[{"editor":[{"full_name":"Harris, Robin","first_name":"Robin","last_name":"Harris"},{"first_name":"John","last_name":"Graham","full_name":"Graham, John"},{"full_name":"Rickwood, David","last_name":"Rickwood","first_name":"David"}],"oa_version":"None","year":"2006","quality_controlled":"1","day":"27","place":"Chichester, UK","date_created":"2022-04-07T07:56:42Z","publisher":"Wiley","extern":"1","publication_identifier":{"eisbn":["9780470033487 "],"isbn":["9780470847589 "]},"type":"book_chapter","_id":"11119","title":"In Vitro Techniques","status":"public","author":[{"full_name":"Harris, J. Robin","first_name":"J. Robin","last_name":"Harris"},{"last_name":"Almouzni","first_name":"Geneviève","full_name":"Almouzni, Geneviève"},{"first_name":"Doris","last_name":"Kirschner","full_name":"Kirschner, Doris"},{"full_name":"Dimitrova, Daniela","last_name":"Dimitrova","first_name":"Daniela"},{"first_name":"Jeffrey A.","last_name":"Nickerson","full_name":"Nickerson, Jeffrey A."},{"first_name":"Jean","last_name":"Underwood","full_name":"Underwood, Jean"},{"first_name":"Stefan","last_name":"Wagner","full_name":"Wagner, Stefan"},{"full_name":"Korbei, Barbara","first_name":"Barbara","last_name":"Korbei"},{"full_name":"Foisner, Roland","first_name":"Roland","last_name":"Foisner"},{"full_name":"Walther, Tobias C.","last_name":"Walther","first_name":"Tobias C."},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"first_name":"Reiner","last_name":"Peters","full_name":"Peters, Reiner"},{"full_name":"Walev, Ivan","last_name":"Walev","first_name":"Ivan"},{"full_name":"de Kroon, Anton I. P. M.","first_name":"Anton I. P. M.","last_name":"de Kroon"},{"first_name":"Rutger W. H. M.","last_name":"Staffhorst","full_name":"Staffhorst, Rutger W. H. M."},{"full_name":"de Kruijff, Ben","last_name":"de Kruijff","first_name":"Ben"},{"first_name":"Koert N. J.","last_name":"Burger","full_name":"Burger, Koert N. J."},{"full_name":"Netto, Luis Eduardo Soares","last_name":"Netto","first_name":"Luis Eduardo Soares"},{"first_name":"Eric","last_name":"Bertrand","full_name":"Bertrand, Eric"},{"full_name":"Alimonti, Judie B.","last_name":"Alimonti","first_name":"Judie B."},{"last_name":"Greenberg","first_name":"Arnold H.","full_name":"Greenberg, Arnold H."},{"first_name":"Jinnan","last_name":"Xiao","full_name":"Xiao, Jinnan"},{"first_name":"Anuradha","last_name":"Pradhan","full_name":"Pradhan, Anuradha"},{"full_name":"Liu, Yuechueng","last_name":"Liu","first_name":"Yuechueng"},{"full_name":"Paiement, Jacques","last_name":"Paiement","first_name":"Jacques"},{"full_name":"Young, Robin","first_name":"Robin","last_name":"Young"},{"full_name":"Goñi, Félix M.","last_name":"Goñi","first_name":"Félix M."},{"first_name":"Ana-Victoria","last_name":"Villar","full_name":"Villar, Ana-Victoria"},{"full_name":"Contreras, F.-Xabier","first_name":"F.-Xabier","last_name":"Contreras"},{"first_name":"Alicia","last_name":"Alonso","full_name":"Alonso, Alicia"},{"last_name":"Peter","first_name":"Brian J.","full_name":"Peter, Brian J."},{"full_name":"Mills, Ian G.","first_name":"Ian G.","last_name":"Mills"},{"full_name":"Higgins, Matthew K.","first_name":"Matthew K.","last_name":"Higgins"},{"last_name":"Brown","first_name":"William J.","full_name":"Brown, William J."},{"full_name":"Chambers, K.","last_name":"Chambers","first_name":"K."},{"full_name":"Doody, A.","first_name":"A.","last_name":"Doody"},{"full_name":"Cheng, C. Yan","first_name":"C. Yan","last_name":"Cheng"},{"full_name":"Mruk, Dolores D.","last_name":"Mruk","first_name":"Dolores D."},{"last_name":"Yang","first_name":"Chunhong","full_name":"Yang, Chunhong"},{"full_name":"Kirchhoff, Helmut","last_name":"Kirchhoff","first_name":"Helmut"},{"full_name":"Haase, Winfried","first_name":"Winfried","last_name":"Haase"},{"first_name":"Stephanie","last_name":"Boggasch","full_name":"Boggasch, Stephanie"},{"last_name":"Paulsen","first_name":"Harald","full_name":"Paulsen, Harald"},{"last_name":"Benesova","first_name":"Julie","full_name":"Benesova, Julie"},{"last_name":"Liffers","first_name":"Sven-T.","full_name":"Liffers, Sven-T."},{"last_name":"Rögner","first_name":"Matthias","full_name":"Rögner, Matthias"},{"first_name":"Ya-sheng","last_name":"Gao","full_name":"Gao, Ya-sheng"},{"first_name":"Elizabeth","last_name":"Sztul","full_name":"Sztul, Elizabeth"},{"full_name":"Thiemann, Meinolf","first_name":"Meinolf","last_name":"Thiemann"},{"full_name":"Fahimi, H. Dariush","first_name":"H. Dariush","last_name":"Fahimi"},{"last_name":"Gniadecki","first_name":"Robert","full_name":"Gniadecki, Robert"},{"full_name":"Gajkowska, Barbara","first_name":"Barbara","last_name":"Gajkowska"},{"full_name":"Bane, Susan L.","last_name":"Bane","first_name":"Susan L."},{"full_name":"Hess, John F.","first_name":"John F.","last_name":"Hess"},{"full_name":"Voss, John C.","last_name":"Voss","first_name":"John C."},{"full_name":"Fitzgerald, Paul G.","last_name":"Fitzgerald","first_name":"Paul G."},{"full_name":"Hisanaga, Shin-ichi","last_name":"Hisanaga","first_name":"Shin-ichi"},{"full_name":"Sasaki, Takahiro","first_name":"Takahiro","last_name":"Sasaki"},{"full_name":"Uéda, Kenji","first_name":"Kenji","last_name":"Uéda"},{"last_name":"Town","first_name":"Terrence","full_name":"Town, Terrence"},{"full_name":"Tan, Jun","first_name":"Jun","last_name":"Tan"},{"full_name":"Milton, Nathaniel G. N.","first_name":"Nathaniel G. N.","last_name":"Milton"},{"first_name":"Richard","last_name":"Chi","full_name":"Chi, Richard"},{"last_name":"Keller","first_name":"Thomas C. S.","full_name":"Keller, Thomas C. S."},{"full_name":"Kriajevska, Marina","last_name":"Kriajevska","first_name":"Marina"},{"last_name":"Bronstein","first_name":"Igor","full_name":"Bronstein, Igor"},{"full_name":"Lukanidin, Eugene","last_name":"Lukanidin","first_name":"Eugene"},{"last_name":"Holmes","first_name":"David F.","full_name":"Holmes, David F."},{"full_name":"Kadler, Karl E.","first_name":"Karl E.","last_name":"Kadler"}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","language":[{"iso":"eng"}],"doi":"10.1002/0470033487.ch6","date_updated":"2022-07-18T08:57:08Z","page":"201-378","publication_status":"published","date_published":"2006-01-27T00:00:00Z","scopus_import":"1","publication":"Cell Biology Protocols","article_processing_charge":"No","month":"01","citation":{"short":"J.R. Harris, G. Almouzni, D. Kirschner, D. Dimitrova, J.A. Nickerson, J. Underwood, S. Wagner, B. Korbei, R. Foisner, T.C. Walther, M. Hetzer, R. Peters, I. Walev, A.I.P.M. de Kroon, R.W.H.M. Staffhorst, B. de Kruijff, K.N.J. Burger, L.E.S. Netto, E. Bertrand, J.B. Alimonti, A.H. Greenberg, J. Xiao, A. Pradhan, Y. Liu, J. Paiement, R. Young, F.M. Goñi, A.-V. Villar, F.-X. Contreras, A. Alonso, B.J. Peter, I.G. Mills, M.K. Higgins, W.J. Brown, K. Chambers, A. Doody, C.Y. Cheng, D.D. Mruk, C. Yang, H. Kirchhoff, W. Haase, S. Boggasch, H. Paulsen, J. Benesova, S.-T. Liffers, M. Rögner, Y. Gao, E. Sztul, M. Thiemann, H.D. Fahimi, R. Gniadecki, B. Gajkowska, S.L. Bane, J.F. Hess, J.C. Voss, P.G. Fitzgerald, S. Hisanaga, T. Sasaki, K. Uéda, T. Town, J. Tan, N.G.N. Milton, R. Chi, T.C.S. Keller, M. Kriajevska, I. Bronstein, E. Lukanidin, D.F. Holmes, K.E. Kadler, in:, R. Harris, J. Graham, D. Rickwood (Eds.), Cell Biology Protocols, Wiley, Chichester, UK, 2006, pp. 201–378.","ista":"Harris JR, Almouzni G, Kirschner D, Dimitrova D, Nickerson JA, Underwood J, Wagner S, Korbei B, Foisner R, Walther TC, Hetzer M, Peters R, Walev I, de Kroon AIPM, Staffhorst RWHM, de Kruijff B, Burger KNJ, Netto LES, Bertrand E, Alimonti JB, Greenberg AH, Xiao J, Pradhan A, Liu Y, Paiement J, Young R, Goñi FM, Villar A-V, Contreras F-X, Alonso A, Peter BJ, Mills IG, Higgins MK, Brown WJ, Chambers K, Doody A, Cheng CY, Mruk DD, Yang C, Kirchhoff H, Haase W, Boggasch S, Paulsen H, Benesova J, Liffers S-T, Rögner M, Gao Y, Sztul E, Thiemann M, Fahimi HD, Gniadecki R, Gajkowska B, Bane SL, Hess JF, Voss JC, Fitzgerald PG, Hisanaga S, Sasaki T, Uéda K, Town T, Tan J, Milton NGN, Chi R, Keller TCS, Kriajevska M, Bronstein I, Lukanidin E, Holmes DF, Kadler KE. 2006.In Vitro Techniques. In: Cell Biology Protocols. , 201–378.","apa":"Harris, J. R., Almouzni, G., Kirschner, D., Dimitrova, D., Nickerson, J. A., Underwood, J., … Kadler, K. E. (2006). In Vitro Techniques. In R. Harris, J. Graham, &#38; D. Rickwood (Eds.), <i>Cell Biology Protocols</i> (pp. 201–378). Chichester, UK: Wiley. <a href=\"https://doi.org/10.1002/0470033487.ch6\">https://doi.org/10.1002/0470033487.ch6</a>","chicago":"Harris, J. Robin, Geneviève Almouzni, Doris Kirschner, Daniela Dimitrova, Jeffrey A. Nickerson, Jean Underwood, Stefan Wagner, et al. “In Vitro Techniques.” In <i>Cell Biology Protocols</i>, edited by Robin Harris, John Graham, and David Rickwood, 201–378. Chichester, UK: Wiley, 2006. <a href=\"https://doi.org/10.1002/0470033487.ch6\">https://doi.org/10.1002/0470033487.ch6</a>.","ieee":"J. R. Harris <i>et al.</i>, “In Vitro Techniques,” in <i>Cell Biology Protocols</i>, R. Harris, J. Graham, and D. Rickwood, Eds. Chichester, UK: Wiley, 2006, pp. 201–378.","mla":"Harris, J. Robin, et al. “In Vitro Techniques.” <i>Cell Biology Protocols</i>, edited by Robin Harris et al., Wiley, 2006, pp. 201–378, doi:<a href=\"https://doi.org/10.1002/0470033487.ch6\">10.1002/0470033487.ch6</a>.","ama":"Harris JR, Almouzni G, Kirschner D, et al. In Vitro Techniques. In: Harris R, Graham J, Rickwood D, eds. <i>Cell Biology Protocols</i>. Chichester, UK: Wiley; 2006:201-378. doi:<a href=\"https://doi.org/10.1002/0470033487.ch6\">10.1002/0470033487.ch6</a>"}},{"month":"06","citation":{"mla":"Schanda, Paul, et al. “Speeding up Three-Dimensional Protein NMR Experiments to a Few Minutes.” <i>Journal of the American Chemical Society</i>, vol. 128, no. 28, American Chemical Society, 2006, pp. 9042–43, doi:<a href=\"https://doi.org/10.1021/ja062025p\">10.1021/ja062025p</a>.","ama":"Schanda P, Van Melckebeke H, Brutscher B. Speeding up three-dimensional protein NMR experiments to a few minutes. <i>Journal of the American Chemical Society</i>. 2006;128(28):9042-9043. doi:<a href=\"https://doi.org/10.1021/ja062025p\">10.1021/ja062025p</a>","short":"P. Schanda, H. Van Melckebeke, B. Brutscher, Journal of the American Chemical Society 128 (2006) 9042–9043.","ista":"Schanda P, Van Melckebeke H, Brutscher B. 2006. Speeding up three-dimensional protein NMR experiments to a few minutes. Journal of the American Chemical Society. 128(28), 9042–9043.","ieee":"P. Schanda, H. Van Melckebeke, and B. Brutscher, “Speeding up three-dimensional protein NMR experiments to a few minutes,” <i>Journal of the American Chemical Society</i>, vol. 128, no. 28. American Chemical Society, pp. 9042–9043, 2006.","chicago":"Schanda, Paul, Hélène Van Melckebeke, and Bernhard Brutscher. “Speeding up Three-Dimensional Protein NMR Experiments to a Few Minutes.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2006. <a href=\"https://doi.org/10.1021/ja062025p\">https://doi.org/10.1021/ja062025p</a>.","apa":"Schanda, P., Van Melckebeke, H., &#38; Brutscher, B. (2006). Speeding up three-dimensional protein NMR experiments to a few minutes. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja062025p\">https://doi.org/10.1021/ja062025p</a>"},"volume":128,"doi":"10.1021/ja062025p","page":"9042-9043","date_updated":"2021-01-12T08:19:37Z","publication_status":"published","date_published":"2006-06-21T00:00:00Z","publication":"Journal of the American Chemical Society","article_processing_charge":"No","title":"Speeding up three-dimensional protein NMR experiments to a few minutes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"full_name":"Van Melckebeke, Hélène","first_name":"Hélène","last_name":"Van Melckebeke"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"}],"status":"public","type":"journal_article","_id":"8488","abstract":[{"text":"We demonstrate for different protein samples that three-dimensional HNCO and HNCA correlation spectra may be recorded in a few minutes acquisition time using the band-selective excitation short-transient sequences presented here. This opens new perspectives for the NMR structural investigation of unstable protein samples and real-time site-resolved studies of protein kinetics.","lang":"eng"}],"intvolume":"       128","publication_identifier":{"issn":["0002-7863","1520-5126"]},"publisher":"American Chemical Society","extern":"1","issue":"28","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"date_created":"2020-09-18T10:13:36Z","oa_version":"None","quality_controlled":"1","year":"2006","day":"21","article_type":"original"},{"title":"HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains","status":"public","language":[{"iso":"eng"}],"author":[{"last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"},{"full_name":"Forge, Vincent","first_name":"Vincent","last_name":"Forge"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8489","type":"journal_article","volume":44,"month":"07","citation":{"ama":"Schanda P, Forge V, Brutscher B. HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains. <i>Magnetic Resonance in Chemistry</i>. 2006;44(S1):S177-S184. doi:<a href=\"https://doi.org/10.1002/mrc.1825\">10.1002/mrc.1825</a>","mla":"Schanda, Paul, et al. “HET-SOFAST NMR for Fast Detection of Structural Compactness and Heterogeneity along Polypeptide Chains.” <i>Magnetic Resonance in Chemistry</i>, vol. 44, no. S1, Wiley, 2006, pp. S177–84, doi:<a href=\"https://doi.org/10.1002/mrc.1825\">10.1002/mrc.1825</a>.","apa":"Schanda, P., Forge, V., &#38; Brutscher, B. (2006). HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains. <i>Magnetic Resonance in Chemistry</i>. Wiley. <a href=\"https://doi.org/10.1002/mrc.1825\">https://doi.org/10.1002/mrc.1825</a>","ieee":"P. Schanda, V. Forge, and B. Brutscher, “HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains,” <i>Magnetic Resonance in Chemistry</i>, vol. 44, no. S1. Wiley, pp. S177–S184, 2006.","chicago":"Schanda, Paul, Vincent Forge, and Bernhard Brutscher. “HET-SOFAST NMR for Fast Detection of Structural Compactness and Heterogeneity along Polypeptide Chains.” <i>Magnetic Resonance in Chemistry</i>. Wiley, 2006. <a href=\"https://doi.org/10.1002/mrc.1825\">https://doi.org/10.1002/mrc.1825</a>.","short":"P. Schanda, V. Forge, B. Brutscher, Magnetic Resonance in Chemistry 44 (2006) S177–S184.","ista":"Schanda P, Forge V, Brutscher B. 2006. HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains. Magnetic Resonance in Chemistry. 44(S1), S177–S184."},"date_published":"2006-07-06T00:00:00Z","publication_status":"published","article_processing_charge":"No","publication":"Magnetic Resonance in Chemistry","doi":"10.1002/mrc.1825","date_updated":"2021-01-12T08:19:37Z","page":"S177-S184","date_created":"2020-09-18T10:13:42Z","issue":"S1","article_type":"original","oa_version":"None","quality_controlled":"1","year":"2006","day":"06","publication_identifier":{"issn":["0749-1581","1097-458X"]},"intvolume":"        44","abstract":[{"lang":"eng","text":"Structure elucidation of proteins by either NMR or X‐ray crystallography often requires the screening of a large number of samples for promising protein constructs and optimum solution conditions. For large‐scale screening of protein samples in solution, robust methods are needed that allow a rapid assessment of the folding of a polypeptide under diverse sample conditions. Here we present HET‐SOFAST NMR, a highly sensitive new method for semi‐quantitative characterization of the structural compactness and heterogeneity of polypeptide chains in solution. On the basis of one‐dimensional 1H HET‐SOFAST NMR data, obtained on well‐folded, molten globular, partially‐ and completely unfolded proteins, we define empirical thresholds that can be used as quantitative benchmarks for protein compactness. For 15N‐enriched protein samples, two‐dimensional 1H‐15N HET‐SOFAST correlation spectra provide site‐specific information about the structural heterogeneity along the polypeptide chain."}],"publisher":"Wiley","extern":"1"},{"doi":"10.1016/j.jmr.2005.10.007","date_updated":"2021-01-12T08:19:38Z","page":"334-339","date_published":"2006-02-01T00:00:00Z","publication_status":"published","publication":"Journal of Magnetic Resonance","article_processing_charge":"No","month":"02","citation":{"ista":"Schanda P, Brutscher B. 2006. Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR. Journal of Magnetic Resonance. 178(2), 334–339.","short":"P. Schanda, B. Brutscher, Journal of Magnetic Resonance 178 (2006) 334–339.","chicago":"Schanda, Paul, and Bernhard Brutscher. “Hadamard Frequency-Encoded SOFAST-HMQC for Ultrafast Two-Dimensional Protein NMR.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.jmr.2005.10.007\">https://doi.org/10.1016/j.jmr.2005.10.007</a>.","ieee":"P. Schanda and B. Brutscher, “Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR,” <i>Journal of Magnetic Resonance</i>, vol. 178, no. 2. Elsevier, pp. 334–339, 2006.","apa":"Schanda, P., &#38; Brutscher, B. (2006). Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2005.10.007\">https://doi.org/10.1016/j.jmr.2005.10.007</a>","mla":"Schanda, Paul, and Bernhard Brutscher. “Hadamard Frequency-Encoded SOFAST-HMQC for Ultrafast Two-Dimensional Protein NMR.” <i>Journal of Magnetic Resonance</i>, vol. 178, no. 2, Elsevier, 2006, pp. 334–39, doi:<a href=\"https://doi.org/10.1016/j.jmr.2005.10.007\">10.1016/j.jmr.2005.10.007</a>.","ama":"Schanda P, Brutscher B. Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR. <i>Journal of Magnetic Resonance</i>. 2006;178(2):334-339. doi:<a href=\"https://doi.org/10.1016/j.jmr.2005.10.007\">10.1016/j.jmr.2005.10.007</a>"},"volume":178,"type":"journal_article","_id":"8490","title":"Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"last_name":"Brutscher","first_name":"Bernhard","full_name":"Brutscher, Bernhard"}],"language":[{"iso":"eng"}],"publisher":"Elsevier","extern":"1","abstract":[{"text":"We demonstrate the feasibility of recording 1H–15N correlation spectra of proteins in only one second of acquisition time. The experiment combines recently proposed SOFAST-HMQC with Hadamard-type 15N frequency encoding. This allows site-resolved real-time NMR studies of kinetic processes in proteins with an increased time resolution. The sensitivity of the experiment is sufficient to be applicable to a wide range of molecular systems available at millimolar concentration on a high magnetic field spectrometer.","lang":"eng"}],"intvolume":"       178","publication_identifier":{"issn":["1090-7807"]},"year":"2006","oa_version":"None","day":"01","article_type":"original","issue":"2","date_created":"2020-09-18T10:13:51Z","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"]},{"day":"01","oa_version":"None","quality_controlled":"1","year":"2006","article_type":"original","issue":"2","date_created":"2020-09-18T10:48:43Z","extern":"1","publisher":"American Institute of Mathematical Sciences (AIMS)","intvolume":"        15","publication_identifier":{"issn":["1553-5231"]},"type":"journal_article","_id":"8513","language":[{"iso":"eng"}],"author":[{"first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"},{"full_name":"Saprykina, Maria","first_name":"Maria","last_name":"Saprykina"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits","date_updated":"2021-01-12T08:19:48Z","page":"611-640","doi":"10.3934/dcds.2006.15.611","publication":"Discrete & Continuous Dynamical Systems - A","article_processing_charge":"No","date_published":"2006-05-01T00:00:00Z","publication_status":"published","citation":{"chicago":"Kaloshin, Vadim, and Maria Saprykina. “Generic 3-Dimensional Volume-Preserving Diffeomorphisms with Superexponential Growth of Number of Periodic Orbits.” <i>Discrete &#38; Continuous Dynamical Systems - A</i>. American Institute of Mathematical Sciences (AIMS), 2006. <a href=\"https://doi.org/10.3934/dcds.2006.15.611\">https://doi.org/10.3934/dcds.2006.15.611</a>.","ieee":"V. Kaloshin and M. Saprykina, “Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits,” <i>Discrete &#38; Continuous Dynamical Systems - A</i>, vol. 15, no. 2. American Institute of Mathematical Sciences (AIMS), pp. 611–640, 2006.","apa":"Kaloshin, V., &#38; Saprykina, M. (2006). Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits. <i>Discrete &#38; Continuous Dynamical Systems - A</i>. American Institute of Mathematical Sciences (AIMS). <a href=\"https://doi.org/10.3934/dcds.2006.15.611\">https://doi.org/10.3934/dcds.2006.15.611</a>","ista":"Kaloshin V, Saprykina M. 2006. Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits. Discrete &#38; Continuous Dynamical Systems - A. 15(2), 611–640.","short":"V. Kaloshin, M. Saprykina, Discrete &#38; Continuous Dynamical Systems - A 15 (2006) 611–640.","ama":"Kaloshin V, Saprykina M. Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits. <i>Discrete &#38; Continuous Dynamical Systems - A</i>. 2006;15(2):611-640. doi:<a href=\"https://doi.org/10.3934/dcds.2006.15.611\">10.3934/dcds.2006.15.611</a>","mla":"Kaloshin, Vadim, and Maria Saprykina. “Generic 3-Dimensional Volume-Preserving Diffeomorphisms with Superexponential Growth of Number of Periodic Orbits.” <i>Discrete &#38; Continuous Dynamical Systems - A</i>, vol. 15, no. 2, American Institute of Mathematical Sciences (AIMS), 2006, pp. 611–40, doi:<a href=\"https://doi.org/10.3934/dcds.2006.15.611\">10.3934/dcds.2006.15.611</a>."},"month":"05","volume":15},{"article_type":"original","year":"2006","oa_version":"None","quality_controlled":"1","day":"01","date_created":"2020-09-18T10:48:52Z","issue":"3","publisher":"Cambridge University Press","extern":"1","publication_identifier":{"issn":["0143-3857","1469-4417"]},"intvolume":"        26","abstract":[{"lang":"eng","text":"We study the extent to which the Hausdorff dimension of a compact subset of an infinite-dimensional Banach space is affected by a typical mapping into a finite-dimensional space. It is possible that the dimension drops under all such mappings, but the amount by which it typically drops is controlled by the ‘thickness exponent’ of the set, which was defined by Hunt and Kaloshin (Nonlinearity12 (1999), 1263–1275). More precisely, let $X$ be a compact subset of a Banach space $B$ with thickness exponent $\\tau$ and Hausdorff dimension $d$. Let $M$ be any subspace of the (locally) Lipschitz functions from $B$ to $\\mathbb{R}^{m}$ that contains the space of bounded linear functions. We prove that for almost every (in the sense of prevalence) function $f \\in M$, the Hausdorff dimension of $f(X)$ is at least $\\min\\{ m, d / (1 + \\tau) \\}$. We also prove an analogous result for a certain part of the dimension spectra of Borel probability measures supported on $X$. The factor $1 / (1 + \\tau)$ can be improved to $1 / (1 + \\tau / 2)$ if $B$ is a Hilbert space. Since dimension cannot increase under a (locally) Lipschitz function, these theorems become dimension preservation results when $\\tau = 0$. We conjecture that many of the attractors associated with the evolution equations of mathematical physics have thickness exponent zero. We also discuss the sharpness of our results in the case $\\tau > 0$."}],"_id":"8514","type":"journal_article","title":"The effect of projections on fractal sets and measures in Banach spaces","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","language":[{"iso":"eng"}],"author":[{"full_name":"OTT, WILLIAM","first_name":"WILLIAM","last_name":"OTT"},{"full_name":"HUNT, BRIAN","last_name":"HUNT","first_name":"BRIAN"},{"orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","last_name":"Kaloshin"}],"date_published":"2006-06-01T00:00:00Z","publication_status":"published","publication":"Ergodic Theory and Dynamical Systems","article_processing_charge":"No","doi":"10.1017/s0143385705000714","date_updated":"2021-01-12T08:19:48Z","page":"869-891","volume":26,"month":"06","citation":{"ama":"OTT W, HUNT B, Kaloshin V. The effect of projections on fractal sets and measures in Banach spaces. <i>Ergodic Theory and Dynamical Systems</i>. 2006;26(3):869-891. doi:<a href=\"https://doi.org/10.1017/s0143385705000714\">10.1017/s0143385705000714</a>","mla":"OTT, WILLIAM, et al. “The Effect of Projections on Fractal Sets and Measures in Banach Spaces.” <i>Ergodic Theory and Dynamical Systems</i>, vol. 26, no. 3, Cambridge University Press, 2006, pp. 869–91, doi:<a href=\"https://doi.org/10.1017/s0143385705000714\">10.1017/s0143385705000714</a>.","apa":"OTT, W., HUNT, B., &#38; Kaloshin, V. (2006). The effect of projections on fractal sets and measures in Banach spaces. <i>Ergodic Theory and Dynamical Systems</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/s0143385705000714\">https://doi.org/10.1017/s0143385705000714</a>","ieee":"W. OTT, B. HUNT, and V. Kaloshin, “The effect of projections on fractal sets and measures in Banach spaces,” <i>Ergodic Theory and Dynamical Systems</i>, vol. 26, no. 3. Cambridge University Press, pp. 869–891, 2006.","chicago":"OTT, WILLIAM, BRIAN HUNT, and Vadim Kaloshin. “The Effect of Projections on Fractal Sets and Measures in Banach Spaces.” <i>Ergodic Theory and Dynamical Systems</i>. Cambridge University Press, 2006. <a href=\"https://doi.org/10.1017/s0143385705000714\">https://doi.org/10.1017/s0143385705000714</a>.","short":"W. OTT, B. HUNT, V. Kaloshin, Ergodic Theory and Dynamical Systems 26 (2006) 869–891.","ista":"OTT W, HUNT B, Kaloshin V. 2006. The effect of projections on fractal sets and measures in Banach spaces. Ergodic Theory and Dynamical Systems. 26(3), 869–891."}},{"title":"Long time behaviour of periodic stochastic flows","author":[{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim"},{"first_name":"D.","last_name":"DOLGOPYAT","full_name":"DOLGOPYAT, D."},{"full_name":"KORALOV, L.","last_name":"KORALOV","first_name":"L."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","language":[{"iso":"eng"}],"_id":"8515","type":"conference","month":"03","citation":{"apa":"Kaloshin, V., DOLGOPYAT, D., &#38; KORALOV, L. (2006). Long time behaviour of periodic stochastic flows. In <i>XIVth International Congress on Mathematical Physics</i> (pp. 290–295). Lisbon, Portugal: World Scientific. <a href=\"https://doi.org/10.1142/9789812704016_0026\">https://doi.org/10.1142/9789812704016_0026</a>","chicago":"Kaloshin, Vadim, D. DOLGOPYAT, and L. KORALOV. “Long Time Behaviour of Periodic Stochastic Flows.” In <i>XIVth International Congress on Mathematical Physics</i>, 290–95. World Scientific, 2006. <a href=\"https://doi.org/10.1142/9789812704016_0026\">https://doi.org/10.1142/9789812704016_0026</a>.","ieee":"V. Kaloshin, D. DOLGOPYAT, and L. KORALOV, “Long time behaviour of periodic stochastic flows,” in <i>XIVth International Congress on Mathematical Physics</i>, Lisbon, Portugal, 2006, pp. 290–295.","ista":"Kaloshin V, DOLGOPYAT D, KORALOV L. 2006. Long time behaviour of periodic stochastic flows. XIVth International Congress on Mathematical Physics. International Congress on Mathematical Physics, 290–295.","short":"V. Kaloshin, D. DOLGOPYAT, L. KORALOV, in:, XIVth International Congress on Mathematical Physics, World Scientific, 2006, pp. 290–295.","ama":"Kaloshin V, DOLGOPYAT D, KORALOV L. Long time behaviour of periodic stochastic flows. In: <i>XIVth International Congress on Mathematical Physics</i>. World Scientific; 2006:290-295. doi:<a href=\"https://doi.org/10.1142/9789812704016_0026\">10.1142/9789812704016_0026</a>","mla":"Kaloshin, Vadim, et al. “Long Time Behaviour of Periodic Stochastic Flows.” <i>XIVth International Congress on Mathematical Physics</i>, World Scientific, 2006, pp. 290–95, doi:<a href=\"https://doi.org/10.1142/9789812704016_0026\">10.1142/9789812704016_0026</a>."},"publication_status":"published","date_published":"2006-03-01T00:00:00Z","publication":"XIVth International Congress on Mathematical Physics","article_processing_charge":"No","doi":"10.1142/9789812704016_0026","page":"290-295","date_updated":"2021-01-12T08:19:49Z","date_created":"2020-09-18T10:48:59Z","quality_controlled":"1","oa_version":"None","year":"2006","day":"01","publication_identifier":{"isbn":["9789812562012","9789812704016"]},"abstract":[{"lang":"eng","text":"We consider the evolution of a set carried by a space periodic incompressible stochastic flow in a Euclidean space. We\r\nreport on three main results obtained in [8, 9, 10] concerning long time behaviour for a typical realization of the stochastic flow. First, at time t most of the particles are at a distance of order √t away from the origin. Moreover, we prove a Central Limit Theorem for the evolution of a measure carried by the flow, which holds for almost every realization of the flow. Second, we show the existence of a zero measure full Hausdorff dimension set of points, which\r\nescape to infinity at a linear rate. Third, in the 2-dimensional case, we study the set of points visited by the original set by time t. Such a set, when scaled down by the factor of t, has a limiting non random shape."}],"conference":{"location":"Lisbon, Portugal","start_date":"2003-07-28","name":"International Congress on Mathematical Physics","end_date":"2003-08-02"},"publisher":"World Scientific","extern":"1"},{"abstract":[{"lang":"eng","text":"Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch - the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ∼1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene."}],"intvolume":"         4","extern":1,"publisher":"Public Library of Science","issue":"3","publist_id":"6794","date_created":"2018-12-11T11:48:51Z","day":"01","year":"2006","quality_controlled":0,"citation":{"ama":"Rogaev E, Moliaka Y, Malyarchuk B, et al. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. <i>PLoS Biology</i>. 2006;4(3):0403-0410. doi:<a href=\"https://doi.org/10.1371/journal.pbio.0040073\">10.1371/journal.pbio.0040073</a>","mla":"Rogaev, Evgeny, et al. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” <i>PLoS Biology</i>, vol. 4, no. 3, Public Library of Science, 2006, pp. 0403–10, doi:<a href=\"https://doi.org/10.1371/journal.pbio.0040073\">10.1371/journal.pbio.0040073</a>.","chicago":"Rogaev, Evgeny, Yuri Moliaka, Boris Malyarchuk, Fyodor Kondrashov, Miroslava Derenko, Ilya Chumakov, and Anastasia Grigorenko. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” <i>PLoS Biology</i>. Public Library of Science, 2006. <a href=\"https://doi.org/10.1371/journal.pbio.0040073\">https://doi.org/10.1371/journal.pbio.0040073</a>.","ieee":"E. Rogaev <i>et al.</i>, “Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius,” <i>PLoS Biology</i>, vol. 4, no. 3. Public Library of Science, pp. 0403–0410, 2006.","apa":"Rogaev, E., Moliaka, Y., Malyarchuk, B., Kondrashov, F., Derenko, M., Chumakov, I., &#38; Grigorenko, A. (2006). Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.0040073\">https://doi.org/10.1371/journal.pbio.0040073</a>","short":"E. Rogaev, Y. Moliaka, B. Malyarchuk, F. Kondrashov, M. Derenko, I. Chumakov, A. Grigorenko, PLoS Biology 4 (2006) 0403–0410.","ista":"Rogaev E, Moliaka Y, Malyarchuk B, Kondrashov F, Derenko M, Chumakov I, Grigorenko A. 2006. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 4(3), 0403–0410."},"month":"03","volume":4,"page":"0403 - 0410","date_updated":"2021-01-12T08:19:58Z","doi":"10.1371/journal.pbio.0040073","publication":"PLoS Biology","date_published":"2006-03-01T00:00:00Z","publication_status":"published","status":"public","author":[{"first_name":"Evgeny","last_name":"Rogaev","full_name":"Rogaev, Evgeny I"},{"last_name":"Moliaka","first_name":"Yuri","full_name":"Moliaka, Yuri K"},{"first_name":"Boris","last_name":"Malyarchuk","full_name":"Malyarchuk, Boris A"},{"orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Derenko","first_name":"Miroslava","full_name":"Derenko, Miroslava V"},{"full_name":"Chumakov, Ilya M","last_name":"Chumakov","first_name":"Ilya"},{"full_name":"Grigorenko, Anastasia P","first_name":"Anastasia","last_name":"Grigorenko"}],"title":"Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius","type":"journal_article","_id":"854","acknowledgement":"FAK is supported by the NSF Graduate Research Fellowship.\nWe thank the Natural History Museum, North-Eastern Research Center, Far Eastern Branch of the Russian Academy of Sciences for photographic material ofM. primigenius leg, V. A. Nikishina for artwork and technical support, Y.B. Yurov, G. Dvoryanchikov, N. Riazanskaya and T. Kolesnikova for technical support, K. Mehren and C. Gray for elephant specimens, and V. Y. Solovyev for help with artwork of animal images."},{"month":"10","citation":{"short":"F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, M. Kondrashova, Biology Direct 1 (2006).","ista":"Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. 2006. Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. Biology Direct. 1.","ieee":"F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, and M. Kondrashova, “Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation,” <i>Biology Direct</i>, vol. 1. BioMed Central, 2006.","chicago":"Kondrashov, Fyodor, Eugene Koonin, Igor Morgunov, Tatiana Finogenova, and Marie Kondrashova. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” <i>Biology Direct</i>. BioMed Central, 2006. <a href=\"https://doi.org/10.1186/1745-6150-1-31\">https://doi.org/10.1186/1745-6150-1-31</a>.","apa":"Kondrashov, F., Koonin, E., Morgunov, I., Finogenova, T., &#38; Kondrashova, M. (2006). Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-1-31\">https://doi.org/10.1186/1745-6150-1-31</a>","mla":"Kondrashov, Fyodor, et al. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” <i>Biology Direct</i>, vol. 1, BioMed Central, 2006, doi:<a href=\"https://doi.org/10.1186/1745-6150-1-31\">10.1186/1745-6150-1-31</a>.","ama":"Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. <i>Biology Direct</i>. 2006;1. doi:<a href=\"https://doi.org/10.1186/1745-6150-1-31\">10.1186/1745-6150-1-31</a>"},"volume":1,"doi":"10.1186/1745-6150-1-31","date_updated":"2021-01-12T08:20:31Z","publication_status":"published","date_published":"2006-10-23T00:00:00Z","publication":"Biology Direct","title":"Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation","status":"public","author":[{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"},{"first_name":"Eugene","last_name":"Koonin","full_name":"Koonin, Eugene V"},{"full_name":"Morgunov, Igor G","last_name":"Morgunov","first_name":"Igor"},{"first_name":"Tatiana","last_name":"Finogenova","full_name":"Finogenova, Tatiana V"},{"first_name":"Marie","last_name":"Kondrashova","full_name":"Kondrashova, Marie N"}],"type":"journal_article","acknowledgement":"The authors thank Alexey Kondrashov for suggesting the possibility of non- orthologous gene displacement in glyoxylate cycle specific enzymes and for critical reading of this manuscript. FAK is a National Science Foundation Graduate Fellow.","_id":"868","intvolume":"         1","abstract":[{"lang":"eng","text":"Background: The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in animal tissues has been reported. In order to clarify the status of the MS and ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic study. Results: Using sequence similarity searches, we identified MS genes in arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in the numerous sequenced genomes of placental mammals. The regions of the placental mammals' genomes expected to code for malate synthase, as determined by comparison of the gene orders in vertebrate genomes, show clear similarity to the opossum MS sequence but contain stop codons, indicating that the MS gene became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable in animals other than the nematodes that possess a bifunctional, fused ICL-MS gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal gene transfer events that probably went in both directions between several bacterial and eukaryotic lineages. The strongest evidence was obtained for the acquisition of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the corresponding operonic organization by the common ancestor of the nematodes. Conclusion: The distribution of the MS and ICL genes in animals suggests that either they encode alternative enzymes of the glyoxylate cycle that are not orthologous to the known MS and ICL or the animal MS acquired a new function that remains to be characterized. Regardless of the ultimate solution to this conundrum, the genes for the glyoxylate cycle enzymes present a remarkable variety of evolutionary events including unusual horizontal gene transfer from bacteria to animals."}],"publisher":"BioMed Central","extern":1,"publist_id":"6778","date_created":"2018-12-11T11:48:56Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":0,"year":"2006","day":"23"},{"day":"21","year":"2006","quality_controlled":0,"issue":"4","publist_id":"6779","date_created":"2018-12-11T11:48:56Z","extern":1,"publisher":"Elsevier","abstract":[{"text":"The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, and the rate of their evolution is used as a proxy for mutation rate. We subdivide all sites into four classes in terms of the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold synonymous sites and intron sites residing outside transposable elements. The distribution of the rate of evolution across all synonymous sites is trimodal. Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed by G, is ∼10% below that at such intron sites. In contrast, rate of evolution at postCpreG synonymous sites is ∼30% above that at such intron sites. Finally, synonymous and intron postC and preG sites evolve at similar rates. The relationship between the levels of polymorphism at the corresponding synonymous and intron sites is very similar to that between their rates of evolution. Within every class, synonymous sites are occupied by G or C much more often than intron sites, whose nucleotide composition is consistent with neutral mutation-drift equilibrium. These patterns suggest that synonymous sites are under weak selection in favor of G and C, with the average coefficient s∼0.25/Ne∼10-5, where Ne is the effective population size. Such selection decelerates evolution and reduces variability at sites with symmetric mutation, but has the opposite effects at sites where the favored nucleotides are more mutable. The amino-acid composition of proteins dictates that many synonymous sites are CpGprone, which causes them, on average, to evolve faster and to be more polymorphic than intron sites. An average genotype carries ∼107 suboptimal nucleotides at synonymous sites, implying synergistic epistasis in selection against them.","lang":"eng"}],"intvolume":"       240","type":"journal_article","_id":"869","acknowledgement":"This research was supported in part by the Intramural Research Program of the NIH, National Library of Medicine.","status":"public","author":[{"orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aleksey","last_name":"Ogurtsov","full_name":"Ogurtsov, Aleksey Yu"},{"first_name":"Alexey","last_name":"Kondrashov","full_name":"Kondrashov, Alexey S"}],"title":"Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites","date_updated":"2021-01-12T08:20:33Z","page":"616 - 626","doi":"10.1016/j.jtbi.2005.10.020","publication":"Journal of Theoretical Biology","date_published":"2006-06-21T00:00:00Z","publication_status":"published","citation":{"apa":"Kondrashov, F., Ogurtsov, A., &#38; Kondrashov, A. (2006). Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2005.10.020\">https://doi.org/10.1016/j.jtbi.2005.10.020</a>","chicago":"Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” <i>Journal of Theoretical Biology</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.jtbi.2005.10.020\">https://doi.org/10.1016/j.jtbi.2005.10.020</a>.","ieee":"F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites,” <i>Journal of Theoretical Biology</i>, vol. 240, no. 4. Elsevier, pp. 616–626, 2006.","short":"F. Kondrashov, A. Ogurtsov, A. Kondrashov, Journal of Theoretical Biology 240 (2006) 616–626.","ista":"Kondrashov F, Ogurtsov A, Kondrashov A. 2006. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. 240(4), 616–626.","ama":"Kondrashov F, Ogurtsov A, Kondrashov A. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. <i>Journal of Theoretical Biology</i>. 2006;240(4):616-626. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2005.10.020\">10.1016/j.jtbi.2005.10.020</a>","mla":"Kondrashov, Fyodor, et al. “Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” <i>Journal of Theoretical Biology</i>, vol. 240, no. 4, Elsevier, 2006, pp. 616–26, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2005.10.020\">10.1016/j.jtbi.2005.10.020</a>."},"month":"06","volume":240},{"date_created":"2018-12-11T11:48:57Z","publist_id":"6773","issue":"2","quality_controlled":0,"year":"2006","day":"21","intvolume":"       239","abstract":[{"text":"New genes commonly appear through complete or partial duplications of pre-existing genes. Duplications of long DNA segments are constantly produced by rare mutations, may become fixed in a population by selection or random drift, and are subject to divergent evolution of the paralogous sequences after fixation, although gene conversion can impede this process. New data shed some light on each of these processes. Mutations which involve duplications can occur through at least two different mechanisms, backward strand slippage during DNA replication and unequal crossing-over. The background rate of duplication of a complete gene in humans is 10-9-10-10 per generation, although many genes located within hot-spots of large-scale mutation are duplicated much more often. Many gene duplications affect fitness strongly, and are responsible, through gene dosage effects, for a number of genetic diseases. However, high levels of intrapopulation polymorphism caused by presence or absence of long, gene-containing DNA segments imply that some duplications are not under strong selection. The polymorphism to fixation ratios appear to be approximately the same for gene duplications and for presumably selectively neutral nucleotide substitutions, which, according to the McDonald-Kreitman test, is consistent with selective neutrality of duplications. However, this pattern can also be due to negative selection against most of segregating duplications and positive selection for at least some duplications which become fixed. Patterns in post-fixation evolution of duplicated genes do not easily reveal the causes of fixations. Many gene duplications which became fixed recently in a variety of organisms were positively selected because the increased expression of the corresponding genes was beneficial. The effects of gene dosage provide a unified framework for studying all phases of the life history of a gene duplication. Application of well-known methods of evolutionary genetics to accumulating data on new, polymorphic, and fixed duplication will enhance our understanding of the role of natural selection in the evolution by gene duplication.","lang":"eng"}],"publisher":"Elsevier","extern":1,"title":"Role of selection in fixation of gene duplications","status":"public","author":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"},{"full_name":"Kondrashov, Alexey S","first_name":"Alexey","last_name":"Kondrashov"}],"_id":"873","type":"journal_article","volume":239,"month":"03","citation":{"ama":"Kondrashov F, Kondrashov A. Role of selection in fixation of gene duplications. <i>Journal of Theoretical Biology</i>. 2006;239(2):141-151. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2005.08.033\">10.1016/j.jtbi.2005.08.033</a>","mla":"Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of Gene Duplications.” <i>Journal of Theoretical Biology</i>, vol. 239, no. 2, Elsevier, 2006, pp. 141–51, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2005.08.033\">10.1016/j.jtbi.2005.08.033</a>.","apa":"Kondrashov, F., &#38; Kondrashov, A. (2006). Role of selection in fixation of gene duplications. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2005.08.033\">https://doi.org/10.1016/j.jtbi.2005.08.033</a>","chicago":"Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of Gene Duplications.” <i>Journal of Theoretical Biology</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.jtbi.2005.08.033\">https://doi.org/10.1016/j.jtbi.2005.08.033</a>.","ieee":"F. Kondrashov and A. Kondrashov, “Role of selection in fixation of gene duplications,” <i>Journal of Theoretical Biology</i>, vol. 239, no. 2. Elsevier, pp. 141–151, 2006.","ista":"Kondrashov F, Kondrashov A. 2006. Role of selection in fixation of gene duplications. Journal of Theoretical Biology. 239(2), 141–151.","short":"F. Kondrashov, A. Kondrashov, Journal of Theoretical Biology 239 (2006) 141–151."},"date_published":"2006-03-21T00:00:00Z","publication_status":"published","publication":"Journal of Theoretical Biology","doi":"10.1016/j.jtbi.2005.08.033","page":"141 - 151","date_updated":"2021-01-12T08:20:47Z"},{"page":"625 - 635","date_updated":"2021-11-16T07:44:15Z","doi":"10.1016/j.cub.2006.02.061","article_processing_charge":"No","publication":"Current Biology","date_published":"2006-04-04T00:00:00Z","publication_status":"published","citation":{"apa":"Dudu, V., Bittig, T., Entchev, E., Kicheva, A., Julicher, F., &#38; González Gaitán, M. (2006). Postsynaptic mad signaling at the Drosophila neuromuscular junction. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2006.02.061\">https://doi.org/10.1016/j.cub.2006.02.061</a>","chicago":"Dudu, Veronika, Thomas Bittig, Eugeni Entchev, Anna Kicheva, Frank Julicher, and Marcos González Gaitán. “Postsynaptic Mad Signaling at the Drosophila Neuromuscular Junction.” <i>Current Biology</i>. Cell Press, 2006. <a href=\"https://doi.org/10.1016/j.cub.2006.02.061\">https://doi.org/10.1016/j.cub.2006.02.061</a>.","ieee":"V. Dudu, T. Bittig, E. Entchev, A. Kicheva, F. Julicher, and M. González Gaitán, “Postsynaptic mad signaling at the Drosophila neuromuscular junction,” <i>Current Biology</i>, vol. 16, no. 7. Cell Press, pp. 625–635, 2006.","short":"V. Dudu, T. Bittig, E. Entchev, A. Kicheva, F. Julicher, M. González Gaitán, Current Biology 16 (2006) 625–635.","ista":"Dudu V, Bittig T, Entchev E, Kicheva A, Julicher F, González Gaitán M. 2006. Postsynaptic mad signaling at the Drosophila neuromuscular junction. Current Biology. 16(7), 625–635.","ama":"Dudu V, Bittig T, Entchev E, Kicheva A, Julicher F, González Gaitán M. Postsynaptic mad signaling at the Drosophila neuromuscular junction. <i>Current Biology</i>. 2006;16(7):625-635. doi:<a href=\"https://doi.org/10.1016/j.cub.2006.02.061\">10.1016/j.cub.2006.02.061</a>","mla":"Dudu, Veronika, et al. “Postsynaptic Mad Signaling at the Drosophila Neuromuscular Junction.” <i>Current Biology</i>, vol. 16, no. 7, Cell Press, 2006, pp. 625–35, doi:<a href=\"https://doi.org/10.1016/j.cub.2006.02.061\">10.1016/j.cub.2006.02.061</a>."},"month":"04","volume":16,"type":"journal_article","_id":"1715","acknowledgement":"This work was supported by the Max Planck Society, HFSP, and Deutsche Forschungsgemeinschaft.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Dudu","first_name":"Veronika","full_name":"Dudu, Veronika"},{"full_name":"Bittig, Thomas","first_name":"Thomas","last_name":"Bittig"},{"last_name":"Entchev","first_name":"Eugeni","full_name":"Entchev, Eugeni"},{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna"},{"first_name":"Frank","last_name":"Julicher","full_name":"Julicher, Frank"},{"full_name":"González Gaitán, Marcos","last_name":"González Gaitán","first_name":"Marcos"}],"language":[{"iso":"eng"}],"status":"public","title":"Postsynaptic mad signaling at the Drosophila neuromuscular junction","extern":"1","publisher":"Cell Press","intvolume":"        16","abstract":[{"lang":"eng","text":"Background: Cell-to-cell communication at the synapse involves synaptic transmission as well as signaling mediated by growth factors, which provide developmental and plasticity cues. There is evidence that a retrograde, presynaptic transforming growth factor-β (TGF-β) signaling event regulates synapse development and function in Drosophila. Results: Here we show that a postsynaptic TGF-β signaling event occurs during larval development. The type I receptor Thick veins (Tkv) and the R-Smad transcription factor Mothers-against-dpp (Mad) are localized postsynaptically in the muscle. Furthermore, Mad phosphorylation occurs in regions facing the presynaptic active zones of neurotransmitter release within the postsynaptic subsynaptic reticulum (SSR). In order to monitor in real time the levels of TGF-β signaling in the synapse during synaptic transmission, we have established a FRAP assay to measure Mad nuclear import/export in the muscle. We show that Mad nuclear trafficking depends on stimulation of the muscle. Conclusions: Our data suggest a mechanism linking synaptic transmission and postsynaptic TGF-β signaling that may coordinate nerve-muscle development and function."}],"day":"04","year":"2006","oa_version":"None","issue":"7","publist_id":"5416","date_created":"2018-12-11T11:53:37Z","related_material":{"link":[{"url":"https://doi.org/10.1016/j.cub.2006.06.020","relation":"erratum"}]}},{"year":"2006","quality_controlled":0,"day":"15","publist_id":"5379","issue":"12","date_created":"2018-12-11T11:53:47Z","publisher":"Elsevier","extern":1,"abstract":[{"lang":"eng","text":"SiGe islands grown by deposition of 10 monolayers of Ge on Si(0 0 1) at 740 °C were investigated by using a combination of selective wet chemical etching and atomic force microscopy. The used etchant, a solution consisting of ammonium hydroxide and hydrogen peroxide, shows a high selectivity of Ge over SixGe1-x and is characterized by relatively slow etching rates for Si-rich alloys. By performing successive etching experiments on the same sample area, we are able to gain a deeper insight into the lateral displacement the islands undergo during post growth annealing."}],"intvolume":"       600","type":"journal_article","_id":"1745","title":"Investigating the lateral motion of SiGe islands by selective chemical etching","status":"public","author":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Georgios Katsaros"},{"full_name":"Rastelli, Armando","first_name":"Armando","last_name":"Rastelli"},{"first_name":"Mathieu","last_name":"Stoffel","full_name":"Stoffel, Mathieu"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"last_name":"Von Känel","first_name":"Hans","full_name":"Von Känel, Hans"},{"full_name":"Bittner, Alexander M","last_name":"Bittner","first_name":"Alexander"},{"first_name":"Jerry","last_name":"Tersoff","full_name":"Tersoff, Jerry"},{"last_name":"Denker","first_name":"Ulrich","full_name":"Denker, Ulrich"},{"full_name":"Schmidt, Oliver G","first_name":"Oliver","last_name":"Schmidt"},{"last_name":"Costantini","first_name":"Giovanni","full_name":"Costantini, Giovanni"},{"full_name":"Kern, Klaus","last_name":"Kern","first_name":"Klaus"}],"doi":"10.1016/j.susc.2006.04.027","page":"2608 - 2613","date_updated":"2021-01-12T06:52:56Z","publication_status":"published","date_published":"2006-06-15T00:00:00Z","publication":"Surface Science","month":"06","citation":{"ama":"Katsaros G, Rastelli A, Stoffel M, et al. Investigating the lateral motion of SiGe islands by selective chemical etching. <i>Surface Science</i>. 2006;600(12):2608-2613. doi:<a href=\"https://doi.org/10.1016/j.susc.2006.04.027\">10.1016/j.susc.2006.04.027</a>","mla":"Katsaros, Georgios, et al. “Investigating the Lateral Motion of SiGe Islands by Selective Chemical Etching.” <i>Surface Science</i>, vol. 600, no. 12, Elsevier, 2006, pp. 2608–13, doi:<a href=\"https://doi.org/10.1016/j.susc.2006.04.027\">10.1016/j.susc.2006.04.027</a>.","apa":"Katsaros, G., Rastelli, A., Stoffel, M., Isella, G., Von Känel, H., Bittner, A., … Kern, K. (2006). Investigating the lateral motion of SiGe islands by selective chemical etching. <i>Surface Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.susc.2006.04.027\">https://doi.org/10.1016/j.susc.2006.04.027</a>","ieee":"G. Katsaros <i>et al.</i>, “Investigating the lateral motion of SiGe islands by selective chemical etching,” <i>Surface Science</i>, vol. 600, no. 12. Elsevier, pp. 2608–2613, 2006.","chicago":"Katsaros, Georgios, Armando Rastelli, Mathieu Stoffel, Giovanni Isella, Hans Von Känel, Alexander Bittner, Jerry Tersoff, et al. “Investigating the Lateral Motion of SiGe Islands by Selective Chemical Etching.” <i>Surface Science</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.susc.2006.04.027\">https://doi.org/10.1016/j.susc.2006.04.027</a>.","ista":"Katsaros G, Rastelli A, Stoffel M, Isella G, Von Känel H, Bittner A, Tersoff J, Denker U, Schmidt O, Costantini G, Kern K. 2006. Investigating the lateral motion of SiGe islands by selective chemical etching. Surface Science. 600(12), 2608–2613.","short":"G. Katsaros, A. Rastelli, M. Stoffel, G. Isella, H. Von Känel, A. Bittner, J. Tersoff, U. Denker, O. Schmidt, G. Costantini, K. Kern, Surface Science 600 (2006) 2608–2613."},"volume":600},{"doi":"10.1103/PhysRevLett.96.226106","date_updated":"2021-01-12T06:52:56Z","publication_status":"published","date_published":"2006-01-01T00:00:00Z","publication":"Physical Review Letters","month":"01","citation":{"ama":"Costantini G, Rastelli A, Manzano C, et al. Interplay between thermodynamics and kinetics in the capping of InAs/GaAs (001) quantum dots. <i>Physical Review Letters</i>. 2006;96(22). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.96.226106\">10.1103/PhysRevLett.96.226106</a>","mla":"Costantini, Giovanni, et al. “Interplay between Thermodynamics and Kinetics in the Capping of InAs/GaAs (001) Quantum Dots.” <i>Physical Review Letters</i>, vol. 96, no. 22, American Physical Society, 2006, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.96.226106\">10.1103/PhysRevLett.96.226106</a>.","apa":"Costantini, G., Rastelli, A., Manzano, C., Acosta Diaz, P., Songmuang, R., Katsaros, G., … Kern, K. (2006). Interplay between thermodynamics and kinetics in the capping of InAs/GaAs (001) quantum dots. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.96.226106\">https://doi.org/10.1103/PhysRevLett.96.226106</a>","chicago":"Costantini, Giovanni, Armando Rastelli, Carlos Manzano, P Acosta Diaz, Rudeeson Songmuang, Georgios Katsaros, Oliver Schmidt, and Klaus Kern. “Interplay between Thermodynamics and Kinetics in the Capping of InAs/GaAs (001) Quantum Dots.” <i>Physical Review Letters</i>. American Physical Society, 2006. <a href=\"https://doi.org/10.1103/PhysRevLett.96.226106\">https://doi.org/10.1103/PhysRevLett.96.226106</a>.","ieee":"G. Costantini <i>et al.</i>, “Interplay between thermodynamics and kinetics in the capping of InAs/GaAs (001) quantum dots,” <i>Physical Review Letters</i>, vol. 96, no. 22. American Physical Society, 2006.","ista":"Costantini G, Rastelli A, Manzano C, Acosta Diaz P, Songmuang R, Katsaros G, Schmidt O, Kern K. 2006. Interplay between thermodynamics and kinetics in the capping of InAs/GaAs (001) quantum dots. Physical Review Letters. 96(22).","short":"G. Costantini, A. Rastelli, C. Manzano, P. Acosta Diaz, R. Songmuang, G. Katsaros, O. Schmidt, K. Kern, Physical Review Letters 96 (2006)."},"volume":96,"type":"journal_article","_id":"1746","title":"Interplay between thermodynamics and kinetics in the capping of InAs/GaAs (001) quantum dots","author":[{"full_name":"Costantini, Giovanni","last_name":"Costantini","first_name":"Giovanni"},{"first_name":"Armando","last_name":"Rastelli","full_name":"Rastelli, Armando"},{"full_name":"Manzano, Carlos","first_name":"Carlos","last_name":"Manzano"},{"last_name":"Acosta Diaz","first_name":"P","full_name":"Acosta-Diaz, P"},{"full_name":"Songmuang, Rudeeson","first_name":"Rudeeson","last_name":"Songmuang"},{"last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Georgios Katsaros"},{"first_name":"Oliver","last_name":"Schmidt","full_name":"Schmidt, Oliver G"},{"last_name":"Kern","first_name":"Klaus","full_name":"Kern, Klaus"}],"status":"public","publisher":"American Physical Society","extern":1,"intvolume":"        96","abstract":[{"text":"A microscopic picture for the GaAs overgrowth of self-organized InAs/GaAs(001) quantum dots is developed. Scanning tunneling microscopy measurements reveal two capping regimes: the first being characterized by a dot shrinking and a backward pyramid-to-dome shape transition. This regime is governed by fast dynamics resulting in island morphologies close to thermodynamic equilibrium. The second regime is marked by a true overgrowth and is controlled by kinetically limited surface diffusion processes. A simple model is developed to describe the observed structural changes which are rationalized in terms of energetic minimization driven by lattice mismatch and alloying.","lang":"eng"}],"quality_controlled":0,"year":"2006","day":"01","publist_id":"5378","issue":"22","date_created":"2018-12-11T11:53:47Z"},{"page":"1471 - 1476","date_updated":"2021-01-12T06:52:57Z","doi":"10.1016/j.mejo.2006.05.029","publication":"Microelectronics Journal","date_published":"2006-12-01T00:00:00Z","publication_status":"published","citation":{"ama":"Rastelli A, Stoffel M, Katsaros G, et al. Reading the footprints of strained islands. <i>Microelectronics Journal</i>. 2006;37(12):1471-1476. doi:<a href=\"https://doi.org/10.1016/j.mejo.2006.05.029\">10.1016/j.mejo.2006.05.029</a>","mla":"Rastelli, Armando, et al. “Reading the Footprints of Strained Islands.” <i>Microelectronics Journal</i>, vol. 37, no. 12, Elsevier, 2006, pp. 1471–76, doi:<a href=\"https://doi.org/10.1016/j.mejo.2006.05.029\">10.1016/j.mejo.2006.05.029</a>.","ieee":"A. Rastelli <i>et al.</i>, “Reading the footprints of strained islands,” <i>Microelectronics Journal</i>, vol. 37, no. 12. Elsevier, pp. 1471–1476, 2006.","chicago":"Rastelli, Armando, Mathieu Stoffel, Georgios Katsaros, Jerry Tersoff, Ulrich Denker, Tsvetelina Merdzhanova, Gouranga Kar, et al. “Reading the Footprints of Strained Islands.” <i>Microelectronics Journal</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.mejo.2006.05.029\">https://doi.org/10.1016/j.mejo.2006.05.029</a>.","apa":"Rastelli, A., Stoffel, M., Katsaros, G., Tersoff, J., Denker, U., Merdzhanova, T., … Schmidt, O. (2006). Reading the footprints of strained islands. <i>Microelectronics Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mejo.2006.05.029\">https://doi.org/10.1016/j.mejo.2006.05.029</a>","short":"A. Rastelli, M. Stoffel, G. Katsaros, J. Tersoff, U. Denker, T. Merdzhanova, G. Kar, G. Costantini, K. Kern, H. Von Känel, O. Schmidt, Microelectronics Journal 37 (2006) 1471–1476.","ista":"Rastelli A, Stoffel M, Katsaros G, Tersoff J, Denker U, Merdzhanova T, Kar G, Costantini G, Kern K, Von Känel H, Schmidt O. 2006. Reading the footprints of strained islands. Microelectronics Journal. 37(12), 1471–1476."},"month":"12","volume":37,"type":"journal_article","_id":"1747","acknowledgement":"This work was supported by the BMBF (03N8711)","status":"public","author":[{"full_name":"Rastelli, Armando","last_name":"Rastelli","first_name":"Armando"},{"full_name":"Stoffel, Mathieu","first_name":"Mathieu","last_name":"Stoffel"},{"last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Georgios Katsaros"},{"first_name":"Jerry","last_name":"Tersoff","full_name":"Tersoff, Jerry"},{"full_name":"Denker, Ulrich","first_name":"Ulrich","last_name":"Denker"},{"last_name":"Merdzhanova","first_name":"Tsvetelina","full_name":"Merdzhanova, Tsvetelina"},{"last_name":"Kar","first_name":"Gouranga","full_name":"Kar, Gouranga S"},{"full_name":"Costantini, Giovanni","last_name":"Costantini","first_name":"Giovanni"},{"full_name":"Kern, Klaus","last_name":"Kern","first_name":"Klaus"},{"last_name":"Von Känel","first_name":"Hans","full_name":"Von Känel, Hans"},{"first_name":"Oliver","last_name":"Schmidt","full_name":"Schmidt, Oliver G"}],"title":"Reading the footprints of strained islands","extern":1,"publisher":"Elsevier","abstract":[{"text":"We report on recent advances in the understanding of surface processes occurring during growth and post-growth annealing of strained islands which may find application as self-assembled quantum dots. We investigate the model system SiGe/Si(0 0 1) by a new approach based on &quot;reading the footprints&quot; which islands leave on the substrate during their growth and evolution. Such footprints consist of trenches carved in the Si substrate. We distinguish between surface footprints and footprints buried below the islands. The former allow us to discriminate islands which are in the process of growing from those which are shrinking. Islands with steep morphologies grow at the expense of smaller and shallower islands, consistent with the kinetics of anomalous coarsening. While shrinking, islands change their shape according to thermodynamic predictions. Buried footprints are investigated by removing the SiGe epilayer by means of selective wet chemical etching. Their reading shows that: (i) during post-growth annealing islands move laterally because of surface-mediated Si-Ge intermixing; (ii) a tree-ring structure of trenches is created by dislocated islands during their &quot;cyclic&quot; growth. This allows us to distinguish coherent from dislocated islands and to establish whether the latter are the result of island coalescence.","lang":"eng"}],"intvolume":"        37","day":"01","year":"2006","quality_controlled":0,"issue":"12","publist_id":"5377","date_created":"2018-12-11T11:53:47Z"},{"date_created":"2018-12-11T11:53:48Z","publist_id":"5376","issue":"25","quality_controlled":0,"year":"2006","day":"01","intvolume":"        89","abstract":[{"text":"The authors apply selective wet chemical etching and atomic force microscopy to reveal the three-dimensional shape of SiGeSi (001) islands after capping with Si. Although the &quot;self-assembled quantum dots&quot; remain practically unaffected by capping in the temperature range of 300-450 °C, significant morphological changes take place on the Si surface. At 450 °C, the morphology of the capping layer (Si matrix) evolves toward an intriguing semifacetted structure, which we call a &quot;ziggurat,&quot; giving the misleading impression of a stepped SiGe island shape.","lang":"eng"}],"publisher":"American Institute of Physics","extern":1,"title":"Evolution of buried semiconductor nanostructures and origin of stepped surface mounds during capping","status":"public","author":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Georgios Katsaros"},{"full_name":"Rastelli, Armando","first_name":"Armando","last_name":"Rastelli"},{"first_name":"Mathieu","last_name":"Stoffel","full_name":"Stoffel, Mathieu"},{"last_name":"Costantini","first_name":"Giovanni","full_name":"Costantini, Giovanni"},{"last_name":"Schmidt","first_name":"Oliver","full_name":"Schmidt, Oliver G"},{"full_name":"Kern, Klaus","first_name":"Klaus","last_name":"Kern"},{"full_name":"Tersoff, Jerry","last_name":"Tersoff","first_name":"Jerry"},{"full_name":"Müller, Elisabeth","first_name":"Elisabeth","last_name":"Müller"},{"first_name":"Hans","last_name":"Von Känel","full_name":"Von Känel, Hans"}],"_id":"1748","type":"journal_article","volume":89,"month":"01","citation":{"apa":"Katsaros, G., Rastelli, A., Stoffel, M., Costantini, G., Schmidt, O., Kern, K., … Von Känel, H. (2006). Evolution of buried semiconductor nanostructures and origin of stepped surface mounds during capping. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.2405876\">https://doi.org/10.1063/1.2405876</a>","ieee":"G. Katsaros <i>et al.</i>, “Evolution of buried semiconductor nanostructures and origin of stepped surface mounds during capping,” <i>Applied Physics Letters</i>, vol. 89, no. 25. American Institute of Physics, 2006.","chicago":"Katsaros, Georgios, Armando Rastelli, Mathieu Stoffel, Giovanni Costantini, Oliver Schmidt, Klaus Kern, Jerry Tersoff, Elisabeth Müller, and Hans Von Känel. “Evolution of Buried Semiconductor Nanostructures and Origin of Stepped Surface Mounds during Capping.” <i>Applied Physics Letters</i>. American Institute of Physics, 2006. <a href=\"https://doi.org/10.1063/1.2405876\">https://doi.org/10.1063/1.2405876</a>.","short":"G. Katsaros, A. Rastelli, M. Stoffel, G. Costantini, O. Schmidt, K. Kern, J. Tersoff, E. Müller, H. Von Känel, Applied Physics Letters 89 (2006).","ista":"Katsaros G, Rastelli A, Stoffel M, Costantini G, Schmidt O, Kern K, Tersoff J, Müller E, Von Känel H. 2006. Evolution of buried semiconductor nanostructures and origin of stepped surface mounds during capping. Applied Physics Letters. 89(25).","ama":"Katsaros G, Rastelli A, Stoffel M, et al. Evolution of buried semiconductor nanostructures and origin of stepped surface mounds during capping. <i>Applied Physics Letters</i>. 2006;89(25). doi:<a href=\"https://doi.org/10.1063/1.2405876\">10.1063/1.2405876</a>","mla":"Katsaros, Georgios, et al. “Evolution of Buried Semiconductor Nanostructures and Origin of Stepped Surface Mounds during Capping.” <i>Applied Physics Letters</i>, vol. 89, no. 25, American Institute of Physics, 2006, doi:<a href=\"https://doi.org/10.1063/1.2405876\">10.1063/1.2405876</a>."},"date_published":"2006-01-01T00:00:00Z","publication_status":"published","publication":"Applied Physics Letters","doi":"10.1063/1.2405876","date_updated":"2021-01-12T06:52:57Z"},{"_id":"1796","type":"journal_article","status":"public","author":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Sandra Siegert"},{"first_name":"Peter","last_name":"Schnierle","full_name":"Schnierle, Peter"},{"full_name":"Schnierle, Barbara S","first_name":"Barbara","last_name":"Schnierle"}],"title":"Novel anti-viral therapy: Drugs that block HIV entry at different target sites","publication":"Mini-Reviews in Medicinal Chemistry","publication_status":"published","date_published":"2006-05-01T00:00:00Z","date_updated":"2021-01-12T06:53:15Z","page":"557 - 562","doi":"10.2174/138955706776876267","volume":6,"citation":{"apa":"Siegert, S., Schnierle, P., &#38; Schnierle, B. (2006). Novel anti-viral therapy: Drugs that block HIV entry at different target sites. <i>Mini-Reviews in Medicinal Chemistry</i>. Bentham Science Publishers. <a href=\"https://doi.org/10.2174/138955706776876267\">https://doi.org/10.2174/138955706776876267</a>","ieee":"S. Siegert, P. Schnierle, and B. Schnierle, “Novel anti-viral therapy: Drugs that block HIV entry at different target sites,” <i>Mini-Reviews in Medicinal Chemistry</i>, vol. 6, no. 5. Bentham Science Publishers, pp. 557–562, 2006.","chicago":"Siegert, Sandra, Peter Schnierle, and Barbara Schnierle. “Novel Anti-Viral Therapy: Drugs That Block HIV Entry at Different Target Sites.” <i>Mini-Reviews in Medicinal Chemistry</i>. Bentham Science Publishers, 2006. <a href=\"https://doi.org/10.2174/138955706776876267\">https://doi.org/10.2174/138955706776876267</a>.","ista":"Siegert S, Schnierle P, Schnierle B. 2006. Novel anti-viral therapy: Drugs that block HIV entry at different target sites. Mini-Reviews in Medicinal Chemistry. 6(5), 557–562.","short":"S. Siegert, P. Schnierle, B. Schnierle, Mini-Reviews in Medicinal Chemistry 6 (2006) 557–562.","ama":"Siegert S, Schnierle P, Schnierle B. Novel anti-viral therapy: Drugs that block HIV entry at different target sites. <i>Mini-Reviews in Medicinal Chemistry</i>. 2006;6(5):557-562. doi:<a href=\"https://doi.org/10.2174/138955706776876267\">10.2174/138955706776876267</a>","mla":"Siegert, Sandra, et al. “Novel Anti-Viral Therapy: Drugs That Block HIV Entry at Different Target Sites.” <i>Mini-Reviews in Medicinal Chemistry</i>, vol. 6, no. 5, Bentham Science Publishers, 2006, pp. 557–62, doi:<a href=\"https://doi.org/10.2174/138955706776876267\">10.2174/138955706776876267</a>."},"month":"05","day":"01","quality_controlled":0,"year":"2006","date_created":"2018-12-11T11:54:03Z","issue":"5","publist_id":"5314","extern":1,"publisher":"Bentham Science Publishers","abstract":[{"lang":"eng","text":"Drugs that block the entry of human immunodeficiency virus type 1 (HIV-1) into host cells abrogate the establishment of a productive infection and should ideally diminish the chances of HIV-1 developing resistance. This review will give an overview of the mechanism by which the envelope glycoprotein mediates HIV-1 entry and will summarize current drug developments."}],"intvolume":"         6"},{"extern":1,"publisher":"American Association for the Advancement of Science","abstract":[{"text":"Respiratory complex I plays a central role in cellular energy production in bacteria and mitochondria. Its dysfunction is implicated in many human neurodegenerative diseases, as well as in aging. The crystal structure of the hydrophilic domain (peripheral arm) of complex I from Thermus thermophilus has been solved at 3.3 angstrom resolution. This subcomplex consists of eight subunits and contains all the redox centers of the enzyme, including nine iron-sulfur clusters. The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway, and of the distal cluster Nia, a possible antioxidant. The structure reveals new aspects of the mechanism and evolution of the enzyme. The terminal cluster N2 is coordinated, uniquely, by two consecutive cysteines. The novel subunit Nqo15 has a similar fold to the mitochondrial iron chaperone frataxin, and it may be involved in iron-sulfur cluster regeneration in the complex.\n","lang":"eng"}],"intvolume":"       311","day":"10","quality_controlled":0,"year":"2006","issue":"5766","publist_id":"5121","date_created":"2018-12-11T11:54:56Z","date_updated":"2021-01-12T06:54:22Z","page":"1430 - 1436","doi":"10.1126/science.1123809","publication":"Science","publication_status":"published","date_published":"2006-03-10T00:00:00Z","citation":{"mla":"Sazanov, Leonid A., and Philip Hinchliffe. “Structure of the Hydrophilic Domain of Respiratory Complex I from Thermus Thermophilus.” <i>Science</i>, vol. 311, no. 5766, American Association for the Advancement of Science, 2006, pp. 1430–36, doi:<a href=\"https://doi.org/10.1126/science.1123809\">10.1126/science.1123809</a>.","ama":"Sazanov LA, Hinchliffe P. Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. <i>Science</i>. 2006;311(5766):1430-1436. doi:<a href=\"https://doi.org/10.1126/science.1123809\">10.1126/science.1123809</a>","short":"L.A. Sazanov, P. Hinchliffe, Science 311 (2006) 1430–1436.","ista":"Sazanov LA, Hinchliffe P. 2006. Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Science. 311(5766), 1430–1436.","apa":"Sazanov, L. A., &#38; Hinchliffe, P. (2006). Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1123809\">https://doi.org/10.1126/science.1123809</a>","ieee":"L. A. Sazanov and P. Hinchliffe, “Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus,” <i>Science</i>, vol. 311, no. 5766. American Association for the Advancement of Science, pp. 1430–1436, 2006.","chicago":"Sazanov, Leonid A, and Philip Hinchliffe. “Structure of the Hydrophilic Domain of Respiratory Complex I from Thermus Thermophilus.” <i>Science</i>. American Association for the Advancement of Science, 2006. <a href=\"https://doi.org/10.1126/science.1123809\">https://doi.org/10.1126/science.1123809</a>."},"month":"03","volume":311,"type":"journal_article","_id":"1961","acknowledgement":"This work was funded by the Medical Research Council.","author":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Leonid Sazanov"},{"full_name":"Hinchliffe, Philip ","last_name":"Hinchliffe","first_name":"Philip"}],"status":"public","title":"Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus"},{"date_created":"2018-12-11T11:54:57Z","publist_id":"5120","issue":"14","quality_controlled":0,"year":"2006","day":"11","intvolume":"        45","abstract":[{"lang":"eng","text":"The hydrophilic domain (peripheral arm) of the proton-translocating NADH:quinone oxidoreductase (complex I) from the thermophilic organism Thermus thermophilus HB8 has been purified and characterized. The subcomplex is stable in sodium dodecyl sulfate up to 80 °C. Of nine iron-sulfur clusters, four to five (one or two binuclear and three tetranuclear) could be detected by EPR in the NADH-reduced enzyme. The preparation consists of eight different polypeptides. Seven of them have been positively identified by peptide mass mapping and N-terminal sequencing as known hydrophilic subunits of T. thermophilus complex I. The eighth polypeptide copurified with the subcomplex at all stages, is strongly associated with the other subunits, and is present in crystals of the subcomplex, used for X-ray data collection. Therefore, it has been identified as a novel complex I subunit and named Nqo15. It is encoded in a locus separate from the nqo operon, containing the 14 other known complex I genes. ORFs encoding Nqo15 homologues are present in the genomes of the closest relatives of T. thermophilus. Our data show that, contrary to previous assumptions, bacterial complex I can contain proteins in addition to a &quot;core&quot; complement of 14 subunits."}],"publisher":"ACS","extern":1,"title":"Identification of a novel subunit of respiratory complex I from Thermus thermophilus","author":[{"full_name":"Hinchliffe, Philip ","first_name":"Philip","last_name":"Hinchliffe"},{"full_name":"Carroll, Joe D","first_name":"Joe","last_name":"Carroll"},{"last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Leonid Sazanov"}],"status":"public","_id":"1966","type":"journal_article","volume":45,"month":"04","citation":{"ama":"Hinchliffe P, Carroll J, Sazanov LA. Identification of a novel subunit of respiratory complex I from Thermus thermophilus. <i>Biochemistry</i>. 2006;45(14):4413-4420. doi:<a href=\"https://doi.org/10.1021/bi0600998\">10.1021/bi0600998</a>","mla":"Hinchliffe, Philip, et al. “Identification of a Novel Subunit of Respiratory Complex I from Thermus Thermophilus.” <i>Biochemistry</i>, vol. 45, no. 14, ACS, 2006, pp. 4413–20, doi:<a href=\"https://doi.org/10.1021/bi0600998\">10.1021/bi0600998</a>.","chicago":"Hinchliffe, Philip, Joe Carroll, and Leonid A Sazanov. “Identification of a Novel Subunit of Respiratory Complex I from Thermus Thermophilus.” <i>Biochemistry</i>. ACS, 2006. <a href=\"https://doi.org/10.1021/bi0600998\">https://doi.org/10.1021/bi0600998</a>.","ieee":"P. Hinchliffe, J. Carroll, and L. A. Sazanov, “Identification of a novel subunit of respiratory complex I from Thermus thermophilus,” <i>Biochemistry</i>, vol. 45, no. 14. ACS, pp. 4413–4420, 2006.","apa":"Hinchliffe, P., Carroll, J., &#38; Sazanov, L. A. (2006). Identification of a novel subunit of respiratory complex I from Thermus thermophilus. <i>Biochemistry</i>. ACS. <a href=\"https://doi.org/10.1021/bi0600998\">https://doi.org/10.1021/bi0600998</a>","ista":"Hinchliffe P, Carroll J, Sazanov LA. 2006. Identification of a novel subunit of respiratory complex I from Thermus thermophilus. Biochemistry. 45(14), 4413–4420.","short":"P. Hinchliffe, J. Carroll, L.A. Sazanov, Biochemistry 45 (2006) 4413–4420."},"date_published":"2006-04-11T00:00:00Z","publication_status":"published","publication":"Biochemistry","doi":"10.1021/bi0600998","date_updated":"2021-01-12T06:54:23Z","page":"4413 - 4420"},{"month":"08","citation":{"apa":"Vicoso, B., &#38; Charlesworth, B. (2006). Evolution on the X chromosome: Unusual patterns and processes. <i>Nature Reviews Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrg1914\">https://doi.org/10.1038/nrg1914</a>","chicago":"Vicoso, Beatriz, and Brian Charlesworth. “Evolution on the X Chromosome: Unusual Patterns and Processes.” <i>Nature Reviews Genetics</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/nrg1914\">https://doi.org/10.1038/nrg1914</a>.","ieee":"B. Vicoso and B. Charlesworth, “Evolution on the X chromosome: Unusual patterns and processes,” <i>Nature Reviews Genetics</i>, vol. 7, no. 8. Nature Publishing Group, pp. 645–653, 2006.","ista":"Vicoso B, Charlesworth B. 2006. Evolution on the X chromosome: Unusual patterns and processes. Nature Reviews Genetics. 7(8), 645–653.","short":"B. Vicoso, B. Charlesworth, Nature Reviews Genetics 7 (2006) 645–653.","ama":"Vicoso B, Charlesworth B. Evolution on the X chromosome: Unusual patterns and processes. <i>Nature Reviews Genetics</i>. 2006;7(8):645-653. doi:<a href=\"https://doi.org/10.1038/nrg1914\">10.1038/nrg1914</a>","mla":"Vicoso, Beatriz, and Brian Charlesworth. “Evolution on the X Chromosome: Unusual Patterns and Processes.” <i>Nature Reviews Genetics</i>, vol. 7, no. 8, Nature Publishing Group, 2006, pp. 645–53, doi:<a href=\"https://doi.org/10.1038/nrg1914\">10.1038/nrg1914</a>."},"volume":7,"doi":"10.1038/nrg1914","date_updated":"2021-01-12T06:55:05Z","page":"645 - 653","date_published":"2006-08-01T00:00:00Z","publication_status":"published","publication":"Nature Reviews Genetics","title":"Evolution on the X chromosome: Unusual patterns and processes","status":"public","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Beatriz Vicoso","orcid":"0000-0002-4579-8306"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"}],"type":"journal_article","acknowledgement":"B.V. is supported by a postgraduate fellowship from the Fundação de Ciência e Tecnologia of Portugal, and B.C. by the Royal Society (UK)","_id":"2066","abstract":[{"text":"Although the X chromosome is usually similar to the autosomes in size and cytogenetic appearance, theoretical models predict that its hemizygosity in males may cause unusual patterns of evolution. The sequencing of several genomes has indeed revealed differences between the X chromosome and the autosomes in the rates of gene divergence, patterns of gene expression and rates of gene movement between chromosomes. A better understanding of these patterns should provide valuable information on the evolution of genes located on the X chromosome. It could also suggest solutions to more general problems in molecular evolution, such as detecting selection and estimating mutational effects on fitness","lang":"eng"}],"intvolume":"         7","publisher":"Nature Publishing Group","extern":1,"publist_id":"4973","issue":"8","date_created":"2018-12-11T11:55:31Z","year":"2006","quality_controlled":0,"day":"01"}]