[{"publisher":"American Chemical Society","author":[{"full_name":"Amero, Carlos","last_name":"Amero","first_name":"Carlos"},{"first_name":"Paul","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"},{"full_name":"Durá, M. Asunción","last_name":"Durá","first_name":"M. Asunción"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"last_name":"Marion","full_name":"Marion, Dominique","first_name":"Dominique"},{"first_name":"Bruno","full_name":"Franzetti, Bruno","last_name":"Franzetti"},{"last_name":"Brutscher","full_name":"Brutscher, Bernhard","first_name":"Bernhard"},{"full_name":"Boisbouvier, Jérôme","last_name":"Boisbouvier","first_name":"Jérôme"}],"extern":"1","abstract":[{"lang":"eng","text":"An optimized NMR experiment that combines the advantages of methyl-TROSY and SOFAST-HMQC has been developed. It allows the recording of high quality methyl 1H−13C correlation spectra of protein assemblies of several hundreds of kDa in a few seconds. The SOFAST-methyl-TROSY-based experiment offers completely new opportunities for the study of structural and dynamic changes occurring in molecular nanomachines while they perform their biological function in vitro."}],"publication_identifier":{"issn":["0002-7863","1520-5126"]},"page":"3448-3449","citation":{"ista":"Amero C, Schanda P, Durá MA, Ayala I, Marion D, Franzetti B, Brutscher B, Boisbouvier J. 2009. Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies. Journal of the American Chemical Society. 131(10), 3448–3449.","ama":"Amero C, Schanda P, Durá MA, et al. Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies. <i>Journal of the American Chemical Society</i>. 2009;131(10):3448-3449. doi:<a href=\"https://doi.org/10.1021/ja809880p\">10.1021/ja809880p</a>","short":"C. Amero, P. Schanda, M.A. Durá, I. Ayala, D. Marion, B. Franzetti, B. Brutscher, J. Boisbouvier, Journal of the American Chemical Society 131 (2009) 3448–3449.","ieee":"C. Amero <i>et al.</i>, “Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies,” <i>Journal of the American Chemical Society</i>, vol. 131, no. 10. American Chemical Society, pp. 3448–3449, 2009.","mla":"Amero, Carlos, et al. “Fast Two-Dimensional NMR Spectroscopy of High Molecular Weight Protein Assemblies.” <i>Journal of the American Chemical Society</i>, vol. 131, no. 10, American Chemical Society, 2009, pp. 3448–49, doi:<a href=\"https://doi.org/10.1021/ja809880p\">10.1021/ja809880p</a>.","apa":"Amero, C., Schanda, P., Durá, M. A., Ayala, I., Marion, D., Franzetti, B., … Boisbouvier, J. (2009). Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja809880p\">https://doi.org/10.1021/ja809880p</a>","chicago":"Amero, Carlos, Paul Schanda, M. Asunción Durá, Isabel Ayala, Dominique Marion, Bruno Franzetti, Bernhard Brutscher, and Jérôme Boisbouvier. “Fast Two-Dimensional NMR Spectroscopy of High Molecular Weight Protein Assemblies.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2009. <a href=\"https://doi.org/10.1021/ja809880p\">https://doi.org/10.1021/ja809880p</a>."},"status":"public","publication":"Journal of the American Chemical Society","intvolume":"       131","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"10","doi":"10.1021/ja809880p","quality_controlled":"1","volume":131,"date_published":"2009-02-25T00:00:00Z","month":"02","year":"2009","date_created":"2020-09-18T10:12:01Z","title":"Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies","article_type":"original","publication_status":"published","type":"journal_article","date_updated":"2021-01-12T08:19:32Z","language":[{"iso":"eng"}],"oa_version":"None","day":"25","_id":"8477","article_processing_charge":"No"},{"article_type":"original","title":"Direct observation of the dynamic process underlying allosteric signal transmission","date_created":"2020-09-18T10:12:14Z","year":"2009","month":"02","date_published":"2009-02-09T00:00:00Z","article_processing_charge":"No","day":"09","_id":"8478","oa_version":"None","language":[{"iso":"eng"}],"type":"journal_article","date_updated":"2021-01-12T08:19:33Z","publication_status":"published","citation":{"chicago":"Brüschweiler, Sven, Paul Schanda, Karin Kloiber, Bernhard Brutscher, Georg Kontaxis, Robert Konrat, and Martin Tollinger. “Direct Observation of the Dynamic Process Underlying Allosteric Signal Transmission.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2009. <a href=\"https://doi.org/10.1021/ja809947w\">https://doi.org/10.1021/ja809947w</a>.","mla":"Brüschweiler, Sven, et al. “Direct Observation of the Dynamic Process Underlying Allosteric Signal Transmission.” <i>Journal of the American Chemical Society</i>, vol. 131, no. 8, American Chemical Society, 2009, pp. 3063–68, doi:<a href=\"https://doi.org/10.1021/ja809947w\">10.1021/ja809947w</a>.","apa":"Brüschweiler, S., Schanda, P., Kloiber, K., Brutscher, B., Kontaxis, G., Konrat, R., &#38; Tollinger, M. (2009). Direct observation of the dynamic process underlying allosteric signal transmission. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja809947w\">https://doi.org/10.1021/ja809947w</a>","ieee":"S. Brüschweiler <i>et al.</i>, “Direct observation of the dynamic process underlying allosteric signal transmission,” <i>Journal of the American Chemical Society</i>, vol. 131, no. 8. American Chemical Society, pp. 3063–3068, 2009.","short":"S. Brüschweiler, P. Schanda, K. Kloiber, B. Brutscher, G. Kontaxis, R. Konrat, M. Tollinger, Journal of the American Chemical Society 131 (2009) 3063–3068.","ista":"Brüschweiler S, Schanda P, Kloiber K, Brutscher B, Kontaxis G, Konrat R, Tollinger M. 2009. Direct observation of the dynamic process underlying allosteric signal transmission. Journal of the American Chemical Society. 131(8), 3063–3068.","ama":"Brüschweiler S, Schanda P, Kloiber K, et al. Direct observation of the dynamic process underlying allosteric signal transmission. <i>Journal of the American Chemical Society</i>. 2009;131(8):3063-3068. doi:<a href=\"https://doi.org/10.1021/ja809947w\">10.1021/ja809947w</a>"},"page":"3063-3068","publication_identifier":{"issn":["0002-7863","1520-5126"]},"abstract":[{"lang":"eng","text":"Allosteric regulation is an effective mechanism of control in biological processes. In allosteric proteins a signal originating at one site in the molecule is communicated through the protein structure to trigger a specific response at a remote site. Using NMR relaxation dispersion techniques we directly observe the dynamic process through which the KIX domain of CREB binding protein communicates allosteric information between binding sites. KIX mediates cooperativity between pairs of transcription factors through binding to two distinct interaction surfaces in an allosteric manner. We show that binding the activation domain of the mixed lineage leukemia (MLL) transcription factor to KIX induces a redistribution of the relative populations of KIX conformations toward a high-energy state in which the allosterically activated second binding site is already preformed, consistent with the Monod−Wyman−Changeux (WMC) model of allostery. The structural rearrangement process that links the two conformers and by which allosteric information is communicated occurs with a time constant of 3 ms at 27 °C. Our dynamic NMR data reveal that an evolutionarily conserved network of hydrophobic amino acids constitutes the pathway through which information is transmitted."}],"extern":"1","author":[{"first_name":"Sven","last_name":"Brüschweiler","full_name":"Brüschweiler, Sven"},{"first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"},{"full_name":"Kloiber, Karin","last_name":"Kloiber","first_name":"Karin"},{"first_name":"Bernhard","last_name":"Brutscher","full_name":"Brutscher, Bernhard"},{"first_name":"Georg","last_name":"Kontaxis","full_name":"Kontaxis, Georg"},{"first_name":"Robert","last_name":"Konrat","full_name":"Konrat, Robert"},{"full_name":"Tollinger, Martin","last_name":"Tollinger","first_name":"Martin"}],"publisher":"American Chemical Society","quality_controlled":"1","doi":"10.1021/ja809947w","volume":131,"issue":"8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       131","publication":"Journal of the American Chemical Society","status":"public"},{"year":"2009","month":"01","date_published":"2009-01-01T00:00:00Z","article_type":"original","title":"An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates","date_created":"2020-09-18T10:12:20Z","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:19:33Z","type":"journal_article","publication_status":"published","article_processing_charge":"No","_id":"8479","day":"01","oa_version":"None","abstract":[{"lang":"eng","text":"Multidimensional NMR spectroscopy is a well-established technique for the characterization of structure and fast-time-scale dynamics of highly populated ground states of biological macromolecules. The investigation of short-lived excited states that are important for molecular folding, misfolding and function, however, remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time kinetic NMR methods allow direct observation of conformational or chemical changes by following peak positions and intensities in a series of spectra recorded during a kinetic event. Because standard multidimensional NMR methods required to yield sufficient atom-resolution are intrinsically time-consuming, many interesting phenomena are excluded from real-time NMR analysis. Recently, spatially encoded ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D NMR experiment within a single transient. In addition, when combined with the SOFAST technique, such ultrafast experiments can be repeated at high rates. One of the problems detected for such ultrafast protein NMR experiments is related to the heteronuclear decoupling during detection with interferences between the pulses and the oscillatory magnetic field gradients arising in this scheme. Here we present a method for improved ultrafast data acquisition yielding higher signal to noise and sharper lines in single-scan 2D NMR spectra. In combination with a fast-mixing device, the recording of 1H–15N correlation spectra with repetition rates of up to a few Hertz becomes feasible, enabling real-time studies of protein kinetics occurring on time scales down to a few seconds."}],"extern":"1","publisher":"Springer Nature","author":[{"full_name":"Gal, Maayan","last_name":"Gal","first_name":"Maayan"},{"last_name":"Kern","full_name":"Kern, Thomas","first_name":"Thomas"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul"},{"first_name":"Lucio","last_name":"Frydman","full_name":"Frydman, Lucio"},{"last_name":"Brutscher","full_name":"Brutscher, Bernhard","first_name":"Bernhard"}],"page":"1-10","citation":{"ieee":"M. Gal, T. Kern, P. Schanda, L. Frydman, and B. Brutscher, “An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates,” <i>Journal of Biomolecular NMR</i>, vol. 43. Springer Nature, pp. 1–10, 2009.","short":"M. Gal, T. Kern, P. Schanda, L. Frydman, B. Brutscher, Journal of Biomolecular NMR 43 (2009) 1–10.","ama":"Gal M, Kern T, Schanda P, Frydman L, Brutscher B. An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates. <i>Journal of Biomolecular NMR</i>. 2009;43:1-10. doi:<a href=\"https://doi.org/10.1007/s10858-008-9284-9\">10.1007/s10858-008-9284-9</a>","ista":"Gal M, Kern T, Schanda P, Frydman L, Brutscher B. 2009. An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates. Journal of Biomolecular NMR. 43, 1–10.","chicago":"Gal, Maayan, Thomas Kern, Paul Schanda, Lucio Frydman, and Bernhard Brutscher. “An Improved Ultrafast 2D NMR Experiment: Towards Atom-Resolved Real-Time Studies of Protein Kinetics at Multi-Hz Rates.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2009. <a href=\"https://doi.org/10.1007/s10858-008-9284-9\">https://doi.org/10.1007/s10858-008-9284-9</a>.","mla":"Gal, Maayan, et al. “An Improved Ultrafast 2D NMR Experiment: Towards Atom-Resolved Real-Time Studies of Protein Kinetics at Multi-Hz Rates.” <i>Journal of Biomolecular NMR</i>, vol. 43, Springer Nature, 2009, pp. 1–10, doi:<a href=\"https://doi.org/10.1007/s10858-008-9284-9\">10.1007/s10858-008-9284-9</a>.","apa":"Gal, M., Kern, T., Schanda, P., Frydman, L., &#38; Brutscher, B. (2009). An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-008-9284-9\">https://doi.org/10.1007/s10858-008-9284-9</a>"},"publication_identifier":{"issn":["0925-2738","1573-5001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        43","keyword":["Spectroscopy","Biochemistry"],"publication":"Journal of Biomolecular NMR","status":"public","doi":"10.1007/s10858-008-9284-9","volume":43,"quality_controlled":"1"},{"month":"12","date_published":"2009-12-01T00:00:00Z","year":"2009","date_created":"2020-09-18T10:48:03Z","title":"Conservative homoclinic bifurcations and some applications","article_type":"original","publication_status":"published","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:19:46Z","type":"journal_article","_id":"8508","day":"01","oa_version":"None","article_processing_charge":"No","extern":"1","publisher":"Springer Nature","author":[{"full_name":"Gorodetski, Anton","last_name":"Gorodetski","first_name":"Anton"},{"first_name":"Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","full_name":"Kaloshin, Vadim"}],"abstract":[{"text":"We study generic unfoldings of homoclinic tangencies of two-dimensional area-preserving diffeomorphisms (conservative New house phenomena) and show that they give rise to invariant hyperbolic sets of arbitrarily large Hausdorff dimension. As applications, we discuss the size of the stochastic layer of a standard map and the Hausdorff dimension of invariant hyperbolic sets for certain restricted three-body problems. We avoid involved technical details and only concentrate on the ideas of the proof of the presented results.","lang":"eng"}],"page":"76-90","citation":{"ieee":"A. Gorodetski and V. Kaloshin, “Conservative homoclinic bifurcations and some applications,” <i>Proceedings of the Steklov Institute of Mathematics</i>, vol. 267, no. 1. Springer Nature, pp. 76–90, 2009.","short":"A. Gorodetski, V. Kaloshin, Proceedings of the Steklov Institute of Mathematics 267 (2009) 76–90.","ista":"Gorodetski A, Kaloshin V. 2009. Conservative homoclinic bifurcations and some applications. Proceedings of the Steklov Institute of Mathematics. 267(1), 76–90.","ama":"Gorodetski A, Kaloshin V. Conservative homoclinic bifurcations and some applications. <i>Proceedings of the Steklov Institute of Mathematics</i>. 2009;267(1):76-90. doi:<a href=\"https://doi.org/10.1134/s0081543809040063\">10.1134/s0081543809040063</a>","chicago":"Gorodetski, Anton, and Vadim Kaloshin. “Conservative Homoclinic Bifurcations and Some Applications.” <i>Proceedings of the Steklov Institute of Mathematics</i>. Springer Nature, 2009. <a href=\"https://doi.org/10.1134/s0081543809040063\">https://doi.org/10.1134/s0081543809040063</a>.","apa":"Gorodetski, A., &#38; Kaloshin, V. (2009). Conservative homoclinic bifurcations and some applications. <i>Proceedings of the Steklov Institute of Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1134/s0081543809040063\">https://doi.org/10.1134/s0081543809040063</a>","mla":"Gorodetski, Anton, and Vadim Kaloshin. “Conservative Homoclinic Bifurcations and Some Applications.” <i>Proceedings of the Steklov Institute of Mathematics</i>, vol. 267, no. 1, Springer Nature, 2009, pp. 76–90, doi:<a href=\"https://doi.org/10.1134/s0081543809040063\">10.1134/s0081543809040063</a>."},"publication_identifier":{"issn":["0081-5438","1531-8605"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the Steklov Institute of Mathematics","intvolume":"       267","keyword":["Mathematics (miscellaneous)"],"issue":"1","doi":"10.1134/s0081543809040063","volume":267,"quality_controlled":"1"},{"_id":"88","day":"25","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:21:06Z","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.osti.gov/biblio/22053583"}],"date_published":"2009-06-25T00:00:00Z","external_id":{"pmid":["    19566203"]},"issue":"6","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7966","publication":"Review of Scientific Instruments","intvolume":"        80","citation":{"ista":"Higginbotham AP, Semonin O, Bruce S, Chan C, Maindi M, Donnelly T, Maurer M, Bang W, Churina I., Osterholz J, Kim I, Bernstein A, Ditmire T. 2009. Generation of Mie size microdroplet aerosols with applications in laser-driven fusion experiments. Review of Scientific Instruments. 80(6), 063503.","ama":"Higginbotham AP, Semonin O, Bruce S, et al. Generation of Mie size microdroplet aerosols with applications in laser-driven fusion experiments. <i>Review of Scientific Instruments</i>. 2009;80(6). doi:<a href=\"https://doi.org/10.1063/1.3155302\">10.1063/1.3155302</a>","short":"A.P. Higginbotham, O. Semonin, S. Bruce, C. Chan, M. Maindi, T. Donnelly, M. Maurer, W. Bang, I.. Churina, J. Osterholz, I. Kim, A. Bernstein, T. Ditmire, Review of Scientific Instruments 80 (2009).","ieee":"A. P. Higginbotham <i>et al.</i>, “Generation of Mie size microdroplet aerosols with applications in laser-driven fusion experiments,” <i>Review of Scientific Instruments</i>, vol. 80, no. 6. American Institute of Physics, 2009.","apa":"Higginbotham, A. P., Semonin, O., Bruce, S., Chan, C., Maindi, M., Donnelly, T., … Ditmire, T. (2009). Generation of Mie size microdroplet aerosols with applications in laser-driven fusion experiments. <i>Review of Scientific Instruments</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.3155302\">https://doi.org/10.1063/1.3155302</a>","mla":"Higginbotham, Andrew P., et al. “Generation of Mie Size Microdroplet Aerosols with Applications in Laser-Driven Fusion Experiments.” <i>Review of Scientific Instruments</i>, vol. 80, no. 6, 063503, American Institute of Physics, 2009, doi:<a href=\"https://doi.org/10.1063/1.3155302\">10.1063/1.3155302</a>.","chicago":"Higginbotham, Andrew P, Octavi Semonin, S Bruce, C Chan, M Maindi, Tom Donnelly, M Maurer, et al. “Generation of Mie Size Microdroplet Aerosols with Applications in Laser-Driven Fusion Experiments.” <i>Review of Scientific Instruments</i>. American Institute of Physics, 2009. <a href=\"https://doi.org/10.1063/1.3155302\">https://doi.org/10.1063/1.3155302</a>."},"oa":1,"oa_version":"Submitted Version","type":"journal_article","publication_status":"published","title":"Generation of Mie size microdroplet aerosols with applications in laser-driven fusion experiments","date_created":"2018-12-11T11:44:34Z","year":"2009","month":"06","quality_controlled":"1","volume":80,"doi":"10.1063/1.3155302","acknowledgement":"This work was supported by the National Science Foundation under Grant Nos. PHY-0456898, PHY-0757989, and PHY-0456870 and the National Nuclear Security Administration under Cooperative Agreement No. DE-FC52-03NA00156. Acknowledgment is made to the Donors of the Petroleum Research Fund administered by the American Chemical Society for partial support of this research.","status":"public","abstract":[{"text":"We have developed a tunable source of Mie scale microdroplet aerosols that can be used for the generation of energetic ions. To demonstrate this potential, a terawatt Ti: Al2 O3 laser focused to 2×10 19 W/cm2 was used to irradiate heavy water (D2 O) aerosols composed of micron-scale droplets. Energetic deuterium ions, which were generated in the laser-droplet interaction, produced deuterium-deuterium fusion with approximately 2×10^3 fusion neutrons measured per joule of incident laser energy. ","lang":"eng"}],"extern":"1","publisher":"American Institute of Physics","article_number":"063503","author":[{"first_name":"Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Semonin","full_name":"Semonin, Octavi","first_name":"Octavi"},{"first_name":"S","last_name":"Bruce","full_name":"Bruce, S"},{"first_name":"C","last_name":"Chan","full_name":"Chan, C"},{"first_name":"M","last_name":"Maindi","full_name":"Maindi, M"},{"first_name":"Tom","full_name":"Donnelly, Tom","last_name":"Donnelly"},{"first_name":"M","full_name":"Maurer, M","last_name":"Maurer"},{"first_name":"Woosuk","full_name":"Bang, Woosuk","last_name":"Bang"},{"last_name":"Churina","full_name":"Churina, I.V","first_name":"I.V"},{"full_name":"Osterholz, Jens","last_name":"Osterholz","first_name":"Jens"},{"full_name":"Kim, I","last_name":"Kim","first_name":"I"},{"full_name":"Bernstein, Aaron","last_name":"Bernstein","first_name":"Aaron"},{"first_name":"Todd","last_name":"Ditmire","full_name":"Ditmire, Todd"}]},{"_id":"908","day":"03","publication_status":"published","type":"journal_article","date_updated":"2021-01-12T08:21:49Z","title":"Translation termination in pyrrolysine-utilizing archaea","date_created":"2018-12-11T11:49:08Z","month":"11","date_published":"2009-11-03T00:00:00Z","year":"2009","issue":"21","quality_controlled":0,"volume":583,"doi":"10.1016/j.febslet.2009.09.044","acknowledgement":"We are grateful to Andrey Poltaraus and his colleagues for sequencing a/eRF1 genes. We thank Tatyana Pestova and Chris Hellen for the gift of plasmids encoding initiation factors eIF1, eIF1A, eIF4A, eIF4B, eIF4G, eIF5, eIF5B, and Anna Yaremchuk and Michael Tukalo for M. jannaschii aRF1. This work was supported by grants from the Presidium of the (Program Molecular and Cell Biology), the Russian Foundation for Basic Research (08-04-01091-а to E.A. and 08-04-00375a to L.F.), the National Institute for General Medical Sciences (to D.S.), the National Science Foundation (to D.S.) and the Office of Basic Energy Sciences, DOE (to D.S.).","status":"public","publist_id":"6740","publication":"FEBS Letters","intvolume":"       583","citation":{"ista":"Alkalaeva E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov F, Gundllapalli S, Frolova L, Söll D, Kisselev L. 2009. Translation termination in pyrrolysine-utilizing archaea. FEBS Letters. 583(21), 3455–3460.","ama":"Alkalaeva E, Eliseev B, Ambrogelly A, et al. Translation termination in pyrrolysine-utilizing archaea. <i>FEBS Letters</i>. 2009;583(21):3455-3460. doi:<a href=\"https://doi.org/10.1016/j.febslet.2009.09.044\">10.1016/j.febslet.2009.09.044</a>","ieee":"E. Alkalaeva <i>et al.</i>, “Translation termination in pyrrolysine-utilizing archaea,” <i>FEBS Letters</i>, vol. 583, no. 21. Elsevier, pp. 3455–3460, 2009.","short":"E. Alkalaeva, B. Eliseev, A. Ambrogelly, P. Vlasov, F. Kondrashov, S. Gundllapalli, L. Frolova, D. Söll, L. Kisselev, FEBS Letters 583 (2009) 3455–3460.","apa":"Alkalaeva, E., Eliseev, B., Ambrogelly, A., Vlasov, P., Kondrashov, F., Gundllapalli, S., … Kisselev, L. (2009). Translation termination in pyrrolysine-utilizing archaea. <i>FEBS Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.febslet.2009.09.044\">https://doi.org/10.1016/j.febslet.2009.09.044</a>","mla":"Alkalaeva, Elena, et al. “Translation Termination in Pyrrolysine-Utilizing Archaea.” <i>FEBS Letters</i>, vol. 583, no. 21, Elsevier, 2009, pp. 3455–60, doi:<a href=\"https://doi.org/10.1016/j.febslet.2009.09.044\">10.1016/j.febslet.2009.09.044</a>.","chicago":"Alkalaeva, Elena, Boris Eliseev, Alexandre Ambrogelly, Peter Vlasov, Fyodor Kondrashov, Sarath Gundllapalli, Ludmila Frolova, Dieter Söll, and Lev Kisselev. “Translation Termination in Pyrrolysine-Utilizing Archaea.” <i>FEBS Letters</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.febslet.2009.09.044\">https://doi.org/10.1016/j.febslet.2009.09.044</a>."},"page":"3455 - 3460","extern":1,"publisher":"Elsevier","author":[{"last_name":"Alkalaeva","full_name":"Alkalaeva, Elena Z","first_name":"Elena"},{"first_name":"Boris","full_name":"Eliseev, Boris D","last_name":"Eliseev"},{"first_name":"Alexandre","full_name":"Ambrogelly, Alexandre","last_name":"Ambrogelly"},{"last_name":"Vlasov","full_name":"Vlasov, Peter K","first_name":"Peter"},{"last_name":"Kondrashov","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor"},{"first_name":"Sarath","full_name":"Gundllapalli, Sarath B","last_name":"Gundllapalli"},{"full_name":"Frolova, Ludmila Y","last_name":"Frolova","first_name":"Ludmila"},{"full_name":"Söll, Dieter G","last_name":"Söll","first_name":"Dieter"},{"first_name":"Lev","full_name":"Kisselev, Lev L","last_name":"Kisselev"}],"abstract":[{"text":"Although some data link archaeal and eukaryotic translation, the overall mechanism of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1) and eukaryotic (eRF1) single release factors recognize all three stop codons. The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis of the last stage of archaeal translation in pyrrolysine-utilizing species. We demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses activity and recognizes all three stop codons. The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed.","lang":"eng"}]},{"article_processing_charge":"No","_id":"9147","day":"01","date_updated":"2022-01-24T13:50:37Z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1175/2009JPO4141.1"}],"date_published":"2009-09-01T00:00:00Z","issue":"9","keyword":["Oceanography"],"publication":"Journal of Physical Oceanography","intvolume":"        39","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"page":"2077-2096","citation":{"chicago":"Muller, Caroline J, and Oliver Bühler. “Saturation of the Internal Tides and Induced Mixing in the Abyssal Ocean.” <i>Journal of Physical Oceanography</i>. American Meteorological Society, 2009. <a href=\"https://doi.org/10.1175/2009jpo4141.1\">https://doi.org/10.1175/2009jpo4141.1</a>.","mla":"Muller, Caroline J., and Oliver Bühler. “Saturation of the Internal Tides and Induced Mixing in the Abyssal Ocean.” <i>Journal of Physical Oceanography</i>, vol. 39, no. 9, American Meteorological Society, 2009, pp. 2077–96, doi:<a href=\"https://doi.org/10.1175/2009jpo4141.1\">10.1175/2009jpo4141.1</a>.","apa":"Muller, C. J., &#38; Bühler, O. (2009). Saturation of the internal tides and induced mixing in the abyssal ocean. <i>Journal of Physical Oceanography</i>. American Meteorological Society. <a href=\"https://doi.org/10.1175/2009jpo4141.1\">https://doi.org/10.1175/2009jpo4141.1</a>","short":"C.J. Muller, O. Bühler, Journal of Physical Oceanography 39 (2009) 2077–2096.","ieee":"C. J. Muller and O. Bühler, “Saturation of the internal tides and induced mixing in the abyssal ocean,” <i>Journal of Physical Oceanography</i>, vol. 39, no. 9. American Meteorological Society, pp. 2077–2096, 2009.","ista":"Muller CJ, Bühler O. 2009. Saturation of the internal tides and induced mixing in the abyssal ocean. Journal of Physical Oceanography. 39(9), 2077–2096.","ama":"Muller CJ, Bühler O. Saturation of the internal tides and induced mixing in the abyssal ocean. <i>Journal of Physical Oceanography</i>. 2009;39(9):2077-2096. doi:<a href=\"https://doi.org/10.1175/2009jpo4141.1\">10.1175/2009jpo4141.1</a>"},"oa_version":"Published Version","type":"journal_article","publication_status":"published","article_type":"original","date_created":"2021-02-15T14:41:08Z","title":"Saturation of the internal tides and induced mixing in the abyssal ocean","year":"2009","month":"09","volume":39,"quality_controlled":"1","doi":"10.1175/2009jpo4141.1","status":"public","publication_identifier":{"issn":["1520-0485","0022-3670"]},"abstract":[{"lang":"eng","text":"As part of an ongoing effort to develop a parameterization of wave-induced abyssal mixing, the authors derive an heuristic model for nonlinear wave breaking and energy dissipation associated with internal tides. Then the saturation and dissipation of internal tides for idealized and observed topography samples are investigated. One of the main results is that the wave-induced mixing could be more intense and more confined to the bottom than previously assumed in numerical models. Furthermore, in this model wave breaking and mixing clearly depend on the small scales of the topography below 10 km or so, which is below the current resolution of global bathymetry. This motivates the use of a statistical approach to represent the unresolved topography when addressing the role of internal tides in mixing the deep ocean."}],"publisher":"American Meteorological Society","author":[{"full_name":"Muller, Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","first_name":"Caroline J"},{"last_name":"Bühler","full_name":"Bühler, Oliver","first_name":"Oliver"}],"extern":"1"},{"article_processing_charge":"No","day":"25","_id":"9148","date_updated":"2022-01-24T13:50:15Z","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1029/2009GL039667","open_access":"1"}],"date_published":"2009-08-25T00:00:00Z","issue":"16","intvolume":"        36","publication":"Geophysical Research Letters","keyword":["General Earth and Planetary Sciences","Geophysics"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"citation":{"short":"C.J. Muller, L.E. Back, P.A. O’Gorman, K.A. Emanuel, Geophysical Research Letters 36 (2009).","ieee":"C. J. Muller, L. E. Back, P. A. O’Gorman, and K. A. Emanuel, “A model for the relationship between tropical precipitation and column water vapor,” <i>Geophysical Research Letters</i>, vol. 36, no. 16. American Geophysical Union, 2009.","ama":"Muller CJ, Back LE, O’Gorman PA, Emanuel KA. A model for the relationship between tropical precipitation and column water vapor. <i>Geophysical Research Letters</i>. 2009;36(16). doi:<a href=\"https://doi.org/10.1029/2009gl039667\">10.1029/2009gl039667</a>","ista":"Muller CJ, Back LE, O’Gorman PA, Emanuel KA. 2009. A model for the relationship between tropical precipitation and column water vapor. Geophysical Research Letters. 36(16), L16804.","chicago":"Muller, Caroline J, Larissa E. Back, Paul A. O’Gorman, and Kerry A. Emanuel. “A Model for the Relationship between Tropical Precipitation and Column Water Vapor.” <i>Geophysical Research Letters</i>. American Geophysical Union, 2009. <a href=\"https://doi.org/10.1029/2009gl039667\">https://doi.org/10.1029/2009gl039667</a>.","mla":"Muller, Caroline J., et al. “A Model for the Relationship between Tropical Precipitation and Column Water Vapor.” <i>Geophysical Research Letters</i>, vol. 36, no. 16, L16804, American Geophysical Union, 2009, doi:<a href=\"https://doi.org/10.1029/2009gl039667\">10.1029/2009gl039667</a>.","apa":"Muller, C. J., Back, L. E., O’Gorman, P. A., &#38; Emanuel, K. A. (2009). A model for the relationship between tropical precipitation and column water vapor. <i>Geophysical Research Letters</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2009gl039667\">https://doi.org/10.1029/2009gl039667</a>"},"oa_version":"Published Version","type":"journal_article","publication_status":"published","article_type":"original","title":"A model for the relationship between tropical precipitation and column water vapor","date_created":"2021-02-15T14:41:28Z","year":"2009","month":"08","doi":"10.1029/2009gl039667","quality_controlled":"1","volume":36,"status":"public","publication_identifier":{"issn":["0094-8276"]},"abstract":[{"text":"Several observational studies have shown a tight relationship between tropical precipitation and column‐integrated water vapor. We show that the observed relationship in the tropics between column‐integrated water vapor, precipitation, and its variance can be qualitatively reproduced by a simple and physically motivated two‐layer model. It has previously been argued that features of this relationship could be explained by analogy with the theory of continuous phase transitions. Instead, our model explicitly assumes that the onset of precipitation is governed by a stability threshold involving boundary‐layer water vapor. This allows us to explain the precipitation‐humidity relationship over a broader range of water vapor values, and may explain the observed temperature dependence of the relationship.","lang":"eng"}],"article_number":"L16804","publisher":"American Geophysical Union","author":[{"first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350"},{"first_name":"Larissa E.","last_name":"Back","full_name":"Back, Larissa E."},{"first_name":"Paul A.","full_name":"O'Gorman, Paul A.","last_name":"O'Gorman"},{"first_name":"Kerry A.","last_name":"Emanuel","full_name":"Emanuel, Kerry A."}],"extern":"1"},{"date_created":"2019-11-19T13:48:32Z","title":"Influence of magnetic fields on structural martensitic transitions","related_material":{"record":[{"id":"11752","relation":"earlier_version","status":"public"}]},"article_type":"original","month":"08","date_published":"2009-08-21T00:00:00Z","year":"2009","_id":"7080","day":"21","oa_version":"None","article_processing_charge":"No","publication_status":"published","language":[{"iso":"eng"}],"date_updated":"2023-02-21T16:26:53Z","type":"journal_article","page":"2083-2091","citation":{"chicago":"Yang, X.-D., P.S. Riseborough, Kimberly A Modic, R.A. Fisher, C.P. Opeil, T.R. Finlayson, J.C. Cooley, et al. “Influence of Magnetic Fields on Structural Martensitic Transitions.” <i>Philosophical Magazine</i>. Taylor &#38; Francis, 2009. <a href=\"https://doi.org/10.1080/14786430902865518\">https://doi.org/10.1080/14786430902865518</a>.","mla":"Yang, X. D., et al. “Influence of Magnetic Fields on Structural Martensitic Transitions.” <i>Philosophical Magazine</i>, vol. 89, no. 22–24, Taylor &#38; Francis, 2009, pp. 2083–91, doi:<a href=\"https://doi.org/10.1080/14786430902865518\">10.1080/14786430902865518</a>.","apa":"Yang, X.-D., Riseborough, P. S., Modic, K. A., Fisher, R. A., Opeil, C. P., Finlayson, T. R., … Lashley, J. C. (2009). Influence of magnetic fields on structural martensitic transitions. <i>Philosophical Magazine</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/14786430902865518\">https://doi.org/10.1080/14786430902865518</a>","ieee":"X.-D. Yang <i>et al.</i>, “Influence of magnetic fields on structural martensitic transitions,” <i>Philosophical Magazine</i>, vol. 89, no. 22–24. Taylor &#38; Francis, pp. 2083–2091, 2009.","short":"X.-D. Yang, P.S. Riseborough, K.A. Modic, R.A. Fisher, C.P. Opeil, T.R. Finlayson, J.C. Cooley, J.L. Smith, P.A. Goddard, A.V. Silhanek, J.C. Lashley, Philosophical Magazine 89 (2009) 2083–2091.","ista":"Yang X-D, Riseborough PS, Modic KA, Fisher RA, Opeil CP, Finlayson TR, Cooley JC, Smith JL, Goddard PA, Silhanek AV, Lashley JC. 2009. Influence of magnetic fields on structural martensitic transitions. Philosophical Magazine. 89(22–24), 2083–2091.","ama":"Yang X-D, Riseborough PS, Modic KA, et al. Influence of magnetic fields on structural martensitic transitions. <i>Philosophical Magazine</i>. 2009;89(22-24):2083-2091. doi:<a href=\"https://doi.org/10.1080/14786430902865518\">10.1080/14786430902865518</a>"},"publication_identifier":{"eissn":["1478-6443"],"issn":["1478-6435"]},"extern":"1","publisher":"Taylor & Francis","author":[{"first_name":"X.-D.","last_name":"Yang","full_name":"Yang, X.-D."},{"first_name":"P.S.","last_name":"Riseborough","full_name":"Riseborough, P.S."},{"first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","last_name":"Modic","full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147"},{"first_name":"R.A.","full_name":"Fisher, R.A.","last_name":"Fisher"},{"first_name":"C.P.","last_name":"Opeil","full_name":"Opeil, C.P."},{"full_name":"Finlayson, T.R.","last_name":"Finlayson","first_name":"T.R."},{"first_name":"J.C.","full_name":"Cooley, J.C.","last_name":"Cooley"},{"first_name":"J.L.","last_name":"Smith","full_name":"Smith, J.L."},{"first_name":"P.A.","full_name":"Goddard, P.A.","last_name":"Goddard"},{"first_name":"A.V.","last_name":"Silhanek","full_name":"Silhanek, A.V."},{"first_name":"J.C.","full_name":"Lashley, J.C.","last_name":"Lashley"}],"abstract":[{"lang":"eng","text":"We show evidence that a structural martensitic transition is related to significant changes in the electronic structure, as revealed in thermodynamic measurements made in high magnetic fields. The effect of the magnetic field is considered unusual as many influential investigations of martensitic transitions have emphasized that the structural transitions are primarily lattice dynamical and are driven by the entropy due to the phonons. We provide a theoretical framework, which can be used to describe the effect of the magnetic field on the lattice dynamics in which the field dependence originates from the dielectric constant."}],"issue":"22-24","quality_controlled":"1","volume":89,"doi":"10.1080/14786430902865518","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Philosophical Magazine","intvolume":"        89"},{"issue":"3","quality_controlled":"1","doi":"10.1149/1.3043422","volume":156,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of The Electrochemical Society","intvolume":"       156","citation":{"ama":"Reum M, Freunberger SA, Wokaun A, Büchi FN. Measuring the current distribution with sub-millimeter resolution in PEFCs: II. Impact of operating parameters. <i>Journal of The Electrochemical Society</i>. 2009;156(3). doi:<a href=\"https://doi.org/10.1149/1.3043422\">10.1149/1.3043422</a>","ista":"Reum M, Freunberger SA, Wokaun A, Büchi FN. 2009. Measuring the current distribution with sub-millimeter resolution in PEFCs: II. Impact of operating parameters. Journal of The Electrochemical Society. 156(3), B301.","short":"M. Reum, S.A. Freunberger, A. Wokaun, F.N. Büchi, Journal of The Electrochemical Society 156 (2009).","ieee":"M. Reum, S. A. Freunberger, A. Wokaun, and F. N. Büchi, “Measuring the current distribution with sub-millimeter resolution in PEFCs: II. Impact of operating parameters,” <i>Journal of The Electrochemical Society</i>, vol. 156, no. 3. The Electrochemical Society, 2009.","mla":"Reum, Mathias, et al. “Measuring the Current Distribution with Sub-Millimeter Resolution in PEFCs: II. Impact of Operating Parameters.” <i>Journal of The Electrochemical Society</i>, vol. 156, no. 3, B301, The Electrochemical Society, 2009, doi:<a href=\"https://doi.org/10.1149/1.3043422\">10.1149/1.3043422</a>.","apa":"Reum, M., Freunberger, S. A., Wokaun, A., &#38; Büchi, F. N. (2009). Measuring the current distribution with sub-millimeter resolution in PEFCs: II. Impact of operating parameters. <i>Journal of The Electrochemical Society</i>. The Electrochemical Society. <a href=\"https://doi.org/10.1149/1.3043422\">https://doi.org/10.1149/1.3043422</a>","chicago":"Reum, Mathias, Stefan Alexander Freunberger, Alexander Wokaun, and Felix N. Büchi. “Measuring the Current Distribution with Sub-Millimeter Resolution in PEFCs: II. Impact of Operating Parameters.” <i>Journal of The Electrochemical Society</i>. The Electrochemical Society, 2009. <a href=\"https://doi.org/10.1149/1.3043422\">https://doi.org/10.1149/1.3043422</a>."},"publication_identifier":{"issn":["0013-4651"]},"extern":"1","author":[{"full_name":"Reum, Mathias","last_name":"Reum","first_name":"Mathias"},{"orcid":"0000-0003-2902-5319","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"},{"full_name":"Wokaun, Alexander","last_name":"Wokaun","first_name":"Alexander"},{"last_name":"Büchi","full_name":"Büchi, Felix N.","first_name":"Felix N."}],"article_number":"B301","publisher":"The Electrochemical Society","abstract":[{"lang":"eng","text":"In the first paper of this series, an experimental technique for measuring the current-density distribution with a resolution better than the sub-millimeter scale of the channel and rib structures in the flow-field plates of polymer electrolyte fuel cells (PEFCs) was introduced. This method is extended to the determination of local membrane resistance with the same spatial resolution in the present paper. The combined measurement of current and resistance allows for investigating the interaction of mass- and charge-transport processes, which determine the local rate distribution across the domain of channels and ribs. Therewith, the influence of relevant operating parameters such as reactant composition, dew points, and cell compression on local current generation is investigated. The results show that the distribution of water and oxidant across the channel and rib are the main reasons for significant current gradients on a scale smaller than a millimeter. Humidity variation mainly affects the membrane resistance under the channel, while reactant concentration predominantly influences current generation under the rib-covered cell area."}],"day":"01","_id":"7319","oa_version":"None","article_processing_charge":"No","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","date_updated":"2021-01-12T08:13:01Z","date_created":"2020-01-15T12:21:24Z","title":"Measuring the current distribution with sub-millimeter resolution in PEFCs: II. Impact of operating parameters","article_type":"original","month":"03","date_published":"2009-03-01T00:00:00Z","year":"2009"},{"year":"2009","date_published":"2009-01-01T00:00:00Z","month":"01","date_created":"2018-12-11T11:48:19Z","title":"Of choices, failures and asynchrony: the many faces of set agreement","type":"conference","date_updated":"2023-02-23T13:10:05Z","language":[{"iso":"eng"}],"publication_status":"published","article_processing_charge":"No","oa_version":"None","day":"01","_id":"752","abstract":[{"text":"Set agreement is a fundamental problem in distributed computing in which processes collectively choose a small subset of values from a larger set of proposals. The impossibility of fault-tolerant set agreement in asynchronous networks is one of the seminal results in distributed computing. The complexity of set agreement in synchronous networks has also been a significant research challenge. Real systems, however, are neither purely synchronous nor purely asynchronous. Rather, they tend to alternate between periods of synchrony and periods of asynchrony. In this paper, we analyze the complexity of set agreement in a &quot;partially synchronous&quot; setting, presenting the first (asymptotically) tight bound on the complexity of set agreement in such systems. We introduce a novel technique for simulating, in fault-prone asynchronous shared memory, executions of an asynchronous and failure-prone messagepassing system in which some fragments appear synchronous to some processes. We use this technique to derive a lower bound on the round complexity of set agreement in a partially synchronous system by a reduction from asynchronous wait-free set agreement. We also present an asymptotically matching algorithm that relies on a distributed asynchrony detection mechanism to decide as soon as possible during periods of synchrony. By relating environments with differing degrees of synchrony, our simulation technique is of independent interest. In particular, it allows us to obtain a new lower bound on the complexity of early deciding k-set agreement complementary to that of [12], and to re-derive the combinatorial topology lower bound of [13] in an algorithmic way.","lang":"eng"}],"publisher":"Springer","author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian"},{"last_name":"Gilbert","full_name":"Gilbert, Seth","first_name":"Seth"},{"last_name":"Guerraoui","full_name":"Guerraoui, Rachid","first_name":"Rachid"},{"last_name":"Travers","full_name":"Travers, Corentin","first_name":"Corentin"}],"extern":"1","conference":{"name":"ISAAC: International Symposium on Algorithms and Computation"},"citation":{"short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, in:, Springer, 2009, pp. 943–953.","ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Of choices, failures and asynchrony: the many faces of set agreement,” presented at the ISAAC: International Symposium on Algorithms and Computation, 2009, vol. 5878 LNCS, pp. 943–953.","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2009. Of choices, failures and asynchrony: the many faces of set agreement. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 5878 LNCS, 943–953.","ama":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Of choices, failures and asynchrony: the many faces of set agreement. In: Vol 5878 LNCS. Springer; 2009:943-953. doi:<a href=\"https://doi.org/10.1007/978-3-642-10631-6_95\">10.1007/978-3-642-10631-6_95</a>","chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement,” 5878 LNCS:943–53. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-10631-6_95\">https://doi.org/10.1007/978-3-642-10631-6_95</a>.","apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., &#38; Travers, C. (2009). Of choices, failures and asynchrony: the many faces of set agreement (Vol. 5878 LNCS, pp. 943–953). Presented at the ISAAC: International Symposium on Algorithms and Computation, Springer. <a href=\"https://doi.org/10.1007/978-3-642-10631-6_95\">https://doi.org/10.1007/978-3-642-10631-6_95</a>","mla":"Alistarh, Dan-Adrian, et al. <i>Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement</i>. Vol. 5878 LNCS, Springer, 2009, pp. 943–53, doi:<a href=\"https://doi.org/10.1007/978-3-642-10631-6_95\">10.1007/978-3-642-10631-6_95</a>."},"page":"943 - 953","publist_id":"6903","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","acknowledgement":"Corentin Travers was supposrted in part by a Sam & Cecilia Neaman Fellowship","volume":"5878 LNCS","doi":"10.1007/978-3-642-10631-6_95","alternative_title":["LNCS"]},{"publication_status":"published","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:15:17Z","type":"journal_article","day":"01","_id":"7751","oa_version":"None","article_processing_charge":"No","month":"04","date_published":"2009-04-01T00:00:00Z","year":"2009","date_created":"2020-04-30T11:01:57Z","title":"The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep","article_type":"original","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Genetics","intvolume":"       181","issue":"4","volume":181,"doi":"10.1534/genetics.108.086801","quality_controlled":"1","extern":"1","publisher":"Genetics Society of America","author":[{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"},{"last_name":"Wilson","full_name":"Wilson, Alastair J.","first_name":"Alastair J."},{"full_name":"Pilkington, Jill G.","last_name":"Pilkington","first_name":"Jill G."},{"last_name":"Clutton-Brock","full_name":"Clutton-Brock, Tim H.","first_name":"Tim H."},{"full_name":"Pemberton, Josephine M.","last_name":"Pemberton","first_name":"Josephine M."},{"first_name":"Loeske E. B.","last_name":"Kruuk","full_name":"Kruuk, Loeske E. B."}],"abstract":[{"text":"This work demonstrates that environmental conditions experienced by individuals can shape their development and affect the stability of genetic associations. The implication of this observation is that the environmental response may influence the evolution of traits in the wild. Here, we examined how the genetic architecture of a suite of sexually dimorphic traits changed as a function of environmental conditions in an unmanaged population of Soay sheep (Ovis aries) on the island of Hirta, St. Kilda, northwest Scotland. We examined the stability of phenotypic, genetic, and environmental (residual) covariance in males during the first year of life between horn length, body weight, and parasite load in environments of different quality. We then examined the same covariance structures across environments within and between the adult sexes. We found significant genotype-by-environment interactions for lamb male body weight and parasite load, leading to a change in the genetic correlation among environments. Horn length was genetically correlated with body weight in males but not females and the genetic correlation among traits within and between the sexes was dependent upon the environmental conditions experienced during adulthood. Genetic correlations were smaller in more favorable environmental conditions, suggesting that in good environments, loci are expressed that have sex-specific effects. The reduction in genetic correlation between the sexes may allow independent evolutionary trajectories for each sex. This study demonstrates that the genetic architecture of traits is not stable under temporally varying environments and highlights the fact that evolutionary processes may depend largely upon ecological conditions.\r\nENVIRONMENTAL heterogeneity has long been recognized as an important factor influencing the evolution of fitness-related traits in the wild (Roff 2002). The evolution of a trait depends upon the selection upon it, underlying genetic variation, and to a large degree the genetic relationships with other traits (Lynch and Walsh 1998). There is evidence that selection can vary considerably from year to year (Price et al. 1984; Robinson et al. 2008) and genetic variability in quantitative traits can change in response to environmental conditions (Hoffmann and Merilä 1999; Charmantier and Garant 2005). However, we know surprisingly little about the influence of environmental conditions on genetic correlations between traits in wild populations. Laboratory evidence suggests that the environment may influence genetic relationships between traits (Sgrò and Hoffmann 2004), but estimates obtained in a controlled or in an arbitrary range of conditions show a lack of concordance with those obtained in wild habitats (Conner et al. 2003). As a result, laboratory and environment-specific estimates of genetic correlations can make predictions for a trait's evolution, but these are valid only for the environment in which they were measured. Therefore, at present, it is difficult to generalize about the evolution of a trait that is expressed in populations that experience variable environmental conditions (Steppan et al. 2002).\r\nThe influence of changing environmental conditions on the G matrix (the matrix of additive genetic variance and covariances corresponding to a set of traits) has been the focus of theoretical quantitative genetic studies (e.g., Jones et al. 2003). There is evidence of genotype-by-environment interaction for many traits expressed in wild populations (Charmantier and Garant 2005) and thus we may also expect that associations between traits may depend upon the environmental conditions encountered by an individual. Genetic correlations among traits may arise from pleiotropy, where a given locus affects more than one trait (Cheverud 1988; Lynch and Walsh 1998), which may limit the potential for those traits to evolve independently. There has recently been much interest in assessing genetic correlations between the sexes (Rice and Chippindale 2001; Foerster et al. 2007; Poissant et al. 2008), but all of these predictions have also been made in average environmental conditions. For sexually dimorphic traits, expectations of between-sex genetic correlations are unclear (Lande 1980; Badyaev 2002). We might expect that the genetic determination of a trait and the patterns of genetic covariance between traits may differ both within and between the sexes, producing the differences in trait growth that are commonly observed (Lande 1980; Badyaev 2002; Roff 2002), but so far evidence suggests that genetic expression in both sexes is influenced by the same developmental pathway (Roff 2002; Jensen et al. 2003; Parker and Garant 2005). However, to our knowledge, no study has yet determined whether genetic correlations, both within and between the sexes, vary across gradients of the environmental conditions encountered by individuals in the wild (Garant et al. 2008).\r\nThis study aims to assess the stability of phenotypic, genetic, and environmental (residual) associations between traits, within and between the sexes, across a range of environmental conditions experienced by a wild population. We focus on the traits of horn length, body weight, and parasite load in a feral population of Soay sheep (Ovis aries) from the island of Hirta, St. Kilda, United Kingdom. Weather conditions, population density, and consequently resource availability fluctuate from year to year, providing substantial differences between individuals in the environments they experience and thus their survival rates (Clutton-Brock and Pemberton 2004). These varying conditions, combined with a large pedigree and extensive repeated morphological measures, provide an excellent opportunity to assess the potential effects of environmental heterogeneity on genetic architecture of traits. Previous studies on this population have shown additive genetic variance for many morphological traits (Milner et al. 2000; Coltman et al. 2001; Wilson et al. 2005), genetic correlations between traits (Coltman et al. 2001), and genotype-by-environment interactions for birth weight (Wilson et al. 2006). Here we apply a random regression animal model approach to assess the extent to which quantitative genetic parameters of a range of morphological traits measured during life vary as a function of environmental conditions. We then extend this methodology to the multivariate case, testing whether the phenotypic covariance structure, and the underlying G matrix, depends on the environmental conditions experienced. Since the traits considered here are known to be sexually dimorphic and there are differences in trait growth and survival across ages, we look at sex-specific traits in lambs and then across all ages.","lang":"eng"}],"citation":{"ama":"Robinson MR, Wilson AJ, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep. <i>Genetics</i>. 2009;181(4):1639-1648. doi:<a href=\"https://doi.org/10.1534/genetics.108.086801\">10.1534/genetics.108.086801</a>","ista":"Robinson MR, Wilson AJ, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. 2009. The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep. Genetics. 181(4), 1639–1648.","short":"M.R. Robinson, A.J. Wilson, J.G. Pilkington, T.H. Clutton-Brock, J.M. Pemberton, L.E.B. Kruuk, Genetics 181 (2009) 1639–1648.","ieee":"M. R. Robinson, A. J. Wilson, J. G. Pilkington, T. H. Clutton-Brock, J. M. Pemberton, and L. E. B. Kruuk, “The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep,” <i>Genetics</i>, vol. 181, no. 4. Genetics Society of America, pp. 1639–1648, 2009.","mla":"Robinson, Matthew Richard, et al. “The Impact of Environmental Heterogeneity on Genetic Architecture in a Wild Population of Soay Sheep.” <i>Genetics</i>, vol. 181, no. 4, Genetics Society of America, 2009, pp. 1639–48, doi:<a href=\"https://doi.org/10.1534/genetics.108.086801\">10.1534/genetics.108.086801</a>.","apa":"Robinson, M. R., Wilson, A. J., Pilkington, J. G., Clutton-Brock, T. H., Pemberton, J. M., &#38; Kruuk, L. E. B. (2009). The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.108.086801\">https://doi.org/10.1534/genetics.108.086801</a>","chicago":"Robinson, Matthew Richard, Alastair J. Wilson, Jill G. Pilkington, Tim H. Clutton-Brock, Josephine M. Pemberton, and Loeske E. B. Kruuk. “The Impact of Environmental Heterogeneity on Genetic Architecture in a Wild Population of Soay Sheep.” <i>Genetics</i>. Genetics Society of America, 2009. <a href=\"https://doi.org/10.1534/genetics.108.086801\">https://doi.org/10.1534/genetics.108.086801</a>."},"page":"1639-1648","publication_identifier":{"issn":["0016-6731","1943-2631"]}},{"_id":"8026","day":"01","article_processing_charge":"No","date_updated":"2021-01-12T08:16:36Z","language":[{"iso":"eng"}],"date_published":"2009-04-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2693069/"}],"pmid":1,"issue":"4","external_id":{"pmid":["19305402"]},"publication":"Nature Neuroscience","intvolume":"        12","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa":1,"citation":{"ieee":"T. P. Vogels and L. F. Abbott, “Gating multiple signals through detailed balance of excitation and inhibition in spiking networks,” <i>Nature Neuroscience</i>, vol. 12, no. 4. Springer Nature, pp. 483–491, 2009.","short":"T.P. Vogels, L.F. Abbott, Nature Neuroscience 12 (2009) 483–491.","ama":"Vogels TP, Abbott LF. Gating multiple signals through detailed balance of excitation and inhibition in spiking networks. <i>Nature Neuroscience</i>. 2009;12(4):483-491. doi:<a href=\"https://doi.org/10.1038/nn.2276\">10.1038/nn.2276</a>","ista":"Vogels TP, Abbott LF. 2009. Gating multiple signals through detailed balance of excitation and inhibition in spiking networks. Nature Neuroscience. 12(4), 483–491.","chicago":"Vogels, Tim P, and L F Abbott. “Gating Multiple Signals through Detailed Balance of Excitation and Inhibition in Spiking Networks.” <i>Nature Neuroscience</i>. Springer Nature, 2009. <a href=\"https://doi.org/10.1038/nn.2276\">https://doi.org/10.1038/nn.2276</a>.","apa":"Vogels, T. P., &#38; Abbott, L. F. (2009). Gating multiple signals through detailed balance of excitation and inhibition in spiking networks. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nn.2276\">https://doi.org/10.1038/nn.2276</a>","mla":"Vogels, Tim P., and L. F. Abbott. “Gating Multiple Signals through Detailed Balance of Excitation and Inhibition in Spiking Networks.” <i>Nature Neuroscience</i>, vol. 12, no. 4, Springer Nature, 2009, pp. 483–91, doi:<a href=\"https://doi.org/10.1038/nn.2276\">10.1038/nn.2276</a>."},"page":"483-491","oa_version":"Submitted Version","publication_status":"published","type":"journal_article","title":"Gating multiple signals through detailed balance of excitation and inhibition in spiking networks","date_created":"2020-06-25T13:10:55Z","article_type":"original","month":"04","year":"2009","quality_controlled":"1","volume":12,"doi":"10.1038/nn.2276","status":"public","publication_identifier":{"issn":["1097-6256","1546-1726"]},"author":[{"first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P","last_name":"Vogels","orcid":"0000-0003-3295-6181"},{"first_name":"L F","full_name":"Abbott, L F","last_name":"Abbott"}],"publisher":"Springer Nature","extern":"1","abstract":[{"lang":"eng","text":"Recent theoretical work has provided a basic understanding of signal propagation in networks of spiking neurons, but mechanisms for gating and controlling these signals have not been investigated previously. Here we introduce an idea for the gating of multiple signals in cortical networks that combines principles of signal propagation with aspects of balanced networks. Specifically, we studied networks in which incoming excitatory signals are normally cancelled by locally evoked inhibition, leaving the targeted layer unresponsive. Transmission can be gated 'on' by modulating excitatory and inhibitory gains to upset this detailed balance. We illustrate gating through detailed balance in large networks of integrate-and-fire neurons. We show successful gating of multiple signals and study failure modes that produce effects reminiscent of clinically observed pathologies. Provided that the individual signals are detectable, detailed balance has a large capacity for gating multiple signals."}]},{"main_file_link":[{"url":"https://arxiv.org/abs/math/0611086","open_access":"1"}],"year":"2009","date_published":"2009-01-31T00:00:00Z","month":"01","arxiv":1,"date_created":"2018-12-11T11:44:58Z","title":"Integral points on cubic hypersurfaces","type":"book_chapter","date_updated":"2021-01-12T06:52:11Z","language":[{"iso":"eng"}],"publication_status":"published","article_processing_charge":"No","oa_version":"Preprint","day":"31","_id":"164","abstract":[{"text":"Let g be a cubic polynomial with integer coefficients and n&gt;9 variables, and assume that the congruence g=0 modulo p^k is soluble for all prime powers p^k. We show that the equation g=0 has infinitely many integer solutions when the cubic part of g defines a projective hypersurface with singular locus of dimension &lt;n-10. The proof is based on the Hardy-Littlewood circle method.","lang":"eng"}],"author":[{"first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","full_name":"Browning, Timothy D"},{"first_name":"Roger","last_name":"Heath Brown","full_name":"Heath Brown, Roger"}],"publisher":"Cambridge University Press","extern":"1","oa":1,"page":"75 - 90","citation":{"chicago":"Browning, Timothy D, and Roger Heath Brown. “Integral Points on Cubic Hypersurfaces.” In <i>Analytic Number Theory: Essays in Honour of Klaus Roth</i>, 75–90. Cambridge University Press, 2009.","apa":"Browning, T. D., &#38; Heath Brown, R. (2009). Integral points on cubic hypersurfaces. In <i>Analytic Number Theory: Essays in honour of Klaus Roth</i> (pp. 75–90). Cambridge University Press.","mla":"Browning, Timothy D., and Roger Heath Brown. “Integral Points on Cubic Hypersurfaces.” <i>Analytic Number Theory: Essays in Honour of Klaus Roth</i>, Cambridge University Press, 2009, pp. 75–90.","ieee":"T. D. Browning and R. Heath Brown, “Integral points on cubic hypersurfaces,” in <i>Analytic Number Theory: Essays in honour of Klaus Roth</i>, Cambridge University Press, 2009, pp. 75–90.","short":"T.D. Browning, R. Heath Brown, in:, Analytic Number Theory: Essays in Honour of Klaus Roth, Cambridge University Press, 2009, pp. 75–90.","ista":"Browning TD, Heath Brown R. 2009.Integral points on cubic hypersurfaces. In: Analytic Number Theory: Essays in honour of Klaus Roth. , 75–90.","ama":"Browning TD, Heath Brown R. Integral points on cubic hypersurfaces. In: <i>Analytic Number Theory: Essays in Honour of Klaus Roth</i>. Cambridge University Press; 2009:75-90."},"publication":"Analytic Number Theory: Essays in honour of Klaus Roth","publist_id":"7757","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","quality_controlled":"1","external_id":{"arxiv":["0611086"]}},{"title":"Resent progress on the quantitative arithmetic of del Pezzo surfaces","date_created":"2018-12-11T11:44:58Z","year":"2009","month":"08","date_published":"2009-08-24T00:00:00Z","day":"24","_id":"165","type":"conference","date_updated":"2021-01-12T06:52:15Z","publication_status":"published","conference":{"name":"Number Theory: Dreaming in dreams"},"citation":{"chicago":"Browning, Timothy D. “Resent Progress on the Quantitative Arithmetic of Del Pezzo Surfaces.” edited by Takashi Aoki, Shigeru Kanemitsu, and Jianya Liu, 6:1–18. World Scientific Publishing, 2009. <a href=\"https://doi.org/10.1142/9789814289924_0001\">https://doi.org/10.1142/9789814289924_0001</a>.","apa":"Browning, T. D. (2009). Resent progress on the quantitative arithmetic of del Pezzo surfaces. In T. Aoki, S. Kanemitsu, &#38; J. Liu (Eds.) (Vol. 6, pp. 1–18). Presented at the Number Theory: Dreaming in dreams, World Scientific Publishing. <a href=\"https://doi.org/10.1142/9789814289924_0001\">https://doi.org/10.1142/9789814289924_0001</a>","mla":"Browning, Timothy D. <i>Resent Progress on the Quantitative Arithmetic of Del Pezzo Surfaces</i>. Edited by Takashi Aoki et al., vol. 6, World Scientific Publishing, 2009, pp. 1–18, doi:<a href=\"https://doi.org/10.1142/9789814289924_0001\">https://doi.org/10.1142/9789814289924_0001</a>.","ieee":"T. D. Browning, “Resent progress on the quantitative arithmetic of del Pezzo surfaces,” presented at the Number Theory: Dreaming in dreams, 2009, vol. 6, pp. 1–18.","short":"T.D. Browning, in:, T. Aoki, S. Kanemitsu, J. Liu (Eds.), World Scientific Publishing, 2009, pp. 1–18.","ama":"Browning TD. Resent progress on the quantitative arithmetic of del Pezzo surfaces. In: Aoki T, Kanemitsu S, Liu J, eds. Vol 6. World Scientific Publishing; 2009:1-18. doi:<a href=\"https://doi.org/10.1142/9789814289924_0001\">https://doi.org/10.1142/9789814289924_0001</a>","ista":"Browning TD. 2009. Resent progress on the quantitative arithmetic of del Pezzo surfaces. Number Theory: Dreaming in dreams, Series on number theory and its application, vol. 6, 1–18."},"page":"1 - 18","abstract":[{"lang":"eng","text":"We survey the state of affairs for the distribution of ℚ-rational points on non-singular del Pezzo surfaces of low degree, highlighting the recent resolution of Manin's conjecture for a non-singular del Pezzo surface of degree 4 by la Bretèche and Browning."}],"extern":1,"publisher":"World Scientific Publishing","author":[{"last_name":"Browning","full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D"}],"quality_controlled":0,"editor":[{"first_name":"Takashi","full_name":"Aoki, Takashi","last_name":"Aoki"},{"full_name":"Kanemitsu, Shigeru","last_name":"Kanemitsu","first_name":"Shigeru"},{"first_name":"Jianya","last_name":"Liu","full_name":"Liu, Jianya"}],"volume":6,"doi":"https://doi.org/10.1142/9789814289924_0001","alternative_title":["Series on number theory and its application"],"publist_id":"7756","intvolume":"         6","acknowledgement":"Proceedings of the 5th China-Japan Seminar","status":"public"},{"publication":"Quadratic Forms - algebra, arithmetic and geometry","intvolume":"       493","publist_id":"7753","status":"public","volume":493,"doi":"http://dx.doi.org/10.1090/conm/493","quality_controlled":0,"alternative_title":["Contemporary Mathematics"],"abstract":[{"lang":"eng","text":"The arithmetic of ternary diagonal equation is considered for degree d &gt;1, with the outcome that the set of coefficients for which the equation admits a non-zero integer solution is shown to have density zero."}],"author":[{"last_name":"Browning","full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D"},{"last_name":"Dietmann","full_name":"Dietmann, Rainer","first_name":"Rainer"}],"publisher":"American Mathematical Society","extern":1,"citation":{"apa":"Browning, T. D., &#38; Dietmann, R. (2009). Solubility of Fermat equations. In <i>Quadratic Forms - algebra, arithmetic and geometry</i> (Vol. 493, pp. 99–106). American Mathematical Society. <a href=\"http://dx.doi.org/10.1090/conm/493\">http://dx.doi.org/10.1090/conm/493</a>","mla":"Browning, Timothy D., and Rainer Dietmann. “Solubility of Fermat Equations.” <i>Quadratic Forms - Algebra, Arithmetic and Geometry</i>, vol. 493, American Mathematical Society, 2009, pp. 99–106, doi:<a href=\"http://dx.doi.org/10.1090/conm/493\">http://dx.doi.org/10.1090/conm/493</a>.","chicago":"Browning, Timothy D, and Rainer Dietmann. “Solubility of Fermat Equations.” In <i>Quadratic Forms - Algebra, Arithmetic and Geometry</i>, 493:99–106. American Mathematical Society, 2009. <a href=\"http://dx.doi.org/10.1090/conm/493\">http://dx.doi.org/10.1090/conm/493</a>.","ama":"Browning TD, Dietmann R. Solubility of Fermat equations. In: <i>Quadratic Forms - Algebra, Arithmetic and Geometry</i>. Vol 493. American Mathematical Society; 2009:99-106. doi:<a href=\"http://dx.doi.org/10.1090/conm/493\">http://dx.doi.org/10.1090/conm/493</a>","ista":"Browning TD, Dietmann R. 2009.Solubility of Fermat equations. In: Quadratic Forms - algebra, arithmetic and geometry. Contemporary Mathematics, vol. 493, 99–106.","short":"T.D. Browning, R. Dietmann, in:, Quadratic Forms - Algebra, Arithmetic and Geometry, American Mathematical Society, 2009, pp. 99–106.","ieee":"T. D. Browning and R. Dietmann, “Solubility of Fermat equations,” in <i>Quadratic Forms - algebra, arithmetic and geometry</i>, vol. 493, American Mathematical Society, 2009, pp. 99–106."},"page":"99 - 106","date_updated":"2021-01-12T06:52:29Z","type":"book_chapter","publication_status":"published","day":"01","_id":"168","main_file_link":[{"open_access":"0","url":"https://arxiv.org/abs/0805.3354"}],"year":"2009","date_published":"2009-01-01T00:00:00Z","month":"01","title":"Solubility of Fermat equations","date_created":"2018-12-11T11:44:59Z"},{"_id":"1718","day":"01","publication_status":"published","type":"journal_article","date_updated":"2021-01-12T06:52:44Z","date_created":"2018-12-11T11:53:38Z","title":"Temporal dynamics of patterning by morphogen gradients","month":"08","date_published":"2009-08-01T00:00:00Z","year":"2009","issue":"4","volume":19,"doi":"10.1016/j.gde.2009.05.004","quality_controlled":0,"acknowledgement":"EK is supported by an EMBO LTF, AK by a FEBS fellowship, and JB by MRC (UK) and the Wellcome Trust","status":"public","publist_id":"5410","publication":"Current Opinion in Genetics & Development","intvolume":"        19","page":"315 - 322","citation":{"mla":"Kutějová, Eva, et al. “Temporal Dynamics of Patterning by Morphogen Gradients.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 19, no. 4, Elsevier, 2009, pp. 315–22, doi:<a href=\"https://doi.org/10.1016/j.gde.2009.05.004\">10.1016/j.gde.2009.05.004</a>.","apa":"Kutějová, E., Briscoe, J., &#38; Kicheva, A. (2009). Temporal dynamics of patterning by morphogen gradients. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2009.05.004\">https://doi.org/10.1016/j.gde.2009.05.004</a>","chicago":"Kutějová, Eva, James Briscoe, and Anna Kicheva. “Temporal Dynamics of Patterning by Morphogen Gradients.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.gde.2009.05.004\">https://doi.org/10.1016/j.gde.2009.05.004</a>.","ama":"Kutějová E, Briscoe J, Kicheva A. Temporal dynamics of patterning by morphogen gradients. <i>Current Opinion in Genetics &#38; Development</i>. 2009;19(4):315-322. doi:<a href=\"https://doi.org/10.1016/j.gde.2009.05.004\">10.1016/j.gde.2009.05.004</a>","ista":"Kutějová E, Briscoe J, Kicheva A. 2009. Temporal dynamics of patterning by morphogen gradients. Current Opinion in Genetics &#38; Development. 19(4), 315–322.","ieee":"E. Kutějová, J. Briscoe, and A. Kicheva, “Temporal dynamics of patterning by morphogen gradients,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 19, no. 4. Elsevier, pp. 315–322, 2009.","short":"E. Kutějová, J. Briscoe, A. Kicheva, Current Opinion in Genetics &#38; Development 19 (2009) 315–322."},"extern":1,"author":[{"last_name":"Kutějová","full_name":"Kutějová, Eva","first_name":"Eva"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Anna Kicheva","first_name":"Anna"}],"publisher":"Elsevier","abstract":[{"text":"Morphogens act as graded positional cues to control cell fate specification in many developing tissues. This concept, in which a signaling gradient regulates differential gene expression in a concentration-dependent manner, has received considerable experimental support. Nevertheless, several recent studies have challenged the straightforward model of morphogen activity. In particular, the observation that pattern formation is a dynamic process has raised questions about the influence of time on morphogen activity. Here we propose that the spatiotemporal dynamics of the cellular response to a morphogen gradient depend on a combination of temporal alterations to the morphogen gradient itself, the dynamics of its signal transduction and downstream interactions between target genes.","lang":"eng"}]},{"status":"public","publication":"Cold Spring Harbor perspectives in biology","intvolume":"         1","publist_id":"5409","issue":"3","volume":1,"quality_controlled":0,"doi":"10.1101/cshperspect.a001255","publisher":"Cold Spring Harbor Laboratory Press","author":[{"first_name":"Ortrud","full_name":"Wartlick, Ortrud","last_name":"Wartlick"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Anna Kicheva","last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna"},{"full_name":"González-Gaitán, Marcos A","last_name":"González Gaitán","first_name":"Marcos"}],"extern":1,"abstract":[{"lang":"eng","text":"How morphogen gradients are formed in target tissues is a key question for understanding the mechanisms of morphological patterning. Here, we review different mechanisms of morphogen gradient formation from theoretical and experimental points of view. First, a simple, comprehensive overview of the underlying biophysical principles of several mechanisms of gradient formation is provided. We then discuss the advantages and limitations of different experimental approaches to gradient formation analysis."}],"citation":{"mla":"Wartlick, Ortrud, et al. “Morphogen Gradient Formation .” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 1, no. 3, Cold Spring Harbor Laboratory Press, 2009, doi:<a href=\"https://doi.org/10.1101/cshperspect.a001255\">10.1101/cshperspect.a001255</a>.","apa":"Wartlick, O., Kicheva, A., &#38; González Gaitán, M. (2009). Morphogen gradient formation . <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a001255\">https://doi.org/10.1101/cshperspect.a001255</a>","chicago":"Wartlick, Ortrud, Anna Kicheva, and Marcos González Gaitán. “Morphogen Gradient Formation .” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2009. <a href=\"https://doi.org/10.1101/cshperspect.a001255\">https://doi.org/10.1101/cshperspect.a001255</a>.","ista":"Wartlick O, Kicheva A, González Gaitán M. 2009. Morphogen gradient formation . Cold Spring Harbor perspectives in biology. 1(3).","ama":"Wartlick O, Kicheva A, González Gaitán M. Morphogen gradient formation . <i>Cold Spring Harbor perspectives in biology</i>. 2009;1(3). doi:<a href=\"https://doi.org/10.1101/cshperspect.a001255\">10.1101/cshperspect.a001255</a>","ieee":"O. Wartlick, A. Kicheva, and M. González Gaitán, “Morphogen gradient formation ,” <i>Cold Spring Harbor perspectives in biology</i>, vol. 1, no. 3. Cold Spring Harbor Laboratory Press, 2009.","short":"O. Wartlick, A. Kicheva, M. González Gaitán, Cold Spring Harbor Perspectives in Biology 1 (2009)."},"publication_status":"published","type":"journal_article","date_updated":"2021-01-12T06:52:45Z","_id":"1720","day":"01","date_published":"2009-09-01T00:00:00Z","month":"09","year":"2009","date_created":"2018-12-11T11:53:39Z","title":"Morphogen gradient formation "},{"title":"Using sideband transitions for two-qubit operations in superconducting circuits","date_created":"2018-12-11T11:53:54Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0812.2678"}],"year":"2009","date_published":"2009-05-01T00:00:00Z","month":"05","_id":"1766","day":"01","type":"journal_article","date_updated":"2021-01-12T06:53:04Z","publication_status":"published","oa":1,"citation":{"chicago":"Leek, Peter, Stefan Filipp, Patrick Maurer, Matthias Baur, R Bianchetti, Johannes M Fink, M Göppl, L. Steffen, and Andreas Wallraff. “Using Sideband Transitions for Two-Qubit Operations in Superconducting Circuits.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2009. <a href=\"https://doi.org/10.1103/PhysRevB.79.180511\">https://doi.org/10.1103/PhysRevB.79.180511</a>.","mla":"Leek, Peter, et al. “Using Sideband Transitions for Two-Qubit Operations in Superconducting Circuits.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 79, no. 18, American Physical Society, 2009, doi:<a href=\"https://doi.org/10.1103/PhysRevB.79.180511\">10.1103/PhysRevB.79.180511</a>.","apa":"Leek, P., Filipp, S., Maurer, P., Baur, M., Bianchetti, R., Fink, J. M., … Wallraff, A. (2009). Using sideband transitions for two-qubit operations in superconducting circuits. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.79.180511\">https://doi.org/10.1103/PhysRevB.79.180511</a>","ieee":"P. Leek <i>et al.</i>, “Using sideband transitions for two-qubit operations in superconducting circuits,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 79, no. 18. American Physical Society, 2009.","short":"P. Leek, S. Filipp, P. Maurer, M. Baur, R. Bianchetti, J.M. Fink, M. Göppl, L. Steffen, A. Wallraff, Physical Review B - Condensed Matter and Materials Physics 79 (2009).","ama":"Leek P, Filipp S, Maurer P, et al. Using sideband transitions for two-qubit operations in superconducting circuits. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2009;79(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.79.180511\">10.1103/PhysRevB.79.180511</a>","ista":"Leek P, Filipp S, Maurer P, Baur M, Bianchetti R, Fink JM, Göppl M, Steffen L, Wallraff A. 2009. Using sideband transitions for two-qubit operations in superconducting circuits. Physical Review B - Condensed Matter and Materials Physics. 79(18)."},"abstract":[{"lang":"eng","text":"We demonstrate the time-resolved driving of two-photon blue sideband transitions between superconducting qubits and a transmission line resonator. As an example of using these sideband transitions for a two-qubit operation, we implement a pulse sequence that first entangles one qubit with the resonator and subsequently distributes the entanglement between two qubits. We show the generation of 75% fidelity Bell states by this method. The full density matrix of the two-qubit system is extracted using joint measurement and quantum state tomography and shows close agreement with numerical simulation."}],"author":[{"full_name":"Leek, Peter J","last_name":"Leek","first_name":"Peter"},{"first_name":"Stefan","full_name":"Filipp, Stefan","last_name":"Filipp"},{"first_name":"Patrick","full_name":"Maurer, Patrick","last_name":"Maurer"},{"first_name":"Matthias","last_name":"Baur","full_name":"Baur, Matthias P"},{"full_name":"Bianchetti, R","last_name":"Bianchetti","first_name":"R"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X"},{"full_name":"Göppl, M","last_name":"Göppl","first_name":"M"},{"full_name":"Steffen, L. Kraig","last_name":"Steffen","first_name":"L."},{"first_name":"Andreas","full_name":"Wallraff, Andreas","last_name":"Wallraff"}],"publisher":"American Physical Society","extern":1,"quality_controlled":0,"volume":79,"doi":"10.1103/PhysRevB.79.180511","issue":"18","publication":"Physical Review B - Condensed Matter and Materials Physics","intvolume":"        79","publist_id":"5354","status":"public","acknowledgement":"This work was supported by ETH Zurich, the Swiss National Science Foundation, and by the EC via the EuroSQIP project and the Marie-Curie program (P. J. L.)"},{"_id":"1767","day":"19","date_updated":"2021-01-12T06:53:04Z","type":"journal_article","publication_status":"published","title":"Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit","date_created":"2018-12-11T11:53:54Z","year":"2009","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0812.4384"}],"month":"06","date_published":"2009-06-19T00:00:00Z","volume":102,"quality_controlled":0,"doi":"10.1103/PhysRevLett.102.243602","issue":"24","publist_id":"5352","publication":"Physical Review Letters","intvolume":"       102","acknowledgement":"This work was supported by the Swiss National Science Foundation and by ETH Zürich. P. J. L. acknowledges support from the EC via an Intra-European Marie-Curie Fellowship. A. B. was supported by NSERC, CIFAR, FQRNT, and Alfred P. Sloan Foundation","status":"public","citation":{"chicago":"Baur, Matthias, Stefan Filipp, R Bianchetti, Johannes M Fink, M Göppl, L. Steffen, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Measurement of Autler-Townes and Mollow Transitions in a Strongly Driven Superconducting Qubit.” <i>Physical Review Letters</i>. American Physical Society, 2009. <a href=\"https://doi.org/10.1103/PhysRevLett.102.243602\">https://doi.org/10.1103/PhysRevLett.102.243602</a>.","apa":"Baur, M., Filipp, S., Bianchetti, R., Fink, J. M., Göppl, M., Steffen, L., … Wallraff, A. (2009). Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.102.243602\">https://doi.org/10.1103/PhysRevLett.102.243602</a>","mla":"Baur, Matthias, et al. “Measurement of Autler-Townes and Mollow Transitions in a Strongly Driven Superconducting Qubit.” <i>Physical Review Letters</i>, vol. 102, no. 24, American Physical Society, 2009, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.102.243602\">10.1103/PhysRevLett.102.243602</a>.","ieee":"M. Baur <i>et al.</i>, “Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit,” <i>Physical Review Letters</i>, vol. 102, no. 24. American Physical Society, 2009.","short":"M. Baur, S. Filipp, R. Bianchetti, J.M. Fink, M. Göppl, L. Steffen, P. Leek, A. Blais, A. Wallraff, Physical Review Letters 102 (2009).","ista":"Baur M, Filipp S, Bianchetti R, Fink JM, Göppl M, Steffen L, Leek P, Blais A, Wallraff A. 2009. Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. Physical Review Letters. 102(24).","ama":"Baur M, Filipp S, Bianchetti R, et al. Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. <i>Physical Review Letters</i>. 2009;102(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.102.243602\">10.1103/PhysRevLett.102.243602</a>"},"oa":1,"abstract":[{"text":"We present spectroscopic measurements of the Autler-Townes doublet and the sidebands of the Mollow triplet in a driven superconducting qubit. The ground to first excited state transition of the qubit is strongly pumped while the resulting dressed qubit spectrum is probed with a weak tone. The corresponding transitions are detected using dispersive readout of the qubit coupled off resonantly to a microwave transmission line resonator. The observed frequencies of the Autler-Townes and Mollow spectral lines are in good agreement with a dispersive Jaynes-Cummings model taking into account higher excited qubit states and dispersive level shifts due to off-resonant drives.","lang":"eng"}],"extern":1,"publisher":"American Physical Society","author":[{"first_name":"Matthias","full_name":"Baur, Matthias P","last_name":"Baur"},{"last_name":"Filipp","full_name":"Filipp, Stefan","first_name":"Stefan"},{"full_name":"Bianchetti, R","last_name":"Bianchetti","first_name":"R"},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink","last_name":"Fink"},{"full_name":"Göppl, M","last_name":"Göppl","first_name":"M"},{"first_name":"L.","full_name":"Steffen, L. Kraig","last_name":"Steffen"},{"first_name":"Peter","last_name":"Leek","full_name":"Leek, Peter J"},{"last_name":"Blais","full_name":"Blais, Alexandre","first_name":"Alexandre"},{"last_name":"Wallraff","full_name":"Wallraff, Andreas","first_name":"Andreas"}]}]