[{"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1142592/"}],"page":"1874 - 1885","month":"05","date_published":"2005-05-18T00:00:00Z","oa":1,"abstract":[{"lang":"eng","text":"The plant hormone auxin elicits many specific context-dependent developmental responses. Auxin promotes degradation of Aux/IAA proteins that prevent transcription factors of the auxin response factor (ARF) family from regulating auxin-responsive target genes. Aux/IAAs and ARFs are represented by large gene families in Arabidopsis. Here we show that stabilization of BDL/IAA12 or its sister protein IAA13 prevents MP/ARF5-dependent embryonic root formation whereas stabilized SHY2/IAA3 interferes with seedling growth. Although both bdl and shy2-2 proteins inhibited MP/ARF5-dependent reporter gene activation, shy2-2 was much less efficient than bdl to interfere with embryonic root initiation when expressed from the BDL promoter. Similarly, MP was much more efficient than ARF16 in this process. When expressed from the SHY2 promoter, both shy2-2 and bdl inhibited cell elongation and auxin-induced gene expression in the seedling hypocotyl. By contrast, gravitropism and auxin-induced gene expression in the root, which were promoted by functionally redundant NPH4/ARF7 and ARF19 proteins, were inhibited by shy2-2, but not by bdl protein. Our results suggest that auxin signals are converted into specific responses by matching pairs of coexpressed ARF and Aux/IAA proteins."}],"publisher":"Wiley-Blackwell","date_updated":"2021-01-12T07:00:22Z","publist_id":"3918","publication_status":"published","issue":"10","_id":"2867","type":"journal_article","publication":"EMBO Journal","extern":1,"citation":{"ista":"Weijers D, Benková E, Jäger K, Schlereth A, Hamann T, Kientz M, Wilmoth J, Reed J, Jürgens G. 2005. Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators. EMBO Journal. 24(10), 1874–1885.","ieee":"D. Weijers <i>et al.</i>, “Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators,” <i>EMBO Journal</i>, vol. 24, no. 10. Wiley-Blackwell, pp. 1874–1885, 2005.","mla":"Weijers, Dolf, et al. “Developmental Specificity of Auxin Response by Pairs of ARF and Aux/IAA Transcriptional Regulators.” <i>EMBO Journal</i>, vol. 24, no. 10, Wiley-Blackwell, 2005, pp. 1874–85, doi:<a href=\"https://doi.org/10.1038/sj.emboj.7600659\">10.1038/sj.emboj.7600659</a>.","apa":"Weijers, D., Benková, E., Jäger, K., Schlereth, A., Hamann, T., Kientz, M., … Jürgens, G. (2005). Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/sj.emboj.7600659\">https://doi.org/10.1038/sj.emboj.7600659</a>","short":"D. Weijers, E. Benková, K. Jäger, A. Schlereth, T. Hamann, M. Kientz, J. Wilmoth, J. Reed, G. Jürgens, EMBO Journal 24 (2005) 1874–1885.","chicago":"Weijers, Dolf, Eva Benková, Katja Jäger, Alexandra Schlereth, Thorsten Hamann, Marika Kientz, Jill Wilmoth, Jason Reed, and Gerd Jürgens. “Developmental Specificity of Auxin Response by Pairs of ARF and Aux/IAA Transcriptional Regulators.” <i>EMBO Journal</i>. Wiley-Blackwell, 2005. <a href=\"https://doi.org/10.1038/sj.emboj.7600659\">https://doi.org/10.1038/sj.emboj.7600659</a>.","ama":"Weijers D, Benková E, Jäger K, et al. Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators. <i>EMBO Journal</i>. 2005;24(10):1874-1885. doi:<a href=\"https://doi.org/10.1038/sj.emboj.7600659\">10.1038/sj.emboj.7600659</a>"},"doi":"10.1038/sj.emboj.7600659","date_created":"2018-12-11T12:00:01Z","quality_controlled":0,"author":[{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Eva Benková"},{"first_name":"Katja","last_name":"Jäger","full_name":"Jäger, Katja E"},{"full_name":"Schlereth, Alexandra","last_name":"Schlereth","first_name":"Alexandra"},{"full_name":"Hamann, Thorsten","last_name":"Hamann","first_name":"Thorsten"},{"first_name":"Marika","last_name":"Kientz","full_name":"Kientz, Marika"},{"first_name":"Jill","last_name":"Wilmoth","full_name":"Wilmoth, Jill C"},{"full_name":"Reed, Jason W","first_name":"Jason","last_name":"Reed"},{"last_name":"Jürgens","first_name":"Gerd","full_name":"Jürgens, Gerd"}],"day":"18","year":"2005","status":"public","intvolume":"        24","volume":24,"title":"Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators"},{"intvolume":"        55","year":"2005","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0196-6774"]},"related_material":{"record":[{"relation":"earlier_version","id":"11926","status":"public"}]},"quality_controlled":"1","citation":{"ama":"Goel A, Henzinger MH, Plotkin S. An online throughput-competitive algorithm for multicast routing and admission control. <i>Journal of Algorithms</i>. 2005;55(1):1-20. doi:<a href=\"https://doi.org/10.1016/j.jalgor.2004.11.001\">10.1016/j.jalgor.2004.11.001</a>","ista":"Goel A, Henzinger MH, Plotkin S. 2005. An online throughput-competitive algorithm for multicast routing and admission control. Journal of Algorithms. 55(1), 1–20.","ieee":"A. Goel, M. H. Henzinger, and S. Plotkin, “An online throughput-competitive algorithm for multicast routing and admission control,” <i>Journal of Algorithms</i>, vol. 55, no. 1. Elsevier, pp. 1–20, 2005.","mla":"Goel, Ashish, et al. “An Online Throughput-Competitive Algorithm for Multicast Routing and Admission Control.” <i>Journal of Algorithms</i>, vol. 55, no. 1, Elsevier, 2005, pp. 1–20, doi:<a href=\"https://doi.org/10.1016/j.jalgor.2004.11.001\">10.1016/j.jalgor.2004.11.001</a>.","apa":"Goel, A., Henzinger, M. H., &#38; Plotkin, S. (2005). An online throughput-competitive algorithm for multicast routing and admission control. <i>Journal of Algorithms</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jalgor.2004.11.001\">https://doi.org/10.1016/j.jalgor.2004.11.001</a>","chicago":"Goel, Ashish, Monika H Henzinger, and Serge Plotkin. “An Online Throughput-Competitive Algorithm for Multicast Routing and Admission Control.” <i>Journal of Algorithms</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.jalgor.2004.11.001\">https://doi.org/10.1016/j.jalgor.2004.11.001</a>.","short":"A. Goel, M.H. Henzinger, S. Plotkin, Journal of Algorithms 55 (2005) 1–20."},"doi":"10.1016/j.jalgor.2004.11.001","extern":"1","abstract":[{"text":"We present the first polylog-competitive online algorithm for the general multicast admission control and routing problem in the throughput model. The ratio of the number of requests accepted by the optimum offline algorithm to the expected number of requests accepted by our algorithm is O((log n + log log M)(log n + log M) log n), where M is the number of multicast groups and n is the number of nodes in the graph. We show that this is close to optimum by presenting an\r\nΩ(log n log M) lower bound on this ratio for any randomized online algorithm against an oblivious adversary, when M is much larger than the link capacities. Our lower bound applies even in the restricted case where the link capacities are much larger than bandwidth requested by a single multicast. We also present a simple proof showing that it is impossible to be competitive against an adaptive online adversary.\r\nAs in the previous online routing algorithms, our algorithm uses edge-costs when deciding on which is the best path to use. In contrast to the previous competitive algorithms in the throughput model, our cost is not a direct function of the edge load. The new cost definition allows us to decouple the effects of routing and admission decisions of different multicast groups.","lang":"eng"}],"oa":1,"page":"1-20","title":"An online throughput-competitive algorithm for multicast routing and admission control","volume":55,"status":"public","day":"01","author":[{"last_name":"Goel","first_name":"Ashish","full_name":"Goel, Ashish"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger"},{"full_name":"Plotkin, Serge","last_name":"Plotkin","first_name":"Serge"}],"date_created":"2022-08-08T12:03:00Z","oa_version":"Published Version","publication":"Journal of Algorithms","article_processing_charge":"No","_id":"11763","type":"journal_article","issue":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-21T16:33:22Z","publisher":"Elsevier","article_type":"original","date_published":"2005-04-01T00:00:00Z","month":"04","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jalgor.2004.11.001"}]},{"author":[{"first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","full_name":"Tamas Hausel"},{"first_name":"Eugénie","last_name":"Hunsicker","full_name":"Hunsicker, Eugénie"},{"first_name":"Rafe","last_name":"Mazzeo","full_name":"Mazzeo, Rafe R"}],"acknowledgement":"Hausel’s work supported by a Miller Research Fellowship at the University of California, Berkeley.\nHunsicker’s work partially supported by Stanford University.\nMazzeo’s work supported by National Science Foundation grant numbers DMS-991975 and DMS-0204730 and\nby the Mathematical Sciences Research Institute.","citation":{"ama":"Hausel T, Hunsicker E, Mazzeo R. Hodge cohomology of gravitational instantons. <i>Duke Mathematical Journal</i>. 2004;122(3):485-548. doi:<a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">10.1215/S0012-7094-04-12233-X</a>","ieee":"T. Hausel, E. Hunsicker, and R. Mazzeo, “Hodge cohomology of gravitational instantons,” <i>Duke Mathematical Journal</i>, vol. 122, no. 3. Duke University Press, pp. 485–548, 2004.","ista":"Hausel T, Hunsicker E, Mazzeo R. 2004. Hodge cohomology of gravitational instantons. Duke Mathematical Journal. 122(3), 485–548.","mla":"Hausel, Tamás, et al. “Hodge Cohomology of Gravitational Instantons.” <i>Duke Mathematical Journal</i>, vol. 122, no. 3, Duke University Press, 2004, pp. 485–548, doi:<a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">10.1215/S0012-7094-04-12233-X</a>.","apa":"Hausel, T., Hunsicker, E., &#38; Mazzeo, R. (2004). Hodge cohomology of gravitational instantons. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">https://doi.org/10.1215/S0012-7094-04-12233-X</a>","chicago":"Hausel, Tamás, Eugénie Hunsicker, and Rafe Mazzeo. “Hodge Cohomology of Gravitational Instantons.” <i>Duke Mathematical Journal</i>. Duke University Press, 2004. <a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">https://doi.org/10.1215/S0012-7094-04-12233-X</a>.","short":"T. Hausel, E. Hunsicker, R. Mazzeo, Duke Mathematical Journal 122 (2004) 485–548."},"doi":"10.1215/S0012-7094-04-12233-X","date_created":"2018-12-11T11:52:08Z","quality_controlled":0,"_id":"1456","type":"journal_article","issue":"3","publication":"Duke Mathematical Journal","extern":1,"title":"Hodge cohomology of gravitational instantons","volume":122,"intvolume":"       122","status":"public","day":"15","year":"2004","page":"485 - 548","main_file_link":[{"url":"http://arxiv.org/abs/math/0207169","open_access":"1"}],"publication_status":"published","publisher":"Duke University Press","date_updated":"2021-01-12T06:50:52Z","publist_id":"5737","oa":1,"abstract":[{"text":"We study the space of L2 harmonic forms on complete manifolds with metrics of fibred boundary or fibred cusp type. These metrics generalize the geometric structures at infinity of several different well-known classes of metrics, including asymptotically locally Euclidean manifolds, the (known types of) gravitational instantons, and also Poincaré metrics on ℚ-rank 1 ends of locally symmetric spaces and on the complements of smooth divisors in Kähler manifolds. The answer in all cases is given in terms of intersection cohomology of a stratified compactification of the manifold. The L2 signature formula implied by our result is closely related to the one proved by Dai and more generally by Vaillant and identifies Dai's τ-invariant directly in terms of intersection cohomology of differing perversities. This work is also closely related to a recent paper of Carron and the forthcoming paper of Cheeger and Dai. We apply our results to a number of examples, gravitational instantons among them, arising in predictions about L2 harmonic forms in duality theories in string theory.","lang":"eng"}],"month":"04","date_published":"2004-04-15T00:00:00Z"},{"publist_id":"5736","date_updated":"2021-01-12T06:50:55Z","publisher":"Oxford University Press","publication_status":"published","date_published":"2004-05-01T00:00:00Z","month":"05","abstract":[{"lang":"eng","text":"The moduli space of stable vector bundles on a Riemann surface is smooth when the rank and degree are coprime, and is diffeomorphic to the space of unitary connections of central constant curvature. A classic result of Newstead and Atiyah and Bott asserts that its rational cohomology ring is generated by the universal classes, that is, by the Kunneth components of the Chern classes of the universal bundle.\n\nThis paper studies the larger, non-compact moduli space of Higgs bundles, as introduced by Hitchin and Simpson, with values in the canonical bundle K. This is diffeomorphic to the space of all connections of central constant curvature, whether unitary or not. The main result of the paper is that, in the rank 2 case, the rational cohomology ring of this space is again generated by universal classes.\n\nThe spaces of Higgs bundles with values in K(n) for n &gt; 0 turn out to be essential to the story. Indeed, we show that their direct limit has the homotopy type of the classifying space of the gauge group, and hence has cohomology generated by universal classes. 2000 Mathematics Subject Classification 14H60 (primary), 14D20, 14H81, 32Q55, 58D27 (secondary). "}],"oa":1,"page":"632 - 658","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/math/0003093"}],"intvolume":"        88","status":"public","title":"Generators for the cohomology ring of the moduli space of rank 2 higgs bundles","volume":88,"year":"2004","day":"01","author":[{"first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","full_name":"Tamas Hausel"},{"full_name":"Thaddeus, Michael","last_name":"Thaddeus","first_name":"Michael"}],"publication":"Proceedings of the London Mathematical Society","extern":1,"_id":"1464","issue":"3","type":"journal_article","quality_controlled":0,"date_created":"2018-12-11T11:52:10Z","doi":"10.1112/S0024611503014618","citation":{"ama":"Hausel T, Thaddeus M. Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. <i>Proceedings of the London Mathematical Society</i>. 2004;88(3):632-658. doi:<a href=\"https://doi.org/10.1112/S0024611503014618\">10.1112/S0024611503014618</a>","mla":"Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring of the Moduli Space of Rank 2 Higgs Bundles.” <i>Proceedings of the London Mathematical Society</i>, vol. 88, no. 3, Oxford University Press, 2004, pp. 632–58, doi:<a href=\"https://doi.org/10.1112/S0024611503014618\">10.1112/S0024611503014618</a>.","ista":"Hausel T, Thaddeus M. 2004. Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. Proceedings of the London Mathematical Society. 88(3), 632–658.","ieee":"T. Hausel and M. Thaddeus, “Generators for the cohomology ring of the moduli space of rank 2 higgs bundles,” <i>Proceedings of the London Mathematical Society</i>, vol. 88, no. 3. Oxford University Press, pp. 632–658, 2004.","short":"T. Hausel, M. Thaddeus, Proceedings of the London Mathematical Society 88 (2004) 632–658.","chicago":"Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring of the Moduli Space of Rank 2 Higgs Bundles.” <i>Proceedings of the London Mathematical Society</i>. Oxford University Press, 2004. <a href=\"https://doi.org/10.1112/S0024611503014618\">https://doi.org/10.1112/S0024611503014618</a>.","apa":"Hausel, T., &#38; Thaddeus, M. (2004). Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. <i>Proceedings of the London Mathematical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1112/S0024611503014618\">https://doi.org/10.1112/S0024611503014618</a>"}},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2004.06.055"}],"publisher":"Elsevier","date_updated":"2021-12-14T08:52:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","date_published":"2004-07-13T00:00:00Z","month":"07","article_type":"original","department":[{"_id":"DaZi"}],"author":[{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Xiaofeng","last_name":"Cao","full_name":"Cao, Xiaofeng"},{"full_name":"Johansen, Lisa K.","first_name":"Lisa K.","last_name":"Johansen"},{"full_name":"Xie, Zhixin","first_name":"Zhixin","last_name":"Xie"},{"last_name":"Carrington","first_name":"James C.","full_name":"Carrington, James C."},{"full_name":"Jacobsen, Steven E.","first_name":"Steven E.","last_name":"Jacobsen"}],"_id":"9493","type":"journal_article","issue":"13","article_processing_charge":"No","publication":"Current Biology","date_created":"2021-06-07T10:33:00Z","oa_version":"Published Version","status":"public","volume":14,"title":"Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats","day":"13","external_id":{"pmid":["15242620 "]},"page":"1214-1220","oa":1,"abstract":[{"lang":"eng","text":"In a number of organisms, transgenes containing transcribed inverted repeats (IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA silencing also causes extensive cytosine methylation of homologous DNA in both the transgene \"trigger\" and any other homologous DNA sequences--\"targets\". Endogenous genomic sequences, including transposable elements and repeated elements, are also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4) is required for maintenance of DNA methylation at several endogenous loci and for the establishment of methylation at the FWA gene. Here, we show that mutation of AGO4 substantially reduces the maintenance of DNA methylation triggered by IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences, while the IR trigger sequences lose methylation in all sequence contexts. Finally, we find that AGO4 and the DRM methyltransferase genes are required for maintenance of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting that AGO4 may function downstream of siRNA production."}],"extern":"1","citation":{"ieee":"D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E. Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats,” <i>Current Biology</i>, vol. 14, no. 13. Elsevier, pp. 1214–1220, 2004.","ista":"Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 14(13), 1214–1220.","mla":"Zilberman, Daniel, et al. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” <i>Current Biology</i>, vol. 14, no. 13, Elsevier, 2004, pp. 1214–20, doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">10.1016/j.cub.2004.06.055</a>.","apa":"Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., &#38; Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">https://doi.org/10.1016/j.cub.2004.06.055</a>","short":"D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen, Current Biology 14 (2004) 1214–1220.","chicago":"Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” <i>Current Biology</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">https://doi.org/10.1016/j.cub.2004.06.055</a>.","ama":"Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. <i>Current Biology</i>. 2004;14(13):1214-1220. doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">10.1016/j.cub.2004.06.055</a>"},"doi":"10.1016/j.cub.2004.06.055","quality_controlled":"1","pmid":1,"intvolume":"        14","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"language":[{"iso":"eng"}],"year":"2004"},{"main_file_link":[{"url":"https://doi.org/10.1186/gb-2004-5-12-249","open_access":"1"}],"scopus_import":"1","month":"11","date_published":"2004-11-16T00:00:00Z","article_type":"review","publisher":"Springer Nature","date_updated":"2021-12-14T08:44:24Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","_id":"9511","article_processing_charge":"No","type":"journal_article","issue":"12","publication":"Genome Biology","date_created":"2021-06-07T12:58:06Z","oa_version":"Published Version","department":[{"_id":"DaZi"}],"author":[{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"}],"day":"16","article_number":"249","status":"public","title":"Silencing of transposons in plant genomes: kick them when they're down","volume":5,"external_id":{"pmid":["15575975"]},"oa":1,"abstract":[{"lang":"eng","text":"Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs. DNA and histone methylation are not always sufficient to maintain silencing, and RNA-based reinforcement can be needed to maintain as well as initiate it."}],"extern":"1","citation":{"ama":"Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them when they’re down. <i>Genome Biology</i>. 2004;5(12). doi:<a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">10.1186/gb-2004-5-12-249</a>","short":"D. Zilberman, S. Henikoff, Genome Biology 5 (2004).","chicago":"Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” <i>Genome Biology</i>. Springer Nature, 2004. <a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">https://doi.org/10.1186/gb-2004-5-12-249</a>.","apa":"Zilberman, D., &#38; Henikoff, S. (2004). Silencing of transposons in plant genomes: kick them when they’re down. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">https://doi.org/10.1186/gb-2004-5-12-249</a>","mla":"Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” <i>Genome Biology</i>, vol. 5, no. 12, 249, Springer Nature, 2004, doi:<a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">10.1186/gb-2004-5-12-249</a>.","ista":"Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 5(12), 249.","ieee":"D. Zilberman and S. Henikoff, “Silencing of transposons in plant genomes: kick them when they’re down,” <i>Genome Biology</i>, vol. 5, no. 12. Springer Nature, 2004."},"doi":"10.1186/gb-2004-5-12-249","quality_controlled":"1","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"language":[{"iso":"eng"}],"year":"2004","pmid":1,"intvolume":"         5"},{"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1371/journal.pbio.0020104","open_access":"1"}],"publisher":"Public Library of Science","date_updated":"2021-12-14T08:43:57Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","date_published":"2004-02-24T00:00:00Z","month":"02","article_type":"original","department":[{"_id":"DaZi"}],"author":[{"full_name":"Xie, Zhixin","last_name":"Xie","first_name":"Zhixin"},{"first_name":"Lisa K.","last_name":"Johansen","full_name":"Johansen, Lisa K."},{"full_name":"Gustafson, Adam M.","last_name":"Gustafson","first_name":"Adam M."},{"last_name":"Kasschau","first_name":"Kristin D.","full_name":"Kasschau, Kristin D."},{"first_name":"Andrew D. ","last_name":"Lellis","full_name":"Lellis, Andrew D. "},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Jacobsen, Steven E.","last_name":"Jacobsen","first_name":"Steven E."},{"full_name":"Carrington, James C.","first_name":"James C.","last_name":"Carrington"}],"_id":"9517","article_processing_charge":"No","type":"journal_article","issue":"5","publication":"PLoS Biology","oa_version":"Published Version","date_created":"2021-06-07T14:12:08Z","status":"public","volume":2,"title":"Genetic and functional diversification of small RNA pathways in plants","day":"24","external_id":{"pmid":["15024409"]},"page":"0642-0652","oa":1,"abstract":[{"lang":"eng","text":"Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense."}],"extern":"1","doi":"10.1371/journal.pbio.0020104","citation":{"ieee":"Z. Xie <i>et al.</i>, “Genetic and functional diversification of small RNA pathways in plants,” <i>PLoS Biology</i>, vol. 2, no. 5. Public Library of Science, pp. 0642–0652, 2004.","ista":"Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. 2(5), 0642–0652.","mla":"Xie, Zhixin, et al. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” <i>PLoS Biology</i>, vol. 2, no. 5, Public Library of Science, 2004, pp. 0642–52, doi:<a href=\"https://doi.org/10.1371/journal.pbio.0020104\">10.1371/journal.pbio.0020104</a>.","apa":"Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D., Zilberman, D., … Carrington, J. C. (2004). Genetic and functional diversification of small RNA pathways in plants. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.0020104\">https://doi.org/10.1371/journal.pbio.0020104</a>","short":"Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman, S.E. Jacobsen, J.C. Carrington, PLoS Biology 2 (2004) 0642–0652.","chicago":"Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D.  Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” <i>PLoS Biology</i>. Public Library of Science, 2004. <a href=\"https://doi.org/10.1371/journal.pbio.0020104\">https://doi.org/10.1371/journal.pbio.0020104</a>.","ama":"Xie Z, Johansen LK, Gustafson AM, et al. Genetic and functional diversification of small RNA pathways in plants. <i>PLoS Biology</i>. 2004;2(5):0642-0652. doi:<a href=\"https://doi.org/10.1371/journal.pbio.0020104\">10.1371/journal.pbio.0020104</a>"},"quality_controlled":"1","pmid":1,"intvolume":"         2","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"language":[{"iso":"eng"}],"year":"2004"},{"date_updated":"2021-01-12T07:52:20Z","publist_id":"2403","publisher":"Wiley-Blackwell","publication_status":"published","date_published":"2004-01-01T00:00:00Z","month":"01","abstract":[{"lang":"eng","text":"The time course of Mg(2+) block and unblock of NMDA receptors (NMDARs) determines the extent they are activated by depolarization. Here, we directly measure the rate of NMDAR channel opening in response to depolarizations at different times after brief (1 ms) and sustained (4.6 s) applications of glutamate to nucleated patches from neocortical pyramidal neurons. The kinetics of Mg(2+) unblock were found to be non-instantaneous and complex, consisting of a prominent fast component (time constant approximately 100 micros) and slower components (time constants 4 and approximately 300 ms), the relative amplitudes of which depended on the timing of the depolarizing pulse. Fitting a kinetic model to these data indicated that Mg(2+) not only blocks the NMDAR channel, but reduces both the open probability and affinity for glutamate, while enhancing desensitization. These effects slow the rate of NMDAR channel opening in response to depolarization in a time-dependent manner such that the slower components of Mg(2+) unblock are enhanced during depolarizations at later times after glutamate application. One physiological consequence of this is that brief depolarizations occurring earlier in time after glutamate application are better able to open NMDAR channels. This finding has important implications for spike-timing-dependent synaptic plasticity (STDP), where the precise (millisecond) timing of action potentials relative to synaptic inputs determines the magnitude and sign of changes in synaptic strength. Indeed, we find that STDP timing curves of NMDAR channel activation elicited by realistic dendritic action potential waveforms are narrower than expected assuming instantaneous Mg(2+) unblock, indicating that slow Mg(2+) unblock of NMDAR channels makes the STDP timing window more precise."}],"oa":1,"page":"337 - 45","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664940/"}],"intvolume":"       556","status":"public","volume":556,"title":"Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity","year":"2004","day":"01","author":[{"full_name":"Kampa, Bjorn M","last_name":"Kampa","first_name":"Bjorn"},{"full_name":"Clements, John","last_name":"Clements","first_name":"John"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Peter Jonas"},{"full_name":"Stuart, Greg J","last_name":"Stuart","first_name":"Greg"}],"extern":1,"publication":"Journal of Physiology","_id":"3807","type":"journal_article","issue":"Pt 2","quality_controlled":0,"date_created":"2018-12-11T12:05:17Z","doi":"10.1113/jphysiol.2003.058842 ","citation":{"ama":"Kampa B, Clements J, Jonas PM, Stuart G. Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity. <i>Journal of Physiology</i>. 2004;556(Pt 2):337-345. doi:<a href=\"https://doi.org/10.1113/jphysiol.2003.058842 \">10.1113/jphysiol.2003.058842 </a>","apa":"Kampa, B., Clements, J., Jonas, P. M., &#38; Stuart, G. (2004). Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity. <i>Journal of Physiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1113/jphysiol.2003.058842 \">https://doi.org/10.1113/jphysiol.2003.058842 </a>","short":"B. Kampa, J. Clements, P.M. Jonas, G. Stuart, Journal of Physiology 556 (2004) 337–45.","chicago":"Kampa, Bjorn, John Clements, Peter M Jonas, and Greg Stuart. “Kinetics of Mg(2+) Unblock of NMDA Receptors: Implications for Spike-Timing Dependent Synaptic Plasticity.” <i>Journal of Physiology</i>. Wiley-Blackwell, 2004. <a href=\"https://doi.org/10.1113/jphysiol.2003.058842 \">https://doi.org/10.1113/jphysiol.2003.058842 </a>.","ieee":"B. Kampa, J. Clements, P. M. Jonas, and G. Stuart, “Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity,” <i>Journal of Physiology</i>, vol. 556, no. Pt 2. Wiley-Blackwell, pp. 337–45, 2004.","ista":"Kampa B, Clements J, Jonas PM, Stuart G. 2004. Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity. Journal of Physiology. 556(Pt 2), 337–45.","mla":"Kampa, Bjorn, et al. “Kinetics of Mg(2+) Unblock of NMDA Receptors: Implications for Spike-Timing Dependent Synaptic Plasticity.” <i>Journal of Physiology</i>, vol. 556, no. Pt 2, Wiley-Blackwell, 2004, pp. 337–45, doi:<a href=\"https://doi.org/10.1113/jphysiol.2003.058842 \">10.1113/jphysiol.2003.058842 </a>."}},{"date_published":"2004-04-01T00:00:00Z","month":"04","abstract":[{"lang":"eng","text":"The BMV conjecture for traces, which states that Tr exp(A - λB) is the Laplace transform of a positive measure, is shown to be equivalent to two other statements: (i) The polynomial λ → Tr(A + λB) p has only non-negative coefficients for all A, B ≥ 0, p ∈ ℕ and (ii) λ → Tr(A + λB)-p is the Laplace transform of a positive measure for A, B ≥ 0, p &gt; 0."}],"oa":1,"publist_id":"4568","date_updated":"2021-01-12T06:56:59Z","publisher":"Springer","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/math-ph/0210027"}],"page":"185 - 190","day":"01","year":"2004","status":"public","intvolume":"       115","volume":115,"title":" Equivalent forms of the Bessis-Moussa-Villani conjecture","extern":1,"publication":"Journal of Statistical Physics","_id":"2355","issue":"1-2","type":"journal_article","quality_controlled":0,"date_created":"2018-12-11T11:57:11Z","citation":{"ama":"Lieb É, Seiringer R.  Equivalent forms of the Bessis-Moussa-Villani conjecture. <i>Journal of Statistical Physics</i>. 2004;115(1-2):185-190. doi:<a href=\"https://doi.org/10.1023/B:JOSS.0000019811.15510.27\">10.1023/B:JOSS.0000019811.15510.27</a>","ista":"Lieb É, Seiringer R. 2004.  Equivalent forms of the Bessis-Moussa-Villani conjecture. Journal of Statistical Physics. 115(1–2), 185–190.","ieee":"É. Lieb and R. Seiringer, “ Equivalent forms of the Bessis-Moussa-Villani conjecture,” <i>Journal of Statistical Physics</i>, vol. 115, no. 1–2. Springer, pp. 185–190, 2004.","mla":"Lieb, Élliott, and Robert Seiringer. “ Equivalent Forms of the Bessis-Moussa-Villani Conjecture.” <i>Journal of Statistical Physics</i>, vol. 115, no. 1–2, Springer, 2004, pp. 185–90, doi:<a href=\"https://doi.org/10.1023/B:JOSS.0000019811.15510.27\">10.1023/B:JOSS.0000019811.15510.27</a>.","apa":"Lieb, É., &#38; Seiringer, R. (2004).  Equivalent forms of the Bessis-Moussa-Villani conjecture. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1023/B:JOSS.0000019811.15510.27\">https://doi.org/10.1023/B:JOSS.0000019811.15510.27</a>","short":"É. Lieb, R. Seiringer, Journal of Statistical Physics 115 (2004) 185–190.","chicago":"Lieb, Élliott, and Robert Seiringer. “ Equivalent Forms of the Bessis-Moussa-Villani Conjecture.” <i>Journal of Statistical Physics</i>. Springer, 2004. <a href=\"https://doi.org/10.1023/B:JOSS.0000019811.15510.27\">https://doi.org/10.1023/B:JOSS.0000019811.15510.27</a>."},"doi":"10.1023/B:JOSS.0000019811.15510.27","author":[{"first_name":"Élliott","last_name":"Lieb","full_name":"Lieb, Élliott H"},{"orcid":"0000-0002-6781-0521","full_name":"Robert Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer"}]},{"volume":244,"title":"One-dimensional behavior of dilute, trapped Bose gases","intvolume":"       244","status":"public","day":"01","year":"2004","author":[{"last_name":"Lieb","first_name":"Élliott","full_name":"Lieb, Élliott H"},{"orcid":"0000-0002-6781-0521","full_name":"Robert Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"}],"citation":{"chicago":"Lieb, Élliott, Robert Seiringer, and Jakob Yngvason. “One-Dimensional Behavior of Dilute, Trapped Bose Gases.” <i>Communications in Mathematical Physics</i>. Springer, 2004. <a href=\"https://doi.org/10.1007/s00220-003-0993-3\">https://doi.org/10.1007/s00220-003-0993-3</a>.","short":"É. Lieb, R. Seiringer, J. Yngvason, Communications in Mathematical Physics 244 (2004) 347–393.","apa":"Lieb, É., Seiringer, R., &#38; Yngvason, J. (2004). One-dimensional behavior of dilute, trapped Bose gases. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-003-0993-3\">https://doi.org/10.1007/s00220-003-0993-3</a>","mla":"Lieb, Élliott, et al. “One-Dimensional Behavior of Dilute, Trapped Bose Gases.” <i>Communications in Mathematical Physics</i>, vol. 244, no. 2, Springer, 2004, pp. 347–93, doi:<a href=\"https://doi.org/10.1007/s00220-003-0993-3\">10.1007/s00220-003-0993-3</a>.","ista":"Lieb É, Seiringer R, Yngvason J. 2004. One-dimensional behavior of dilute, trapped Bose gases. Communications in Mathematical Physics. 244(2), 347–393.","ieee":"É. Lieb, R. Seiringer, and J. Yngvason, “One-dimensional behavior of dilute, trapped Bose gases,” <i>Communications in Mathematical Physics</i>, vol. 244, no. 2. Springer, pp. 347–393, 2004.","ama":"Lieb É, Seiringer R, Yngvason J. One-dimensional behavior of dilute, trapped Bose gases. <i>Communications in Mathematical Physics</i>. 2004;244(2):347-393. doi:<a href=\"https://doi.org/10.1007/s00220-003-0993-3\">10.1007/s00220-003-0993-3</a>"},"doi":"10.1007/s00220-003-0993-3","date_created":"2018-12-11T11:57:11Z","quality_controlled":0,"issue":"2","_id":"2356","type":"journal_article","extern":1,"publication":"Communications in Mathematical Physics","publication_status":"published","publisher":"Springer","date_updated":"2021-01-12T06:56:59Z","publist_id":"4569","oa":1,"abstract":[{"lang":"eng","text":"Recent experimental and theoretical work has shown that there are conditions in which a trapped, low-density Bose gas behaves like the one-dimensional delta-function Bose gas solved years ago by Lieb and Liniger. This is an intrinsically quantum-mechanical phenomenon because it is not necessary to have a trap width that is the size of an atom - as might have been supposed - but it suffices merely to have a trap width such that the energy gap for motion in the transverse direction is large compared to the energy associated with the motion along the trap. Up to now the theoretical arguments have been based on variational - perturbative ideas or numerical investigations. In contrast, this paper gives a rigorous proof of the one-dimensional behavior as far as the ground state energy and particle density are concerned. There are four parameters involved: the particle number, N, transverse and longitudinal dimensions of the trap, r and L, and the scattering length a of the interaction potential. Our main result is that if r/L → 0 and N → ∞ the ground state energy and density can be obtained by minimizing a one-dimensional density functional involving the Lieb-Liniger energy density with coupling constant ∼ a/r 2. This density functional simplifies in various limiting cases and we identify five asymptotic parameter regions altogether. Three of these, corresponding to the weak coupling regime, can also be obtained as limits of a three-dimensional Gross-Pitaevskii theory. We also show that Bose-Einstein condensation in the ground state persists in a part of this regime. In the strong coupling regime the longitudinal motion of the particles is strongly correlated. The Gross-Pitaevskii description is not valid in this regime and new mathematical methods come into play."}],"month":"01","date_published":"2004-01-01T00:00:00Z","page":"347 - 393","main_file_link":[{"url":"http://arxiv.org/abs/math-ph/0305025","open_access":"1"}]},{"abstract":[{"text":"An optical lattice model developed that is similar to the Bose-Hubbard model to describe the transition between Bose-Einstein condensation (BEC) and a Mott insulator state was analyzed. It was found that the system was a hard core lattice gas at half of the maximum density and the optical lattice was modeled by a periodic potential of strength λ. It was also observed that the interparticle interaction was essential for this transition that occurred even in the ground state. The results show that all the essential features could be proved rigorously such as the existence of BEC for small λ and its suppression for a large λ.","lang":"eng"}],"oa":1,"date_published":"2004-08-01T00:00:00Z","month":"08","publication_status":"published","date_updated":"2021-01-12T06:57:01Z","publist_id":"4567","publisher":"American Physical Society","main_file_link":[{"url":"http://arxiv.org/abs/cond-mat/0403240","open_access":"1"}],"page":"023612 - 1-0236121-2","day":"01","year":"2004","title":"Bose-Einstein quantum phase transition in an optical lattice model","volume":70,"status":"public","intvolume":"        70","quality_controlled":0,"date_created":"2018-12-11T11:57:12Z","citation":{"chicago":"Aizenman, Michael, Élliott Lieb, Robert Seiringer, Jan Solovej, and Jakob Yngvason. “Bose-Einstein Quantum Phase Transition in an Optical Lattice Model.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2004. <a href=\"https://doi.org/10.1103/PhysRevA.70.023612\">https://doi.org/10.1103/PhysRevA.70.023612</a>.","short":"M. Aizenman, É. Lieb, R. Seiringer, J. Solovej, J. Yngvason, Physical Review A - Atomic, Molecular, and Optical Physics 70 (2004) 023612-1-0236121-2.","apa":"Aizenman, M., Lieb, É., Seiringer, R., Solovej, J., &#38; Yngvason, J. (2004). Bose-Einstein quantum phase transition in an optical lattice model. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.70.023612\">https://doi.org/10.1103/PhysRevA.70.023612</a>","mla":"Aizenman, Michael, et al. “Bose-Einstein Quantum Phase Transition in an Optical Lattice Model.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 70, no. 2, American Physical Society, 2004, pp. 023612-1-0236121-2, doi:<a href=\"https://doi.org/10.1103/PhysRevA.70.023612\">10.1103/PhysRevA.70.023612</a>.","ieee":"M. Aizenman, É. Lieb, R. Seiringer, J. Solovej, and J. Yngvason, “Bose-Einstein quantum phase transition in an optical lattice model,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 70, no. 2. American Physical Society, pp. 023612-1-0236121-2, 2004.","ista":"Aizenman M, Lieb É, Seiringer R, Solovej J, Yngvason J. 2004. Bose-Einstein quantum phase transition in an optical lattice model. Physical Review A - Atomic, Molecular, and Optical Physics. 70(2), 023612-1-0236121-2.","ama":"Aizenman M, Lieb É, Seiringer R, Solovej J, Yngvason J. Bose-Einstein quantum phase transition in an optical lattice model. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2004;70(2):023612-1-0236121-2. doi:<a href=\"https://doi.org/10.1103/PhysRevA.70.023612\">10.1103/PhysRevA.70.023612</a>"},"doi":"10.1103/PhysRevA.70.023612","extern":1,"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","type":"journal_article","_id":"2360","issue":"2","author":[{"first_name":"Michael","last_name":"Aizenman","full_name":"Aizenman, Michael"},{"full_name":"Lieb, Élliott H","last_name":"Lieb","first_name":"Élliott"},{"full_name":"Robert Seiringer","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Solovej, Jan P","last_name":"Solovej","first_name":"Jan"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"}]},{"doi":"10.1080/15427951.2004.10129079","citation":{"ama":"Henzinger MH. Algorithmic challenges in web search engines. <i>Internet Mathematics</i>. 2004;1(1):115-123. doi:<a href=\"https://doi.org/10.1080/15427951.2004.10129079\">10.1080/15427951.2004.10129079</a>","apa":"Henzinger, M. H. (2004). Algorithmic challenges in web search engines. <i>Internet Mathematics</i>. Internet Mathematics. <a href=\"https://doi.org/10.1080/15427951.2004.10129079\">https://doi.org/10.1080/15427951.2004.10129079</a>","short":"M.H. Henzinger, Internet Mathematics 1 (2004) 115–123.","chicago":"Henzinger, Monika H. “Algorithmic Challenges in Web Search Engines.” <i>Internet Mathematics</i>. Internet Mathematics, 2004. <a href=\"https://doi.org/10.1080/15427951.2004.10129079\">https://doi.org/10.1080/15427951.2004.10129079</a>.","ieee":"M. H. Henzinger, “Algorithmic challenges in web search engines,” <i>Internet Mathematics</i>, vol. 1, no. 1. Internet Mathematics, pp. 115–123, 2004.","ista":"Henzinger MH. 2004. Algorithmic challenges in web search engines. Internet Mathematics. 1(1), 115–123.","mla":"Henzinger, Monika H. “Algorithmic Challenges in Web Search Engines.” <i>Internet Mathematics</i>, vol. 1, no. 1, Internet Mathematics, 2004, pp. 115–23, doi:<a href=\"https://doi.org/10.1080/15427951.2004.10129079\">10.1080/15427951.2004.10129079</a>."},"quality_controlled":"1","extern":"1","year":"2004","publication_identifier":{"eissn":["1944-9488"],"issn":["1542-7951"]},"language":[{"iso":"eng"}],"intvolume":"         1","page":"115-123","oa":1,"abstract":[{"text":"In this paper, we describe six algorithmic problems that arise in web search engines and that are not or only partially solved: (1) Uniformly sampling of web pages; (2) modeling the web graph; (3) finding duplicate hosts; (4) finding top gainers and losers in data streams; (5) finding large dense bipartite graphs; and (6) understanding how eigenvectors partition the web.","lang":"eng"}],"date_created":"2022-08-08T11:55:53Z","oa_version":"Published Version","_id":"11762","article_processing_charge":"No","type":"journal_article","issue":"1","publication":"Internet Mathematics","author":[{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger"}],"day":"01","volume":1,"title":"Algorithmic challenges in web search engines","status":"public","main_file_link":[{"url":"https://doi.org/10.1080/15427951.2004.10129079","open_access":"1"}],"scopus_import":"1","date_published":"2004-01-01T00:00:00Z","month":"01","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Internet Mathematics","date_updated":"2023-02-10T07:47:21Z"},{"pmid":1,"intvolume":"       101","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"year":"2004","extern":"1","citation":{"apa":"Henzinger, M. H., &#38; Lawrence, S. (2004). Extracting knowledge from the World Wide Web. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0307528100\">https://doi.org/10.1073/pnas.0307528100</a>","chicago":"Henzinger, Monika H, and Steve Lawrence. “Extracting Knowledge from the World Wide Web.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2004. <a href=\"https://doi.org/10.1073/pnas.0307528100\">https://doi.org/10.1073/pnas.0307528100</a>.","short":"M.H. Henzinger, S. Lawrence, Proceedings of the National Academy of Sciences 101 (2004) 5186–5191.","ieee":"M. H. Henzinger and S. Lawrence, “Extracting knowledge from the World Wide Web,” <i>Proceedings of the National Academy of Sciences</i>, vol. 101, no. suppl_1. Proceedings of the National Academy of Sciences, pp. 5186–5191, 2004.","ista":"Henzinger MH, Lawrence S. 2004. Extracting knowledge from the World Wide Web. Proceedings of the National Academy of Sciences. 101(suppl_1), 5186–5191.","mla":"Henzinger, Monika H., and Steve Lawrence. “Extracting Knowledge from the World Wide Web.” <i>Proceedings of the National Academy of Sciences</i>, vol. 101, no. suppl_1, Proceedings of the National Academy of Sciences, 2004, pp. 5186–91, doi:<a href=\"https://doi.org/10.1073/pnas.0307528100\">10.1073/pnas.0307528100</a>.","ama":"Henzinger MH, Lawrence S. Extracting knowledge from the World Wide Web. <i>Proceedings of the National Academy of Sciences</i>. 2004;101(suppl_1):5186-5191. doi:<a href=\"https://doi.org/10.1073/pnas.0307528100\">10.1073/pnas.0307528100</a>"},"doi":"10.1073/pnas.0307528100","quality_controlled":"1","oa":1,"abstract":[{"text":"The World Wide Web provides a unprecedented opportunity to automatically analyze a large sample of interests and activity in the world. We discuss methods for extracting knowledge from the web by randomly sampling and analyzing hosts and pages, and by analyzing the link structure of the web and how links accumulate over time. A variety of interesting and valuable information can be extracted, such as the distribution of web pages over domains, the distribution of interest in different areas, communities related to different topics, the nature of competition in different categories of sites, and the degree of communication between different communities or countries.","lang":"eng"}],"external_id":{"pmid":["14745041"]},"page":"5186-5191","status":"public","title":"Extracting knowledge from the World Wide Web","volume":101,"day":"06","author":[{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Lawrence, Steve","last_name":"Lawrence","first_name":"Steve"}],"_id":"11877","type":"journal_article","article_processing_charge":"No","issue":"suppl_1","publication":"Proceedings of the National Academy of Sciences","date_created":"2022-08-16T13:06:10Z","oa_version":"Published Version","publisher":"Proceedings of the National Academy of Sciences","date_updated":"2023-02-17T12:21:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","month":"04","date_published":"2004-04-06T00:00:00Z","article_type":"original","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC387294/"}]},{"external_id":{"arxiv":["1311.1665"]},"alternative_title":["Bonner mathematische Schriften"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.1665"}],"publist_id":"7755","date_updated":"2021-01-12T06:52:20Z","publisher":"Mathematisches Institut der Universität Bonn","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","date_published":"2003-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"For any number field k, upper bounds are established for the number of k-rational points of bounded height on non-singular del Pezzo surfaces defined over k, which are equipped with suitable conic bundle structures over k."}],"oa":1,"author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"M","last_name":"Swarbick Jones","full_name":"Swarbick Jones, M"}],"publication":"Proceedings of the Bonn session in analytic number theory and diophantine equations","extern":"1","type":"journal_article","_id":"166","date_created":"2018-12-11T11:44:58Z","oa_version":"None","citation":{"ama":"Browning TD, Swarbick Jones M. Counting rational points on del Pezzo surfaces of degree 5. <i>Proceedings of the Bonn session in analytic number theory and diophantine equations</i>. 2003;360.","apa":"Browning, T. D., &#38; Swarbick Jones, M. (2003). Counting rational points on del Pezzo surfaces of degree 5. <i>Proceedings of the Bonn Session in Analytic Number Theory and Diophantine Equations</i>. Mathematisches Institut der Universität Bonn.","short":"T.D. Browning, M. Swarbick Jones, Proceedings of the Bonn Session in Analytic Number Theory and Diophantine Equations 360 (2003).","chicago":"Browning, Timothy D, and M Swarbick Jones. “Counting Rational Points on Del Pezzo Surfaces of Degree 5.” <i>Proceedings of the Bonn Session in Analytic Number Theory and Diophantine Equations</i>. Mathematisches Institut der Universität Bonn, 2003.","ista":"Browning TD, Swarbick Jones M. 2003. Counting rational points on del Pezzo surfaces of degree 5. Proceedings of the Bonn session in analytic number theory and diophantine equations. 360.","ieee":"T. D. Browning and M. Swarbick Jones, “Counting rational points on del Pezzo surfaces of degree 5,” <i>Proceedings of the Bonn session in analytic number theory and diophantine equations</i>, vol. 360. Mathematisches Institut der Universität Bonn, 2003.","mla":"Browning, Timothy D., and M. Swarbick Jones. “Counting Rational Points on Del Pezzo Surfaces of Degree 5.” <i>Proceedings of the Bonn Session in Analytic Number Theory and Diophantine Equations</i>, vol. 360, Mathematisches Institut der Universität Bonn, 2003."},"intvolume":"       360","status":"public","arxiv":1,"volume":360,"title":"Counting rational points on del Pezzo surfaces of degree 5","language":[{"iso":"eng"}],"day":"01","year":"2003"},{"publication_status":"published","date_updated":"2021-01-12T06:50:52Z","publist_id":"5738","publisher":"Springer","abstract":[{"lang":"eng","text":"Among the major mathematical approaches to mirror symmetry are those of Batyrev-Borisov and Stromdnger-Yau-Zaslow (SYZ). The first is explicit and amenable to computation but is not clearly related to the physical motivation; the second is the opposite. Furthermore, it is far from obvious that mirror partners in one sense will also be mirror partners in the other. This paper concerns a class of examples that can be shown to satisfy the requirements of SYZ, but whose Hodge numbers are also equal. This provides significant evidence in support of SYZ. Moreover, the examples are of great interest in their own right: they are spaces of flat SLr-connections on a smooth curve. The mirror is the corresponding space for the Langlands dual group PGLr. These examples therefore throw a bridge from mirror symmetry to the duality theory of Lie groups and, more broadly, to the geometric Langlands program."}],"oa":1,"date_published":"2003-07-01T00:00:00Z","month":"07","page":"197 - 229","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/math/0205236"}],"title":"Mirror symmetry, langlands duality, and the Hitchin system","volume":153,"intvolume":"       153","status":"public","year":"2003","day":"01","author":[{"first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","full_name":"Tamas Hausel"},{"first_name":"Michael","last_name":"Thaddeus","full_name":"Thaddeus, Michael"}],"date_created":"2018-12-11T11:52:08Z","quality_controlled":0,"citation":{"ama":"Hausel T, Thaddeus M. Mirror symmetry, langlands duality, and the Hitchin system. <i>Inventiones Mathematicae</i>. 2003;153(1):197-229. doi:<a href=\"https://doi.org/10.1007/s00222-003-0286-7\">10.1007/s00222-003-0286-7</a>","chicago":"Hausel, Tamás, and Michael Thaddeus. “Mirror Symmetry, Langlands Duality, and the Hitchin System.” <i>Inventiones Mathematicae</i>. Springer, 2003. <a href=\"https://doi.org/10.1007/s00222-003-0286-7\">https://doi.org/10.1007/s00222-003-0286-7</a>.","short":"T. Hausel, M. Thaddeus, Inventiones Mathematicae 153 (2003) 197–229.","apa":"Hausel, T., &#38; Thaddeus, M. (2003). Mirror symmetry, langlands duality, and the Hitchin system. <i>Inventiones Mathematicae</i>. Springer. <a href=\"https://doi.org/10.1007/s00222-003-0286-7\">https://doi.org/10.1007/s00222-003-0286-7</a>","mla":"Hausel, Tamás, and Michael Thaddeus. “Mirror Symmetry, Langlands Duality, and the Hitchin System.” <i>Inventiones Mathematicae</i>, vol. 153, no. 1, Springer, 2003, pp. 197–229, doi:<a href=\"https://doi.org/10.1007/s00222-003-0286-7\">10.1007/s00222-003-0286-7</a>.","ista":"Hausel T, Thaddeus M. 2003. Mirror symmetry, langlands duality, and the Hitchin system. Inventiones Mathematicae. 153(1), 197–229.","ieee":"T. Hausel and M. Thaddeus, “Mirror symmetry, langlands duality, and the Hitchin system,” <i>Inventiones Mathematicae</i>, vol. 153, no. 1. Springer, pp. 197–229, 2003."},"doi":"10.1007/s00222-003-0286-7","extern":1,"publication":"Inventiones Mathematicae","issue":"1","_id":"1457","type":"journal_article"},{"year":"2003","day":"01","status":"public","intvolume":"        16","title":"Relations in the cohomology ring of the moduli space of rank 2 Higgs bundles","volume":16,"_id":"1458","issue":"2","type":"journal_article","publication":"Journal of the American Mathematical Society","extern":1,"citation":{"ista":"Hausel T, Thaddeus M. 2003. Relations in the cohomology ring of the moduli space of rank 2 Higgs bundles. Journal of the American Mathematical Society. 16(2), 303–329.","ieee":"T. Hausel and M. Thaddeus, “Relations in the cohomology ring of the moduli space of rank 2 Higgs bundles,” <i>Journal of the American Mathematical Society</i>, vol. 16, no. 2. American Mathematical Society, pp. 303–329, 2003.","mla":"Hausel, Tamás, and Michael Thaddeus. “Relations in the Cohomology Ring of the Moduli Space of Rank 2 Higgs Bundles.” <i>Journal of the American Mathematical Society</i>, vol. 16, no. 2, American Mathematical Society, 2003, pp. 303–29, doi:<a href=\"https://doi.org/10.1090/S0894-0347-02-00417-4\">10.1090/S0894-0347-02-00417-4</a>.","apa":"Hausel, T., &#38; Thaddeus, M. (2003). Relations in the cohomology ring of the moduli space of rank 2 Higgs bundles. <i>Journal of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/S0894-0347-02-00417-4\">https://doi.org/10.1090/S0894-0347-02-00417-4</a>","short":"T. Hausel, M. Thaddeus, Journal of the American Mathematical Society 16 (2003) 303–329.","chicago":"Hausel, Tamás, and Michael Thaddeus. “Relations in the Cohomology Ring of the Moduli Space of Rank 2 Higgs Bundles.” <i>Journal of the American Mathematical Society</i>. American Mathematical Society, 2003. <a href=\"https://doi.org/10.1090/S0894-0347-02-00417-4\">https://doi.org/10.1090/S0894-0347-02-00417-4</a>.","ama":"Hausel T, Thaddeus M. Relations in the cohomology ring of the moduli space of rank 2 Higgs bundles. <i>Journal of the American Mathematical Society</i>. 2003;16(2):303-329. doi:<a href=\"https://doi.org/10.1090/S0894-0347-02-00417-4\">10.1090/S0894-0347-02-00417-4</a>"},"doi":"10.1090/S0894-0347-02-00417-4","date_created":"2018-12-11T11:52:08Z","quality_controlled":0,"acknowledgement":"The first author was supported by NSF grant DMS-97-29992. The second author was supported by NSF grant DMS-98-08529.","author":[{"last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","full_name":"Tamas Hausel"},{"full_name":"Thaddeus, Michael","first_name":"Michael","last_name":"Thaddeus"}],"date_published":"2003-04-01T00:00:00Z","month":"04","oa":1,"abstract":[{"text":"The moduli space of stable bundles of rank $2$ and degree $1$ on a Riemann surface has rational cohomology generated by the so-called universal classes. The work of Baranovsky, King-Newstead, Siebert-Tian and Zagier provided a complete set of relations between these classes, expressed in terms of a recursion in the genus. This paper accomplishes the same thing for the noncompact moduli spaces of Higgs bundles, in the sense of Hitchin and Simpson. There are many more independent relations than for stable bundles, but in a sense the answer is simpler, since the formulas are completely explicit, not recursive. The results of Kirwan on equivariant cohomology for holomorphic circle actions are of key importance.","lang":"eng"}],"publisher":"American Mathematical Society","publist_id":"5739","date_updated":"2021-01-12T06:50:53Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/math/0003094"}],"page":"303 - 329"},{"extern":1,"publication":"Communications in Mathematical Physics","type":"journal_article","_id":"1459","issue":"2","date_created":"2018-12-11T11:52:09Z","quality_controlled":0,"doi":"10.1007/s00220-003-0806-8","citation":{"apa":"Etesi, G., &#38; Hausel, T. (2003). On Yang-Mills instantons over multi-centered gravitational instantons. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-003-0806-8\">https://doi.org/10.1007/s00220-003-0806-8</a>","chicago":"Etesi, Gábor, and Tamás Hausel. “On Yang-Mills Instantons over Multi-Centered Gravitational Instantons.” <i>Communications in Mathematical Physics</i>. Springer, 2003. <a href=\"https://doi.org/10.1007/s00220-003-0806-8\">https://doi.org/10.1007/s00220-003-0806-8</a>.","short":"G. Etesi, T. Hausel, Communications in Mathematical Physics 235 (2003) 275–288.","ieee":"G. Etesi and T. Hausel, “On Yang-Mills instantons over multi-centered gravitational instantons,” <i>Communications in Mathematical Physics</i>, vol. 235, no. 2. Springer, pp. 275–288, 2003.","ista":"Etesi G, Hausel T. 2003. On Yang-Mills instantons over multi-centered gravitational instantons. Communications in Mathematical Physics. 235(2), 275–288.","mla":"Etesi, Gábor, and Tamás Hausel. “On Yang-Mills Instantons over Multi-Centered Gravitational Instantons.” <i>Communications in Mathematical Physics</i>, vol. 235, no. 2, Springer, 2003, pp. 275–88, doi:<a href=\"https://doi.org/10.1007/s00220-003-0806-8\">10.1007/s00220-003-0806-8</a>.","ama":"Etesi G, Hausel T. On Yang-Mills instantons over multi-centered gravitational instantons. <i>Communications in Mathematical Physics</i>. 2003;235(2):275-288. doi:<a href=\"https://doi.org/10.1007/s00220-003-0806-8\">10.1007/s00220-003-0806-8</a>"},"acknowledgement":"We would like to acknowledge the financial support by Prof. P. Major (R ́ enyi Institute, Hungary) from his OTKA grant No. T26176 and of the Miller Institute for Basic Research in Science at UC Berkeley.","author":[{"last_name":"Etesi","first_name":"Gábor","full_name":"Etesi, Gábor"},{"first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","full_name":"Tamas Hausel"}],"year":"2003","day":"01","intvolume":"       235","status":"public","volume":235,"title":"On Yang-Mills instantons over multi-centered gravitational instantons","main_file_link":[{"url":"http://arxiv.org/abs/hep-th/0207196","open_access":"1"}],"page":"275 - 288","date_published":"2003-04-01T00:00:00Z","month":"04","abstract":[{"text":"In this paper we explicitly calculate the analogue of the 't Hooft SU (2) Yang-Mills instantons on Gibbons-Hawking multi-centered gravitational instantons, which come in two parallel families: the multi-Eguchi-Hanson, or Ak ALE gravitational instantons and the multi-Taub-NUT spaces, or Ak ALF gravitational instantons. We calculate their energy and find the reducible ones. Following Kronheimer we also exploit the U(1) invariance of our solutions and study the corresponding explicit singular SU (2) magnetic monopole solutions of the Bogomolny equations on flat ℝ3.","lang":"eng"}],"oa":1,"publist_id":"5740","date_updated":"2021-01-12T06:50:53Z","publisher":"Springer","publication_status":"published"},{"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2003.11.052","open_access":"1"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","publisher":"Elsevier","date_updated":"2021-12-14T08:41:38Z","month":"12","date_published":"2003-12-16T00:00:00Z","article_type":"original","author":[{"full_name":"Cao, Xiaofeng","last_name":"Cao","first_name":"Xiaofeng"},{"last_name":"Aufsatz","first_name":"Werner","full_name":"Aufsatz, Werner"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"},{"full_name":"Mette, M.Florian","last_name":"Mette","first_name":"M.Florian"},{"last_name":"Huang","first_name":"Michael S.","full_name":"Huang, Michael S."},{"full_name":"Matzke, Marjori","first_name":"Marjori","last_name":"Matzke"},{"last_name":"Jacobsen","first_name":"Steven E.","full_name":"Jacobsen, Steven E."}],"department":[{"_id":"DaZi"}],"date_created":"2021-06-07T10:43:02Z","oa_version":"Published Version","article_processing_charge":"No","_id":"9495","type":"journal_article","issue":"24","publication":"Current Biology","volume":13,"title":"Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation","status":"public","day":"16","page":"2212-2217","external_id":{"pmid":["14680640"]},"oa":1,"abstract":[{"lang":"eng","text":"RNA interference is a conserved process in which double-stranded RNA is processed into 21–25 nucleotide siRNAs that trigger posttranscriptional gene silencing. In addition, plants display a phenomenon termed RNA-directed DNA methylation (RdDM) in which DNA with sequence identity to silenced RNA is de novo methylated at its cytosine residues. This methylation is not only at canonical CpG sites but also at cytosines in CpNpG and asymmetric sequence contexts. In this report, we study the role of the DRM and CMT3 DNA methyltransferase genes in the initiation and maintenance of RdDM. Neither drm nor cmt3 mutants affected the maintenance of preestablished RNA-directed CpG methylation. However, drm mutants showed a nearly complete loss of asymmetric methylation and a partial loss of CpNpG methylation. The remaining asymmetric and CpNpG methylation was dependent on the activity of CMT3, showing that DRM and CMT3 act redundantly to maintain non-CpG methylation. These DNA methyltransferases appear to act downstream of siRNAs, since drm1 drm2 cmt3 triple mutants show a lack of non-CpG methylation but elevated levels of siRNAs. Finally, we demonstrate that DRM activity is required for the initial establishment of RdDM in all sequence contexts including CpG, CpNpG, and asymmetric sites."}],"citation":{"chicago":"Cao, Xiaofeng, Werner Aufsatz, Daniel Zilberman, M.Florian Mette, Michael S. Huang, Marjori Matzke, and Steven E. Jacobsen. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation.” <i>Current Biology</i>. Elsevier, 2003. <a href=\"https://doi.org/10.1016/j.cub.2003.11.052\">https://doi.org/10.1016/j.cub.2003.11.052</a>.","short":"X. Cao, W. Aufsatz, D. Zilberman, M.F. Mette, M.S. Huang, M. Matzke, S.E. Jacobsen, Current Biology 13 (2003) 2212–2217.","apa":"Cao, X., Aufsatz, W., Zilberman, D., Mette, M. F., Huang, M. S., Matzke, M., &#38; Jacobsen, S. E. (2003). Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2003.11.052\">https://doi.org/10.1016/j.cub.2003.11.052</a>","mla":"Cao, Xiaofeng, et al. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation.” <i>Current Biology</i>, vol. 13, no. 24, Elsevier, 2003, pp. 2212–17, doi:<a href=\"https://doi.org/10.1016/j.cub.2003.11.052\">10.1016/j.cub.2003.11.052</a>.","ieee":"X. Cao <i>et al.</i>, “Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation,” <i>Current Biology</i>, vol. 13, no. 24. Elsevier, pp. 2212–2217, 2003.","ista":"Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE. 2003. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Current Biology. 13(24), 2212–2217.","ama":"Cao X, Aufsatz W, Zilberman D, et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. <i>Current Biology</i>. 2003;13(24):2212-2217. doi:<a href=\"https://doi.org/10.1016/j.cub.2003.11.052\">10.1016/j.cub.2003.11.052</a>"},"doi":"10.1016/j.cub.2003.11.052","quality_controlled":"1","extern":"1","pmid":1,"intvolume":"        13","year":"2003","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"language":[{"iso":"eng"}]},{"year":"2003","day":"01","intvolume":"        22","status":"public","title":"Unfolding pathways of native bacteriorhodopsin depend on temperature","volume":22,"extern":1,"publication":"EMBO Journal","_id":"3725","type":"journal_article","issue":"19","date_created":"2018-12-11T12:04:50Z","quality_controlled":0,"citation":{"chicago":"Janovjak, Harald L, Max Kessler, Dieter Oesterhelt, Hermann Gaub, and Daniel Mueller. “Unfolding Pathways of Native Bacteriorhodopsin Depend on Temperature.” <i>EMBO Journal</i>. Wiley-Blackwell, 2003. <a href=\"https://doi.org/10.1093/emboj/cdg509\">https://doi.org/10.1093/emboj/cdg509</a>.","short":"H.L. Janovjak, M. Kessler, D. Oesterhelt, H. Gaub, D. Mueller, EMBO Journal 22 (2003) 5220–5229.","apa":"Janovjak, H. L., Kessler, M., Oesterhelt, D., Gaub, H., &#38; Mueller, D. (2003). Unfolding pathways of native bacteriorhodopsin depend on temperature. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1093/emboj/cdg509\">https://doi.org/10.1093/emboj/cdg509</a>","mla":"Janovjak, Harald L., et al. “Unfolding Pathways of Native Bacteriorhodopsin Depend on Temperature.” <i>EMBO Journal</i>, vol. 22, no. 19, Wiley-Blackwell, 2003, pp. 5220–29, doi:<a href=\"https://doi.org/10.1093/emboj/cdg509\">10.1093/emboj/cdg509</a>.","ista":"Janovjak HL, Kessler M, Oesterhelt D, Gaub H, Mueller D. 2003. Unfolding pathways of native bacteriorhodopsin depend on temperature. EMBO Journal. 22(19), 5220–5229.","ieee":"H. L. Janovjak, M. Kessler, D. Oesterhelt, H. Gaub, and D. Mueller, “Unfolding pathways of native bacteriorhodopsin depend on temperature,” <i>EMBO Journal</i>, vol. 22, no. 19. Wiley-Blackwell, pp. 5220–5229, 2003.","ama":"Janovjak HL, Kessler M, Oesterhelt D, Gaub H, Mueller D. Unfolding pathways of native bacteriorhodopsin depend on temperature. <i>EMBO Journal</i>. 2003;22(19):5220-5229. doi:<a href=\"https://doi.org/10.1093/emboj/cdg509\">10.1093/emboj/cdg509</a>"},"doi":"10.1093/emboj/cdg509","author":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Harald Janovjak"},{"full_name":"Kessler, Max","first_name":"Max","last_name":"Kessler"},{"full_name":"Oesterhelt, Dieter","first_name":"Dieter","last_name":"Oesterhelt"},{"first_name":"Hermann","last_name":"Gaub","full_name":"Gaub, Hermann"},{"last_name":"Mueller","first_name":"Daniel","full_name":"Mueller, Daniel J"}],"date_published":"2003-01-01T00:00:00Z","month":"01","abstract":[{"text":"The combination of high-resolution atomic force microscopy (AFM) imaging and single-molecule force-spectroscopy was employed to unfold single bacteriorhodopsins (BR) from native purple membrane patches at various physiologically relevant temperatures. The unfolding spectra reveal detailed insight into the stability of individual structural elements of BR against mechanical unfolding. Intermittent states in the unfolding process are associated with the stepwise unfolding of alpha-helices, whereas other states are associated with the unfolding of polypeptide loops connecting the alpha-helices. It was found that the unfolding forces of the secondary structures considerably decreased upon increasing the temperature from 8 to 52°C. Associated with this effect, the probability of individual unfolding pathways of BR was significantly influenced by the temperature. At lower temperatures, transmembrane alpha-helices and extracellular polypeptide loops exhibited sufficient stability to individually establish potential barriers against unfolding, whereas they predominantly unfolded collectively at elevated temperatures. This suggests that increasing the temperature decreases the mechanical stability of secondary structural elements and changes molecular interactions between secondary structures, thereby forcing them to act as grouped structures.","lang":"eng"}],"oa":1,"date_updated":"2021-01-12T07:51:45Z","publist_id":"2506","publisher":"Wiley-Blackwell","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC204492/"}],"page":"5220 - 5229"},{"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2172934/?tool=pubmed"}],"page":"471 - 476","date_published":"2003-01-12T00:00:00Z","month":"01","abstract":[{"lang":"eng","text":"We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We integrate three different levels of description (molecular, cellular, and that of cell population) into a single model, which seems to capture many experimental aspects of the system."}],"oa":1,"date_updated":"2021-01-12T07:51:57Z","publist_id":"2475","publisher":"Rockefeller University Press","publication_status":"published","publication":"Journal of Cell Biology","extern":1,"type":"journal_article","_id":"3752","issue":"3","date_created":"2018-12-11T12:04:58Z","quality_controlled":0,"citation":{"ama":"Vilar J, Guet CC, Leibler S. Modeling network dynamics: the lac operon, a case study. <i>Journal of Cell Biology</i>. 2003;161(3):471-476. doi:<a href=\"https://doi.org/10.1083/jcb.200301125\">10.1083/jcb.200301125</a>","short":"J. Vilar, C.C. Guet, S. Leibler, Journal of Cell Biology 161 (2003) 471–476.","chicago":"Vilar, Jose, Calin C Guet, and Stanislas Leibler. “Modeling Network Dynamics: The Lac Operon, a Case Study.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2003. <a href=\"https://doi.org/10.1083/jcb.200301125\">https://doi.org/10.1083/jcb.200301125</a>.","apa":"Vilar, J., Guet, C. C., &#38; Leibler, S. (2003). Modeling network dynamics: the lac operon, a case study. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.200301125\">https://doi.org/10.1083/jcb.200301125</a>","mla":"Vilar, Jose, et al. “Modeling Network Dynamics: The Lac Operon, a Case Study.” <i>Journal of Cell Biology</i>, vol. 161, no. 3, Rockefeller University Press, 2003, pp. 471–76, doi:<a href=\"https://doi.org/10.1083/jcb.200301125\">10.1083/jcb.200301125</a>.","ista":"Vilar J, Guet CC, Leibler S. 2003. Modeling network dynamics: the lac operon, a case study. Journal of Cell Biology. 161(3), 471–476.","ieee":"J. Vilar, C. C. Guet, and S. Leibler, “Modeling network dynamics: the lac operon, a case study,” <i>Journal of Cell Biology</i>, vol. 161, no. 3. Rockefeller University Press, pp. 471–476, 2003."},"doi":"10.1083/jcb.200301125","author":[{"last_name":"Vilar","first_name":"Jose","full_name":"Vilar,Jose M"},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Calin Guet","orcid":"0000-0001-6220-2052"},{"full_name":"Leibler, Stanislas","first_name":"Stanislas","last_name":"Leibler"}],"year":"2003","day":"12","intvolume":"       161","status":"public","volume":161,"title":"Modeling network dynamics: the lac operon, a case study"}]