[{"pmid":1,"date_published":"2004-02-24T00:00:00Z","publisher":"Public Library of Science","title":"Genetic and functional diversification of small RNA pathways in plants","publication_status":"published","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."}],"external_id":{"pmid":["15024409"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"extern":"1","date_updated":"2021-12-14T08:43:57Z","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.","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>","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.","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>.","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>","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>.","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."},"intvolume":"         2","publication":"PLoS Biology","scopus_import":"1","day":"24","year":"2004","page":"0642-0652","doi":"10.1371/journal.pbio.0020104","oa":1,"language":[{"iso":"eng"}],"volume":2,"article_processing_charge":"No","month":"02","issue":"5","author":[{"last_name":"Xie","first_name":"Zhixin","full_name":"Xie, Zhixin"},{"full_name":"Johansen, Lisa K.","last_name":"Johansen","first_name":"Lisa K."},{"full_name":"Gustafson, Adam M.","first_name":"Adam M.","last_name":"Gustafson"},{"last_name":"Kasschau","first_name":"Kristin D.","full_name":"Kasschau, Kristin D."},{"last_name":"Lellis","first_name":"Andrew D. ","full_name":"Lellis, Andrew D. "},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Steven E.","last_name":"Jacobsen","full_name":"Jacobsen, Steven E."},{"full_name":"Carrington, James C.","last_name":"Carrington","first_name":"James C."}],"quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1371/journal.pbio.0020104","open_access":"1"}],"status":"public","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"date_created":"2021-06-07T14:12:08Z","article_type":"original","_id":"9517","type":"journal_article"},{"language":[{"iso":"eng"}],"date_published":"2004-07-01T00:00:00Z","publisher":"Springer Nature","title":"The past, present, and future of web search engines","volume":3142,"article_processing_charge":"No","month":"07","publication_status":"published","abstract":[{"text":"Web search engines have emerged as one of the central applications on the Internet. In fact, search has become one of the most important activities that people engage in on the the Internet. Even beyond becoming the number one source of information, a growing number of businesses are depending on web search engines for customer acquisition.\r\n\r\nThe first generation of web search engines used text-only retrieval techniques. Google revolutionized the field by deploying the PageRank technology – an eigenvector-based analysis of the hyperlink structure – to analyze the web in order to produce relevant results. Moving forward, our goal is to achieve a better understanding of a page with a view towards producing even more relevant results.","lang":"eng"}],"author":[{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H"}],"alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","quality_controlled":"1","date_updated":"2023-02-13T11:45:25Z","citation":{"mla":"Henzinger, Monika H. “The Past, Present, and Future of Web Search Engines.” <i>31st International Colloquium on Automata, Languages and Programming</i>, vol. 3142, Springer Nature, 2004, p. 3, doi:<a href=\"https://doi.org/10.1007/978-3-540-27836-8_2\">10.1007/978-3-540-27836-8_2</a>.","short":"M.H. Henzinger, in:, 31st International Colloquium on Automata, Languages and Programming, Springer Nature, 2004, p. 3.","apa":"Henzinger, M. H. (2004). The past, present, and future of web search engines. In <i>31st International Colloquium on Automata, Languages and Programming</i> (Vol. 3142, p. 3). Turku, Finland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-540-27836-8_2\">https://doi.org/10.1007/978-3-540-27836-8_2</a>","ista":"Henzinger MH. 2004. The past, present, and future of web search engines. 31st International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 3142, 3.","chicago":"Henzinger, Monika H. “The Past, Present, and Future of Web Search Engines.” In <i>31st International Colloquium on Automata, Languages and Programming</i>, 3142:3. Springer Nature, 2004. <a href=\"https://doi.org/10.1007/978-3-540-27836-8_2\">https://doi.org/10.1007/978-3-540-27836-8_2</a>.","ama":"Henzinger MH. The past, present, and future of web search engines. In: <i>31st International Colloquium on Automata, Languages and Programming</i>. Vol 3142. Springer Nature; 2004:3. doi:<a href=\"https://doi.org/10.1007/978-3-540-27836-8_2\">10.1007/978-3-540-27836-8_2</a>","ieee":"M. H. Henzinger, “The past, present, and future of web search engines,” in <i>31st International Colloquium on Automata, Languages and Programming</i>, Turku, Finland, 2004, vol. 3142, p. 3."},"oa_version":"None","conference":{"end_date":"2004-07-16","start_date":"2004-07-12","name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Turku, Finland"},"intvolume":"      3142","publication":"31st International Colloquium on Automata, Languages and Programming","scopus_import":"1","day":"01","year":"2004","status":"public","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"]},"page":"3","doi":"10.1007/978-3-540-27836-8_2","date_created":"2022-08-11T12:38:58Z","_id":"11800","type":"conference"},{"scopus_import":"1","publication":"2th Annual European Symposium on Algorithms","conference":{"name":"ESA: European Symposium on Algorithms","location":"Bergen, Norway","end_date":"2004-09-17","start_date":"2004-09-14"},"intvolume":"      3221","type":"conference","_id":"11801","date_created":"2022-08-11T13:18:05Z","doi":"10.1007/978-3-540-30140-0_2","publication_identifier":{"isbn":[" 3540230254"],"issn":["0302-9743"],"eissn":["1611-3349"]},"page":"3","day":"01","year":"2004","status":"public","publication_status":"published","month":"09","abstract":[{"lang":"eng","text":"Web search engines have emerged as one of the central applications on the internet. In fact, search has become one of the most important activities that people engage in on the Internet. Even beyond becoming the number one source of information, a growing number of businesses are depending on web search engines for customer acquisition. In this talk I will brief review the history of web search engines: The first generation of web search engines used text-only retrieval techniques. Google revolutionized the field by deploying the PageRank technology – an eigenvector-based analysis of the hyperlink structure- to analyze the web in order to produce relevant results. Moving forward, our goal is to achieve a better understanding of a page with a view towards producing even more relevant results.\r\n\r\nGoogle is powered by a large number of PCs. Using this infrastructure and striving to be as efficient as possible poses challenging systems problems but also various algorithmic challenges. I will discuss some of them in my talk."}],"volume":3221,"title":"Algorithmic aspects of web search engines","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2004-09-01T00:00:00Z","publisher":"Springer Nature","citation":{"short":"M.H. Henzinger, in:, 2th Annual European Symposium on Algorithms, Springer Nature, 2004, p. 3.","mla":"Henzinger, Monika H. “Algorithmic Aspects of Web Search Engines.” <i>2th Annual European Symposium on Algorithms</i>, vol. 3221, Springer Nature, 2004, p. 3, doi:<a href=\"https://doi.org/10.1007/978-3-540-30140-0_2\">10.1007/978-3-540-30140-0_2</a>.","ieee":"M. H. Henzinger, “Algorithmic aspects of web search engines,” in <i>2th Annual European Symposium on Algorithms</i>, Bergen, Norway, 2004, vol. 3221, p. 3.","ama":"Henzinger MH. Algorithmic aspects of web search engines. In: <i>2th Annual European Symposium on Algorithms</i>. Vol 3221. Springer Nature; 2004:3. doi:<a href=\"https://doi.org/10.1007/978-3-540-30140-0_2\">10.1007/978-3-540-30140-0_2</a>","chicago":"Henzinger, Monika H. “Algorithmic Aspects of Web Search Engines.” In <i>2th Annual European Symposium on Algorithms</i>, 3221:3. Springer Nature, 2004. <a href=\"https://doi.org/10.1007/978-3-540-30140-0_2\">https://doi.org/10.1007/978-3-540-30140-0_2</a>.","ista":"Henzinger MH. 2004. Algorithmic aspects of web search engines. 2th Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LNCS, vol. 3221, 3.","apa":"Henzinger, M. H. (2004). Algorithmic aspects of web search engines. In <i>2th Annual European Symposium on Algorithms</i> (Vol. 3221, p. 3). Bergen, Norway: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-540-30140-0_2\">https://doi.org/10.1007/978-3-540-30140-0_2</a>"},"oa_version":"None","extern":"1","quality_controlled":"1","date_updated":"2023-02-13T11:47:26Z","alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"}]},{"conference":{"end_date":"2004-01-22","start_date":"2004-01-21","location":"San Jose, CA, United States","name":"Document Recognition and Retrieval XI"},"intvolume":"      5296","publication":"SPIE Proceedings","scopus_import":"1","day":"01","status":"public","publication_identifier":{"issn":["0277-786X"]},"year":"2004","page":"23 - 26","doi":"10.1117/12.537534","date_created":"2022-08-16T08:46:41Z","_id":"11859","type":"conference","date_published":"2004-01-01T00:00:00Z","publisher":"Society of Photo-Optical Instrumentation Engineers","language":[{"iso":"eng"}],"volume":5296,"title":"The past, present, and future of web information retrieval","article_processing_charge":"No","publication_status":"published","month":"01","abstract":[{"text":"In this article we describe the approach taken by the first web search engines, discuss the state of the art, and present some of the challenges for the future.","lang":"eng"}],"author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","quality_controlled":"1","date_updated":"2023-02-17T10:05:19Z","citation":{"apa":"Henzinger, M. H. (2004). The past, present, and future of web information retrieval. In <i>SPIE Proceedings</i> (Vol. 5296, pp. 23–26). San Jose, CA, United States: Society of Photo-Optical Instrumentation Engineers. <a href=\"https://doi.org/10.1117/12.537534\">https://doi.org/10.1117/12.537534</a>","chicago":"Henzinger, Monika H. “The Past, Present, and Future of Web Information Retrieval.” In <i>SPIE Proceedings</i>, 5296:23–26. Society of Photo-Optical Instrumentation Engineers, 2004. <a href=\"https://doi.org/10.1117/12.537534\">https://doi.org/10.1117/12.537534</a>.","ama":"Henzinger MH. The past, present, and future of web information retrieval. In: <i>SPIE Proceedings</i>. Vol 5296. Society of Photo-Optical Instrumentation Engineers; 2004:23-26. doi:<a href=\"https://doi.org/10.1117/12.537534\">10.1117/12.537534</a>","ista":"Henzinger MH. 2004. The past, present, and future of web information retrieval. SPIE Proceedings. Document Recognition and Retrieval XI vol. 5296, 23–26.","ieee":"M. H. Henzinger, “The past, present, and future of web information retrieval,” in <i>SPIE Proceedings</i>, San Jose, CA, United States, 2004, vol. 5296, pp. 23–26.","mla":"Henzinger, Monika H. “The Past, Present, and Future of Web Information Retrieval.” <i>SPIE Proceedings</i>, vol. 5296, Society of Photo-Optical Instrumentation Engineers, 2004, pp. 23–26, doi:<a href=\"https://doi.org/10.1117/12.537534\">10.1117/12.537534</a>.","short":"M.H. Henzinger, in:, SPIE Proceedings, Society of Photo-Optical Instrumentation Engineers, 2004, pp. 23–26."},"oa_version":"None"},{"citation":{"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.","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>","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>.","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>","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>.","short":"M.H. Henzinger, S. Lawrence, Proceedings of the National Academy of Sciences 101 (2004) 5186–5191."},"date_updated":"2023-02-17T12:21:43Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["14745041"]},"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"}],"publication_status":"published","title":"Extracting knowledge from the World Wide Web","date_published":"2004-04-06T00:00:00Z","publisher":"Proceedings of the National Academy of Sciences","pmid":1,"oa":1,"year":"2004","page":"5186-5191","doi":"10.1073/pnas.0307528100","day":"06","scopus_import":"1","publication":"Proceedings of the National Academy of Sciences","intvolume":"       101","oa_version":"Published Version","quality_controlled":"1","author":[{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"first_name":"Steve","last_name":"Lawrence","full_name":"Lawrence, Steve"}],"issue":"suppl_1","month":"04","article_processing_charge":"No","volume":101,"language":[{"iso":"eng"}],"_id":"11877","type":"journal_article","article_type":"original","date_created":"2022-08-16T13:06:10Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC387294/","open_access":"1"}]},{"keyword":["Endocrinology","Genetics","Molecular Biology","Biochemistry"],"scopus_import":"1","intvolume":"        15","publication":"DNA Sequence","acknowledgement":"This study was financially supported by China National High-Tech “863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences, Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic tree.","page":"153-158","year":"2004","doi":"10.1080/10425170410001667348","publication_status":"published","abstract":[{"lang":"eng","text":"Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide biosynthesis. Here we reported for the first time the cloning of a new full-length cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal, which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed that GbGGPPS was a member of polyprenyltransferases with two highly conserved aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs."}],"pmid":1,"date_published":"2004-01-01T00:00:00Z","publisher":"Informa UK Limited","title":"A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides","department":[{"_id":"XiFe"}],"extern":"1","date_updated":"2023-05-08T10:58:29Z","citation":{"mla":"Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>.","short":"Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang, DNA Sequence 15 (2004) 153–158.","ieee":"Z. Liao <i>et al.</i>, “A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,” <i>DNA Sequence</i>, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004.","chicago":"Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng, Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>. Informa UK Limited, 2004. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>.","ista":"Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158.","ama":"Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. 2004;15(2):153-158. doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>","apa":"Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004). A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>"},"external_id":{"pmid":["15352294"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-01-16T09:24:50Z","article_type":"original","type":"journal_article","_id":"12203","status":"public","publication_identifier":{"issn":["1042-5179"]},"issue":"2","language":[{"iso":"eng"}],"volume":15,"article_processing_charge":"No","quality_controlled":"1","oa_version":"None","author":[{"first_name":"Zhihua","last_name":"Liao","full_name":"Liao, Zhihua"},{"full_name":"Chen, Min","first_name":"Min","last_name":"Chen"},{"full_name":"Gong, Yifu","last_name":"Gong","first_name":"Yifu"},{"last_name":"Guo","first_name":"Liang","full_name":"Guo, Liang"},{"last_name":"Tan","first_name":"Qiumin","full_name":"Tan, Qiumin"},{"first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi"},{"first_name":"Xiaofen","last_name":"Sun","full_name":"Sun, Xiaofen"},{"first_name":"Feng","last_name":"Tan","full_name":"Tan, Feng"},{"last_name":"Tang","first_name":"Kexuan","full_name":"Tang, Kexuan"}]},{"publication":"Journal of Geophysical Research: Atmospheres","intvolume":"       109","keyword":["Paleontology","Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Earth-Surface Processes","Geochemistry and Petrology","Soil Science","Water Science and Technology","Ecology","Aquatic Science","Forestry","Oceanography","Geophysics"],"scopus_import":"1","day":"16","doi":"10.1029/2003jd003973","year":"2004","title":"Spatial and temporal variability of meteorological variables at Haut Glacier d'Arolla (Switzerland) during the ablation season 2001: Measurements and simulations","publisher":"American Geophysical Union","date_published":"2004-02-16T00:00:00Z","abstract":[{"text":"[1] During the ablation period 2001 a glaciometeorological experiment was carried out on Haut Glacier d'Arolla, Switzerland. Five meteorological stations were installed on the glacier, and one permanent automatic weather station in the glacier foreland. The altitudes of the stations ranged between 2500 and 3000 m a.s.l., and they were in operation from end of May to beginning of September 2001. The spatial arrangement of the stations and temporal duration of the measurements generated a unique data set enabling the analysis of the spatial and temporal variability of the meteorological variables across an alpine glacier. All measurements were taken at a nominal height of 2 m, and hourly averages were derived for the analysis. The wind regime was dominated by the glacier wind (mean value 2.8 m s−1) but due to erosion by the synoptic gradient wind, occasionally the wind would blow up the valley. A slight decrease in mean 2 m air temperatures with altitude was found, however the 2 m air temperature gradient varied greatly and frequently changed its sign. Mean relative humidity was 71% and exhibited limited spatial variation. Mean incoming shortwave radiation and albedo both generally increased with elevation. The different components of shortwave radiation are quantified with a parameterization scheme. Resulting spatial variations are mainly due to horizon obstruction and reflections from surrounding slopes, i.e., topography. The effect of clouds accounts for a loss of 30% of the extraterrestrial flux. Albedos derived from a Landsat TM image of 30 July show remarkably constant values, in the range 0.49 to 0.50, across snow covered parts of the glacier, while albedo is highly spatially variable below the zone of continuous snow cover. These results are verified with ground measurements and compared with parameterized albedo. Mean longwave radiative fluxes decreased with elevation due to lower air temperatures and the effect of upper hemisphere slopes. It is shown through parameterization that this effect would even be more pronounced without the effect of clouds. Results are discussed with respect to a similar study which has been carried out on Pasterze Glacier (Austria). The presented algorithms for interpolating, parameterizing and simulating variables and parameters in alpine regions are integrated in the software package AMUNDSEN which is freely available to be adapted and further developed by the community.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, and M. Funk, “Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 109, no. D3. American Geophysical Union, 2004.","ista":"Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. 2004. Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. Journal of Geophysical Research: Atmospheres. 109(D3), D03103.","chicago":"Strasser, Ulrich, Javier Corripio, Francesca Pellicciotti, Paolo Burlando, Ben Brock, and Martin Funk. “Spatial and Temporal Variability of Meteorological Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001: Measurements and Simulations.” <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union, 2004. <a href=\"https://doi.org/10.1029/2003jd003973\">https://doi.org/10.1029/2003jd003973</a>.","ama":"Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. <i>Journal of Geophysical Research: Atmospheres</i>. 2004;109(D3). doi:<a href=\"https://doi.org/10.1029/2003jd003973\">10.1029/2003jd003973</a>","apa":"Strasser, U., Corripio, J., Pellicciotti, F., Burlando, P., Brock, B., &#38; Funk, M. (2004). Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2003jd003973\">https://doi.org/10.1029/2003jd003973</a>","short":"U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, M. Funk, Journal of Geophysical Research: Atmospheres 109 (2004).","mla":"Strasser, Ulrich, et al. “Spatial and Temporal Variability of Meteorological Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001: Measurements and Simulations.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 109, no. D3, D03103, American Geophysical Union, 2004, doi:<a href=\"https://doi.org/10.1029/2003jd003973\">10.1029/2003jd003973</a>."},"date_updated":"2023-02-20T08:40:21Z","extern":"1","status":"public","publication_identifier":{"issn":["0148-0227"]},"type":"journal_article","_id":"12658","article_type":"original","date_created":"2023-02-20T08:18:57Z","article_processing_charge":"No","volume":109,"language":[{"iso":"eng"}],"issue":"D3","article_number":"D03103","month":"02","author":[{"full_name":"Strasser, Ulrich","last_name":"Strasser","first_name":"Ulrich"},{"first_name":"Javier","last_name":"Corripio","full_name":"Corripio, Javier"},{"last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"},{"last_name":"Burlando","first_name":"Paolo","full_name":"Burlando, Paolo"},{"full_name":"Brock, Ben","first_name":"Ben","last_name":"Brock"},{"full_name":"Funk, Martin","last_name":"Funk","first_name":"Martin"}],"oa_version":"None","quality_controlled":"1"},{"_id":"3419","type":"journal_article","date_created":"2018-12-11T12:03:14Z","day":"01","status":"public","year":"2004","doi":"10.1016/j.str.2004.03.016","page":"871 - 879","publication":"Structure","publist_id":"2982","intvolume":"        12","citation":{"ieee":"H. L. Janovjak, J. Struckmeier, M. Hubain, M. Kessler, A. Kedrov, and D. Mueller, “Probing the energy landscape of the membrane protein bacteriorhodopsin,” <i>Structure</i>, vol. 12, no. 5. Cell Press, pp. 871–879, 2004.","chicago":"Janovjak, Harald L, Jens Struckmeier, Maurice Hubain, Max Kessler, Alexej Kedrov, and Daniel Mueller. “Probing the Energy Landscape of the Membrane Protein Bacteriorhodopsin.” <i>Structure</i>. Cell Press, 2004. <a href=\"https://doi.org/10.1016/j.str.2004.03.016\">https://doi.org/10.1016/j.str.2004.03.016</a>.","ama":"Janovjak HL, Struckmeier J, Hubain M, Kessler M, Kedrov A, Mueller D. Probing the energy landscape of the membrane protein bacteriorhodopsin. <i>Structure</i>. 2004;12(5):871-879. doi:<a href=\"https://doi.org/10.1016/j.str.2004.03.016\">10.1016/j.str.2004.03.016</a>","ista":"Janovjak HL, Struckmeier J, Hubain M, Kessler M, Kedrov A, Mueller D. 2004. Probing the energy landscape of the membrane protein bacteriorhodopsin. Structure. 12(5), 871–879.","apa":"Janovjak, H. L., Struckmeier, J., Hubain, M., Kessler, M., Kedrov, A., &#38; Mueller, D. (2004). Probing the energy landscape of the membrane protein bacteriorhodopsin. <i>Structure</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.str.2004.03.016\">https://doi.org/10.1016/j.str.2004.03.016</a>","mla":"Janovjak, Harald L., et al. “Probing the Energy Landscape of the Membrane Protein Bacteriorhodopsin.” <i>Structure</i>, vol. 12, no. 5, Cell Press, 2004, pp. 871–79, doi:<a href=\"https://doi.org/10.1016/j.str.2004.03.016\">10.1016/j.str.2004.03.016</a>.","short":"H.L. Janovjak, J. Struckmeier, M. Hubain, M. Kessler, A. Kedrov, D. Mueller, Structure 12 (2004) 871–879."},"quality_controlled":0,"extern":1,"date_updated":"2021-01-12T07:43:20Z","author":[{"full_name":"Harald Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L"},{"last_name":"Struckmeier","first_name":"Jens","full_name":"Struckmeier, Jens"},{"full_name":"Hubain, Maurice","last_name":"Hubain","first_name":"Maurice"},{"full_name":"Kessler, Max","first_name":"Max","last_name":"Kessler"},{"full_name":"Kedrov, Alexej","first_name":"Alexej","last_name":"Kedrov"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"issue":"5","month":"05","publication_status":"published","abstract":[{"text":"The folding and stability of transmembrane proteins is a fundamental and unsolved biological problem. Here, single bacteriorhodopsin molecules were mechanically unfolded from native purple membranes using atomic force microscopy and force spectroscopy. The energy landscape of individual transmembrane α helices and polypeptide loops was mapped by monitoring the pulling speed dependence of the unfolding forces and applying Monte Carlo simulations. Single helices formed independently stable units stabilized by a single potential barrier. Mechanical unfolding of the helices was triggered by 3.9–7.7 Å extension, while natural unfolding rates were of the order of 10−3 s−1. Besides acting as individually stable units, helices associated pairwise, establishing a collective potential barrier. The unfolding pathways of individual proteins reflect distinct pulling speed-dependent unfolding routes in their energy landscapes. These observations support the two-stage model of membrane protein folding in which α helices insert into the membrane as stable units and then assemble into the functional protein.","lang":"eng"}],"title":"Probing the energy landscape of the membrane protein bacteriorhodopsin","volume":12,"publisher":"Cell Press","date_published":"2004-05-01T00:00:00Z"},{"day":"23","year":"2004","status":"public","page":"1143 - 1152","doi":"10.1016/j.jmb.2004.05.026","type":"journal_article","_id":"3420","date_created":"2018-12-11T12:03:14Z","publication":"Journal of Molecular Biology","intvolume":"       340","publist_id":"2981","author":[{"first_name":"Alexej","last_name":"Kedrov","full_name":"Kedrov, Alexej"},{"full_name":"Ziegler,  Christine","first_name":"Christine","last_name":"Ziegler"},{"full_name":"Harald Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L"},{"full_name":"Kühlbrandt, Werner","first_name":"Werner","last_name":"Kühlbrandt"},{"full_name":"Mueller, Daniel J","first_name":"Daniel","last_name":"Mueller"}],"citation":{"apa":"Kedrov, A., Ziegler, C., Janovjak, H. L., Kühlbrandt, W., &#38; Mueller, D. (2004). Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2004.05.026\">https://doi.org/10.1016/j.jmb.2004.05.026</a>","ista":"Kedrov A, Ziegler C, Janovjak HL, Kühlbrandt W, Mueller D. 2004. Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy. Journal of Molecular Biology. 340(5), 1143–1152.","ama":"Kedrov A, Ziegler C, Janovjak HL, Kühlbrandt W, Mueller D. Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy. <i>Journal of Molecular Biology</i>. 2004;340(5):1143-1152. doi:<a href=\"https://doi.org/10.1016/j.jmb.2004.05.026\">10.1016/j.jmb.2004.05.026</a>","chicago":"Kedrov, Alexej, Christine Ziegler, Harald L Janovjak, Werner Kühlbrandt, and Daniel Mueller. “Controlled Unfolding and Refolding of a Single Sodium/Proton Antiporter Using Atomic Force Microscopy.” <i>Journal of Molecular Biology</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.jmb.2004.05.026\">https://doi.org/10.1016/j.jmb.2004.05.026</a>.","ieee":"A. Kedrov, C. Ziegler, H. L. Janovjak, W. Kühlbrandt, and D. Mueller, “Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy,” <i>Journal of Molecular Biology</i>, vol. 340, no. 5. Elsevier, pp. 1143–1152, 2004.","short":"A. Kedrov, C. Ziegler, H.L. Janovjak, W. Kühlbrandt, D. Mueller, Journal of Molecular Biology 340 (2004) 1143–1152.","mla":"Kedrov, Alexej, et al. “Controlled Unfolding and Refolding of a Single Sodium/Proton Antiporter Using Atomic Force Microscopy.” <i>Journal of Molecular Biology</i>, vol. 340, no. 5, Elsevier, 2004, pp. 1143–52, doi:<a href=\"https://doi.org/10.1016/j.jmb.2004.05.026\">10.1016/j.jmb.2004.05.026</a>."},"date_updated":"2021-01-12T07:43:21Z","quality_controlled":0,"extern":1,"title":"Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy","volume":340,"publisher":"Elsevier","date_published":"2004-07-23T00:00:00Z","issue":"5","abstract":[{"lang":"eng","text":"Single-molecule force-spectroscopy was employed to unfold and refold single sodium-proton antiporters (NhaA) of Escherichia coli from membrane patches. Although transmembrane α-helices and extracellular polypeptide loops exhibited sufficient stability to individually establish potential barriers against unfolding, two helices predominantly unfolded pairwise, thereby acting as one structural unit. Many of the potential barriers were detected unfolding NhaA either from the C-terminal or the N-terminal end. It was found that some molecular interactions stabilizing secondary structural elements were directional, while others were not. Additionally, some interactions appeared to occur between the secondary structural elements. After unfolding ten of the 12 helices, the extracted polypeptide was allowed to refold back into the membrane. After five seconds, the refolded polypeptide established all secondary structure elements of the native protein. One helical pair showed a characteristic spring like “snap in” into its folded conformation, while the refolding process of other helices was not detected in particular. Additionally, individual helices required characteristic periods of time to fold. Correlating these results with the primary structure of NhaA allowed us to obtain the first insights into how potential barriers establish and determine the folding kinetics of the secondary structure elements."}],"publication_status":"published","month":"07"},{"day":"15","main_file_link":[{"url":"http://www.cs.duke.edu/~edels/Papers/2004-B-01-BiologicalApplicationsTopology.pdf","open_access":"0"}],"page":"1395 - 1412","status":"public","year":"2004","type":"book_chapter","_id":"3574","date_created":"2018-12-11T12:04:02Z","publication":"Handbook of Discrete and Computational Geometry","publist_id":"2811","author":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Herbert Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ista":"Edelsbrunner H. 2004.Biological applications of computational topology. In: Handbook of Discrete and Computational Geometry. , 1395–1412.","chicago":"Edelsbrunner, Herbert. “Biological Applications of Computational Topology.” In <i>Handbook of Discrete and Computational Geometry</i>, 1395–1412. CRC Press, 2004.","ama":"Edelsbrunner H. Biological applications of computational topology. In: <i>Handbook of Discrete and Computational Geometry</i>. CRC Press; 2004:1395-1412.","apa":"Edelsbrunner, H. (2004). Biological applications of computational topology. In <i>Handbook of Discrete and Computational Geometry</i> (pp. 1395–1412). CRC Press.","ieee":"H. Edelsbrunner, “Biological applications of computational topology,” in <i>Handbook of Discrete and Computational Geometry</i>, CRC Press, 2004, pp. 1395–1412.","mla":"Edelsbrunner, Herbert. “Biological Applications of Computational Topology.” <i>Handbook of Discrete and Computational Geometry</i>, CRC Press, 2004, pp. 1395–412.","short":"H. Edelsbrunner, in:, Handbook of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–1412."},"quality_controlled":0,"extern":1,"date_updated":"2021-01-12T07:44:24Z","title":"Biological applications of computational topology","publisher":"CRC Press","date_published":"2004-04-15T00:00:00Z","month":"04","publication_status":"published"},{"publist_id":"2810","intvolume":"       312","publication":"Foundations of Computational Mathematics","date_created":"2018-12-11T12:04:02Z","_id":"3575","type":"book_chapter","day":"01","page":"37 - 57","doi":"10.1017/CBO9781139106962.003","status":"public","year":"2004","month":"01","publication_status":"published","abstract":[{"lang":"eng","text":"The Jacobi set of two Morse functions defined on a common - manifold is the set of critical points of the restrictions of one func- tion to the level sets of the other function. Equivalently, it is the set of points where the gradients of the functions are parallel. For a generic pair of Morse functions, the Jacobi set is a smoothly embed- ded 1-manifold. We give a polynomial-time algorithm that com- putes the piecewise linear analog of the Jacobi set for functions specified at the vertices of a triangulation, and we generalize all results to more than two but at most Morse functions."}],"publisher":"Springer","date_published":"2004-01-01T00:00:00Z","volume":312,"title":"Jacobi sets of multiple Morse functions","extern":1,"quality_controlled":0,"date_updated":"2021-01-12T07:44:24Z","citation":{"ieee":"H. Edelsbrunner and J. Harer, “Jacobi sets of multiple Morse functions,” in <i>Foundations of Computational Mathematics</i>, vol. 312, Springer, 2004, pp. 37–57.","chicago":"Edelsbrunner, Herbert, and John Harer. “Jacobi Sets of Multiple Morse Functions.” In <i>Foundations of Computational Mathematics</i>, 312:37–57. Springer, 2004. <a href=\"https://doi.org/10.1017/CBO9781139106962.003\">https://doi.org/10.1017/CBO9781139106962.003</a>.","ista":"Edelsbrunner H, Harer J. 2004.Jacobi sets of multiple Morse functions. In: Foundations of Computational Mathematics. London Mathematical Society Lecture Note, vol. 312, 37–57.","ama":"Edelsbrunner H, Harer J. Jacobi sets of multiple Morse functions. In: <i>Foundations of Computational Mathematics</i>. Vol 312. Springer; 2004:37-57. doi:<a href=\"https://doi.org/10.1017/CBO9781139106962.003\">10.1017/CBO9781139106962.003</a>","apa":"Edelsbrunner, H., &#38; Harer, J. (2004). Jacobi sets of multiple Morse functions. In <i>Foundations of Computational Mathematics</i> (Vol. 312, pp. 37–57). Springer. <a href=\"https://doi.org/10.1017/CBO9781139106962.003\">https://doi.org/10.1017/CBO9781139106962.003</a>","mla":"Edelsbrunner, Herbert, and John Harer. “Jacobi Sets of Multiple Morse Functions.” <i>Foundations of Computational Mathematics</i>, vol. 312, Springer, 2004, pp. 37–57, doi:<a href=\"https://doi.org/10.1017/CBO9781139106962.003\">10.1017/CBO9781139106962.003</a>.","short":"H. Edelsbrunner, J. Harer, in:, Foundations of Computational Mathematics, Springer, 2004, pp. 37–57."},"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Herbert Edelsbrunner","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"full_name":"Harer, John","first_name":"John","last_name":"Harer"}],"alternative_title":["London Mathematical Society Lecture Note"]},{"date_created":"2018-12-11T12:04:06Z","type":"book_chapter","_id":"3587","day":"01","status":"public","year":"2004","page":"39 - 86","editor":[{"full_name":"Korzh, Vladimir","last_name":"Korzh","first_name":"Vladimir"},{"last_name":"Gong","first_name":"Zhiyuan","full_name":"Gong, Zhiyuan"}],"publist_id":"2796","intvolume":"         2","publication":"Fish development and genetics : the zebrafish and medaka models","extern":"1","date_updated":"2021-01-12T07:44:29Z","citation":{"mla":"Ulrich, Florian, and Carl-Philipp J. Heisenberg. “Gastrulation in Zebrafish.” <i>Fish Development and Genetics : The Zebrafish and Medaka Models</i>, edited by Vladimir Korzh and Zhiyuan Gong, vol. 2, World Scientific Publishing, 2004, pp. 39–86.","short":"F. Ulrich, C.-P.J. Heisenberg, in:, V. Korzh, Z. Gong (Eds.), Fish Development and Genetics : The Zebrafish and Medaka Models, World Scientific Publishing, 2004, pp. 39–86.","apa":"Ulrich, F., &#38; Heisenberg, C.-P. J. (2004). Gastrulation in zebrafish. In V. Korzh &#38; Z. Gong (Eds.), <i>Fish development and genetics : the zebrafish and medaka models</i> (Vol. 2, pp. 39–86). World Scientific Publishing.","ista":"Ulrich F, Heisenberg C-PJ. 2004.Gastrulation in zebrafish. In: Fish development and genetics : the zebrafish and medaka models. Molecular Aspects of Fish and Marine Biology, vol. 2, 39–86.","chicago":"Ulrich, Florian, and Carl-Philipp J Heisenberg. “Gastrulation in Zebrafish.” In <i>Fish Development and Genetics : The Zebrafish and Medaka Models</i>, edited by Vladimir Korzh and Zhiyuan Gong, 2:39–86. World Scientific Publishing, 2004.","ama":"Ulrich F, Heisenberg C-PJ. Gastrulation in zebrafish. In: Korzh V, Gong Z, eds. <i>Fish Development and Genetics : The Zebrafish and Medaka Models</i>. Vol 2. World Scientific Publishing; 2004:39-86.","ieee":"F. Ulrich and C.-P. J. Heisenberg, “Gastrulation in zebrafish,” in <i>Fish development and genetics : the zebrafish and medaka models</i>, vol. 2, V. Korzh and Z. Gong, Eds. World Scientific Publishing, 2004, pp. 39–86."},"oa_version":"None","author":[{"full_name":"Ulrich, Florian","first_name":"Florian","last_name":"Ulrich"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"alternative_title":["Molecular Aspects of Fish and Marine Biology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","month":"11","publisher":"World Scientific Publishing","date_published":"2004-11-01T00:00:00Z","language":[{"iso":"eng"}],"title":"Gastrulation in zebrafish","volume":2,"article_processing_charge":"No"},{"publication":"Current Biology","publist_id":"2788","intvolume":"        14","_id":"3595","type":"review","date_created":"2018-12-11T12:04:09Z","page":"R233 - R235","doi":"10.1016/j.cub.2004.02.054","status":"public","day":"01","year":"2004","issue":"6","month":"03","publication_status":"published","abstract":[{"lang":"eng","text":"Genome sizes vary enormously. This variation in DNA content correlates with effective population size, suggesting that deleterious additions to the genome can accumulate in small populations. On this view, the increased complexity of biological functions associated with large genomes partly reflects evolutionary degeneration."}],"title":"Genome size: Does bigger mean worse?","volume":14,"publisher":"Cell Press","date_published":"2004-03-01T00:00:00Z","citation":{"mla":"Charlesworth, Brian, and Nicholas H. Barton. “Genome Size: Does Bigger Mean Worse?” <i>Current Biology</i>, vol. 14, no. 6, Cell Press, 2004, pp. R233–35, doi:<a href=\"https://doi.org/10.1016/j.cub.2004.02.054\">10.1016/j.cub.2004.02.054</a>.","short":"B. Charlesworth, N.H. Barton, Current Biology 14 (2004) R233–R235.","ieee":"B. Charlesworth and N. H. Barton, “Genome size: Does bigger mean worse?,” <i>Current Biology</i>, vol. 14, no. 6. Cell Press, pp. R233–R235, 2004.","ama":"Charlesworth B, Barton NH. Genome size: Does bigger mean worse? <i>Current Biology</i>. 2004;14(6):R233-R235. doi:<a href=\"https://doi.org/10.1016/j.cub.2004.02.054\">10.1016/j.cub.2004.02.054</a>","ista":"Charlesworth B, Barton NH. 2004. Genome size: Does bigger mean worse? Current Biology. 14(6), R233–R235.","chicago":"Charlesworth, Brian, and Nicholas H Barton. “Genome Size: Does Bigger Mean Worse?” <i>Current Biology</i>. Cell Press, 2004. <a href=\"https://doi.org/10.1016/j.cub.2004.02.054\">https://doi.org/10.1016/j.cub.2004.02.054</a>.","apa":"Charlesworth, B., &#38; Barton, N. H. (2004). Genome size: Does bigger mean worse? <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2004.02.054\">https://doi.org/10.1016/j.cub.2004.02.054</a>"},"quality_controlled":0,"extern":1,"date_updated":"2019-04-26T07:22:31Z","author":[{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Nicholas Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}]},{"date_created":"2018-12-11T12:04:15Z","_id":"3614","type":"journal_article","doi":"10.1111/j.0014-3820.2004.tb01591.x","status":"public","page":"2111 - 2132","day":"01","year":"2004","publist_id":"2769","intvolume":"        58","publication":"Evolution; International Journal of Organic Evolution","extern":1,"quality_controlled":0,"date_updated":"2021-01-12T07:44:40Z","citation":{"ieee":"N. H. Barton and M. Turelli, “Effects of allele frequency changes on variance components under a general model of epistasis,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 58, no. 10. Wiley-Blackwell, pp. 2111–2132, 2004.","ista":"Barton NH, Turelli M. 2004. Effects of allele frequency changes on variance components under a general model of epistasis. Evolution; International Journal of Organic Evolution. 58(10), 2111–2132.","chicago":"Barton, Nicholas H, and Michael Turelli. “Effects of Allele Frequency Changes on Variance Components under a General Model of Epistasis.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell, 2004. <a href=\"https://doi.org/10.1111/j.0014-3820.2004.tb01591.x\">https://doi.org/10.1111/j.0014-3820.2004.tb01591.x</a>.","ama":"Barton NH, Turelli M. Effects of allele frequency changes on variance components under a general model of epistasis. <i>Evolution; International Journal of Organic Evolution</i>. 2004;58(10):2111-2132. doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2004.tb01591.x\">10.1111/j.0014-3820.2004.tb01591.x</a>","apa":"Barton, N. H., &#38; Turelli, M. (2004). Effects of allele frequency changes on variance components under a general model of epistasis. <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.0014-3820.2004.tb01591.x\">https://doi.org/10.1111/j.0014-3820.2004.tb01591.x</a>","short":"N.H. Barton, M. Turelli, Evolution; International Journal of Organic Evolution 58 (2004) 2111–2132.","mla":"Barton, Nicholas H., and Michael Turelli. “Effects of Allele Frequency Changes on Variance Components under a General Model of Epistasis.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 58, no. 10, Wiley-Blackwell, 2004, pp. 2111–32, doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2004.tb01591.x\">10.1111/j.0014-3820.2004.tb01591.x</a>."},"author":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","full_name":"Nicholas Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"}],"month":"10","publication_status":"published","abstract":[{"text":"We analyze the changes in the mean and variance components of a quantitative trait caused by changes in allele frequencies, concentrating on the effects of genetic drift. We use a general representation of epistasis and dominance that allows an arbitrary relation between genotype and phenotype for any number of diallelic loci. We assume initial and final Hardy-Weinberg and linkage equilibrium in our analyses of drift-induced changes. Random drift generates transient linkage disequilibria that cause correlations between allele frequency fluctuations at different loci. However, we show that these have negligible effects, at least for interactions among small numbers of loci. Our analyses are based on diffusion approximations that summarize the effects of drift in terms of F, the inbreeding coefficient, interpreted as the expected proportional decrease in heterozygosity at each locus. For haploids, the variance of the trait mean after a population bottleneck is var(Δ&amp;#x007a;̄) =inline imagewhere n is the number of loci contributing to the trait variance, VA(1)=VA is the additive genetic variance, and VA(k) is the kth-order additive epistatic variance. The expected additive genetic variance after the bottleneck, denoted (V*A), is closely related to var(Δ&amp;#x007a;̄); (V*A) (1 –F)inline imageThus, epistasis inflates the expected additive variance above VA(1 –F), the expectation under additivity. For haploids (and diploids without dominance), the expected value of every variance component is inflated by the existence of higher order interactions (e.g., third-order epistasis inflates (V*AA)). This is not true in general with diploidy, because dominance alone can reduce (V*A) below VA(1 –F) (e.g., when dominant alleles are rare). Without dominance, diploidy produces simple expressions: var(Δ&amp;#x007a;̄)=inline image=1 (2F) kVA(k) and (V*A) = (1 –F)inline imagek(2F)k-1VA(k) With dominance (and even without epistasis), var(Δ&amp;#x007a;̄)and (V*A) no longer depend solely on the variance components in the base population. For small F, the expected additive variance simplifies to (V*A)(1 –F) VA+ 4FVAA+2FVD+2FCAD, where CAD is a sum of two terms describing covariances between additive effects and dominance and additive × dominance interactions. Whether population bottlenecks lead to expected increases in additive variance depends primarily on the ratio of nonadditive to additive genetic variance in the base population, but dominance precludes simple predictions based solely on variance components. We illustrate these results using a model in which genotypic values are drawn at random, allowing extreme and erratic epistatic interactions. Although our analyses clarify the conditions under which drift is expected to increase VA, we question the evolutionary importance of such increases.","lang":"eng"}],"issue":"10","publisher":"Wiley-Blackwell","date_published":"2004-10-01T00:00:00Z","volume":58,"title":"Effects of allele frequency changes on variance components under a general model of epistasis"},{"abstract":[{"text":"We investigate three alternative selection-based scenarios proposed to maintain polygenic variation: pleiotropic balancing selection, G x E interactions (with spatial or temporal variation in allelic effects), and sex-dependent allelic effects. Each analysis assumes an additive polygenic trait with n diallelic loci under stabilizing selection. We allow loci to have different effects and consider equilibria at which the population mean departs from the stabilizing-selection optimum. Under weak selection, each model produces essentially identical, approximate allele-frequency dynamics. Variation is maintained under pleiotropic balancing selection only at loci for which the strength of balancing selection exceeds the effective strength of stabilizing selection. In addition, for all models, polymorphism requires that the population mean be close enough to the optimum that directional selection does not overwhelm balancing selection. This balance allows many simultaneously stable equilibria, and we explore their properties numerically. Both spatial and temporal G x E can maintain variation at loci for which the coefficient of variation (across environments) of the effect of a substitution exceeds a critical value greater than one. The critical value depends on the correlation between substitution effects at different loci. For large positive correlations (e.g., ρ2ij &gt; 3/4), even extreme fluctuations in allelic effects cannot maintain variation. Surprisingly, this constraint on correlations implies that sex-dependent allelic effects cannot maintain polygenic variation. We present numerical results that support our analytical approximations and discuss our results in connection to relevant data and alternative variance-maintaining mechanisms.","lang":"eng"}],"month":"02","publication_status":"published","issue":"2","publisher":"Genetics Society of America","date_published":"2004-02-01T00:00:00Z","title":"Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions","volume":166,"date_updated":"2021-01-12T07:44:41Z","extern":1,"quality_controlled":0,"citation":{"ieee":"M. Turelli and N. H. Barton, “Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions,” <i>Genetics</i>, vol. 166, no. 2. Genetics Society of America, pp. 1053–1079, 2004.","apa":"Turelli, M., &#38; Barton, N. H. (2004). Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.166.2.1053\">https://doi.org/10.1534/genetics.166.2.1053</a>","ama":"Turelli M, Barton NH. Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions. <i>Genetics</i>. 2004;166(2):1053-1079. doi:<a href=\"https://doi.org/10.1534/genetics.166.2.1053\">10.1534/genetics.166.2.1053</a>","chicago":"Turelli, Michael, and Nicholas H Barton. “Polygenic Variation Maintained by Balancing Selection: Pleiotropy, Sex-Dependent Allelic Effects and GxE Interactions.” <i>Genetics</i>. Genetics Society of America, 2004. <a href=\"https://doi.org/10.1534/genetics.166.2.1053\">https://doi.org/10.1534/genetics.166.2.1053</a>.","ista":"Turelli M, Barton NH. 2004. Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions. Genetics. 166(2), 1053–1079.","mla":"Turelli, Michael, and Nicholas H. Barton. “Polygenic Variation Maintained by Balancing Selection: Pleiotropy, Sex-Dependent Allelic Effects and GxE Interactions.” <i>Genetics</i>, vol. 166, no. 2, Genetics Society of America, 2004, pp. 1053–79, doi:<a href=\"https://doi.org/10.1534/genetics.166.2.1053\">10.1534/genetics.166.2.1053</a>.","short":"M. Turelli, N.H. Barton, Genetics 166 (2004) 1053–1079."},"author":[{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Nicholas Barton"}],"intvolume":"       166","publist_id":"2768","publication":"Genetics","date_created":"2018-12-11T12:04:15Z","_id":"3615","type":"journal_article","status":"public","doi":"10.1534/genetics.166.2.1053","page":"1053 - 1079","year":"2004","day":"01"},{"year":"2004","page":"R603 - R604","doi":"10.1016/j.cub.2004.07.037","day":"10","status":"public","type":"review","_id":"3616","date_created":"2018-12-11T12:04:16Z","publication":"Current Biology","intvolume":"        14","publist_id":"2767","author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Nicholas Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Barton, Nicholas H. “Speciation: Why, How, Where and When?” <i>Current Biology</i>, vol. 14, no. 15, Cell Press, 2004, pp. R603–04, doi:<a href=\"https://doi.org/10.1016/j.cub.2004.07.037\">10.1016/j.cub.2004.07.037</a>.","short":"N.H. Barton, Current Biology 14 (2004) R603–R604.","ieee":"N. H. Barton, “Speciation: Why, how, where and when?,” <i>Current Biology</i>, vol. 14, no. 15. Cell Press, pp. R603–R604, 2004.","apa":"Barton, N. H. (2004). Speciation: Why, how, where and when? <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2004.07.037\">https://doi.org/10.1016/j.cub.2004.07.037</a>","chicago":"Barton, Nicholas H. “Speciation: Why, How, Where and When?” <i>Current Biology</i>. Cell Press, 2004. <a href=\"https://doi.org/10.1016/j.cub.2004.07.037\">https://doi.org/10.1016/j.cub.2004.07.037</a>.","ista":"Barton NH. 2004. Speciation: Why, how, where and when? Current Biology. 14(15), R603–R604.","ama":"Barton NH. Speciation: Why, how, where and when? <i>Current Biology</i>. 2004;14(15):R603-R604. doi:<a href=\"https://doi.org/10.1016/j.cub.2004.07.037\">10.1016/j.cub.2004.07.037</a>"},"date_updated":"2019-04-26T07:22:31Z","extern":1,"quality_controlled":0,"title":"Speciation: Why, how, where and when?","volume":14,"date_published":"2004-08-10T00:00:00Z","publisher":"Cell Press","issue":"15","month":"08","publication_status":"published"},{"type":"journal_article","_id":"3617","date_created":"2018-12-11T12:04:16Z","day":"01","page":"1115 - 1131","doi":"10.1534/genetics.166.2.1115","year":"2004","status":"public","publication":"Genetics","publist_id":"2766","intvolume":"       166","citation":{"short":"N.H. Barton, A. Etheridge, Genetics 166 (2004) 1115–1131.","mla":"Barton, Nicholas H., and Alison Etheridge. “The Effect of Selection on Genealogies.” <i>Genetics</i>, vol. 166, no. 2, Genetics Society of America, 2004, pp. 1115–31, doi:<a href=\"https://doi.org/10.1534/genetics.166.2.1115\">10.1534/genetics.166.2.1115</a>.","ama":"Barton NH, Etheridge A. The effect of selection on genealogies. <i>Genetics</i>. 2004;166(2):1115-1131. doi:<a href=\"https://doi.org/10.1534/genetics.166.2.1115\">10.1534/genetics.166.2.1115</a>","chicago":"Barton, Nicholas H, and Alison Etheridge. “The Effect of Selection on Genealogies.” <i>Genetics</i>. Genetics Society of America, 2004. <a href=\"https://doi.org/10.1534/genetics.166.2.1115\">https://doi.org/10.1534/genetics.166.2.1115</a>.","ista":"Barton NH, Etheridge A. 2004. The effect of selection on genealogies. Genetics. 166(2), 1115–1131.","apa":"Barton, N. H., &#38; Etheridge, A. (2004). The effect of selection on genealogies. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.166.2.1115\">https://doi.org/10.1534/genetics.166.2.1115</a>","ieee":"N. H. Barton and A. Etheridge, “The effect of selection on genealogies,” <i>Genetics</i>, vol. 166, no. 2. Genetics Society of America, pp. 1115–1131, 2004."},"quality_controlled":0,"extern":1,"date_updated":"2021-01-12T07:44:41Z","author":[{"full_name":"Nicholas Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Etheridge, Alison M","last_name":"Etheridge","first_name":"Alison"}],"issue":"2","publication_status":"published","month":"02","abstract":[{"text":"The coalescent process can describe the effects of selection at linked loci only if selection is so strong that genotype frequencies evolve deterministically. Here, we develop methods proposed by Kaplan, Darden, and Hudson to find the effects of weak selection. We show that the overall effect is given by an extension to Price's equation: the change in properties such as moments of coalescence times is equal to the covariance between those properties and the fitness of the sample of genes. The distribution of coalescence times differs substantially between allelic classes, even in the absence of selection. However, the average coalescence time between randomly chosen genes is insensitive to the current allele frequency and is affected significantly by purifying selection only if deleterious mutations are common and selection is strong (i.e., the product of population size and selection coefficient, Ns &gt; 3). Balancing selection increases mean coalescence times, but the effect becomes large only when mutation rates between allelic classes are low and when selection is extremely strong. Our analysis supports previous simulations that show that selection has surprisingly little effect on genealogies. Moreover, small fluctuations in allele frequency due to random drift can greatly reduce any such effects. This will make it difficult to detect the action of selection from neutral variation alone.","lang":"eng"}],"title":"The effect of selection on genealogies","volume":166,"publisher":"Genetics Society of America","date_published":"2004-02-01T00:00:00Z"},{"abstract":[{"text":"Capturing images of documents using handheld digital cameras has a variety of applications in academia, research, knowledge management, retail, and office settings. The ultimate goal of such systems is to achieve image quality comparable to that currently achieved with flatbed scanners even for curved, warped, or curled pages. This can be achieved by high-accuracy 3D modeling of the page surface, followed by a &quot;flattening&quot; of the surface. A number of previous systems have either assumed only perspective distortions, or used techniques like structured lighting, shading, or side-imaging for obtaining 3D shape. This paper describes a system for handheld camera-based document capture using general purpose stereo vision methods followed by a new document dewarping technique. Examples of shape modeling and dewarping of book images is shown.","lang":"eng"}],"publication_status":"published","month":"01","title":"Document capture using stereo vision","date_published":"2004-01-01T00:00:00Z","publisher":"ACM","citation":{"ieee":"A. Ulges, C. Lampert, and T. Breuel, “Document capture using stereo vision,” presented at the DocEng: ACM Symposium on Document Engineering, 2004, pp. 198–200.","apa":"Ulges, A., Lampert, C., &#38; Breuel, T. (2004). Document capture using stereo vision (pp. 198–200). Presented at the DocEng: ACM Symposium on Document Engineering, ACM. <a href=\"https://doi.org/10.1145/1030397.1030434\">https://doi.org/10.1145/1030397.1030434</a>","chicago":"Ulges, Adrian, Christoph Lampert, and Thomas Breuel. “Document Capture Using Stereo Vision,” 198–200. ACM, 2004. <a href=\"https://doi.org/10.1145/1030397.1030434\">https://doi.org/10.1145/1030397.1030434</a>.","ista":"Ulges A, Lampert C, Breuel T. 2004. Document capture using stereo vision. DocEng: ACM Symposium on Document Engineering, 198–200.","ama":"Ulges A, Lampert C, Breuel T. Document capture using stereo vision. In: ACM; 2004:198-200. doi:<a href=\"https://doi.org/10.1145/1030397.1030434\">10.1145/1030397.1030434</a>","mla":"Ulges, Adrian, et al. <i>Document Capture Using Stereo Vision</i>. ACM, 2004, pp. 198–200, doi:<a href=\"https://doi.org/10.1145/1030397.1030434\">10.1145/1030397.1030434</a>.","short":"A. Ulges, C. Lampert, T. Breuel, in:, ACM, 2004, pp. 198–200."},"date_updated":"2021-01-12T07:48:58Z","quality_controlled":0,"extern":1,"author":[{"full_name":"Ulges, Adrian","first_name":"Adrian","last_name":"Ulges"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Christoph Lampert","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887"},{"full_name":"Breuel,Thomas M","last_name":"Breuel","first_name":"Thomas"}],"conference":{"name":"DocEng: ACM Symposium on Document Engineering"},"publist_id":"2679","type":"conference","_id":"3688","date_created":"2018-12-11T12:04:38Z","main_file_link":[{"url":"http://pub.ist.ac.at/~chl/papers/ulges-doceng2004.pdf","open_access":"0"}],"status":"public","doi":"10.1145/1030397.1030434","page":"198 - 200","year":"2004","day":"01"},{"author":[{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Peter Jonas"},{"full_name":"Bischofberger, Josef","last_name":"Bischofberger","first_name":"Josef"},{"full_name":"Fricker, Desdemona","first_name":"Desdemona","last_name":"Fricker"},{"full_name":"Miles, Richard","last_name":"Miles","first_name":"Richard"}],"citation":{"short":"P.M. Jonas, J. Bischofberger, D. Fricker, R. Miles, Trends in Neurosciences 27 (2004) 30–40.","mla":"Jonas, Peter M., et al. “Interneuron Diversity Series: Fast in, Fast out--Temporal and Spatial Signal Processing in Hippocampal Interneurons.” <i>Trends in Neurosciences</i>, vol. 27, no. 1, Elsevier, 2004, pp. 30–40, doi:<a href=\"https://doi.org/doi:10.1016/j.tins.2003.10.010\">doi:10.1016/j.tins.2003.10.010</a>.","ieee":"P. M. Jonas, J. Bischofberger, D. Fricker, and R. Miles, “Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons,” <i>Trends in Neurosciences</i>, vol. 27, no. 1. Elsevier, pp. 30–40, 2004.","ista":"Jonas PM, Bischofberger J, Fricker D, Miles R. 2004. Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons. Trends in Neurosciences. 27(1), 30–40.","chicago":"Jonas, Peter M, Josef Bischofberger, Desdemona Fricker, and Richard Miles. “Interneuron Diversity Series: Fast in, Fast out--Temporal and Spatial Signal Processing in Hippocampal Interneurons.” <i>Trends in Neurosciences</i>. Elsevier, 2004. <a href=\"https://doi.org/doi:10.1016/j.tins.2003.10.010\">https://doi.org/doi:10.1016/j.tins.2003.10.010</a>.","ama":"Jonas PM, Bischofberger J, Fricker D, Miles R. Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons. <i>Trends in Neurosciences</i>. 2004;27(1):30-40. doi:<a href=\"https://doi.org/doi:10.1016/j.tins.2003.10.010\">doi:10.1016/j.tins.2003.10.010</a>","apa":"Jonas, P. M., Bischofberger, J., Fricker, D., &#38; Miles, R. (2004). Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons. <i>Trends in Neurosciences</i>. Elsevier. <a href=\"https://doi.org/doi:10.1016/j.tins.2003.10.010\">https://doi.org/doi:10.1016/j.tins.2003.10.010</a>"},"date_updated":"2021-01-12T07:52:19Z","quality_controlled":0,"extern":1,"volume":27,"title":"Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons","publisher":"Elsevier","date_published":"2004-01-01T00:00:00Z","issue":"1","abstract":[{"text":"The operation of neuronal networks crucially depends on a fast time course of signaling in inhibitory interneurons. Synapses that excite interneurons generate fast currents, owing to the expression of glutamate receptors of specific subunit composition. Interneurons generate brief action potentials in response to transient synaptic activation and discharge repetitively at very high frequencies during sustained stimulation. The ability to generate short-duration action potentials at high frequencies depends on the expression of specific voltage-gated K+ channels. Factors facilitating fast action potential initiation following synaptic excitation include depolarized interneuron resting potential, subthreshold conductances and active dendrites. Finally, GABA release at interneuron output synapses is rapid and highly synchronized, leading to a faster inhibition in postsynaptic interneurons than in principal cells. Thus, the expression of distinct transmitter receptors and voltage-gated ion channels ensures that interneurons operate with high speed and temporal precision.","lang":"eng"}],"publication_status":"published","month":"01","day":"01","year":"2004","doi":"doi:10.1016/j.tins.2003.10.010","status":"public","page":"30 - 40","_id":"3805","type":"journal_article","date_created":"2018-12-11T12:05:16Z","publication":"Trends in Neurosciences","intvolume":"        27","publist_id":"2404"},{"date_created":"2018-12-11T12:05:17Z","oa":1,"type":"journal_article","_id":"3807","status":"public","day":"01","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664940/"}],"year":"2004","doi":"10.1113/jphysiol.2003.058842 ","page":"337 - 45","publist_id":"2403","intvolume":"       556","publication":"Journal of Physiology","extern":1,"quality_controlled":0,"date_updated":"2021-01-12T07:52:20Z","citation":{"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>.","short":"B. Kampa, J. Clements, P.M. Jonas, G. Stuart, Journal of Physiology 556 (2004) 337–45.","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>","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>","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.","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."},"author":[{"full_name":"Kampa, Bjorn M","first_name":"Bjorn","last_name":"Kampa"},{"first_name":"John","last_name":"Clements","full_name":"Clements, John"},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Peter Jonas"},{"full_name":"Stuart, Greg J","first_name":"Greg","last_name":"Stuart"}],"month":"01","publication_status":"published","abstract":[{"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.","lang":"eng"}],"issue":"Pt 2","date_published":"2004-01-01T00:00:00Z","publisher":"Wiley-Blackwell","title":"Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity","volume":556}]