.112.026801","external_id":{"arxiv":["1306.2720"]},"date_published":"2014-01-14T00:00:00Z","publisher":"American Physiological Society","status":"public","author":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"},{"full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand","last_name":"Kuemmeth"},{"full_name":"Hanson, Micah","first_name":"Micah","last_name":"Hanson"},{"full_name":"Gossard, Arthur","first_name":"Arthur","last_name":"Gossard"},{"full_name":"Marcus, Charles","first_name":"Charles","last_name":"Marcus"}],"citation":{"ama":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations and screening in multielectron spin qubits. <i>APS Physics, Physical Review Letters</i>. 2014;112(2). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">10.1103/PhysRevLett.112.026801</a>","ista":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. 112(2), 026801.","mla":"Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron Spin Qubits.” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 2, 026801, American Physiological Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">10.1103/PhysRevLett.112.026801</a>.","short":"A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics, Physical Review Letters 112 (2014).","ieee":"A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent operations and screening in multielectron spin qubits,” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 2. American Physiological Society, 2014.","apa":"Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., &#38; Marcus, C. (2014). Coherent operations and screening in multielectron spin qubits. <i>APS Physics, Physical Review Letters</i>. American Physiological Society. <a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">https://doi.org/10.1103/PhysRevLett.112.026801</a>","chicago":"Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard, and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.” <i>APS Physics, Physical Review Letters</i>. American Physiological Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">https://doi.org/10.1103/PhysRevLett.112.026801</a>."},"quality_controlled":"1","article_number":"026801","issue":"2","acknowledgement":"The research is supported by the Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish National Research Foundation.","extern":"1","type":"journal_article","title":"Coherent operations and screening in multielectron spin qubits","intvolume":"       112","publist_id":"7958","year":"2014","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1306.2720"}],"abstract":[{"text":"Multielectron spin qubits are demonstrated, and performance examined by comparing coherent exchange oscillations in coupled single-electron and multielectron quantum dots, measured in the same device. Fast (&gt;1 GHz) exchange oscillations with a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for the single-electron case, the latter consistent with experiments in the literature. A model of dephasing that includes voltage and hyperfine noise is developed that is in good agreement with both single- and multielectron data, though in both cases additional exchange-independent dephasing is needed to obtain quantitative agreement across a broad parameter range.","lang":"eng"}],"arxiv":1,"date_updated":"2021-01-12T08:22:14Z","month":"01","publication":"APS Physics, Physical Review Letters"},{"article_processing_charge":"No","type":"journal_article","extern":"1","pmid":1,"issue":"2","publication":"Journal of Structural Biology","file":[{"relation":"main_file","success":1,"creator":"asandaue","content_type":"application/pdf","checksum":"a322991b43cdc5935c99db88d285aa3a","date_created":"2021-07-22T08:06:34Z","file_size":3454628,"access_level":"open_access","file_id":"9701","file_name":"2014_JournalOfStructuralBiology_Perkovic.pdf","date_updated":"2021-07-22T08:06:34Z"}],"month":"05","date_updated":"2021-07-22T08:26:32Z","has_accepted_license":"1","title":"Correlative light- and electron microscopy with chemical tags","intvolume":"       186","abstract":[{"lang":"eng","text":"Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x–y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells."}],"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","year":"2014","oa":1,"publication_status":"published","volume":186,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode"},"fulldoi":"https://doi.org/10.1016/j.jsb.2014.03.018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9655","scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"date_created":"2021-07-14T09:05:42Z","day":"01","ddc":["570"],"status":"public","publisher":"Elsevier","quality_controlled":"1","citation":{"ama":"Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy with chemical tags. <i>Journal of Structural Biology</i>. 2014;186(2):205-213. doi:<a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">10.1016/j.jsb.2014.03.018</a>","ista":"Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 186(2), 205–213.","mla":"Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” <i>Journal of Structural Biology</i>, vol. 186, no. 2, Elsevier, 2014, pp. 205–13, doi:<a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">10.1016/j.jsb.2014.03.018</a>.","short":"M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau, M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis, Journal of Structural Biology 186 (2014) 205–213.","ieee":"M. Perkovic <i>et al.</i>, “Correlative light- and electron microscopy with chemical tags,” <i>Journal of Structural Biology</i>, vol. 186, no. 2. Elsevier, pp. 205–213, 2014.","apa":"Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis, A. S. (2014). Correlative light- and electron microscopy with chemical tags. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">https://doi.org/10.1016/j.jsb.2014.03.018</a>","chicago":"Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” <i>Journal of Structural Biology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">https://doi.org/10.1016/j.jsb.2014.03.018</a>."},"page":"205-213","author":[{"first_name":"Mario","full_name":"Perkovic, Mario","last_name":"Perkovic"},{"full_name":"Kunz, Michael","first_name":"Michael","last_name":"Kunz"},{"full_name":"Endesfelder, Ulrike","first_name":"Ulrike","last_name":"Endesfelder"},{"last_name":"Bunse","full_name":"Bunse, Stefanie","first_name":"Stefanie"},{"last_name":"Wigge","full_name":"Wigge, Christoph","first_name":"Christoph"},{"full_name":"Yu, Zhou","first_name":"Zhou","last_name":"Yu"},{"full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Scheffer, Margot P.","first_name":"Margot P.","last_name":"Scheffer"},{"last_name":"Seybert","first_name":"Anja","full_name":"Seybert, Anja"},{"last_name":"Malkusch","full_name":"Malkusch, Sebastian","first_name":"Sebastian"},{"first_name":"Erin M.","full_name":"Schuman, Erin M.","last_name":"Schuman"},{"first_name":"Mike","full_name":"Heilemann, Mike","last_name":"Heilemann"},{"full_name":"Frangakis, Achilleas S.","first_name":"Achilleas S.","last_name":"Frangakis"}],"file_date_updated":"2021-07-22T08:06:34Z","doi":"10.1016/j.jsb.2014.03.018","article_type":"original","date_published":"2014-05-01T00:00:00Z","publication_identifier":{"issn":["1047-8477"]},"external_id":{"pmid":["24698954"]}},{"status":"public","publisher":"AIP Publishing","citation":{"ieee":"B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation ratios,” <i>The Journal of Chemical Physics</i>, vol. 141, no. 24. AIP Publishing, 2014.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2014. <a href=\"https://doi.org/10.1063/1.4904293\">https://doi.org/10.1063/1.4904293</a>.","apa":"Cheng, B., &#38; Ceriotti, M. (2014). Direct path integral estimators for isotope fractionation ratios. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4904293\">https://doi.org/10.1063/1.4904293</a>","ama":"Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation ratios. <i>The Journal of Chemical Physics</i>. 2014;141(24). doi:<a href=\"https://doi.org/10.1063/1.4904293\">10.1063/1.4904293</a>","mla":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” <i>The Journal of Chemical Physics</i>, vol. 141, no. 24, 244112, AIP Publishing, 2014, doi:<a href=\"https://doi.org/10.1063/1.4904293\">10.1063/1.4904293</a>.","ista":"Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 141(24), 244112."},"quality_controlled":"1","author":[{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"doi":"10.1063/1.4904293","article_type":"original","external_id":{"pmid":["25554138"],"arxiv":["1412.1308"]},"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"date_published":"2014-12-28T00:00:00Z","publication_status":"published","oa":1,"volume":141,"fulldoi":"https://doi.org/10.1063/1.4904293","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9662","oa_version":"Preprint","language":[{"iso":"eng"}],"scopus_import":"1","day":"28","date_created":"2021-07-15T09:22:49Z","publication":"The Journal of Chemical Physics","arxiv":1,"date_updated":"2021-08-09T12:32:24Z","month":"12","intvolume":"       141","title":"Direct path integral estimators for isotope fractionation ratios","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.1308"}],"abstract":[{"lang":"eng","text":"Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons."}],"year":"2014","article_processing_charge":"No","type":"journal_article","extern":"1","pmid":1,"article_number":"244112","issue":"24"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","fulldoi":"https://doi.org/10.1080/14786435.2014.897008","volume":95,"publication_status":"published","day":"23","date_created":"2021-07-19T09:27:15Z","scopus_import":"1","oa_version":"None","language":[{"iso":"eng"}],"_id":"9686","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing","full_name":"Cheng, Bingqing"},{"first_name":"H.S.","full_name":"Leung, H.S.","last_name":"Leung"},{"last_name":"Ngan","first_name":"A.H.W.","full_name":"Ngan, A.H.W."}],"page":"1845-1865","quality_controlled":"1","citation":{"short":"B. Cheng, H.S. Leung, A.H.W. Ngan, Philosophical Magazine 95 (2014) 1845–1865.","ieee":"B. Cheng, H. S. Leung, and A. H. W. Ngan, “Strength of metals under vibrations – dislocation-density-function dynamics simulations,” <i>Philosophical Magazine</i>, vol. 95, no. 16–18. Taylor &#38; Francis, pp. 1845–1865, 2014.","apa":"Cheng, B., Leung, H. S., &#38; Ngan, A. H. W. (2014). Strength of metals under vibrations – dislocation-density-function dynamics simulations. <i>Philosophical Magazine</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/14786435.2014.897008\">https://doi.org/10.1080/14786435.2014.897008</a>","chicago":"Cheng, Bingqing, H.S. Leung, and A.H.W. Ngan. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” <i>Philosophical Magazine</i>. Taylor &#38; Francis, 2014. <a href=\"https://doi.org/10.1080/14786435.2014.897008\">https://doi.org/10.1080/14786435.2014.897008</a>.","ama":"Cheng B, Leung HS, Ngan AHW. Strength of metals under vibrations – dislocation-density-function dynamics simulations. <i>Philosophical Magazine</i>. 2014;95(16-18):1845-1865. doi:<a href=\"https://doi.org/10.1080/14786435.2014.897008\">10.1080/14786435.2014.897008</a>","ista":"Cheng B, Leung HS, Ngan AHW. 2014. Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. 95(16–18), 1845–1865.","mla":"Cheng, Bingqing, et al. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” <i>Philosophical Magazine</i>, vol. 95, no. 16–18, Taylor &#38; Francis, 2014, pp. 1845–65, doi:<a href=\"https://doi.org/10.1080/14786435.2014.897008\">10.1080/14786435.2014.897008</a>."},"publisher":"Taylor & Francis","status":"public","date_published":"2014-06-23T00:00:00Z","publication_identifier":{"eissn":["1478-6443"],"issn":["1478-6435"]},"article_type":"original","doi":"10.1080/14786435.2014.897008","extern":"1","type":"journal_article","article_processing_charge":"No","issue":"16-18","month":"06","date_updated":"2023-02-23T14:04:59Z","publication":"Philosophical Magazine","year":"2014","abstract":[{"text":"It is well known that ultrasonic vibration can soften metals, and this phenomenon has been widely exploited in industrial applications concerning metal forming and bonding. Recent experiments show that the simultaneous application of oscillatory stresses from audible to ultrasonic frequency ranges can lead to not only softening but also significant dislocation annihilation and subgrain formation in metal samples from the nano- to macro-size range. These findings indicate that the existing understanding of ultrasound softening – that the vibrations either impose additional stress waves to augment the quasi-static applied load, or cause heating of the metal, whereas the metal’s intrinsic deformation resistance or mechanism remains unaltered – is far from complete. To understand the softening and the associated enhanced subgrain formation and dislocation annihilation, a new simulator based on the dynamics of dislocation-density functions is employed. This new simulator considers the flux, production and annihilation, as well as the Taylor and elastic interactions between dislocation densities. Softening during vibrations as well as enhanced cell formation is predicted. The simulations reveal the main mechanism for subcell formation under oscillatory loadings to be the enhanced elimination of statistically stored dislocations (SSDs) by the oscillatory stress, leaving behind geometrically necessary dislocations with low Schmid factors which then form the subgrain walls. The oscillatory stress helps the depletion of the SSDs, because the chance for them to meet up and annihilate is increased with reversals of dislocation motions. This is the first simulation effort to successfully predict the cell formation phenomenon under vibratory loadings.","lang":"eng"}],"title":"Strength of metals under vibrations – dislocation-density-function dynamics simulations","intvolume":"        95"},{"publication":"APS Physics, Physical Review Letters","arxiv":1,"date_updated":"2021-01-12T08:22:19Z","month":"05","intvolume":"       112","title":"Antilocalization of coulomb blockade in a Ge/Si nanowire","abstract":[{"text":"The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length (lso < 20 nm), consistent with values extracted in the Coulomb blockade regime (lso < 25 nm).","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1401.2948","open_access":"1"}],"publist_id":"7957","year":"2014","type":"journal_article","extern":"1","article_number":"216806","acknowledgement":"Research supported by the Danish National Research Foundation, the Office of Science at the U.S. Department of Energy, the National Science Foundation (PHY-1104528), and the Defense Advanced Research Projects Agency through the QuEST Program.","issue":"21","status":"public","publisher":"American Physical Society","citation":{"ama":"Higginbotham AP, Kuemmeth F, Larsen T, et al. Antilocalization of coulomb blockade in a Ge/Si nanowire. <i>APS Physics, Physical Review Letters</i>. 2014;112(21). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">10.1103/PhysRevLett.112.216806</a>","mla":"Higginbotham, Andrew P., et al. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 21, 216806, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">10.1103/PhysRevLett.112.216806</a>.","ista":"Higginbotham AP, Kuemmeth F, Larsen T, Fitzpatrick M, Yao J, Yan H, Lieber C, Marcus C. 2014. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. 112(21), 216806.","ieee":"A. P. Higginbotham <i>et al.</i>, “Antilocalization of coulomb blockade in a Ge/Si nanowire,” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 21. American Physical Society, 2014.","short":"A.P. Higginbotham, F. Kuemmeth, T. Larsen, M. Fitzpatrick, J. Yao, H. Yan, C. Lieber, C. Marcus, APS Physics, Physical Review Letters 112 (2014).","chicago":"Higginbotham, Andrew P, Ferdinand Kuemmeth, Thorvald Larsen, Mattias Fitzpatrick, Jun Yao, Hao Yan, Charles Lieber, and Charles Marcus. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” <i>APS Physics, Physical Review Letters</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">https://doi.org/10.1103/PhysRevLett.112.216806</a>.","apa":"Higginbotham, A. P., Kuemmeth, F., Larsen, T., Fitzpatrick, M., Yao, J., Yan, H., … Marcus, C. (2014). Antilocalization of coulomb blockade in a Ge/Si nanowire. <i>APS Physics, Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">https://doi.org/10.1103/PhysRevLett.112.216806</a>"},"quality_controlled":"1","author":[{"first_name":"Andrew P","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363"},{"first_name":"Ferdinand","full_name":"Kuemmeth, Ferdinand","last_name":"Kuemmeth"},{"last_name":"Larsen","full_name":"Larsen, Thorvald","first_name":"Thorvald"},{"last_name":"Fitzpatrick","full_name":"Fitzpatrick, Mattias","first_name":"Mattias"},{"last_name":"Yao","first_name":"Jun","full_name":"Yao, Jun"},{"first_name":"Hao","full_name":"Yan, Hao","last_name":"Yan"},{"last_name":"Lieber","first_name":"Charles","full_name":"Lieber, Charles"},{"first_name":"Charles","full_name":"Marcus, Charles","last_name":"Marcus"}],"doi":"10.1103/PhysRevLett.112.216806","external_id":{"arxiv":["1401.2948"]},"date_published":"2014-05-29T00:00:00Z","publication_status":"published","oa":1,"volume":112,"fulldoi":"https://doi.org/10.1103/PhysRevLett.112.216806","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"97","oa_version":"None","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:44:36Z","day":"29"},{"fulldoi":"https://doi.org/10.1371/journal.pone.0111430.s006","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","day":"14","date_created":"2021-07-26T14:35:00Z","_id":"9722","oa_version":"Published Version","citation":{"chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>.","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &#38; Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>","ieee":"A. Lovrics <i>et al.</i>, “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014).","mla":"Lovrics, Anna, et al. <i>Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>"},"author":[{"last_name":"Lovrics","first_name":"Anna","full_name":"Lovrics, Anna"},{"last_name":"Gao","full_name":"Gao, Yu","first_name":"Yu"},{"last_name":"Juhász","full_name":"Juhász, Bianka","first_name":"Bianka"},{"first_name":"István","full_name":"Bock, István","last_name":"Bock"},{"first_name":"Helen M.","full_name":"Byrne, Helen M.","last_name":"Byrne"},{"last_name":"Dinnyés","full_name":"Dinnyés, András","first_name":"András"},{"full_name":"Kovács, Krisztián","first_name":"Krisztián","last_name":"Kovács","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-09-29T12:02:47Z","month":"11","status":"public","publisher":"Public Library of Science","date_published":"2014-11-14T00:00:00Z","year":"2014","title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2","department":[{"_id":"JoCs"}],"doi":"10.1371/journal.pone.0111430.s006","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2004"}]}},{"citation":{"ista":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for “The time scale of evolutionary innovation”, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Detailed Proofs for “The Time Scale of Evolutionary Innovation.”</i> Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time scale of evolutionary innovation.” 2014. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., &#38; Novak, M. (2014). Detailed proofs for “The time scale of evolutionary innovation.” Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak. “Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014."},"date_updated":"2025-09-29T11:53:46Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"},{"full_name":"Adlam, Ben","first_name":"Ben","last_name":"Adlam"},{"last_name":"Novak","full_name":"Novak, Martin","first_name":"Martin"}],"month":"09","status":"public","publisher":"Public Library of Science","date_published":"2014-09-11T00:00:00Z","year":"2014","title":"Detailed proofs for “The time scale of evolutionary innovation”","department":[{"_id":"KrCh"}],"doi":"10.1371/journal.pcbi.1003818.s001","related_material":{"record":[{"id":"2039","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","fulldoi":"https://doi.org/10.1371/journal.pcbi.1003818.s001","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","day":"11","date_created":"2021-07-28T08:13:57Z","_id":"9739","oa_version":"Published Version"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.vm0vc"}],"abstract":[{"lang":"eng","text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens."}],"year":"2014","date_published":"2014-11-13T00:00:00Z","title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","department":[{"_id":"SyCr"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1993"}]},"doi":"10.5061/dryad.vm0vc","citation":{"ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad, <a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","mla":"Konrad, Matthias, et al. <i>Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>","apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2014). Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Dryad. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014).","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host.” Dryad, 2014."},"author":[{"last_name":"Konrad","id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias","first_name":"Matthias"},{"last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","first_name":"Anna V"},{"full_name":"Tragust, Simon","first_name":"Simon","last_name":"Tragust","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","first_name":"Sylvia"}],"date_updated":"2025-09-23T07:55:02Z","month":"11","status":"public","publisher":"Dryad","date_created":"2021-07-28T08:38:40Z","day":"13","_id":"9740","corr_author":"1","oa_version":"Published Version","type":"research_data_reference","fulldoi":"https://doi.org/10.5061/dryad.vm0vc","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","oa":1},{"_id":"9747","oa_version":"Published Version","day":"17","date_created":"2021-07-28T15:32:55Z","article_processing_charge":"No","oa":1,"type":"research_data_reference","fulldoi":"https://doi.org/10.5061/dryad.s42n1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Role of sex and migration in adaptation to sink environments","doi":"10.5061/dryad.s42n1","related_material":{"record":[{"id":"2083","relation":"used_in_publication","status":"public"}]},"department":[{"_id":"CaGu"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.s42n1","open_access":"1"}],"abstract":[{"text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.","lang":"eng"}],"year":"2014","date_published":"2014-04-17T00:00:00Z","status":"public","publisher":"Dryad","citation":{"ama":"Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>","mla":"Lagator, Mato, et al. <i>Data from: Role of Sex and Migration in Adaptation to Sink Environments</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, <a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>.","apa":"Lagator, M., Morgan, A., Neve, P., &#38; Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>"},"month":"04","date_updated":"2025-09-29T11:46:47Z","author":[{"full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Morgan","first_name":"Andrew","full_name":"Morgan, Andrew"},{"first_name":"Paul","full_name":"Neve, Paul","last_name":"Neve"},{"full_name":"Colegrave, Nick","first_name":"Nick","last_name":"Colegrave"}]},{"status":"public","publisher":"Dryad","citation":{"short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).","ieee":"K. Simmons <i>et al.</i>, “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>.","ama":"Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>","ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad, <a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","mla":"Simmons, Kristina, et al. <i>Data from: Transformation of Stimulus Correlations by the Retina</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>."},"date_updated":"2025-09-29T14:27:23Z","author":[{"last_name":"Simmons","first_name":"Kristina","full_name":"Simmons, Kristina"},{"full_name":"Prentice, Jason","first_name":"Jason","last_name":"Prentice"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"last_name":"Homann","full_name":"Homann, Jan","first_name":"Jan"},{"first_name":"Heather","full_name":"Yee, Heather","last_name":"Yee"},{"full_name":"Palmer, Stephanie","first_name":"Stephanie","last_name":"Palmer"},{"full_name":"Nelson, Philip","first_name":"Philip","last_name":"Nelson"},{"last_name":"Balasubramanian","first_name":"Vijay","full_name":"Balasubramanian, Vijay"}],"month":"11","title":"Data from: Transformation of stimulus correlations by the retina","department":[{"_id":"GaTk"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2277"}]},"doi":"10.5061/dryad.246qg","abstract":[{"lang":"eng","text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.246qg"}],"date_published":"2014-11-07T00:00:00Z","year":"2014","oa":1,"article_processing_charge":"No","type":"research_data_reference","fulldoi":"https://doi.org/10.5061/dryad.246qg","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9752","oa_version":"Published Version","day":"07","date_created":"2021-07-30T08:13:52Z"},{"volume":14,"oa":1,"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1021/nl501242b","language":[{"iso":"eng"}],"oa_version":"Preprint","_id":"98","day":"05","date_created":"2018-12-11T11:44:37Z","publisher":"American Chemical Society","status":"public","page":"3582 - 3586","author":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"},{"full_name":"Larsen, Thorvald","first_name":"Thorvald","last_name":"Larsen"},{"last_name":"Yao","full_name":"Yao, Jun","first_name":"Jun"},{"full_name":"Yan, Hao","first_name":"Hao","last_name":"Yan"},{"last_name":"Lieber","full_name":"Lieber, Charles","first_name":"Charles"},{"full_name":"Marcus, Charles","first_name":"Charles","last_name":"Marcus"},{"first_name":"Ferdinand","full_name":"Kuemmeth, Ferdinand","last_name":"Kuemmeth"}],"citation":{"ama":"Higginbotham AP, Larsen T, Yao J, et al. Hole spin coherence in a Ge/Si heterostructure nanowire. <i>Nano Letters</i>. 2014;14(6):3582-3586. doi:<a href=\"https://doi.org/10.1021/nl501242b\">10.1021/nl501242b</a>","ista":"Higginbotham AP, Larsen T, Yao J, Yan H, Lieber C, Marcus C, Kuemmeth F. 2014. Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 14(6), 3582–3586.","mla":"Higginbotham, Andrew P., et al. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” <i>Nano Letters</i>, vol. 14, no. 6, American Chemical Society, 2014, pp. 3582–86, doi:<a href=\"https://doi.org/10.1021/nl501242b\">10.1021/nl501242b</a>.","short":"A.P. Higginbotham, T. Larsen, J. Yao, H. Yan, C. Lieber, C. Marcus, F. Kuemmeth, Nano Letters 14 (2014) 3582–3586.","ieee":"A. P. Higginbotham <i>et al.</i>, “Hole spin coherence in a Ge/Si heterostructure nanowire,” <i>Nano Letters</i>, vol. 14, no. 6. American Chemical Society, pp. 3582–3586, 2014.","apa":"Higginbotham, A. P., Larsen, T., Yao, J., Yan, H., Lieber, C., Marcus, C., &#38; Kuemmeth, F. (2014). Hole spin coherence in a Ge/Si heterostructure nanowire. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/nl501242b\">https://doi.org/10.1021/nl501242b</a>","chicago":"Higginbotham, Andrew P, Thorvald Larsen, Jun Yao, Hao Yan, Charles Lieber, Charles Marcus, and Ferdinand Kuemmeth. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” <i>Nano Letters</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/nl501242b\">https://doi.org/10.1021/nl501242b</a>."},"quality_controlled":"1","doi":"10.1021/nl501242b","external_id":{"arxiv":["1403.2093"]},"date_published":"2014-05-05T00:00:00Z","extern":"1","type":"journal_article","issue":"6","acknowledgement":"Funding from the Department of Energy, Office of Science & SCGF, the EC FP7-ICT project SiSPIN no. 323841, and the Danish National Research Foundation is acknowledged.","date_updated":"2021-01-12T08:22:24Z","arxiv":1,"month":"05","publication":"Nano Letters","intvolume":"        14","title":"Hole spin coherence in a Ge/Si heterostructure nanowire","year":"2014","publist_id":"7956","abstract":[{"lang":"eng","text":"Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing."}],"main_file_link":[{"url":"https://arxiv.org/abs/1403.2093","open_access":"1"}]},{"issue":"9","type":"journal_article","extern":"1","title":"From polar to Reed-Muller codes: A technique to improve the finite-length performance","intvolume":"        62","abstract":[{"text":"We explore the relationship between polar and RM codes and we describe a coding scheme which improves upon the performance of the standard polar code at practical block lengths. Our starting point is the experimental observation that RM codes have a smaller error probability than polar codes under MAP decoding. This motivates us to introduce a family of codes that “interpolates” between RM and polar codes, call this family C inter = {C α : α ∈ [0, 1j}, where C α|α=1 is the original polar code, and C α|α=0 is an RM code. Based on numerical observations, we remark that the error probability under MAP decoding is an increasing function of α. MAP decoding has in general exponential complexity, but empirically the performance of polar codes at finite block lengths is boosted by moving along the family Cinter even under low-complexity decoding schemes such as, for instance, belief propagation or successive cancellation list decoder. We demonstrate the performance gain via numerical simulations for transmission over the erasure channel as well as the Gaussian channel.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1401.3127"}],"year":"2014","publication":"IEEE Transactions on Communications","month":"09","arxiv":1,"date_updated":"2021-01-12T08:08:46Z","_id":"6739","language":[{"iso":"eng"}],"oa_version":"Preprint","date_created":"2019-07-31T07:20:21Z","day":"01","publication_status":"published","oa":1,"volume":62,"fulldoi":"https://doi.org/10.1109/tcomm.2014.2345069","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1109/tcomm.2014.2345069","date_published":"2014-09-01T00:00:00Z","external_id":{"arxiv":["1401.3127"]},"publication_identifier":{"issn":["0090-6778"]},"status":"public","publisher":"IEEE","quality_controlled":"1","citation":{"ista":"Mondelli M, Hassani H, Urbanke R. 2014. From polar to Reed-Muller codes: A technique to improve the finite-length performance. IEEE Transactions on Communications. 62(9), 3084–3091.","mla":"Mondelli, Marco, et al. “From Polar to Reed-Muller Codes: A Technique to Improve the Finite-Length Performance.” <i>IEEE Transactions on Communications</i>, vol. 62, no. 9, IEEE, 2014, pp. 3084–91, doi:<a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">10.1109/tcomm.2014.2345069</a>.","ama":"Mondelli M, Hassani H, Urbanke R. From polar to Reed-Muller codes: A technique to improve the finite-length performance. <i>IEEE Transactions on Communications</i>. 2014;62(9):3084-3091. doi:<a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">10.1109/tcomm.2014.2345069</a>","apa":"Mondelli, M., Hassani, H., &#38; Urbanke, R. (2014). From polar to Reed-Muller codes: A technique to improve the finite-length performance. <i>IEEE Transactions on Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">https://doi.org/10.1109/tcomm.2014.2345069</a>","chicago":"Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “From Polar to Reed-Muller Codes: A Technique to Improve the Finite-Length Performance.” <i>IEEE Transactions on Communications</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">https://doi.org/10.1109/tcomm.2014.2345069</a>.","short":"M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Communications 62 (2014) 3084–3091.","ieee":"M. Mondelli, H. Hassani, and R. Urbanke, “From polar to Reed-Muller codes: A technique to improve the finite-length performance,” <i>IEEE Transactions on Communications</i>, vol. 62, no. 9. IEEE, pp. 3084–3091, 2014."},"page":"3084-3091","author":[{"orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","first_name":"Marco"},{"last_name":"Hassani","full_name":"Hassani, Hamed","first_name":"Hamed"},{"last_name":"Urbanke","first_name":"Rudiger","full_name":"Urbanke, Rudiger"}]},{"extern":"1","type":"conference","month":"10","date_updated":"2023-02-23T12:49:36Z","arxiv":1,"publication":"52nd Annual Allerton Conference on Communication, Control, and Computing","related_material":{"record":[{"id":"6678","status":"public","relation":"later_version"}]},"title":"How to achieve the capacity of asymmetric channels","year":"2014","abstract":[{"lang":"eng","text":"We describe coding techniques that achieve the capacity of a discrete memoryless asymmetric channel. To do so, we discuss how recent advances in coding for symmetric channels yield more efficient solutions also for the asymmetric case. In more detail, we consider three basic approaches. The first one is Gallager's scheme that concatenates a linear code with a non-linear mapper, in order to bias the input distribution. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Further, we derive a scaling law between the gap to capacity, the cardinality of channel input and output alphabets, and the required size of the mapper. The second one is an integrated approach in which the coding scheme is used both for source coding, in order to create codewords with the capacity-achieving distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third approach is based on an idea due to Böcherer and Mathar and separates completely the two tasks of source coding and channel coding by “chaining” together several codewords. We prove that we can combine any suitable source code with any suitable channel code in order to provide optimal schemes for asymmetric channels. In particular, polar codes and spatially coupled codes fulfill the required conditions."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1406.7373"}],"conference":{"end_date":"2014-10-03","location":"Monticello, IL, United States","start_date":"2014-09-30","name":"Allerton Conference on Communication, Control, and Computing"},"oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1109/allerton.2014.7028535","language":[{"iso":"eng"}],"oa_version":"Preprint","_id":"6740","day":"01","date_created":"2019-07-31T07:24:23Z","publisher":"IEEE","status":"public","author":[{"orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","first_name":"Marco"},{"last_name":"Urbanke","full_name":"Urbanke, Rudiger","first_name":"Rudiger"},{"last_name":"Hassani","full_name":"Hassani, Hamed","first_name":"Hamed"}],"page":"789-796","quality_controlled":"1","citation":{"ista":"Mondelli M, Urbanke R, Hassani H. 2014. How to achieve the capacity of asymmetric channels. 52nd Annual Allerton Conference on Communication, Control, and Computing. Allerton Conference on Communication, Control, and Computing, 789–796.","mla":"Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.” <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>, IEEE, 2014, pp. 789–96, doi:<a href=\"https://doi.org/10.1109/allerton.2014.7028535\">10.1109/allerton.2014.7028535</a>.","ama":"Mondelli M, Urbanke R, Hassani H. How to achieve the capacity of asymmetric channels. In: <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>. IEEE; 2014:789-796. doi:<a href=\"https://doi.org/10.1109/allerton.2014.7028535\">10.1109/allerton.2014.7028535</a>","apa":"Mondelli, M., Urbanke, R., &#38; Hassani, H. (2014). How to achieve the capacity of asymmetric channels. In <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i> (pp. 789–796). Monticello, IL, United States: IEEE. <a href=\"https://doi.org/10.1109/allerton.2014.7028535\">https://doi.org/10.1109/allerton.2014.7028535</a>","chicago":"Mondelli, Marco, Rudiger Urbanke, and Hamed Hassani. “How to Achieve the Capacity of Asymmetric Channels.” In <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>, 789–96. IEEE, 2014. <a href=\"https://doi.org/10.1109/allerton.2014.7028535\">https://doi.org/10.1109/allerton.2014.7028535</a>.","short":"M. Mondelli, R. Urbanke, H. Hassani, in:, 52nd Annual Allerton Conference on Communication, Control, and Computing, IEEE, 2014, pp. 789–796.","ieee":"M. Mondelli, R. Urbanke, and H. Hassani, “How to achieve the capacity of asymmetric channels,” in <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>, Monticello, IL, United States, 2014, pp. 789–796."},"doi":"10.1109/allerton.2014.7028535","date_published":"2014-10-01T00:00:00Z","publication_identifier":{"eisbn":["978-1-4799-8009-3"]},"external_id":{"arxiv":["1406.7373"]}},{"issue":"3","date_created":"2019-07-31T09:05:07Z","day":"20","oa_version":"None","language":[{"iso":"eng"}],"_id":"6744","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1109/twc.2014.020914.130669","type":"journal_article","volume":13,"publication_status":"published","date_published":"2014-03-20T00:00:00Z","year":"2014","abstract":[{"lang":"eng","text":"With the aim of extending the coverage and improving the performance of impulse radio ultra-wideband (UWB) systems, this paper focuses on developing a novel single differential encoded decode and forward (DF) non-cooperative relaying scheme (NCR). To favor simple receiver structures, differential noncoherent detection is employed which enables effective energy capture without any channel estimation. Putting emphasis on the general case of multi-hop relaying, we illustrate an original algorithm for the joint power allocation and path selection (JPAPS), minimizing an approximate expression of the overall bit error rate (BER). In particular, after deriving a closed-form power allocation strategy, the optimal path selection is reduced to a shortest path problem on a connected graph, which can be solved without any topology information with complexity O(N 3 ), N being the number of available relays of the network. An approximate scheme is also presented, which reduces the complexity to O(N 2 ) while showing a negligible performance loss, and for benchmarking purposes, an exhaustive-search based multi-hop DF cooperative strategy is derived. Simulation results for various network setups corroborate the effectiveness of the proposed low-complexity JPAPS algorithm, which favorably compares to existing AF and DF relaying methods."}],"doi":"10.1109/twc.2014.020914.130669","title":"Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications","intvolume":"        13","author":[{"first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli"},{"first_name":"Qi","full_name":"Zhou, Qi","last_name":"Zhou"},{"full_name":"Lottici, Vincenzo","first_name":"Vincenzo","last_name":"Lottici"},{"first_name":"Xiaoli","full_name":"Ma, Xiaoli","last_name":"Ma"}],"date_updated":"2021-01-12T08:08:48Z","page":"1397-1409","month":"03","citation":{"apa":"Mondelli, M., Zhou, Q., Lottici, V., &#38; Ma, X. (2014). Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. <i>IEEE Transactions on Wireless Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">https://doi.org/10.1109/twc.2014.020914.130669</a>","chicago":"Mondelli, Marco, Qi Zhou, Vincenzo Lottici, and Xiaoli Ma. “Joint Power Allocation and Path Selection for Multi-Hop Noncoherent Decode and Forward UWB Communications.” <i>IEEE Transactions on Wireless Communications</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">https://doi.org/10.1109/twc.2014.020914.130669</a>.","short":"M. Mondelli, Q. Zhou, V. Lottici, X. Ma, IEEE Transactions on Wireless Communications 13 (2014) 1397–1409.","ieee":"M. Mondelli, Q. Zhou, V. Lottici, and X. Ma, “Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications,” <i>IEEE Transactions on Wireless Communications</i>, vol. 13, no. 3. IEEE, pp. 1397–1409, 2014.","ista":"Mondelli M, Zhou Q, Lottici V, Ma X. 2014. Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. IEEE Transactions on Wireless Communications. 13(3), 1397–1409.","mla":"Mondelli, Marco, et al. “Joint Power Allocation and Path Selection for Multi-Hop Noncoherent Decode and Forward UWB Communications.” <i>IEEE Transactions on Wireless Communications</i>, vol. 13, no. 3, IEEE, 2014, pp. 1397–409, doi:<a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">10.1109/twc.2014.020914.130669</a>.","ama":"Mondelli M, Zhou Q, Lottici V, Ma X. Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. <i>IEEE Transactions on Wireless Communications</i>. 2014;13(3):1397-1409. doi:<a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">10.1109/twc.2014.020914.130669</a>"},"publication":"IEEE Transactions on Wireless Communications","quality_controlled":"1","publisher":"IEEE","status":"public"},{"doi":"10.1007/978-3-319-05957-0","department":[{"_id":"HeEd"}],"date_published":"2014-01-01T00:00:00Z","publication_identifier":{"eissn":["2191-5318"],"issn":["2191-530X"],"isbn":["9-783-3190-5956-3"],"eisbn":["9-783-3190-5957-0"]},"status":"public","publisher":"Springer Nature","quality_controlled":"1","citation":{"ama":"Edelsbrunner H. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. Cham: Springer Nature; 2014. doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>","ista":"Edelsbrunner H. 2014. 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The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields."}],"year":"2014","series_title":"SpringerBriefs in Applied Sciences and Technology","place":"Cham","month":"01","date_updated":"2022-03-04T07:47:54Z","alternative_title":["SpringerBriefs in Applied Sciences and Technology"],"article_processing_charge":"No","type":"book"},{"type":"working_paper","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"draft","oa":1,"article_processing_charge":"No","day":"30","date_created":"2019-11-18T15:57:05Z","ddc":["510"],"_id":"7038","corr_author":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"apa":"Huszár, K., &#38; Rolinek, M. (n.d.). <i>Playful Math - An introduction to mathematical games</i>. 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