[{"type":"journal_article","status":"public","author":[{"first_name":"Francesca","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"full_name":"Brock, Ben","first_name":"Ben","last_name":"Brock"},{"last_name":"Strasser","full_name":"Strasser, Ulrich","first_name":"Ulrich"},{"full_name":"Burlando, Paolo","first_name":"Paolo","last_name":"Burlando"},{"full_name":"Funk, Martin","first_name":"Martin","last_name":"Funk"},{"last_name":"Corripio","first_name":"Javier","full_name":"Corripio, Javier"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.3189/172756505781829124","open_access":"1"}],"day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"language":[{"iso":"eng"}],"publication":"Journal of Glaciology","title":"An enhanced temperature-index glacier melt model including the shortwave radiation balance: Development and testing for Haut Glacier d’Arolla, Switzerland","oa":1,"date_updated":"2023-02-20T08:45:37Z","article_processing_charge":"No","issue":"175","intvolume":"        51","scopus_import":"1","extern":"1","page":"573-587","quality_controlled":"1","volume":51,"publisher":"Cambridge University Press","date_published":"2005-10-19T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"An enhanced temperature-index glacier melt model, incorporating incoming shortwave radiation and albedo, is presented. The model is an attempt to combine the high temporal resolution and accuracy of physically based melt models with the lower data requirements and computational simplicity of empirical melt models, represented by the ‘degree-day’ method and its variants. The model is run with both measured and modelled radiation data, to test its applicability to glaciers with differing data availability. Five automatic weather stations were established on Haut Glacier d’Arolla, Switzerland, between May and September 2001. Reference surface melt rates were calculated using a physically based energy-balance melt model. The performance of the enhanced temperature-index model was tested at each of the four validation stations by comparing predicted hourly melt rates with reference melt rates. Predictions made with three other temperature-index models were evaluated in the same way for comparison. The enhanced temperature-index model offers significant improvements over the other temperature-index models, and accounts for 90–95% of the variation in the reference melt rate. The improvement is lower, but still significant, when the model is forced by modelled shortwave radiation data, thus offering a better alternative to existing models that require only temperature data input."}],"article_type":"original","_id":"12657","doi":"10.3189/172756505781829124","citation":{"apa":"Pellicciotti, F., Brock, B., Strasser, U., Burlando, P., Funk, M., &#38; Corripio, J. (2005). An enhanced temperature-index glacier melt model including the shortwave radiation balance: Development and testing for Haut Glacier d’Arolla, Switzerland. <i>Journal of Glaciology</i>. Cambridge University Press. <a href=\"https://doi.org/10.3189/172756505781829124\">https://doi.org/10.3189/172756505781829124</a>","ieee":"F. Pellicciotti, B. Brock, U. Strasser, P. Burlando, M. Funk, and J. Corripio, “An enhanced temperature-index glacier melt model including the shortwave radiation balance: Development and testing for Haut Glacier d’Arolla, Switzerland,” <i>Journal of Glaciology</i>, vol. 51, no. 175. Cambridge University Press, pp. 573–587, 2005.","ama":"Pellicciotti F, Brock B, Strasser U, Burlando P, Funk M, Corripio J. An enhanced temperature-index glacier melt model including the shortwave radiation balance: Development and testing for Haut Glacier d’Arolla, Switzerland. <i>Journal of Glaciology</i>. 2005;51(175):573-587. doi:<a href=\"https://doi.org/10.3189/172756505781829124\">10.3189/172756505781829124</a>","short":"F. Pellicciotti, B. Brock, U. Strasser, P. Burlando, M. Funk, J. Corripio, Journal of Glaciology 51 (2005) 573–587.","mla":"Pellicciotti, Francesca, et al. “An Enhanced Temperature-Index Glacier Melt Model Including the Shortwave Radiation Balance: Development and Testing for Haut Glacier d’Arolla, Switzerland.” <i>Journal of Glaciology</i>, vol. 51, no. 175, Cambridge University Press, 2005, pp. 573–87, doi:<a href=\"https://doi.org/10.3189/172756505781829124\">10.3189/172756505781829124</a>.","chicago":"Pellicciotti, Francesca, Ben Brock, Ulrich Strasser, Paolo Burlando, Martin Funk, and Javier Corripio. “An Enhanced Temperature-Index Glacier Melt Model Including the Shortwave Radiation Balance: Development and Testing for Haut Glacier d’Arolla, Switzerland.” <i>Journal of Glaciology</i>. Cambridge University Press, 2005. <a href=\"https://doi.org/10.3189/172756505781829124\">https://doi.org/10.3189/172756505781829124</a>.","ista":"Pellicciotti F, Brock B, Strasser U, Burlando P, Funk M, Corripio J. 2005. An enhanced temperature-index glacier melt model including the shortwave radiation balance: Development and testing for Haut Glacier d’Arolla, Switzerland. Journal of Glaciology. 51(175), 573–587."},"date_created":"2023-02-20T08:18:51Z","year":"2005"},{"date_created":"2018-12-11T11:51:13Z","title":"In vivo performance of genetically encoded indicators of neural activity in flies","publist_id":"5975","citation":{"apa":"Reiff, D., Ihring, A., Guerrero, G., Isacoff, E., Jösch, M. A., Nakai, J., &#38; Borst, A. (2005). In vivo performance of genetically encoded indicators of neural activity in flies. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.4900-04.2005\">https://doi.org/10.1523/JNEUROSCI.4900-04.2005</a>","short":"D. Reiff, A. Ihring, G. Guerrero, E. Isacoff, M.A. Jösch, J. Nakai, A. Borst, Journal of Neuroscience 25 (2005) 4766–4778.","ieee":"D. Reiff <i>et al.</i>, “In vivo performance of genetically encoded indicators of neural activity in flies,” <i>Journal of Neuroscience</i>, vol. 25, no. 19. Society for Neuroscience, pp. 4766–4778, 2005.","ama":"Reiff D, Ihring A, Guerrero G, et al. In vivo performance of genetically encoded indicators of neural activity in flies. <i>Journal of Neuroscience</i>. 2005;25(19):4766-4778. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.4900-04.2005\">10.1523/JNEUROSCI.4900-04.2005</a>","mla":"Reiff, Dierk, et al. “In Vivo Performance of Genetically Encoded Indicators of Neural Activity in Flies.” <i>Journal of Neuroscience</i>, vol. 25, no. 19, Society for Neuroscience, 2005, pp. 4766–78, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.4900-04.2005\">10.1523/JNEUROSCI.4900-04.2005</a>.","ista":"Reiff D, Ihring A, Guerrero G, Isacoff E, Jösch MA, Nakai J, Borst A. 2005. In vivo performance of genetically encoded indicators of neural activity in flies. Journal of Neuroscience. 25(19), 4766–4778.","chicago":"Reiff, Dierk, Alexandra Ihring, Giovanna Guerrero, Ehud Isacoff, Maximilian A Jösch, Junichi Nakai, and Alexander Borst. “In Vivo Performance of Genetically Encoded Indicators of Neural Activity in Flies.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2005. <a href=\"https://doi.org/10.1523/JNEUROSCI.4900-04.2005\">https://doi.org/10.1523/JNEUROSCI.4900-04.2005</a>."},"date_updated":"2021-01-12T06:49:42Z","acknowledgement":"This work was supported by the Max-Planck-Society.","issue":"19","year":"2005","intvolume":"        25","_id":"1298","doi":"10.1523/JNEUROSCI.4900-04.2005","publication":"Journal of Neuroscience","author":[{"last_name":"Reiff","full_name":"Reiff, Dierk F","first_name":"Dierk"},{"last_name":"Ihring","full_name":"Ihring, Alexandra","first_name":"Alexandra"},{"first_name":"Giovanna","full_name":"Guerrero, Giovanna","last_name":"Guerrero"},{"full_name":"Isacoff, Ehud Y","first_name":"Ehud","last_name":"Isacoff"},{"first_name":"Maximilian A","full_name":"Maximilian Jösch","orcid":"0000-0002-3937-1330","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nakai","full_name":"Nakai, Junichi","first_name":"Junichi"},{"last_name":"Borst","first_name":"Alexander","full_name":"Borst, Alexander"}],"publication_status":"published","day":"11","abstract":[{"lang":"eng","text":"Genetically encoded fluorescent probes of neural activity represent new promising tools for systems neuroscience. Here, we present a comparative in vivo analysis of 10 different genetically encoded calcium indicators, as well as the pH-sensitive synapto-pHluorin. We analyzed their fluorescence changes in presynaptic boutons of the Drosophila larval neuromuscular junction. Robust neural activity did not result in any or noteworthy fluorescence changes when Flash-Pericam, Camgaroo-1, and Camgaroo-2 were expressed. However, calculated on the raw data, fractional fluorescence changes up to 18% were reported by synapto-pHluorin, Yellow Cameleon 2.0, 2.3, and 3.3, Inverse-Pericam, GCaMP1.3, GCaMP1.6, and the troponin C-based calcium sensor TN-L15. The response characteristics of all of these indicators differed considerably from each other, with GCaMP1.6 reporting high rates of neural activity with the largest and fastest fluorescence changes. However, GCaMP1.6 suffered from photobleaching, whereas the fluorescence signals of the double-chromophore indicators were in general smaller but more photostable and reproducible, with TN-L15 showing the fastest rise of the signals at lower activity rates. We show for GCaMP1.3 and YC3.3 that an expanded range of neural activity evoked fairly linear fluorescence changes and a corresponding linear increase in the signal-to-noise ratio (SNR). The expression level of the indicator biased the signal kinetics and SNR, whereas the signal amplitude was independent. The presented data will be useful for in vivo experiments with respect to the selection of an appropriate indicator, as well as for the correct interpretation of the optical signals."}],"month":"03","page":"4766 - 4778","extern":1,"quality_controlled":0,"volume":25,"publisher":"Society for Neuroscience","date_published":"2005-03-11T00:00:00Z","status":"public","type":"journal_article"},{"publication_status":"published","author":[{"full_name":"Yampolsky, Lev Y","first_name":"Lev","last_name":"Yampolsky"},{"full_name":"Fyodor Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"},{"full_name":"Kondrashov, Alexey S","first_name":"Alexey","last_name":"Kondrashov"}],"month":"11","day":"01","abstract":[{"lang":"eng","text":"The impact of an amino acid replacement on the organism's fitness can vary from lethal to selectively neutral and even, in rare cases, beneficial. Substantial data are available on either pathogenic or acceptable replacements. However, the whole distribution of coefficients of selection against individual replacements is not known for any organism. To ascertain this distribution for human proteins, we combined data on pathogenic missense mutations, on human non-synonymous SNPs and on human-chimpanzee divergence of orthologous proteins. Fractions of amino acid replacements which reduce fitness by &gt;10-2, 10-2-10-4, 10-4-10-5 and &lt;10-5 are 25, 49, 14 and 12%, respectively. On average, the strength of selection against a replacement is substantially higher when chemically dissimilar amino acids are involved, and the Grantham's index of a replacement explains 35% of variance in the average logarithm of selection coefficients associated with different replacements. Still, the impact of a replacement depends on its context within the protein more than on its own nature. Reciprocal replacements are often associated with rather different selection coefficients, in particular, replacements of non-polar amino acids with polar ones are typically much more deleterious than replacements in the opposite direction. However, differences between evolutionary fluxes of reciprocal replacements are only weakly correlated with the differences between the corresponding selection coefficients."}],"publisher":"Oxford University Press","type":"journal_article","status":"public","date_published":"2005-11-01T00:00:00Z","page":"3191 - 3201","extern":1,"volume":14,"quality_controlled":0,"date_updated":"2021-01-12T08:19:13Z","issue":"21","year":"2005","title":"Distribution of the strength of selection against amino acid replacements in human proteins","publist_id":"6807","citation":{"apa":"Yampolsky, L., Kondrashov, F., &#38; Kondrashov, A. (2005). Distribution of the strength of selection against amino acid replacements in human proteins. <i>Human Molecular Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/hmg/ddi350\">https://doi.org/10.1093/hmg/ddi350</a>","ama":"Yampolsky L, Kondrashov F, Kondrashov A. Distribution of the strength of selection against amino acid replacements in human proteins. <i>Human Molecular Genetics</i>. 2005;14(21):3191-3201. doi:<a href=\"https://doi.org/10.1093/hmg/ddi350\">10.1093/hmg/ddi350</a>","ieee":"L. Yampolsky, F. Kondrashov, and A. Kondrashov, “Distribution of the strength of selection against amino acid replacements in human proteins,” <i>Human Molecular Genetics</i>, vol. 14, no. 21. Oxford University Press, pp. 3191–3201, 2005.","short":"L. Yampolsky, F. Kondrashov, A. Kondrashov, Human Molecular Genetics 14 (2005) 3191–3201.","mla":"Yampolsky, Lev, et al. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” <i>Human Molecular Genetics</i>, vol. 14, no. 21, Oxford University Press, 2005, pp. 3191–201, doi:<a href=\"https://doi.org/10.1093/hmg/ddi350\">10.1093/hmg/ddi350</a>.","ista":"Yampolsky L, Kondrashov F, Kondrashov A. 2005. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 14(21), 3191–3201.","chicago":"Yampolsky, Lev, Fyodor Kondrashov, and Alexey Kondrashov. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” <i>Human Molecular Genetics</i>. Oxford University Press, 2005. <a href=\"https://doi.org/10.1093/hmg/ddi350\">https://doi.org/10.1093/hmg/ddi350</a>."},"date_created":"2018-12-11T11:48:48Z","intvolume":"        14","_id":"843","publication":"Human Molecular Genetics","doi":"10.1093/hmg/ddi350"},{"intvolume":"        33","keyword":["Spectroscopy","Biochemistry"],"title":"SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds","citation":{"short":"P. Schanda, Ē. Kupče, B. Brutscher, Journal of Biomolecular NMR 33 (2005) 199–211.","ama":"Schanda P, Kupče Ē, Brutscher B. SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. <i>Journal of Biomolecular NMR</i>. 2005;33(4):199-211. doi:<a href=\"https://doi.org/10.1007/s10858-005-4425-x\">10.1007/s10858-005-4425-x</a>","ieee":"P. Schanda, Ē. Kupče, and B. Brutscher, “SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds,” <i>Journal of Biomolecular NMR</i>, vol. 33, no. 4. Springer Nature, pp. 199–211, 2005.","ista":"Schanda P, Kupče Ē, Brutscher B. 2005. SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. Journal of Biomolecular NMR. 33(4), 199–211.","mla":"Schanda, Paul, et al. “SOFAST-HMQC Experiments for Recording Two-Dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds.” <i>Journal of Biomolecular NMR</i>, vol. 33, no. 4, Springer Nature, 2005, pp. 199–211, doi:<a href=\"https://doi.org/10.1007/s10858-005-4425-x\">10.1007/s10858-005-4425-x</a>.","chicago":"Schanda, Paul, Ēriks Kupče, and Bernhard Brutscher. “SOFAST-HMQC Experiments for Recording Two-Dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2005. <a href=\"https://doi.org/10.1007/s10858-005-4425-x\">https://doi.org/10.1007/s10858-005-4425-x</a>.","apa":"Schanda, P., Kupče, Ē., &#38; Brutscher, B. (2005). SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-005-4425-x\">https://doi.org/10.1007/s10858-005-4425-x</a>"},"date_created":"2020-09-18T10:13:59Z","year":"2005","article_processing_charge":"No","issue":"4","date_updated":"2021-01-12T08:19:38Z","doi":"10.1007/s10858-005-4425-x","publication":"Journal of Biomolecular NMR","article_type":"original","_id":"8491","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Fast multidimensional NMR with a time resolution of a few seconds provides a new tool for high throughput screening and site-resolved real-time studies of kinetic molecular processes by NMR. Recently we have demonstrated the feasibility to record protein 1H–15N correlation spectra in a few seconds of acquisition time using a new SOFAST-HMQC experiment (Schanda and Brutscher (2005) J. Am. Chem. Soc. 127, 8014). Here, we investigate in detail the performance of SOFAST-HMQC to record 1H–15N and 1H−13C correlation spectra of proteins of different size and at different magnetic field strengths. Compared to standard 1H–15N correlation experiments SOFAST-HMQC provides a significant gain in sensitivity, especially for fast repetition rates. Guidelines are provided on how to set up SOFAST-HMQC experiments for a given protein sample. In addition, an alternative pulse scheme, IPAP-SOFAST-HMQC is presented that allows application on NMR spectrometers equipped with cryogenic probes, and fast measurement of one-bond 1H–13C and 1H–15N scalar and residual dipolar coupling constants."}],"day":"01","oa_version":"None","publication_identifier":{"issn":["0925-2738","1573-5001"]},"month":"12","author":[{"full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606"},{"first_name":"Ēriks","full_name":"Kupče, Ēriks","last_name":"Kupče"},{"first_name":"Bernhard","full_name":"Brutscher, Bernhard","last_name":"Brutscher"}],"publication_status":"published","volume":33,"quality_controlled":"1","page":"199-211","extern":"1","type":"journal_article","status":"public","date_published":"2005-12-01T00:00:00Z","publisher":"Springer Nature"},{"doi":"10.1021/ja051306e","publication":"Journal of the American Chemical Society","_id":"8492","language":[{"iso":"eng"}],"article_type":"original","intvolume":"       127","citation":{"ista":"Schanda P, Brutscher B. 2005. Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. Journal of the American Chemical Society. 127(22), 8014–8015.","chicago":"Schanda, Paul, and Bernhard Brutscher. “Very Fast Two-Dimensional NMR Spectroscopy for Real-Time Investigation of Dynamic Events in Proteins on the Time Scale of Seconds.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2005. <a href=\"https://doi.org/10.1021/ja051306e\">https://doi.org/10.1021/ja051306e</a>.","mla":"Schanda, Paul, and Bernhard Brutscher. “Very Fast Two-Dimensional NMR Spectroscopy for Real-Time Investigation of Dynamic Events in Proteins on the Time Scale of Seconds.” <i>Journal of the American Chemical Society</i>, vol. 127, no. 22, American Chemical Society, 2005, pp. 8014–15, doi:<a href=\"https://doi.org/10.1021/ja051306e\">10.1021/ja051306e</a>.","ama":"Schanda P, Brutscher B. Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. <i>Journal of the American Chemical Society</i>. 2005;127(22):8014-8015. doi:<a href=\"https://doi.org/10.1021/ja051306e\">10.1021/ja051306e</a>","ieee":"P. Schanda and B. Brutscher, “Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds,” <i>Journal of the American Chemical Society</i>, vol. 127, no. 22. American Chemical Society, pp. 8014–8015, 2005.","short":"P. Schanda, B. Brutscher, Journal of the American Chemical Society 127 (2005) 8014–8015.","apa":"Schanda, P., &#38; Brutscher, B. (2005). Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja051306e\">https://doi.org/10.1021/ja051306e</a>"},"date_created":"2020-09-18T10:14:05Z","title":"Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"date_updated":"2021-01-12T08:19:39Z","issue":"22","article_processing_charge":"No","year":"2005","extern":"1","page":"8014-8015","quality_controlled":"1","volume":127,"publisher":"American Chemical Society","date_published":"2005-05-14T00:00:00Z","status":"public","type":"journal_article","day":"14","oa_version":"None","abstract":[{"text":"We demonstrate for different protein samples that 2D 1H−15N correlation NMR spectra can be recorded in a few seconds of acquisition time using a new band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence experiment. This has enabled us to measure fast hydrogen−deuterium exchange rate constants along the backbone of a small globular protein fragment by real-time 2D NMR.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","publication_identifier":{"issn":["0002-7863","1520-5126"]},"publication_status":"published","author":[{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"}]},{"author":[{"last_name":"Bourgain","full_name":"Bourgain, Jean","first_name":"Jean"},{"first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin"}],"publication_status":"published","oa_version":"None","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The purpose of this paper is to construct examples of diffusion for E-Hamiltonian perturbations\r\nof completely integrable Hamiltonian systems in 2d-dimensional phase space, with d large.\r\nIn the first part of the paper, simple and explicit examples are constructed illustrating absence\r\nof ‘long-time’ stability for size E Hamiltonian perturbations of quasi-convex integrable systems\r\nalready when the dimension 2d of phase space becomes as large as log 1/E . We first produce\r\nthe example in Gevrey class and then a real analytic one, with some additional work.\r\nIn the second part, we consider again E-Hamiltonian perturbations of completely integrable\r\nHamiltonian system in 2d-dimensional space with E-small but not too small, |E| > exp(−d), with\r\nd the number of degrees of freedom assumed large. It is shown that for a class of analytic\r\ntime-periodic perturbations, there exist linearly diffusing trajectories. The underlying idea for\r\nboth examples is similar and consists in coupling a fixed degree of freedom with a large\r\nnumber of them. The procedure and analytical details are however significantly different. As\r\nmentioned, the construction in Part I is totally elementary while Part II is more involved, relying\r\nin particular on the theory of normally hyperbolic invariant manifolds, methods of generating\r\nfunctions, Aubry–Mather theory, and Mather’s variational methods.","lang":"eng"}],"publication_identifier":{"issn":["0022-1236"]},"month":"12","page":"1-61","extern":"1","quality_controlled":"1","volume":229,"publisher":"Elsevier","type":"journal_article","date_published":"2005-12-01T00:00:00Z","status":"public","citation":{"mla":"Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian Systems.” <i>Journal of Functional Analysis</i>, vol. 229, no. 1, Elsevier, 2005, pp. 1–61, doi:<a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">10.1016/j.jfa.2004.09.006</a>.","chicago":"Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian Systems.” <i>Journal of Functional Analysis</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">https://doi.org/10.1016/j.jfa.2004.09.006</a>.","ista":"Bourgain J, Kaloshin V. 2005. On diffusion in high-dimensional Hamiltonian systems. Journal of Functional Analysis. 229(1), 1–61.","short":"J. Bourgain, V. Kaloshin, Journal of Functional Analysis 229 (2005) 1–61.","ama":"Bourgain J, Kaloshin V. On diffusion in high-dimensional Hamiltonian systems. <i>Journal of Functional Analysis</i>. 2005;229(1):1-61. doi:<a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">10.1016/j.jfa.2004.09.006</a>","ieee":"J. Bourgain and V. Kaloshin, “On diffusion in high-dimensional Hamiltonian systems,” <i>Journal of Functional Analysis</i>, vol. 229, no. 1. Elsevier, pp. 1–61, 2005.","apa":"Bourgain, J., &#38; Kaloshin, V. (2005). On diffusion in high-dimensional Hamiltonian systems. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">https://doi.org/10.1016/j.jfa.2004.09.006</a>"},"title":"On diffusion in high-dimensional Hamiltonian systems","date_created":"2020-09-18T10:49:06Z","keyword":["Analysis"],"date_updated":"2021-01-12T08:19:49Z","year":"2005","issue":"1","article_processing_charge":"No","intvolume":"       229","article_type":"original","_id":"8516","language":[{"iso":"eng"}],"doi":"10.1016/j.jfa.2004.09.006","publication":"Journal of Functional Analysis"},{"pmid":1,"type":"journal_article","status":"public","author":[{"first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov"}],"main_file_link":[{"url":"http://pleiades.online/abstract/biophys/5/biophys0349_abstract.pdf"}],"oa_version":"None","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","language":[{"iso":"eng"}],"publication":"Biofizika","title":"The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution","date_updated":"2021-01-12T08:21:01Z","issue":"3","article_processing_charge":"No","intvolume":"        50","page":"389 - 395","extern":"1","quality_controlled":"1","volume":50,"publisher":"Pleiades Publishing","date_published":"2005-05-01T00:00:00Z","publication_status":"published","external_id":{"pmid":["15977826"]},"abstract":[{"text":"Sequence analysis of protein and mitochondrially encoded tRNA genes shows that substitutions\r\nproducing pathogenic effects in humans are often found in normal, healthy individuals from other species.\r\nAnalysis of stability of protein and tRNA structures shows that the disease-causing effects of pathogenic\r\nmutations can be neutralized by other, compensatory substitutions that restore the structural stability of the\r\nmolecule. Further study of such substitutions will, hopefully, lead to new methods for curing genetic dis-\r\neases that may be based on the correction of molecule stability as a whole instead of reversing an individual\r\npathogenic mutation.","lang":"eng"}],"article_type":"original","_id":"877","citation":{"short":"F. Kondrashov, Biofizika 50 (2005) 389–395.","ama":"Kondrashov F. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. <i>Biofizika</i>. 2005;50(3):389-395.","ieee":"F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution,” <i>Biofizika</i>, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005.","chicago":"Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” <i>Biofizika</i>. Pleiades Publishing, 2005.","mla":"Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” <i>Biofizika</i>, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 389–95.","ista":"Kondrashov F. 2005. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. 50(3), 389–395.","apa":"Kondrashov, F. (2005). The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. <i>Biofizika</i>. Pleiades Publishing."},"date_created":"2018-12-11T11:48:58Z","publist_id":"6769","year":"2005"},{"publication_status":"published","author":[{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","first_name":"Fyodor"}],"month":"01","abstract":[{"lang":"eng","text":"Negative trade-offs are thought to be a pervasive phenomenon and to inhibit evolution at all levels. New evidence shows that at the molecular level, there may be no trade-offs preventing the emergence of an enzyme with multiple functions.\n"}],"day":"01","type":"journal_article","date_published":"2005-01-01T00:00:00Z","status":"public","publisher":"Nature Publishing Group","quality_controlled":0,"volume":37,"extern":1,"page":"9 - 10","year":"2005","issue":"1","date_updated":"2021-01-12T08:21:02Z","citation":{"apa":"Kondrashov, F. (2005). In search of the limits of evolution. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng0105-9\">https://doi.org/10.1038/ng0105-9</a>","chicago":"Kondrashov, Fyodor. “In Search of the Limits of Evolution.” <i>Nature Genetics</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/ng0105-9\">https://doi.org/10.1038/ng0105-9</a>.","mla":"Kondrashov, Fyodor. “In Search of the Limits of Evolution.” <i>Nature Genetics</i>, vol. 37, no. 1, Nature Publishing Group, 2005, pp. 9–10, doi:<a href=\"https://doi.org/10.1038/ng0105-9\">10.1038/ng0105-9</a>.","ista":"Kondrashov F. 2005. In search of the limits of evolution. Nature Genetics. 37(1), 9–10.","short":"F. Kondrashov, Nature Genetics 37 (2005) 9–10.","ama":"Kondrashov F. In search of the limits of evolution. <i>Nature Genetics</i>. 2005;37(1):9-10. doi:<a href=\"https://doi.org/10.1038/ng0105-9\">10.1038/ng0105-9</a>","ieee":"F. Kondrashov, “In search of the limits of evolution,” <i>Nature Genetics</i>, vol. 37, no. 1. Nature Publishing Group, pp. 9–10, 2005."},"date_created":"2018-12-11T11:48:59Z","publist_id":"6770","title":"In search of the limits of evolution","intvolume":"        37","_id":"878","publication":"Nature Genetics","doi":"10.1038/ng0105-9"},{"volume":50,"quality_controlled":"1","page":"396 - 403","extern":"1","status":"public","date_published":"2005-05-01T00:00:00Z","type":"journal_article","pmid":1,"publisher":"Pleiades Publishing","publication_status":"published","author":[{"first_name":"Fyodor","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"}],"abstract":[{"lang":"eng","text":"Here, I describe a case of loss of the D-arm by mitochondrial cysteine tRNA in the nine-banded armadillo (Dasypus novemcinctus) convergent with mt tRNASer(AGY). Such evolution sheds light on the relationship between structure and function of tRNA molecules and its impact on the patterns of molecular evolution."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","external_id":{"pmid":["15977827"]},"day":"01","main_file_link":[{"url":"http://pleiades.online/abstract/biophys/5/biophys0356_abstract.pdf"}],"month":"05","_id":"880","language":[{"iso":"eng"}],"publication":"Biofizika","date_created":"2018-12-11T11:48:59Z","title":"The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus","publist_id":"6768","citation":{"apa":"Kondrashov, F. (2005). The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. <i>Biofizika</i>. Pleiades Publishing.","mla":"Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” <i>Biofizika</i>, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 396–403.","ista":"Kondrashov F. 2005. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. 50(3), 396–403.","chicago":"Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” <i>Biofizika</i>. Pleiades Publishing, 2005.","ama":"Kondrashov F. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. <i>Biofizika</i>. 2005;50(3):396-403.","ieee":"F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” <i>Biofizika</i>, vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005.","short":"F. Kondrashov, Biofizika 50 (2005) 396–403."},"article_processing_charge":"No","issue":"3","year":"2005","date_updated":"2021-01-12T08:21:07Z","intvolume":"        50"},{"publisher":"Oxford University Press","status":"public","type":"journal_article","date_published":"2005-08-15T00:00:00Z","page":"2415 - 2419","extern":1,"quality_controlled":0,"volume":14,"author":[{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","first_name":"Fyodor"}],"publication_status":"published","month":"08","day":"15","abstract":[{"lang":"eng","text":"Some mutations in human mitochondrial tRNAs are severely pathogenic. The available computational methods have a poor record of predicting the impact of a tRNA mutation on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms were compared. Mutations that are pathogenic to humans occupy more conservative sites, are only rarely fixed in closely related species, and, when located in stem structures, often disrupt Watson-Crick pairing and display signs of compensatory evolution. These observations make it possible to classify ∼90% of all known pathogenic mutations as deleterious together with only ∼30% of polymorphisms. These polymorphisms segregate at frequencies that are more than two times lower than frequencies of polymorphisms classified as benign, indicating that at least ∼30% of known polymorphisms in mitochondrial tRNAs affect fitness negatively."}],"_id":"882","publication":"Human Molecular Genetics","doi":"10.1093/hmg/ddi243","acknowledgement":"The author thanks P. Andolfatto, D. Bachtrog, N. Esipova, S. Makeev, A. Kondrashov, V. Ramensky, V. Tumanyan and P. Vlasov for a critical reading of the manuscript. The author is an NSF Graduate Research Fellow. This work was supported by a Contract of the Russian Ministry of Science and Education (02.434.11.1008) and a grant on Molecular and Cellular Biology from RAS.\n","date_updated":"2021-01-12T08:21:10Z","year":"2005","issue":"16","publist_id":"6767","date_created":"2018-12-11T11:49:00Z","citation":{"ama":"Kondrashov F. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. <i>Human Molecular Genetics</i>. 2005;14(16):2415-2419. doi:<a href=\"https://doi.org/10.1093/hmg/ddi243\">10.1093/hmg/ddi243</a>","ieee":"F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded human tRNAs,” <i>Human Molecular Genetics</i>, vol. 14, no. 16. Oxford University Press, pp. 2415–2419, 2005.","short":"F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419.","mla":"Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” <i>Human Molecular Genetics</i>, vol. 14, no. 16, Oxford University Press, 2005, pp. 2415–19, doi:<a href=\"https://doi.org/10.1093/hmg/ddi243\">10.1093/hmg/ddi243</a>.","ista":"Kondrashov F. 2005. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. 14(16), 2415–2419.","chicago":"Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” <i>Human Molecular Genetics</i>. Oxford University Press, 2005. <a href=\"https://doi.org/10.1093/hmg/ddi243\">https://doi.org/10.1093/hmg/ddi243</a>.","apa":"Kondrashov, F. (2005). Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. <i>Human Molecular Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/hmg/ddi243\">https://doi.org/10.1093/hmg/ddi243</a>"},"title":"Prediction of pathogenic mutations in mitochondrially encoded human tRNAs","intvolume":"        14"},{"author":[{"first_name":"Ingo","full_name":"Jordan, Ingo K","last_name":"Jordan"},{"full_name":"Fyodor Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Adzhubeǐ, Ivan A","first_name":"Ivan","last_name":"Adzhubeǐ"},{"last_name":"Wolf","first_name":"Yuri","full_name":"Wolf, Yuri I"},{"full_name":"Koonin, Eugene V","first_name":"Eugene","last_name":"Koonin"},{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey S"},{"last_name":"Sunyaev","first_name":"Shamil","full_name":"Sunyaev, Shamil R"}],"publication_status":"published","abstract":[{"text":"Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G+C)-rich (or (A+T)-rich) genomes contain more (or fewer) amino acids encoded by (G+C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day.","lang":"eng"}],"day":"10","month":"02","quality_controlled":0,"volume":433,"extern":1,"page":"633 - 638","type":"journal_article","status":"public","date_published":"2005-02-10T00:00:00Z","publisher":"Nature Publishing Group","publist_id":"6757","date_created":"2018-12-11T11:49:03Z","title":"A universal trend of amino acid gain and loss in protein evolution","citation":{"mla":"Jordan, Ingo, et al. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” <i>Nature</i>, vol. 433, no. 7026, Nature Publishing Group, 2005, pp. 633–38, doi:<a href=\"https://doi.org/10.1038/nature03306\">10.1038/nature03306</a>.","chicago":"Jordan, Ingo, Fyodor Kondrashov, Ivan Adzhubeǐ, Yuri Wolf, Eugene Koonin, Alexey Kondrashov, and Shamil Sunyaev. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” <i>Nature</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/nature03306\">https://doi.org/10.1038/nature03306</a>.","ista":"Jordan I, Kondrashov F, Adzhubeǐ I, Wolf Y, Koonin E, Kondrashov A, Sunyaev S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature. 433(7026), 633–638.","ieee":"I. Jordan <i>et al.</i>, “A universal trend of amino acid gain and loss in protein evolution,” <i>Nature</i>, vol. 433, no. 7026. Nature Publishing Group, pp. 633–638, 2005.","ama":"Jordan I, Kondrashov F, Adzhubeǐ I, et al. A universal trend of amino acid gain and loss in protein evolution. <i>Nature</i>. 2005;433(7026):633-638. doi:<a href=\"https://doi.org/10.1038/nature03306\">10.1038/nature03306</a>","short":"I. Jordan, F. Kondrashov, I. Adzhubeǐ, Y. Wolf, E. Koonin, A. Kondrashov, S. Sunyaev, Nature 433 (2005) 633–638.","apa":"Jordan, I., Kondrashov, F., Adzhubeǐ, I., Wolf, Y., Koonin, E., Kondrashov, A., &#38; Sunyaev, S. (2005). A universal trend of amino acid gain and loss in protein evolution. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature03306\">https://doi.org/10.1038/nature03306</a>"},"year":"2005","issue":"7026","acknowledgement":"S.S. and I.A.A. were supported by the Genome Canada Foundation.","date_updated":"2021-01-12T08:21:23Z","intvolume":"       433","_id":"893","doi":"10.1038/nature03306","publication":"Nature"},{"article_type":"original","_id":"8028","doi":"10.1523/jneurosci.3508-05.2005","year":"2005","citation":{"apa":"Vogels, T. P., &#38; Abbott, L. F. (2005). Signal propagation and logic gating in networks of integrate-and-fire neurons. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">https://doi.org/10.1523/jneurosci.3508-05.2005</a>","mla":"Vogels, Tim P., and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” <i>Journal of Neuroscience</i>, vol. 25, no. 46, Society for Neuroscience, 2005, pp. 10786–95, doi:<a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">10.1523/jneurosci.3508-05.2005</a>.","chicago":"Vogels, Tim P, and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2005. <a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">https://doi.org/10.1523/jneurosci.3508-05.2005</a>.","ista":"Vogels TP, Abbott LF. 2005. Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. 25(46), 10786–10795.","short":"T.P. Vogels, L.F. Abbott, Journal of Neuroscience 25 (2005) 10786–10795.","ama":"Vogels TP, Abbott LF. Signal propagation and logic gating in networks of integrate-and-fire neurons. <i>Journal of Neuroscience</i>. 2005;25(46):10786-10795. doi:<a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">10.1523/jneurosci.3508-05.2005</a>","ieee":"T. P. Vogels and L. F. Abbott, “Signal propagation and logic gating in networks of integrate-and-fire neurons,” <i>Journal of Neuroscience</i>, vol. 25, no. 46. Society for Neuroscience, pp. 10786–10795, 2005."},"date_created":"2020-06-25T13:12:33Z","date_published":"2005-11-16T00:00:00Z","publisher":"Society for Neuroscience","volume":25,"quality_controlled":"1","page":"10786-10795","extern":"1","publication_status":"published","abstract":[{"text":"Transmission of signals within the brain is essential for cognitive function, but it is not clear how neural circuits support reliable and accurate signal propagation over a sufficiently large dynamic range. Two modes of propagation have been studied: synfire chains, in which synchronous activity travels through feedforward layers of a neuronal network, and the propagation of fluctuations in firing rate across these layers. In both cases, a sufficient amount of noise, which was added to previous models from an external source, had to be included to support stable propagation. Sparse, randomly connected networks of spiking model neurons can generate chaotic patterns of activity. We investigate whether this activity, which is a more realistic noise source, is sufficient to allow for signal transmission. We find that, for rate-coded signals but not for synfire chains, such networks support robust and accurate signal reproduction through up to six layers if appropriate adjustments are made in synaptic strengths. We investigate the factors affecting transmission and show that multiple signals can propagate simultaneously along different pathways. Using this feature, we show how different types of logic gates can arise within the architecture of the random network through the strengthening of specific synapses.","lang":"eng"}],"external_id":{"pmid":["16291952"]},"language":[{"iso":"eng"}],"publication":"Journal of Neuroscience","issue":"46","article_processing_charge":"No","oa":1,"date_updated":"2021-01-12T08:16:37Z","title":"Signal propagation and logic gating in networks of integrate-and-fire neurons","intvolume":"        25","type":"journal_article","status":"public","pmid":1,"author":[{"first_name":"Tim P","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","orcid":"0000-0003-3295-6181"},{"first_name":"L. F.","full_name":"Abbott, L. F.","last_name":"Abbott"}],"publication_identifier":{"issn":["0270-6474","1529-2401"]},"month":"11","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa_version":"Published Version","day":"16","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6725859/"}]},{"publication_status":"published","abstract":[{"lang":"eng","text":"Neural network modeling is often concerned with stimulus-driven responses, but most of the activity in the brain is internally generated. Here, we review network models of internally generated activity, focusing on three types of network dynamics: (a) sustained responses to transient stimuli, which provide a model of working memory; (b) oscillatory network activity; and (c) chaotic activity, which models complex patterns of background spiking in cortical and other circuits. We also review propagation of stimulus-driven activity through spontaneously active networks. Exploring these aspects of neural network dynamics is critical for understanding how neural circuits produce cognitive function."}],"external_id":{"pmid":["16022600"]},"quality_controlled":"1","volume":28,"page":"357-376","extern":"1","date_published":"2005-07-21T00:00:00Z","publisher":"Annual Reviews","date_created":"2020-06-25T13:13:11Z","citation":{"apa":"Vogels, T. P., Rajan, K., &#38; Abbott, L. F. (2005). Neural network dynamics. <i>Annual Review of Neuroscience</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">https://doi.org/10.1146/annurev.neuro.28.061604.135637</a>","chicago":"Vogels, Tim P, Kanaka Rajan, and L.F. Abbott. “Neural Network Dynamics.” <i>Annual Review of Neuroscience</i>. Annual Reviews, 2005. <a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">https://doi.org/10.1146/annurev.neuro.28.061604.135637</a>.","mla":"Vogels, Tim P., et al. “Neural Network Dynamics.” <i>Annual Review of Neuroscience</i>, vol. 28, no. 1, Annual Reviews, 2005, pp. 357–76, doi:<a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">10.1146/annurev.neuro.28.061604.135637</a>.","ista":"Vogels TP, Rajan K, Abbott LF. 2005. Neural network dynamics. Annual Review of Neuroscience. 28(1), 357–376.","short":"T.P. Vogels, K. Rajan, L.F. Abbott, Annual Review of Neuroscience 28 (2005) 357–376.","ama":"Vogels TP, Rajan K, Abbott LF. Neural network dynamics. <i>Annual Review of Neuroscience</i>. 2005;28(1):357-376. doi:<a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">10.1146/annurev.neuro.28.061604.135637</a>","ieee":"T. P. Vogels, K. Rajan, and L. F. Abbott, “Neural network dynamics,” <i>Annual Review of Neuroscience</i>, vol. 28, no. 1. Annual Reviews, pp. 357–376, 2005."},"year":"2005","article_type":"review","_id":"8029","doi":"10.1146/annurev.neuro.28.061604.135637","author":[{"last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P","full_name":"Vogels, Tim P"},{"first_name":"Kanaka","full_name":"Rajan, Kanaka","last_name":"Rajan"},{"first_name":"L.F.","full_name":"Abbott, L.F.","last_name":"Abbott"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa_version":"None","day":"21","publication_identifier":{"issn":["0147-006X","1545-4126"]},"month":"07","status":"public","type":"journal_article","pmid":1,"title":"Neural network dynamics","article_processing_charge":"No","issue":"1","date_updated":"2021-01-12T08:16:37Z","intvolume":"        28","language":[{"iso":"eng"}],"publication":"Annual Review of Neuroscience"},{"publication_status":"published","author":[{"first_name":"Giovanni","full_name":"Costantini, Giovanni","last_name":"Costantini"},{"full_name":"Rastelli, Armando","first_name":"Armando","last_name":"Rastelli"},{"first_name":"Carlos","full_name":"Manzano, Carlos","last_name":"Manzano"},{"first_name":"P","full_name":"Acosta-Diaz, P","last_name":"Acosta Diaz"},{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Georgios Katsaros","first_name":"Georgios"},{"last_name":"Songmuang","first_name":"Rudeeson","full_name":"Songmuang, Rudeeson"},{"first_name":"Oliver","full_name":"Schmidt, Oliver G","last_name":"Schmidt"},{"first_name":"Hans","full_name":"Von Känel, Hans","last_name":"Von Känel"},{"last_name":"Kern","full_name":"Kern, Klaus","first_name":"Klaus"}],"day":"01","abstract":[{"lang":"eng","text":"A systematic study of the morphology of self-organized islands in the InAs/GaAs(0 0 1) and Ge/Si(0 0 1) systems is presented, based on high-resolution scanning tunneling microscopy measurements. We demonstrate that in both cases two main island families coexist: smaller pyramids bound by one type of shallow facets and larger multifaceted domes. Their structure and facet orientation are precisely determined, thus solving a highly debated argument in the case of InAs/GaAs(0 0 1). The comparison between the two material systems reveals the existence of striking similarities that extend even to the nature of island precursors and to the islands that form when depositing InGaAs or GeSi alloys. The implications of these observations on a possible universal description of the Stranski-Krastanow growth mode are discussed with respect to recent theoretical results."}],"month":"05","page":"38 - 45","extern":1,"quality_controlled":0,"volume":278,"publisher":"Elsevier","status":"public","date_published":"2005-05-01T00:00:00Z","type":"journal_article","citation":{"chicago":"Costantini, Giovanni, Armando Rastelli, Carlos Manzano, P Acosta Diaz, Georgios Katsaros, Rudeeson Songmuang, Oliver Schmidt, Hans Von Känel, and Klaus Kern. “Pyramids and Domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) Systems.” <i>Journal of Crystal Growth</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.jcrysgro.2004.12.047\">https://doi.org/10.1016/j.jcrysgro.2004.12.047</a>.","mla":"Costantini, Giovanni, et al. “Pyramids and Domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) Systems.” <i>Journal of Crystal Growth</i>, vol. 278, no. 1–4, Elsevier, 2005, pp. 38–45, doi:<a href=\"https://doi.org/10.1016/j.jcrysgro.2004.12.047\">10.1016/j.jcrysgro.2004.12.047</a>.","ista":"Costantini G, Rastelli A, Manzano C, Acosta Diaz P, Katsaros G, Songmuang R, Schmidt O, Von Känel H, Kern K. 2005. Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) systems. Journal of Crystal Growth. 278(1–4), 38–45.","ama":"Costantini G, Rastelli A, Manzano C, et al. Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) systems. <i>Journal of Crystal Growth</i>. 2005;278(1-4):38-45. doi:<a href=\"https://doi.org/10.1016/j.jcrysgro.2004.12.047\">10.1016/j.jcrysgro.2004.12.047</a>","ieee":"G. Costantini <i>et al.</i>, “Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) systems,” <i>Journal of Crystal Growth</i>, vol. 278, no. 1–4. Elsevier, pp. 38–45, 2005.","short":"G. Costantini, A. Rastelli, C. Manzano, P. Acosta Diaz, G. Katsaros, R. Songmuang, O. Schmidt, H. Von Känel, K. Kern, Journal of Crystal Growth 278 (2005) 38–45.","apa":"Costantini, G., Rastelli, A., Manzano, C., Acosta Diaz, P., Katsaros, G., Songmuang, R., … Kern, K. (2005). Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) systems. <i>Journal of Crystal Growth</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcrysgro.2004.12.047\">https://doi.org/10.1016/j.jcrysgro.2004.12.047</a>"},"date_created":"2018-12-11T11:53:45Z","title":"Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) systems","publist_id":"5384","date_updated":"2021-01-12T06:52:54Z","issue":"1-4","year":"2005","intvolume":"       278","_id":"1740","doi":"10.1016/j.jcrysgro.2004.12.047","publication":"Journal of Crystal Growth"},{"extern":1,"volume":94,"quality_controlled":0,"publisher":"American Physical Society","type":"journal_article","status":"public","date_published":"2005-06-03T00:00:00Z","publication_status":"published","author":[{"first_name":"Ulrich","full_name":"Denker, Ulrich","last_name":"Denker"},{"first_name":"Armando","full_name":"Rastelli, Armando","last_name":"Rastelli"},{"last_name":"Stoffel","first_name":"Mathieu","full_name":"Stoffel, Mathieu"},{"last_name":"Tersoff","first_name":"Jerry","full_name":"Tersoff, Jerry"},{"full_name":"Georgios Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"},{"first_name":"Giovanni","full_name":"Costantini, Giovanni","last_name":"Costantini"},{"last_name":"Kern","first_name":"Klaus","full_name":"Kern, Klaus"},{"last_name":"Jin Phillipp","full_name":"Jin-Phillipp, Neng Y","first_name":"Neng"},{"full_name":"Jesson, David E","first_name":"David","last_name":"Jesson"},{"last_name":"Schmidt","first_name":"Oliver","full_name":"Schmidt, Oliver G"}],"day":"03","abstract":[{"lang":"eng","text":"SiGe islands move laterally on a Si(001) substrate during in situ postgrowth annealing. This surprising behavior is revealed by an analysis of the substrate surface morphology after island removal using wet chemical etching. We explain the island motion by asymmetric surface-mediated alloying. Material leaves one side of the island by surface diffusion, and mixes with additional Si from the surrounding surface as it redeposits on the other side. Thus the island moves laterally while becoming larger and more dilute."}],"month":"06","_id":"1741","doi":"10.1103/PhysRevLett.94.216103","publication":"Physical Review Letters","date_created":"2018-12-11T11:53:46Z","publist_id":"5383","citation":{"chicago":"Denker, Ulrich, Armando Rastelli, Mathieu Stoffel, Jerry Tersoff, Georgios Katsaros, Giovanni Costantini, Klaus Kern, Neng Jin Phillipp, David Jesson, and Oliver Schmidt. “Lateral Motion of SiGe Islands Driven by Surface-Mediated Alloying.” <i>Physical Review Letters</i>. American Physical Society, 2005. <a href=\"https://doi.org/10.1103/PhysRevLett.94.216103\">https://doi.org/10.1103/PhysRevLett.94.216103</a>.","ista":"Denker U, Rastelli A, Stoffel M, Tersoff J, Katsaros G, Costantini G, Kern K, Jin Phillipp N, Jesson D, Schmidt O. 2005. Lateral motion of SiGe islands driven by surface-mediated alloying. Physical Review Letters. 94(21).","mla":"Denker, Ulrich, et al. “Lateral Motion of SiGe Islands Driven by Surface-Mediated Alloying.” <i>Physical Review Letters</i>, vol. 94, no. 21, American Physical Society, 2005, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.94.216103\">10.1103/PhysRevLett.94.216103</a>.","ieee":"U. Denker <i>et al.</i>, “Lateral motion of SiGe islands driven by surface-mediated alloying,” <i>Physical Review Letters</i>, vol. 94, no. 21. American Physical Society, 2005.","ama":"Denker U, Rastelli A, Stoffel M, et al. Lateral motion of SiGe islands driven by surface-mediated alloying. <i>Physical Review Letters</i>. 2005;94(21). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.94.216103\">10.1103/PhysRevLett.94.216103</a>","short":"U. Denker, A. Rastelli, M. Stoffel, J. Tersoff, G. Katsaros, G. Costantini, K. Kern, N. Jin Phillipp, D. Jesson, O. Schmidt, Physical Review Letters 94 (2005).","apa":"Denker, U., Rastelli, A., Stoffel, M., Tersoff, J., Katsaros, G., Costantini, G., … Schmidt, O. (2005). Lateral motion of SiGe islands driven by surface-mediated alloying. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.94.216103\">https://doi.org/10.1103/PhysRevLett.94.216103</a>"},"title":"Lateral motion of SiGe islands driven by surface-mediated alloying","acknowledgement":"The work was supported by the BMBF (03N8711)","date_updated":"2021-01-12T06:52:54Z","year":"2005","issue":"21","intvolume":"        94"},{"publication":"Physical Review B - Condensed Matter and Materials Physics","doi":"10.1103/PhysRevB.72.195320","_id":"1742","intvolume":"        72","acknowledgement":"G. K. acknowledges the financial support of DAAD (Deutscher Akademischer Austausch Dienst)","date_updated":"2021-01-12T06:52:55Z","year":"2005","issue":"19","date_created":"2018-12-11T11:53:46Z","citation":{"mla":"Katsaros, Georgios, et al. “Kinetic Origin of Island Intermixing during the Growth of Ge on Si (001).” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 72, no. 19, American Physical Society, 2005, doi:<a href=\"https://doi.org/10.1103/PhysRevB.72.195320\">10.1103/PhysRevB.72.195320</a>.","chicago":"Katsaros, Georgios, Giovanni Costantini, Mathieu Stoffel, Rubén Esteban, Alexander Bittner, Armando Rastelli, Ulrich Denker, Oliver Schmidt, and Klaus Kern. “Kinetic Origin of Island Intermixing during the Growth of Ge on Si (001).” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2005. <a href=\"https://doi.org/10.1103/PhysRevB.72.195320\">https://doi.org/10.1103/PhysRevB.72.195320</a>.","ista":"Katsaros G, Costantini G, Stoffel M, Esteban R, Bittner A, Rastelli A, Denker U, Schmidt O, Kern K. 2005. Kinetic origin of island intermixing during the growth of Ge on Si (001). Physical Review B - Condensed Matter and Materials Physics. 72(19).","ama":"Katsaros G, Costantini G, Stoffel M, et al. Kinetic origin of island intermixing during the growth of Ge on Si (001). <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2005;72(19). doi:<a href=\"https://doi.org/10.1103/PhysRevB.72.195320\">10.1103/PhysRevB.72.195320</a>","ieee":"G. Katsaros <i>et al.</i>, “Kinetic origin of island intermixing during the growth of Ge on Si (001),” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 72, no. 19. American Physical Society, 2005.","short":"G. Katsaros, G. Costantini, M. Stoffel, R. Esteban, A. Bittner, A. Rastelli, U. Denker, O. Schmidt, K. Kern, Physical Review B - Condensed Matter and Materials Physics 72 (2005).","apa":"Katsaros, G., Costantini, G., Stoffel, M., Esteban, R., Bittner, A., Rastelli, A., … Kern, K. (2005). Kinetic origin of island intermixing during the growth of Ge on Si (001). <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.72.195320\">https://doi.org/10.1103/PhysRevB.72.195320</a>"},"title":"Kinetic origin of island intermixing during the growth of Ge on Si (001)","publist_id":"5382","publisher":"American Physical Society","status":"public","type":"journal_article","date_published":"2005-11-15T00:00:00Z","extern":1,"volume":72,"quality_controlled":0,"month":"11","day":"15","abstract":[{"text":"The effects of substrate temperature, growth rate, and postgrowth annealing on the composition of Ge islands grown on Si(001) were investigated with a combination of selective wet chemical etching and atomic force microscopy. A simple kinetic model comprising only surface diffusion processes can explain all the experimentally observed compositional profiles for pyramid and dome islands grown in the 560-620°C range. From this model three-dimensional compositional maps were extracted. By performing annealing experiments a change in the composition of the domes was observed. This could be explained as the result of the islands' movement induced by alloying-driven energy minimization. Also in this case kinetically hindered bulk diffusion processes are not needed to explain the experimental observations.","lang":"eng"}],"publication_status":"published","author":[{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Georgios Katsaros"},{"first_name":"Giovanni","full_name":"Costantini, Giovanni","last_name":"Costantini"},{"first_name":"Mathieu","full_name":"Stoffel, Mathieu","last_name":"Stoffel"},{"full_name":"Esteban, Rubén","first_name":"Rubén","last_name":"Esteban"},{"first_name":"Alexander","full_name":"Bittner, Alexander M","last_name":"Bittner"},{"last_name":"Rastelli","full_name":"Rastelli, Armando","first_name":"Armando"},{"last_name":"Denker","full_name":"Denker, Ulrich","first_name":"Ulrich"},{"full_name":"Schmidt, Oliver G","first_name":"Oliver","last_name":"Schmidt"},{"first_name":"Klaus","full_name":"Kern, Klaus","last_name":"Kern"}]},{"intvolume":"        87","citation":{"short":"Z. Zhong, G. Katsaros, M. Stoffel, G. Costantini, K. Kern, O. Schmidt, N. Jin Phillipp, G. Bauer, Applied Physics Letters 87 (2005) 1–3.","ieee":"Z. Zhong <i>et al.</i>, “Periodic pillar structures by Si etching of multilayer GeSi/Si islands,” <i>Applied Physics Letters</i>, vol. 87, no. 26. American Institute of Physics, pp. 1–3, 2005.","ama":"Zhong Z, Katsaros G, Stoffel M, et al. Periodic pillar structures by Si etching of multilayer GeSi/Si islands. <i>Applied Physics Letters</i>. 2005;87(26):1-3. doi:<a href=\"https://doi.org/10.1063/1.2150278\">10.1063/1.2150278</a>","ista":"Zhong Z, Katsaros G, Stoffel M, Costantini G, Kern K, Schmidt O, Jin Phillipp N, Bauer G. 2005. Periodic pillar structures by Si etching of multilayer GeSi/Si islands. Applied Physics Letters. 87(26), 1–3.","mla":"Zhong, Zheyang, et al. “Periodic Pillar Structures by Si Etching of Multilayer GeSi/Si Islands.” <i>Applied Physics Letters</i>, vol. 87, no. 26, American Institute of Physics, 2005, pp. 1–3, doi:<a href=\"https://doi.org/10.1063/1.2150278\">10.1063/1.2150278</a>.","chicago":"Zhong, Zheyang, Georgios Katsaros, Mathieu Stoffel, Giovanni Costantini, Klaus Kern, Oliver Schmidt, Neng Jin Phillipp, and Günther Bauer. “Periodic Pillar Structures by Si Etching of Multilayer GeSi/Si Islands.” <i>Applied Physics Letters</i>. American Institute of Physics, 2005. <a href=\"https://doi.org/10.1063/1.2150278\">https://doi.org/10.1063/1.2150278</a>.","apa":"Zhong, Z., Katsaros, G., Stoffel, M., Costantini, G., Kern, K., Schmidt, O., … Bauer, G. (2005). Periodic pillar structures by Si etching of multilayer GeSi/Si islands. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.2150278\">https://doi.org/10.1063/1.2150278</a>"},"date_created":"2018-12-11T11:53:46Z","title":"Periodic pillar structures by Si etching of multilayer GeSi/Si islands","publist_id":"5381","date_updated":"2021-01-12T06:52:55Z","acknowledgement":"This work was supported by the BMBF (03N8711) and the EU NOE SANDiE","year":"2005","issue":"26","doi":"10.1063/1.2150278","publication":"Applied Physics Letters","_id":"1743","day":"01","abstract":[{"lang":"eng","text":"Laterally aligned multilayer GeSiSi islands grown on a patterned Si (001) substrate are disclosed by selective etching of Si in a KOH solution. This procedure allows us to visualize the vertical alignment of the islands in a three-dimensional perspective. Our technique reveals that partly coalesced double islands in the initial layer do not merge together, but instead gradually reproduce into well-separated double islands in upper layers. We attribute this effect to very thin spacer layers, which efficiently transfer the strain modulation of each island through the spacer layer to the surface. The etching rate of Si is reduced in tensile strained regions, which helps to preserve sufficient Si between the stacked islands to form a periodic array of freestanding and vertically modulated heterostructure pillars."}],"month":"01","publication_status":"published","author":[{"last_name":"Zhong","first_name":"Zheyang","full_name":"Zhong, Zheyang"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Georgios Katsaros"},{"last_name":"Stoffel","first_name":"Mathieu","full_name":"Stoffel, Mathieu"},{"last_name":"Costantini","first_name":"Giovanni","full_name":"Costantini, Giovanni"},{"first_name":"Klaus","full_name":"Kern, Klaus","last_name":"Kern"},{"last_name":"Schmidt","full_name":"Schmidt, Oliver G","first_name":"Oliver"},{"last_name":"Jin Phillipp","first_name":"Neng","full_name":"Jin-Phillipp, Neng Y"},{"full_name":"Bauer, Günther","first_name":"Günther","last_name":"Bauer"}],"extern":1,"page":"1 - 3","quality_controlled":0,"volume":87,"publisher":"American Institute of Physics","type":"journal_article","status":"public","date_published":"2005-01-01T00:00:00Z"},{"date_created":"2018-12-11T11:53:46Z","title":"Non linear transmission effects in duobinary and dicode optical systems","publist_id":"5380","citation":{"apa":"Katsaros, G., Darwazeh, I., &#38; Lane, P. (2005). Non linear transmission effects in duobinary and dicode optical systems. <i>IEE Proceedings - Optoelectronics</i>. Institute of Electrical Engineers. <a href=\"https://doi.org/10.1049/ip-opt:20045067\">https://doi.org/10.1049/ip-opt:20045067</a>","short":"G. Katsaros, I. Darwazeh, P. Lane, IEE Proceedings - Optoelectronics 152 (2005) 344–352.","ieee":"G. Katsaros, I. Darwazeh, and P. Lane, “Non linear transmission effects in duobinary and dicode optical systems,” <i>IEE Proceedings - Optoelectronics</i>, vol. 152, no. 6. Institute of Electrical Engineers, pp. 344–352, 2005.","ama":"Katsaros G, Darwazeh I, Lane P. Non linear transmission effects in duobinary and dicode optical systems. <i>IEE Proceedings - Optoelectronics</i>. 2005;152(6):344-352. doi:<a href=\"https://doi.org/10.1049/ip-opt:20045067\">10.1049/ip-opt:20045067</a>","mla":"Katsaros, Georgios, et al. “Non Linear Transmission Effects in Duobinary and Dicode Optical Systems.” <i>IEE Proceedings - Optoelectronics</i>, vol. 152, no. 6, Institute of Electrical Engineers, 2005, pp. 344–52, doi:<a href=\"https://doi.org/10.1049/ip-opt:20045067\">10.1049/ip-opt:20045067</a>.","ista":"Katsaros G, Darwazeh I, Lane P. 2005. Non linear transmission effects in duobinary and dicode optical systems. IEE Proceedings - Optoelectronics. 152(6), 344–352.","chicago":"Katsaros, Georgios, Izzat Darwazeh, and Phil Lane. “Non Linear Transmission Effects in Duobinary and Dicode Optical Systems.” <i>IEE Proceedings - Optoelectronics</i>. Institute of Electrical Engineers, 2005. <a href=\"https://doi.org/10.1049/ip-opt:20045067\">https://doi.org/10.1049/ip-opt:20045067</a>."},"issue":"6","year":"2005","date_updated":"2021-01-12T06:52:55Z","acknowledgement":"IET","intvolume":"       152","_id":"1744","doi":"10.1049/ip-opt:20045067","publication":"IEE Proceedings - Optoelectronics","publication_status":"published","author":[{"full_name":"Georgios Katsaros","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Darwazeh","full_name":"Darwazeh, Izzat Z","first_name":"Izzat"},{"last_name":"Lane","full_name":"Lane, Phil M","first_name":"Phil"}],"abstract":[{"text":"This paper presents optical duobinary and dicode signalling, as alternatives to the binary format, in order to improve the transmission performance in the presense of non-linear effects in a dense wavelength division multiplex (WDM) optical system. Duobinary signalling is applied to an optical system to explore the reduction of stimulated Brillouin scattering (SBS) effects. Duobinary signalling suppresses the SBS effects, and an eye-opening improvement of 0.25 to 1.2 dB is achieved relative to binary transmission over a range of input power levels. An experimental study demonstrates that duobinary modulation suppresses the four wave mixing (FWM) products of a dense WDM system by a maximum of 3 dB. The suppression is maintained over a range of channel spacings. An investigation of the impact of fibre dispersion on FWM products under binary, duobinary and dicode modulation in a dense WDM system is then performed, with interchannel spacing and optical power variation. This leads to the development of a set of guidelines for the application areas, in which it is appropriate to use duobinary or dicode modulation in WDM systems as a means of mitigating the impact of FWM.","lang":"eng"}],"day":"01","month":"12","volume":152,"quality_controlled":0,"page":"344 - 352","extern":1,"status":"public","type":"journal_article","date_published":"2005-12-01T00:00:00Z","publisher":"Institute of Electrical Engineers"},{"doi":"10.1186/1742-6405-2-7","publication":"AIDS Research and Therapy","_id":"1795","intvolume":"         2","date_created":"2018-12-11T11:54:03Z","title":"Assessment of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors","publist_id":"5315","citation":{"chicago":"Siegert, Sandra, Sonja Thaler, Ralf Wagner, and Barbara Schnierle. “Assessment of HIV-1 Entry Inhibitors by MLV/HIV-1 Pseudotyped Vectors.” <i>AIDS Research and Therapy</i>. BioMed Central, 2005. <a href=\"https://doi.org/10.1186/1742-6405-2-7\">https://doi.org/10.1186/1742-6405-2-7</a>.","mla":"Siegert, Sandra, et al. “Assessment of HIV-1 Entry Inhibitors by MLV/HIV-1 Pseudotyped Vectors.” <i>AIDS Research and Therapy</i>, vol. 2, no. 1, BioMed Central, 2005, doi:<a href=\"https://doi.org/10.1186/1742-6405-2-7\">10.1186/1742-6405-2-7</a>.","ista":"Siegert S, Thaler S, Wagner R, Schnierle B. 2005. Assessment of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors. AIDS Research and Therapy. 2(1).","ama":"Siegert S, Thaler S, Wagner R, Schnierle B. Assessment of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors. <i>AIDS Research and Therapy</i>. 2005;2(1). doi:<a href=\"https://doi.org/10.1186/1742-6405-2-7\">10.1186/1742-6405-2-7</a>","ieee":"S. Siegert, S. Thaler, R. Wagner, and B. Schnierle, “Assessment of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors,” <i>AIDS Research and Therapy</i>, vol. 2, no. 1. BioMed Central, 2005.","short":"S. Siegert, S. Thaler, R. Wagner, B. Schnierle, AIDS Research and Therapy 2 (2005).","apa":"Siegert, S., Thaler, S., Wagner, R., &#38; Schnierle, B. (2005). Assessment of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors. <i>AIDS Research and Therapy</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1742-6405-2-7\">https://doi.org/10.1186/1742-6405-2-7</a>"},"date_updated":"2021-01-12T06:53:15Z","year":"2005","issue":"1","extern":1,"quality_controlled":0,"volume":2,"publisher":"BioMed Central","status":"public","type":"journal_article","date_published":"2005-09-12T00:00:00Z","day":"12","abstract":[{"lang":"eng","text":"Background: Murine leukemia virus (MLV) vector particles can be pseudotyped with a truncated variant of the human immunodeficiency virus type 1 (HIV-1) envelope protein (Env) and selectively target gene transfer to human cells expressing both CD4 and an appropriate co-receptor. Vector transduction mimics the HIV-1 entry process and is therefore a safe tool to study HIV-1 entry. Results: Using FLY cells, which express the MLV gag and pol genes, we generated stable producer cell lines that express the HIV-1 envelope gene and a retroviral vector genome encoding the green fluorescent protein (GFP). The BH10 or 89.6 P HIV-1 Env was expressed from a bicistronic vector which allowed the rapid selection of stable cell lines. A codon-usage-optimized synthetic env gene permitted high, Rev-independent Env expression. Vectors generated by these producer cells displayed different sensitivity to entry inhibitors. Conclusion: These data illustrate that MLV/HIV-1 vectors are a valuable screening system for entry inhibitors or neutralizing antisera generated by vaccines."}],"month":"09","publication_status":"published","author":[{"full_name":"Sandra Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","orcid":"0000-0001-8635-0877"},{"last_name":"Thaler","full_name":"Thaler, Sonja","first_name":"Sonja"},{"first_name":"Ralf","full_name":"Wagner, Ralf","last_name":"Wagner"},{"last_name":"Schnierle","full_name":"Schnierle, Barbara S","first_name":"Barbara"}]},{"publisher":"American Association for the Advancement of Science","date_published":"2005-07-29T00:00:00Z","type":"journal_article","status":"public","extern":1,"page":"771 - 774","volume":309,"quality_controlled":0,"month":"07","day":"29","abstract":[{"lang":"eng","text":"\n\nComplex I of respiratory chains plays a central role in bioenergetics and is implicated in many human neurodegenerative diseases. An understanding of its mechanism requires a knowledge of the organization of redox centers. The arrangement of iron-sulfur clusters in the hydrophilic domain of complex I from Thermus thermophilus has been determined with the use of x-ray crystallography. One binuclear and six tetranuclear clusters are arranged, maximally 14 angstroms apart, in an 84-angstrom-long electron transfer chain. The binuclear cluster N1a and the tetranuclear cluster N7 are not in this pathway. Cluster N1a may play a role in the prevention of oxidative damage. The structure provides a framework for the interpretation of the large amounts of data accumulated on complex I."}],"author":[{"last_name":"Hinchliffe","full_name":"Hinchliffe, Philip ","first_name":"Philip"},{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Leonid Sazanov","first_name":"Leonid A"}],"publication_status":"published","publication":"Science","doi":"10.1126/science.1113988","_id":"1962","intvolume":"       309","acknowledgement":"This work was funded by the Medical Research Council.","date_updated":"2021-01-12T06:54:22Z","issue":"5735","year":"2005","date_created":"2018-12-11T11:54:56Z","publist_id":"5122","title":"Biochemistry: Organization of iron-sulfur clusters in respiratory complex I","citation":{"apa":"Hinchliffe, P., &#38; Sazanov, L. A. (2005). Biochemistry: Organization of iron-sulfur clusters in respiratory complex I. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1113988\">https://doi.org/10.1126/science.1113988</a>","short":"P. Hinchliffe, L.A. Sazanov, Science 309 (2005) 771–774.","ieee":"P. Hinchliffe and L. A. Sazanov, “Biochemistry: Organization of iron-sulfur clusters in respiratory complex I,” <i>Science</i>, vol. 309, no. 5735. American Association for the Advancement of Science, pp. 771–774, 2005.","ama":"Hinchliffe P, Sazanov LA. Biochemistry: Organization of iron-sulfur clusters in respiratory complex I. <i>Science</i>. 2005;309(5735):771-774. doi:<a href=\"https://doi.org/10.1126/science.1113988\">10.1126/science.1113988</a>","chicago":"Hinchliffe, Philip, and Leonid A Sazanov. “Biochemistry: Organization of Iron-Sulfur Clusters in Respiratory Complex I.” <i>Science</i>. American Association for the Advancement of Science, 2005. <a href=\"https://doi.org/10.1126/science.1113988\">https://doi.org/10.1126/science.1113988</a>.","mla":"Hinchliffe, Philip, and Leonid A. Sazanov. “Biochemistry: Organization of Iron-Sulfur Clusters in Respiratory Complex I.” <i>Science</i>, vol. 309, no. 5735, American Association for the Advancement of Science, 2005, pp. 771–74, doi:<a href=\"https://doi.org/10.1126/science.1113988\">10.1126/science.1113988</a>.","ista":"Hinchliffe P, Sazanov LA. 2005. Biochemistry: Organization of iron-sulfur clusters in respiratory complex I. Science. 309(5735), 771–774."}}]