[{"acknowledgement":"This work was supported in part by NIH grants R01 GM078598 and U54 LM008748.","author":[{"first_name":"Steffen","full_name":"Schmidt, Steffen","last_name":"Schmidt"},{"first_name":"Anna","last_name":"Gerasimova","full_name":"Gerasimova, Anna"},{"orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","last_name":"Kondrashov"},{"first_name":"Ivan","last_name":"Adzuhbei","full_name":"Adzuhbei, Ivan A"},{"first_name":"Alexey","full_name":"Kondrashov, Alexey S","last_name":"Kondrashov"},{"full_name":"Sunyaev, Shamil R","last_name":"Sunyaev","first_name":"Shamil"}],"publist_id":"6800","intvolume":"         4","title":"Hypermutable non-synonymous sites are under stronger negative selection","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":4,"publisher":"Public Library of Science","day":"01","date_published":"2008-11-01T00:00:00Z","month":"11","extern":1,"quality_controlled":0,"doi":"10.1371/journal.pgen.1000281","status":"public","publication":"PLoS Genetics","date_created":"2018-12-11T11:48:48Z","_id":"844","year":"2008","date_updated":"2021-01-12T08:19:16Z","issue":"11","citation":{"ista":"Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. 2008. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. 4(11).","apa":"Schmidt, S., Gerasimova, A., Kondrashov, F., Adzuhbei, I., Kondrashov, A., &#38; Sunyaev, S. (2008). Hypermutable non-synonymous sites are under stronger negative selection. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1000281\">https://doi.org/10.1371/journal.pgen.1000281</a>","short":"S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S. Sunyaev, PLoS Genetics 4 (2008).","ama":"Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. Hypermutable non-synonymous sites are under stronger negative selection. <i>PLoS Genetics</i>. 2008;4(11). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000281\">10.1371/journal.pgen.1000281</a>","chicago":"Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” <i>PLoS Genetics</i>. Public Library of Science, 2008. <a href=\"https://doi.org/10.1371/journal.pgen.1000281\">https://doi.org/10.1371/journal.pgen.1000281</a>.","mla":"Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” <i>PLoS Genetics</i>, vol. 4, no. 11, Public Library of Science, 2008, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000281\">10.1371/journal.pgen.1000281</a>.","ieee":"S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,” <i>PLoS Genetics</i>, vol. 4, no. 11. Public Library of Science, 2008."},"abstract":[{"text":"Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by an order of magnitude. Mutations also vary widely in their effect on the molecular function, phenotype, and fitness. Independence of the probability of occurrence of a new mutation's effect has been a fundamental premise in genetics. However, highly mutable contexts may be preserved by negative selection at important sites but destroyed by mutation at sites under no selection. Thus, there may be a positive correlation between the rate of mutations at a nucleotide site and the magnitude of their effect on fitness. We studied the impact of CpG context on the rate of human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous coding sites. We compared nucleotides that occupy identical positions within codons of identical amino acids and only differ by being within versus outside CpG context. Nucleotides within CpG context are under a stronger negative selection, as revealed by their lower, proportionally to the mutation rate, rate of evolution and nucleotide diversity. In particular, the probability of fixation of a non-synonymous transition at a CpG site is two times lower than at a CpG site. Thus, sites with different mutation rates are not necessarily selectively equivalent. This suggests that the mutation rate may complement sequence conservation as a characteristic predictive of functional importance of nucleotide sites.","lang":"eng"}],"publication_status":"published","type":"journal_article"},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The KIX domain of the transcription co-activator CBP is a three-helix bundle protein that folds via rapid accumulation of an intermediate state, followed by a slower folding phase. Recent NMR relaxation dispersion studies revealed the presence of a low-populated (excited) state of KIX that exists in equilibrium with the natively folded form under non-denaturing conditions, and likely represents the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium exchange measurements using rapid NMR data acquisition techniques with backbone 15N and 13C relaxation dispersion experiments to further investigate the equilibrium folding of the KIX domain. Residual structure within the folding intermediate is detected by both methods, and their combination enables reliable quantification of the amount of persistent residual structure. Three well-defined folding subunits are found, which display variable stability and correspond closely to the individual helices in the native state. While two of the three helices (α2 and α3) are partially formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C), the third helix is disordered. The observed helical content within the excited state exceeds the helical propensities predicted for the corresponding peptide regions, suggesting that the two helices are weakly mutually stabilized, while methyl 13C relaxation dispersion data indicate that a defined packing arrangement is unlikely. Temperature-dependent experiments reveal that the largest enthalpy and entropy changes along the folding reaction occur during the final transition from the intermediate to the native state. Our experimental data are consistent with a folding mechanism where helices α2 and α3 form rapidly, although to different extents, while helix α1 consolidates only as folding proceeds to complete the native state-structure.","lang":"eng"}],"page":"726-741","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","issue":"4","citation":{"ama":"Schanda P, Brutscher B, Konrat R, Tollinger M. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. <i>Journal of Molecular Biology</i>. 2008;380(4):726-741. doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">10.1016/j.jmb.2008.05.040</a>","chicago":"Schanda, Paul, Bernhard Brutscher, Robert Konrat, and Martin Tollinger. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” <i>Journal of Molecular Biology</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">https://doi.org/10.1016/j.jmb.2008.05.040</a>.","short":"P. Schanda, B. Brutscher, R. Konrat, M. Tollinger, Journal of Molecular Biology 380 (2008) 726–741.","apa":"Schanda, P., Brutscher, B., Konrat, R., &#38; Tollinger, M. (2008). Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">https://doi.org/10.1016/j.jmb.2008.05.040</a>","ieee":"P. Schanda, B. Brutscher, R. Konrat, and M. Tollinger, “Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy,” <i>Journal of Molecular Biology</i>, vol. 380, no. 4. Elsevier, pp. 726–741, 2008.","mla":"Schanda, Paul, et al. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” <i>Journal of Molecular Biology</i>, vol. 380, no. 4, Elsevier, 2008, pp. 726–41, doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">10.1016/j.jmb.2008.05.040</a>.","ista":"Schanda P, Brutscher B, Konrat R, Tollinger M. 2008. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal of Molecular Biology. 380(4), 726–741."},"keyword":["Molecular Biology"],"_id":"8480","year":"2008","date_updated":"2021-01-12T08:19:34Z","article_type":"original","publication":"Journal of Molecular Biology","date_created":"2020-09-18T10:12:29Z","status":"public","doi":"10.1016/j.jmb.2008.05.040","publication_identifier":{"issn":["0022-2836"]},"extern":"1","quality_controlled":"1","publisher":"Elsevier","volume":380,"day":"18","date_published":"2008-07-18T00:00:00Z","month":"07","author":[{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"},{"first_name":"Bernhard","last_name":"Brutscher","full_name":"Brutscher, Bernhard"},{"first_name":"Robert","full_name":"Konrat, Robert","last_name":"Konrat"},{"full_name":"Tollinger, Martin","last_name":"Tollinger","first_name":"Martin"}],"title":"Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy","article_processing_charge":"No","intvolume":"       380"},{"date_updated":"2021-01-12T08:19:34Z","_id":"8481","year":"2008","article_type":"original","publication":"Journal of Molecular Biology","date_created":"2020-09-18T10:12:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","page":"386-403","abstract":[{"text":"The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans CH34 within the complex cop cluster of genes, for which 21 genes have been identified. The expression of the corresponding periplasmic CopK protein is strongly upregulated in the presence of copper, leading to a high periplasmic accumulation. The structure and metal-binding properties of CopK were investigated by NMR and mass spectrometry. The protein is dimeric in the apo state with a dissociation constant in the range of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed that CopK has two high-affinity Cu(I)-binding sites per monomer with different Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific. The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets in perpendicular orientation with an unstructured C-terminal tail. The dimer interface is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion induces a major structural modification involving dissociation of the dimeric apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm the conservation of the N-terminal β-sheet, while the last strand of the C-terminal sheet appears in slow conformational exchange. We hypothesize that the partial disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange data acquired on the apo-protein are consistent with a lower thermodynamic stability of the C-terminal sheet. CopK contains seven methionine residues, five of which appear highly conserved. Chemical shift data suggest implication of two or three methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second Cu(I) ion further increases protein plasticity. Comparison of the structural and metal-binding properties of CopK with other periplasmic copper-binding proteins reveals two conserved features within these functionally related proteins: the all-β fold and the methionine-rich Cu(I)-binding site.","lang":"eng"}],"language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","issue":"2","citation":{"ista":"Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M, Wattiez R. 2008. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. Journal of Molecular Biology. 380(2), 386–403.","apa":"Bersch, B., Favier, A., Schanda, P., van Aelst, S., Vallaeys, T., Covès, J., … Wattiez, R. (2008). Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">https://doi.org/10.1016/j.jmb.2008.05.017</a>","short":"B. Bersch, A. Favier, P. Schanda, S. van Aelst, T. Vallaeys, J. Covès, M. Mergeay, R. Wattiez, Journal of Molecular Biology 380 (2008) 386–403.","ama":"Bersch B, Favier A, Schanda P, et al. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. <i>Journal of Molecular Biology</i>. 2008;380(2):386-403. doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">10.1016/j.jmb.2008.05.017</a>","chicago":"Bersch, Beate, Adrien Favier, Paul Schanda, Sébastien van Aelst, Tatiana Vallaeys, Jacques Covès, Max Mergeay, and Ruddy Wattiez. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” <i>Journal of Molecular Biology</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">https://doi.org/10.1016/j.jmb.2008.05.017</a>.","mla":"Bersch, Beate, et al. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” <i>Journal of Molecular Biology</i>, vol. 380, no. 2, Elsevier, 2008, pp. 386–403, doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">10.1016/j.jmb.2008.05.017</a>.","ieee":"B. Bersch <i>et al.</i>, “Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge,” <i>Journal of Molecular Biology</i>, vol. 380, no. 2. Elsevier, pp. 386–403, 2008."},"keyword":["Molecular Biology"],"publisher":"Elsevier","day":"04","volume":380,"month":"07","date_published":"2008-07-04T00:00:00Z","author":[{"full_name":"Bersch, Beate","last_name":"Bersch","first_name":"Beate"},{"first_name":"Adrien","last_name":"Favier","full_name":"Favier, Adrien"},{"full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul"},{"first_name":"Sébastien","last_name":"van Aelst","full_name":"van Aelst, Sébastien"},{"last_name":"Vallaeys","full_name":"Vallaeys, Tatiana","first_name":"Tatiana"},{"last_name":"Covès","full_name":"Covès, Jacques","first_name":"Jacques"},{"full_name":"Mergeay, Max","last_name":"Mergeay","first_name":"Max"},{"first_name":"Ruddy","last_name":"Wattiez","full_name":"Wattiez, Ruddy"}],"article_processing_charge":"No","title":"Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge","intvolume":"       380","doi":"10.1016/j.jmb.2008.05.017","status":"public","publication_identifier":{"issn":["0022-2836"]},"extern":"1","quality_controlled":"1"},{"intvolume":"       190","article_processing_charge":"No","title":"Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load","author":[{"first_name":"Thomas","full_name":"Kern, Thomas","last_name":"Kern"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul"},{"last_name":"Brutscher","full_name":"Brutscher, Bernhard","first_name":"Bernhard"}],"month":"02","date_published":"2008-02-01T00:00:00Z","volume":190,"publisher":"Elsevier","day":"01","quality_controlled":"1","extern":"1","publication_identifier":{"issn":["1090-7807"]},"doi":"10.1016/j.jmr.2007.11.015","status":"public","date_created":"2020-09-18T10:12:46Z","publication":"Journal of Magnetic Resonance","article_type":"letter_note","_id":"8482","year":"2008","date_updated":"2021-01-12T08:19:35Z","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"citation":{"short":"T. Kern, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 190 (2008) 333–338.","apa":"Kern, T., Schanda, P., &#38; Brutscher, B. (2008). Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">https://doi.org/10.1016/j.jmr.2007.11.015</a>","chicago":"Kern, Thomas, Paul Schanda, and Bernhard Brutscher. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">https://doi.org/10.1016/j.jmr.2007.11.015</a>.","ama":"Kern T, Schanda P, Brutscher B. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. <i>Journal of Magnetic Resonance</i>. 2008;190(2):333-338. doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">10.1016/j.jmr.2007.11.015</a>","mla":"Kern, Thomas, et al. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” <i>Journal of Magnetic Resonance</i>, vol. 190, no. 2, Elsevier, 2008, pp. 333–38, doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">10.1016/j.jmr.2007.11.015</a>.","ieee":"T. Kern, P. Schanda, and B. Brutscher, “Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load,” <i>Journal of Magnetic Resonance</i>, vol. 190, no. 2. Elsevier, pp. 333–338, 2008.","ista":"Kern T, Schanda P, Brutscher B. 2008. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance. 190(2), 333–338."},"issue":"2","oa_version":"None","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording two-dimensional correlation spectra of macromolecules such as proteins in only a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC experiments are preferably performed on high-field NMR spectrometers equipped with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC experiments, however, may cause problems when using a cryogenic probe. Here we introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection, and thus significantly reducing the radiofrequency load of the probe during the experiment. The experiment is also attractive for fast and sensitive measurement of heteronuclear one-bond spin coupling constants.","lang":"eng"}],"page":"333-338","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"status":"public","doi":"10.1137/070703235","extern":"1","publication_identifier":{"issn":["0036-1445","1095-7200"]},"quality_controlled":"1","volume":50,"day":"05","publisher":"Society for Industrial & Applied Mathematics","date_published":"2008-11-05T00:00:00Z","month":"11","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","first_name":"Vadim","orcid":"0000-0002-6051-2628"},{"first_name":"Mark","full_name":"Levi, Mark","last_name":"Levi"}],"intvolume":"        50","article_processing_charge":"No","title":"Geometry of Arnold diffusion","abstract":[{"lang":"eng","text":"The goal of this paper is to present to nonspecialists what is perhaps the simplest possible geometrical picture explaining the mechanism of Arnold diffusion. We choose to speak of a specific model—that of geometric rays in a periodic optical medium. This model is equivalent to that of a particle in a periodic potential in ${\\mathbb R}^{n}$ with energy prescribed and to the geodesic flow in a Riemannian metric on ${\\mathbb R}^{n} $."}],"page":"702-720","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"None","issue":"4","keyword":["Theoretical Computer Science","Applied Mathematics","Computational Mathematics"],"citation":{"ista":"Kaloshin V, Levi M. 2008. Geometry of Arnold diffusion. SIAM Review. 50(4), 702–720.","short":"V. Kaloshin, M. Levi, SIAM Review 50 (2008) 702–720.","apa":"Kaloshin, V., &#38; Levi, M. (2008). Geometry of Arnold diffusion. <i>SIAM Review</i>. Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/070703235\">https://doi.org/10.1137/070703235</a>","ama":"Kaloshin V, Levi M. Geometry of Arnold diffusion. <i>SIAM Review</i>. 2008;50(4):702-720. doi:<a href=\"https://doi.org/10.1137/070703235\">10.1137/070703235</a>","chicago":"Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” <i>SIAM Review</i>. Society for Industrial &#38; Applied Mathematics, 2008. <a href=\"https://doi.org/10.1137/070703235\">https://doi.org/10.1137/070703235</a>.","mla":"Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” <i>SIAM Review</i>, vol. 50, no. 4, Society for Industrial &#38; Applied Mathematics, 2008, pp. 702–20, doi:<a href=\"https://doi.org/10.1137/070703235\">10.1137/070703235</a>.","ieee":"V. Kaloshin and M. Levi, “Geometry of Arnold diffusion,” <i>SIAM Review</i>, vol. 50, no. 4. Society for Industrial &#38; Applied Mathematics, pp. 702–720, 2008."},"article_type":"original","_id":"8509","year":"2008","date_updated":"2021-01-12T08:19:46Z","publication":"SIAM Review","date_created":"2020-09-18T10:48:12Z"},{"page":"409-427","abstract":[{"text":"In this paper, using the ideas of Bessi and Mather, we present a simple mechanical system exhibiting Arnold diffusion. This system of a particle in a small periodic potential can be also interpreted as ray propagation in a periodic optical medium with a near-constant index of refraction. Arnold diffusion in this context manifests itself as an arbitrary finite change of direction for nearly constant index of refraction.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"None","issue":"3","keyword":["Applied Mathematics","General Mathematics"],"citation":{"ista":"Kaloshin V, Levi M. 2008. An example of Arnold diffusion for near-integrable Hamiltonians. Bulletin of the American Mathematical Society. 45(3), 409–427.","ieee":"V. Kaloshin and M. Levi, “An example of Arnold diffusion for near-integrable Hamiltonians,” <i>Bulletin of the American Mathematical Society</i>, vol. 45, no. 3. American Mathematical Society, pp. 409–427, 2008.","mla":"Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable Hamiltonians.” <i>Bulletin of the American Mathematical Society</i>, vol. 45, no. 3, American Mathematical Society, 2008, pp. 409–27, doi:<a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">10.1090/s0273-0979-08-01211-1</a>.","chicago":"Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable Hamiltonians.” <i>Bulletin of the American Mathematical Society</i>. American Mathematical Society, 2008. <a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">https://doi.org/10.1090/s0273-0979-08-01211-1</a>.","ama":"Kaloshin V, Levi M. An example of Arnold diffusion for near-integrable Hamiltonians. <i>Bulletin of the American Mathematical Society</i>. 2008;45(3):409-427. doi:<a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">10.1090/s0273-0979-08-01211-1</a>","apa":"Kaloshin, V., &#38; Levi, M. (2008). An example of Arnold diffusion for near-integrable Hamiltonians. <i>Bulletin of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">https://doi.org/10.1090/s0273-0979-08-01211-1</a>","short":"V. Kaloshin, M. Levi, Bulletin of the American Mathematical Society 45 (2008) 409–427."},"article_type":"original","date_updated":"2021-01-12T08:19:47Z","_id":"8510","year":"2008","publication":"Bulletin of the American Mathematical Society","date_created":"2020-09-18T10:48:20Z","doi":"10.1090/s0273-0979-08-01211-1","status":"public","extern":"1","publication_identifier":{"issn":["0273-0979"]},"quality_controlled":"1","publisher":"American Mathematical Society","day":"01","volume":45,"month":"07","date_published":"2008-07-01T00:00:00Z","author":[{"full_name":"Kaloshin, Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim"},{"first_name":"Mark","last_name":"Levi","full_name":"Levi, Mark"}],"intvolume":"        45","title":"An example of Arnold diffusion for near-integrable Hamiltonians","article_processing_charge":"No"},{"citation":{"ista":"Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L. 2008. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1).","ama":"Donaldson Z, Kondrashov F, Putnam A, et al. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. <i>BMC Evolutionary Biology</i>. 2008;8(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-8-180\">10.1186/1471-2148-8-180</a>","chicago":"Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski, Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2008. <a href=\"https://doi.org/10.1186/1471-2148-8-180\">https://doi.org/10.1186/1471-2148-8-180</a>.","apa":"Donaldson, Z., Kondrashov, F., Putnam, A., Bai, Y., Stoinski, T., Hammock, E., &#38; Young, L. (2008). Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-8-180\">https://doi.org/10.1186/1471-2148-8-180</a>","short":"Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock, L. Young, BMC Evolutionary Biology 8 (2008).","ieee":"Z. Donaldson <i>et al.</i>, “Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene,” <i>BMC Evolutionary Biology</i>, vol. 8, no. 1. BioMed Central, 2008.","mla":"Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” <i>BMC Evolutionary Biology</i>, vol. 8, no. 1, BioMed Central, 2008, doi:<a href=\"https://doi.org/10.1186/1471-2148-8-180\">10.1186/1471-2148-8-180</a>."},"issue":"1","type":"journal_article","publication_status":"published","abstract":[{"lang":"eng","text":"Background. The arginine vasopressin V1a receptor (V1aR) modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex (CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Results. Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB) and duplicated alleles (containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. Conclusion. There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated alleles in chimpanzees provides a unique opportunity to assess the functional role of this duplication in contributing to variation in social behavior in primates. While our initial studies show no signs of directional selection on this locus in chimps, pharmacological and genetic association studies support a potential role for this region in influencing V1aR expression and social behavior."}],"date_created":"2018-12-11T11:49:04Z","publication":"BMC Evolutionary Biology","year":"2008","_id":"895","date_updated":"2021-01-12T08:21:29Z","quality_controlled":0,"extern":1,"doi":"10.1186/1471-2148-8-180","status":"public","title":"Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene","publist_id":"6753","intvolume":"         8","author":[{"first_name":"Zoe","full_name":"Donaldson, Zoe R","last_name":"Donaldson"},{"orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","last_name":"Kondrashov"},{"first_name":"Andrea","last_name":"Putnam","full_name":"Putnam, Andrea S"},{"last_name":"Bai","full_name":"Bai, Yaohui","first_name":"Yaohui"},{"full_name":"Stoinski, Tara S","last_name":"Stoinski","first_name":"Tara"},{"last_name":"Hammock","full_name":"Hammock, Elizabeth A","first_name":"Elizabeth"},{"first_name":"Larry","full_name":"Young, Larry","last_name":"Young"}],"acknowledgement":"We thank the caretakers at Zoo Atlanta and Yerkes National Primate Center for help with procuring specimens. Additional DNA samples were supplied by Bill Hopkins, Emory University (chimpanzee), Allyson Bennet, Wake Forest University (chimpanzee, rhesus macaque, bonnet macaque), Mar Sanchez, Emory University (rhesus macaque), and Anne Yoder, Duke University (galago). Susan Lambeth, M.D. Anderson Cancer Center, and Katie Chace, Yerkes National Primate Center, helped provide records regarding the origins of wild born chimps at these centers. We would like to thank Dr Lisa McGraw and two anonymous reviewers for their com- ments on this manuscript. This work was supported by NSF IBN-9876754, NIH RR00165, NIMH56897 (LJY), MH64692 (LJY) and a Howard Hughes Predoctoral Fellowship (ZRD).\n","month":"01","date_published":"2008-01-01T00:00:00Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":8,"publisher":"BioMed Central","day":"01"},{"extern":1,"quality_controlled":0,"doi":"10.1016/j.ceb.2008.01.008","status":"public","acknowledgement":"This work was supported by the University of Geneva, Max Planck Society, VW, EU, SNF, and HFSP","author":[{"full_name":"Anna Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna"},{"full_name":"González-Gaitán, Marcos A","last_name":"González Gaitán","first_name":"Marcos"}],"intvolume":"        20","publist_id":"5412","title":"The Decapentaplegic morphogen gradient a precise definition","publisher":"Elsevier","volume":20,"day":"01","date_published":"2008-04-01T00:00:00Z","month":"04","issue":"2","citation":{"mla":"Kicheva, Anna, and Marcos González Gaitán. “The Decapentaplegic Morphogen Gradient a Precise Definition.” <i>Current Opinion in Cell Biology</i>, vol. 20, no. 2, Elsevier, 2008, pp. 137–43, doi:<a href=\"https://doi.org/10.1016/j.ceb.2008.01.008\">10.1016/j.ceb.2008.01.008</a>.","ieee":"A. Kicheva and M. González Gaitán, “The Decapentaplegic morphogen gradient a precise definition,” <i>Current Opinion in Cell Biology</i>, vol. 20, no. 2. Elsevier, pp. 137–143, 2008.","apa":"Kicheva, A., &#38; González Gaitán, M. (2008). The Decapentaplegic morphogen gradient a precise definition. <i>Current Opinion in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ceb.2008.01.008\">https://doi.org/10.1016/j.ceb.2008.01.008</a>","short":"A. Kicheva, M. González Gaitán, Current Opinion in Cell Biology 20 (2008) 137–143.","chicago":"Kicheva, Anna, and Marcos González Gaitán. “The Decapentaplegic Morphogen Gradient a Precise Definition.” <i>Current Opinion in Cell Biology</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.ceb.2008.01.008\">https://doi.org/10.1016/j.ceb.2008.01.008</a>.","ama":"Kicheva A, González Gaitán M. The Decapentaplegic morphogen gradient a precise definition. <i>Current Opinion in Cell Biology</i>. 2008;20(2):137-143. doi:<a href=\"https://doi.org/10.1016/j.ceb.2008.01.008\">10.1016/j.ceb.2008.01.008</a>","ista":"Kicheva A, González Gaitán M. 2008. The Decapentaplegic morphogen gradient a precise definition. Current Opinion in Cell Biology. 20(2), 137–143."},"page":"137 - 143","abstract":[{"lang":"eng","text":"Two key processes are in the basis of morphogenesis: the spatial allocation of cell types in fields of naïve cells and the regulation of growth. Both are controlled by morphogens, which activate target genes in the growing tissue in a concentration-dependent manner. Thus the morphogen model is an intrinsically quantitative concept. However, quantitative studies were performed only in recent years on two morphogens: Bicoid and Decapentaplegic. This review covers quantitative aspects of the formation and precision of the Decapentaplegic morphogen gradient. The morphogen gradient concept is transitioning from a soft definition to a precise idea of what the gradient could really do."}],"publication_status":"published","type":"journal_article","publication":"Current Opinion in Cell Biology","date_created":"2018-12-11T11:53:38Z","date_updated":"2021-01-12T06:52:44Z","_id":"1717","year":"2008"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We study the mechanics of tissue growth via cell division and cell death (apoptosis). The rearrangements of cells can on large scales and times be captured by a continuum theory which describes the tissue as an effective viscous material with active stresses generated by cell division. We study the effects of anisotropies of cell division on cell rearrangements and show that average cellular trajectories exhibit anisotropic scaling behaviors. If cell division and apoptosis balance, there is no net growth, but for anisotropic cell division the tissue undergoes spontaneous shear deformations. Our description is relevant for the study of developing tissues such as the imaginal disks of the fruit fly Drosophila melanogaster, which grow anisotropically."}],"publication_status":"published","citation":{"chicago":"Bittig, Thomas, Ortrud Wartlick, Anna Kicheva, Marcos González Gaitárr, and Frank Julicher. “Dynamics of Anisotropic Tissue Growth.” <i>New Journal of Physics</i>. IOP Publishing Ltd., 2008. <a href=\"https://doi.org/10.1088/1367-2630/10/6/063001\">https://doi.org/10.1088/1367-2630/10/6/063001</a>.","ama":"Bittig T, Wartlick O, Kicheva A, González Gaitárr M, Julicher F. Dynamics of anisotropic tissue growth. <i>New Journal of Physics</i>. 2008;10. doi:<a href=\"https://doi.org/10.1088/1367-2630/10/6/063001\">10.1088/1367-2630/10/6/063001</a>","apa":"Bittig, T., Wartlick, O., Kicheva, A., González Gaitárr, M., &#38; Julicher, F. (2008). Dynamics of anisotropic tissue growth. <i>New Journal of Physics</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1367-2630/10/6/063001\">https://doi.org/10.1088/1367-2630/10/6/063001</a>","short":"T. Bittig, O. Wartlick, A. Kicheva, M. González Gaitárr, F. Julicher, New Journal of Physics 10 (2008).","ieee":"T. Bittig, O. Wartlick, A. Kicheva, M. González Gaitárr, and F. Julicher, “Dynamics of anisotropic tissue growth,” <i>New Journal of Physics</i>, vol. 10. IOP Publishing Ltd., 2008.","mla":"Bittig, Thomas, et al. “Dynamics of Anisotropic Tissue Growth.” <i>New Journal of Physics</i>, vol. 10, IOP Publishing Ltd., 2008, doi:<a href=\"https://doi.org/10.1088/1367-2630/10/6/063001\">10.1088/1367-2630/10/6/063001</a>.","ista":"Bittig T, Wartlick O, Kicheva A, González Gaitárr M, Julicher F. 2008. Dynamics of anisotropic tissue growth. New Journal of Physics. 10."},"year":"2008","_id":"1719","date_updated":"2021-01-12T06:52:44Z","date_created":"2018-12-11T11:53:39Z","publication":"New Journal of Physics","doi":"10.1088/1367-2630/10/6/063001","status":"public","quality_controlled":0,"extern":1,"month":"06","date_published":"2008-06-03T00:00:00Z","volume":10,"day":"03","publisher":"IOP Publishing Ltd.","intvolume":"        10","publist_id":"5411","title":"Dynamics of anisotropic tissue growth","author":[{"full_name":"Bittig, Thomas","last_name":"Bittig","first_name":"Thomas"},{"full_name":"Wartlick, Ortrud","last_name":"Wartlick","first_name":"Ortrud"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Anna Kicheva","last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998"},{"first_name":"Marcos","full_name":"González-Gaitárr, Marcos","last_name":"González Gaitárr"},{"first_name":"Frank","full_name":"Julicher, Frank","last_name":"Julicher"}]},{"day":"01","publisher":"American Chemical Society","volume":8,"date_published":"2008-05-01T00:00:00Z","month":"05","acknowledgement":"This work was supported by the BMBF (No. 03N8711) and the EU project D-DotFET (No. 012150)","author":[{"first_name":"Armando","full_name":"Rastelli, Armando","last_name":"Rastelli"},{"last_name":"Stoffel","full_name":"Stoffel, Mathieu","first_name":"Mathieu"},{"first_name":"Ângelo","full_name":"Malachias, Ângelo S","last_name":"Malachias"},{"last_name":"Merdzhanova","full_name":"Merdzhanova, Tsvetelina","first_name":"Tsvetelina"},{"full_name":"Georgios Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"},{"last_name":"Kern","full_name":"Kern, Klaus","first_name":"Klaus"},{"last_name":"Metzger","full_name":"Metzger, Till H","first_name":"Till"},{"last_name":"Schmidt","full_name":"Schmidt, Oliver G","first_name":"Oliver"}],"publist_id":"5374","intvolume":"         8","title":"Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography","doi":"10.1021/nl080290y","status":"public","extern":1,"quality_controlled":0,"date_updated":"2021-01-12T06:52:57Z","_id":"1749","year":"2008","publication":"Nano Letters","date_created":"2018-12-11T11:53:48Z","abstract":[{"lang":"eng","text":"Scanning probe microscopy; Semiconductor quantum dots; Composition gradients; Composition profiles; Nanotomography; Single quantum dots; Strained sige/si; Three-dimensional (3D); Wet-chemical etchings; X-ray scattering measurements; quantum dot; methodology; nanotechnology; optical tomography; scanning probe microscopy; three dimensional imaging; Imaging, Three-Dimensional; Materials Testing; Microscopy, Scanning Probe; Nanotechnology; Quantum Dots; Tomography,"}],"page":"1404 - 1409","publication_status":"published","type":"journal_article","issue":"5","citation":{"ista":"Rastelli A, Stoffel M, Malachias Â, Merdzhanova T, Katsaros G, Kern K, Metzger T, Schmidt O. 2008. Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography. Nano Letters. 8(5), 1404–1409.","ieee":"A. Rastelli <i>et al.</i>, “Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography,” <i>Nano Letters</i>, vol. 8, no. 5. American Chemical Society, pp. 1404–1409, 2008.","mla":"Rastelli, Armando, et al. “Three-Dimensional Composition Profiles of Single Quantum Dots Determined by Scanning-Probe-Microscopy-Based Nanotomography.” <i>Nano Letters</i>, vol. 8, no. 5, American Chemical Society, 2008, pp. 1404–09, doi:<a href=\"https://doi.org/10.1021/nl080290y\">10.1021/nl080290y</a>.","ama":"Rastelli A, Stoffel M, Malachias Â, et al. Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography. <i>Nano Letters</i>. 2008;8(5):1404-1409. doi:<a href=\"https://doi.org/10.1021/nl080290y\">10.1021/nl080290y</a>","chicago":"Rastelli, Armando, Mathieu Stoffel, Ângelo Malachias, Tsvetelina Merdzhanova, Georgios Katsaros, Klaus Kern, Till Metzger, and Oliver Schmidt. “Three-Dimensional Composition Profiles of Single Quantum Dots Determined by Scanning-Probe-Microscopy-Based Nanotomography.” <i>Nano Letters</i>. American Chemical Society, 2008. <a href=\"https://doi.org/10.1021/nl080290y\">https://doi.org/10.1021/nl080290y</a>.","short":"A. Rastelli, M. Stoffel, Â. Malachias, T. Merdzhanova, G. Katsaros, K. Kern, T. Metzger, O. Schmidt, Nano Letters 8 (2008) 1404–1409.","apa":"Rastelli, A., Stoffel, M., Malachias, Â., Merdzhanova, T., Katsaros, G., Kern, K., … Schmidt, O. (2008). Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/nl080290y\">https://doi.org/10.1021/nl080290y</a>"}},{"month":"08","date_published":"2008-08-29T00:00:00Z","volume":101,"day":"29","publisher":"American Physical Society","title":"Positioning of strained islands by interaction with surface nanogrooves","publist_id":"5373","intvolume":"       101","author":[{"full_name":"Georgios Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"},{"last_name":"Tersoff","full_name":"Tersoff, Jerry","first_name":"Jerry"},{"first_name":"Mathieu","full_name":"Stoffel, Mathieu","last_name":"Stoffel"},{"last_name":"Rastelli","full_name":"Rastelli, Armando","first_name":"Armando"},{"last_name":"Acosta Diaz","full_name":"Acosta-Diaz, P","first_name":"P"},{"first_name":"Gouranga","full_name":"Kar, Gouranga S","last_name":"Kar"},{"full_name":"Costantini, Giovanni","last_name":"Costantini","first_name":"Giovanni"},{"last_name":"Schmidt","full_name":"Schmidt, Oliver G","first_name":"Oliver"},{"full_name":"Kern, Klaus","last_name":"Kern","first_name":"Klaus"}],"status":"public","doi":"10.1103/PhysRevLett.101.096103","quality_controlled":0,"extern":1,"_id":"1751","date_updated":"2021-01-12T06:52:58Z","year":"2008","date_created":"2018-12-11T11:53:49Z","publication":"Physical Review Letters","type":"journal_article","publication_status":"published","abstract":[{"lang":"eng","text":"When strained Stranski-Krastanow islands are used as &quot;self-assembled quantum dots,&quot; a key goal is to control the island position. Here we show that nanoscale grooves can control the nucleation of epitaxial Ge islands on Si(001), and can drive lateral motion of existing islands onto the grooves, even when the grooves are very narrow and shallow compared to the islands. A position centered on the groove minimizes energy. We use as prototype grooves the trenches which form naturally around islands. During coarsening, the shrinking islands move laterally to sit directly astride that trench. In subsequent growth, we demonstrate that islands nucleate on the &quot;empty trenches&quot; which remain on the surface after complete dissolution of the original islands."}],"citation":{"ista":"Katsaros G, Tersoff J, Stoffel M, Rastelli A, Acosta Diaz P, Kar G, Costantini G, Schmidt O, Kern K. 2008. Positioning of strained islands by interaction with surface nanogrooves. Physical Review Letters. 101(9).","short":"G. Katsaros, J. Tersoff, M. Stoffel, A. Rastelli, P. Acosta Diaz, G. Kar, G. Costantini, O. Schmidt, K. Kern, Physical Review Letters 101 (2008).","apa":"Katsaros, G., Tersoff, J., Stoffel, M., Rastelli, A., Acosta Diaz, P., Kar, G., … Kern, K. (2008). Positioning of strained islands by interaction with surface nanogrooves. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.101.096103\">https://doi.org/10.1103/PhysRevLett.101.096103</a>","chicago":"Katsaros, Georgios, Jerry Tersoff, Mathieu Stoffel, Armando Rastelli, P Acosta Diaz, Gouranga Kar, Giovanni Costantini, Oliver Schmidt, and Klaus Kern. “Positioning of Strained Islands by Interaction with Surface Nanogrooves.” <i>Physical Review Letters</i>. American Physical Society, 2008. <a href=\"https://doi.org/10.1103/PhysRevLett.101.096103\">https://doi.org/10.1103/PhysRevLett.101.096103</a>.","ama":"Katsaros G, Tersoff J, Stoffel M, et al. Positioning of strained islands by interaction with surface nanogrooves. <i>Physical Review Letters</i>. 2008;101(9). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.101.096103\">10.1103/PhysRevLett.101.096103</a>","mla":"Katsaros, Georgios, et al. “Positioning of Strained Islands by Interaction with Surface Nanogrooves.” <i>Physical Review Letters</i>, vol. 101, no. 9, American Physical Society, 2008, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.101.096103\">10.1103/PhysRevLett.101.096103</a>.","ieee":"G. Katsaros <i>et al.</i>, “Positioning of strained islands by interaction with surface nanogrooves,” <i>Physical Review Letters</i>, vol. 101, no. 9. American Physical Society, 2008."},"issue":"9"},{"publication_status":"published","abstract":[{"text":"The field of cavity quantum electrodynamics (QED), traditionally studied in atomic systems, has gained new momentum by recent reports of quantum optical experiments with solid-state semiconducting and superconducting systems. In cavity QED, the observation of the vacuum Rabi mode splitting is used to investigate the nature of matter-light interaction at a quantum-mechanical level. However, this effect can, at least in principle, be explained classically as the normal mode splitting of two coupled linear oscillators. It has been suggested that an observation of the scaling of the resonant atom-photon coupling strength in the Jaynes-Cummings energy ladder with the square root of photon number n is sufficient to prove that the system is quantum mechanical in nature. Here we report a direct spectroscopic observation of this characteristic quantum nonlinearity. Measuring the photonic degree of freedom of the coupled system, our measurements provide unambiguous spectroscopic evidence for the quantum nature of the resonant atom-field interaction in cavity QED. We explore atom-photon superposition states involving up to two photons, using a spectroscopic pump and probe technique. The experiments have been performed in a circuit QED set-up, in which very strong coupling is realized by the large dipole coupling strength and the long coherence time of a superconducting qubit embedded in a high-quality on-chip microwave cavity. Circuit QED systems also provide a natural quantum interface between flying qubits (photons) and stationary qubits for applications in quantum information processing and communication.","lang":"eng"}],"page":"315 - 318","type":"journal_article","issue":"7202","citation":{"mla":"Fink, Johannes M., et al. “Climbing the Jaynes-Cummings Ladder and Observing Its √n Nonlinearity in a Cavity QED System.” <i>Nature</i>, vol. 454, no. 7202, Nature Publishing Group, 2008, pp. 315–18, doi:<a href=\"https://doi.org/10.1038/nature07112\">10.1038/nature07112</a>.","ieee":"J. M. Fink <i>et al.</i>, “Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system,” <i>Nature</i>, vol. 454, no. 7202. Nature Publishing Group, pp. 315–318, 2008.","short":"J.M. Fink, M. Göppl, M. Baur, R. Bianchetti, P. Leek, A. Blais, A. Wallraff, Nature 454 (2008) 315–318.","apa":"Fink, J. M., Göppl, M., Baur, M., Bianchetti, R., Leek, P., Blais, A., &#38; Wallraff, A. (2008). Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature07112\">https://doi.org/10.1038/nature07112</a>","ama":"Fink JM, Göppl M, Baur M, et al. Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system. <i>Nature</i>. 2008;454(7202):315-318. doi:<a href=\"https://doi.org/10.1038/nature07112\">10.1038/nature07112</a>","chicago":"Fink, Johannes M, M Göppl, Matthias Baur, R Bianchetti, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Climbing the Jaynes-Cummings Ladder and Observing Its √n Nonlinearity in a Cavity QED System.” <i>Nature</i>. Nature Publishing Group, 2008. <a href=\"https://doi.org/10.1038/nature07112\">https://doi.org/10.1038/nature07112</a>.","ista":"Fink JM, Göppl M, Baur M, Bianchetti R, Leek P, Blais A, Wallraff A. 2008. Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system. Nature. 454(7202), 315–318."},"_id":"1763","date_updated":"2021-01-12T06:53:03Z","year":"2008","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/0902.1827","open_access":"1"}],"publication":"Nature","date_created":"2018-12-11T11:53:53Z","status":"public","doi":"10.1038/nature07112","extern":1,"quality_controlled":0,"volume":454,"publisher":"Nature Publishing Group","day":"17","date_published":"2008-07-17T00:00:00Z","month":"07","author":[{"full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X"},{"full_name":"Göppl, M","last_name":"Göppl","first_name":"M"},{"first_name":"Matthias","last_name":"Baur","full_name":"Baur, Matthias P"},{"first_name":"R","last_name":"Bianchetti","full_name":"Bianchetti, R"},{"full_name":"Leek, Peter J","last_name":"Leek","first_name":"Peter"},{"last_name":"Blais","full_name":"Blais, Alexandre","first_name":"Alexandre"},{"first_name":"Andreas","full_name":"Wallraff, Andreas","last_name":"Wallraff"}],"acknowledgement":"This work was supported by SNF and ETHZ. P.J.L. was supported by the EU with an MC-EIF. A.B. was supported by NSERC, CIFAR and FQRNT","title":"Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system","intvolume":"       454","publist_id":"5358"},{"author":[{"full_name":"Fragner, A","last_name":"Fragner","first_name":"A"},{"first_name":"M","last_name":"Göppl","full_name":"Göppl, M"},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink","last_name":"Fink"},{"full_name":"Baur, Matthias P","last_name":"Baur","first_name":"Matthias"},{"first_name":"R","full_name":"Bianchetti, R","last_name":"Bianchetti"},{"first_name":"Peter","full_name":"Leek, Peter J","last_name":"Leek"},{"last_name":"Blais","full_name":"Blais, Alexandre","first_name":"Alexandre"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}],"acknowledgement":"This work was supported by the Swiss National Science Foundation and ETHZ. P.J.L. was supported by the European Commission with a Marie Curie Intra-European Fellowship. A.B. was supported by the Natural Sciences and Engineering Research Council of Canada, Canadian Institute for Advanced Research, and Fonds Québécois de la Recherche sur la Nature et les Technologies","title":"Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift","intvolume":"       322","publist_id":"5357","day":"28","volume":322,"publisher":"American Association for the Advancement of Science","month":"11","date_published":"2008-11-28T00:00:00Z","extern":1,"quality_controlled":0,"doi":"10.1126/science.1164482","status":"public","publication":"Science","date_created":"2018-12-11T11:53:53Z","_id":"1764","date_updated":"2021-01-12T06:53:03Z","year":"2008","issue":"5906","citation":{"ista":"Fragner A, Göppl M, Fink JM, Baur M, Bianchetti R, Leek P, Blais A, Wallraff A. 2008. Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift. Science. 322(5906), 1357–1360.","mla":"Fragner, A., et al. “Resolving Vacuum Fluctuations in an Electrical Circuit by Measuring the Lamb Shift.” <i>Science</i>, vol. 322, no. 5906, American Association for the Advancement of Science, 2008, pp. 1357–60, doi:<a href=\"https://doi.org/10.1126/science.1164482\">10.1126/science.1164482</a>.","ieee":"A. Fragner <i>et al.</i>, “Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift,” <i>Science</i>, vol. 322, no. 5906. American Association for the Advancement of Science, pp. 1357–1360, 2008.","apa":"Fragner, A., Göppl, M., Fink, J. M., Baur, M., Bianchetti, R., Leek, P., … Wallraff, A. (2008). Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1164482\">https://doi.org/10.1126/science.1164482</a>","short":"A. Fragner, M. Göppl, J.M. Fink, M. Baur, R. Bianchetti, P. Leek, A. Blais, A. Wallraff, Science 322 (2008) 1357–1360.","ama":"Fragner A, Göppl M, Fink JM, et al. Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift. <i>Science</i>. 2008;322(5906):1357-1360. doi:<a href=\"https://doi.org/10.1126/science.1164482\">10.1126/science.1164482</a>","chicago":"Fragner, A, M Göppl, Johannes M Fink, Matthias Baur, R Bianchetti, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Resolving Vacuum Fluctuations in an Electrical Circuit by Measuring the Lamb Shift.” <i>Science</i>. American Association for the Advancement of Science, 2008. <a href=\"https://doi.org/10.1126/science.1164482\">https://doi.org/10.1126/science.1164482</a>."},"publication_status":"published","abstract":[{"lang":"eng","text":"Quantum theory predicts that empty space is not truly empty. Even in the absence of any particles or radiation, in pure vacuum, virtual particles are constantly created and annihilated. In an electromagnetic field, the presence of virtual photons manifests itself as a small renormalization of the energy of a quantum system, known as the Lamb shift. We present an experimental observation of the Lamb shift in a solid-state system. The strong dispersive coupling of a superconducting electronic circuit acting as a quantum bit (qubit) to the vacuum field in a transmission-line resonator leads to measurable Lamb shifts of up to 1.4% of the qubit transition frequency. The qubit is also observed to couple more strongly to the vacuum field than to a single photon inside the cavity, an effect that is explained by taking into account the limited anharmonicity of the higher excited qubit states."}],"page":"1357 - 1360","type":"journal_article"},{"acknowledgement":"This work was supported by Swiss National Fund (SNF) and ETH Zürich. P.J.L. was supported by the EC with a MC-EIF","author":[{"first_name":"M","last_name":"Göppl","full_name":"Göppl, M"},{"full_name":"Fragner, A","last_name":"Fragner","first_name":"A"},{"first_name":"Matthias","last_name":"Baur","full_name":"Baur, Matthias P"},{"last_name":"Bianchetti","full_name":"Bianchetti, R","first_name":"R"},{"full_name":"Filipp, Stefan","last_name":"Filipp","first_name":"Stefan"},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Leek, Peter J","last_name":"Leek","first_name":"Peter"},{"full_name":"Puebla, G","last_name":"Puebla","first_name":"G"},{"full_name":"Steffen, L. Kraig","last_name":"Steffen","first_name":"L."},{"full_name":"Wallraff, Andreas","last_name":"Wallraff","first_name":"Andreas"}],"intvolume":"       104","publist_id":"5355","title":"Coplanar waveguide resonators for circuit quantum electrodynamics","volume":104,"day":"01","publisher":"American Institute of Physics","month":"01","date_published":"2008-01-01T00:00:00Z","extern":1,"quality_controlled":0,"status":"public","doi":"10.1063/1.3010859","publication":"Journal of Applied Physics","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0807.4094"}],"date_created":"2018-12-11T11:53:53Z","date_updated":"2021-01-12T06:53:03Z","_id":"1765","year":"2008","issue":"11","citation":{"chicago":"Göppl, M, A Fragner, Matthias Baur, R Bianchetti, Stefan Filipp, Johannes M Fink, Peter Leek, G Puebla, L. Steffen, and Andreas Wallraff. “Coplanar Waveguide Resonators for Circuit Quantum Electrodynamics.” <i>Journal of Applied Physics</i>. American Institute of Physics, 2008. <a href=\"https://doi.org/10.1063/1.3010859\">https://doi.org/10.1063/1.3010859</a>.","ama":"Göppl M, Fragner A, Baur M, et al. Coplanar waveguide resonators for circuit quantum electrodynamics. <i>Journal of Applied Physics</i>. 2008;104(11). doi:<a href=\"https://doi.org/10.1063/1.3010859\">10.1063/1.3010859</a>","short":"M. Göppl, A. Fragner, M. Baur, R. Bianchetti, S. Filipp, J.M. Fink, P. Leek, G. Puebla, L. Steffen, A. Wallraff, Journal of Applied Physics 104 (2008).","apa":"Göppl, M., Fragner, A., Baur, M., Bianchetti, R., Filipp, S., Fink, J. M., … Wallraff, A. (2008). Coplanar waveguide resonators for circuit quantum electrodynamics. <i>Journal of Applied Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.3010859\">https://doi.org/10.1063/1.3010859</a>","ieee":"M. Göppl <i>et al.</i>, “Coplanar waveguide resonators for circuit quantum electrodynamics,” <i>Journal of Applied Physics</i>, vol. 104, no. 11. American Institute of Physics, 2008.","mla":"Göppl, M., et al. “Coplanar Waveguide Resonators for Circuit Quantum Electrodynamics.” <i>Journal of Applied Physics</i>, vol. 104, no. 11, American Institute of Physics, 2008, doi:<a href=\"https://doi.org/10.1063/1.3010859\">10.1063/1.3010859</a>.","ista":"Göppl M, Fragner A, Baur M, Bianchetti R, Filipp S, Fink JM, Leek P, Puebla G, Steffen L, Wallraff A. 2008. Coplanar waveguide resonators for circuit quantum electrodynamics. Journal of Applied Physics. 104(11)."},"abstract":[{"text":"High quality on-chip microwave resonators have recently found prominent new applications in quantum optics and quantum information processing experiments with superconducting electronic circuits, a field now known as circuit quantum electrodynamics (QED). They are also used as single photon detectors and parametric amplifiers. Here we analyze the physical properties of coplanar waveguide resonators and their relation to the materials properties for use in circuit QED. We have designed and fabricated resonators with fundamental frequencies from 2 to 9 GHz and quality factors ranging from a few hundreds to a several hundred thousands controlled by appropriately designed input and output coupling capacitors. The microwave transmission spectra measured at temperatures of 20 mK are shown to be in good agreement with theoretical lumped element and distributed element transmission matrix models. In particular, the experimentally determined resonance frequencies, quality factors, and insertion losses are fully and consistently explained by the two models for all measured devices. The high level of control and flexibility in design renders these resonators ideal for storing and manipulating quantum electromagnetic fields in integrated superconducting electronic circuits.","lang":"eng"}],"publication_status":"published","type":"journal_article"},{"intvolume":"       101","publist_id":"5280","title":"Cellular properties and population asymptotics in the population balance equation","author":[{"last_name":"Friedlander","full_name":"Tamar Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar"},{"first_name":"Naama","full_name":"Brenner, Naama","last_name":"Brenner"}],"month":"07","date_published":"2008-07-01T00:00:00Z","publisher":"American Physical Society","day":"01","volume":101,"quality_controlled":0,"extern":1,"status":"public","doi":"10.1103/PhysRevLett.101.018104","date_created":"2018-12-11T11:54:13Z","publication":"Physical Review Letters","main_file_link":[{"open_access":"0","url":"http://arxiv.org/abs/0804.4804"}],"year":"2008","_id":"1826","date_updated":"2021-01-12T06:53:27Z","citation":{"ieee":"T. Friedlander and N. Brenner, “Cellular properties and population asymptotics in the population balance equation,” <i>Physical Review Letters</i>, vol. 101, no. 1. American Physical Society, 2008.","mla":"Friedlander, Tamar, and Naama Brenner. “Cellular Properties and Population Asymptotics in the Population Balance Equation.” <i>Physical Review Letters</i>, vol. 101, no. 1, American Physical Society, 2008, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.101.018104\">10.1103/PhysRevLett.101.018104</a>.","ama":"Friedlander T, Brenner N. Cellular properties and population asymptotics in the population balance equation. <i>Physical Review Letters</i>. 2008;101(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.101.018104\">10.1103/PhysRevLett.101.018104</a>","chicago":"Friedlander, Tamar, and Naama Brenner. “Cellular Properties and Population Asymptotics in the Population Balance Equation.” <i>Physical Review Letters</i>. American Physical Society, 2008. <a href=\"https://doi.org/10.1103/PhysRevLett.101.018104\">https://doi.org/10.1103/PhysRevLett.101.018104</a>.","apa":"Friedlander, T., &#38; Brenner, N. (2008). Cellular properties and population asymptotics in the population balance equation. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.101.018104\">https://doi.org/10.1103/PhysRevLett.101.018104</a>","short":"T. Friedlander, N. Brenner, Physical Review Letters 101 (2008).","ista":"Friedlander T, Brenner N. 2008. Cellular properties and population asymptotics in the population balance equation. Physical Review Letters. 101(1)."},"issue":"1","type":"journal_article","abstract":[{"lang":"eng","text":"Proliferating cell populations at steady-state growth often exhibit broad protein distributions with exponential tails. The sources of this variation and its universality are of much theoretical interest. Here we address the problem by asymptotic analysis of the population balance equation. We show that the steady-state distribution tail is determined by a combination of protein production and cell division and is insensitive to other model details. Under general conditions this tail is exponential with a dependence on parameters consistent with experiment. We discuss the conditions for this effect to be dominant over other sources of variation and the relation to experiments."}],"publication_status":"published"},{"extern":1,"quality_controlled":0,"status":"public","doi":"10.1021/bi801160u","author":[{"full_name":"Berrisford, John M","last_name":"Berrisford","first_name":"John"},{"first_name":"Christopher","full_name":"Thompson, Christopher J","last_name":"Thompson"},{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Leonid Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"acknowledgement":"This research was funded by the Medical Research Council.","title":"Chemical and NADH-induced, ROS-dependent, cross-linking between sublimits of complex I from Escherichia coli and Thermus thermophilus","intvolume":"        47","publist_id":"5115","day":"30","volume":47,"publisher":"ACS","date_published":"2008-09-30T00:00:00Z","month":"09","issue":"39","citation":{"short":"J. Berrisford, C. Thompson, L.A. Sazanov, Biochemistry 47 (2008) 10262–10270.","apa":"Berrisford, J., Thompson, C., &#38; Sazanov, L. A. (2008). Chemical and NADH-induced, ROS-dependent, cross-linking between sublimits of complex I from Escherichia coli and Thermus thermophilus. <i>Biochemistry</i>. ACS. <a href=\"https://doi.org/10.1021/bi801160u\">https://doi.org/10.1021/bi801160u</a>","ama":"Berrisford J, Thompson C, Sazanov LA. Chemical and NADH-induced, ROS-dependent, cross-linking between sublimits of complex I from Escherichia coli and Thermus thermophilus. <i>Biochemistry</i>. 2008;47(39):10262-10270. doi:<a href=\"https://doi.org/10.1021/bi801160u\">10.1021/bi801160u</a>","chicago":"Berrisford, John, Christopher Thompson, and Leonid A Sazanov. “Chemical and NADH-Induced, ROS-Dependent, Cross-Linking between Sublimits of Complex I from Escherichia Coli and Thermus Thermophilus.” <i>Biochemistry</i>. ACS, 2008. <a href=\"https://doi.org/10.1021/bi801160u\">https://doi.org/10.1021/bi801160u</a>.","mla":"Berrisford, John, et al. “Chemical and NADH-Induced, ROS-Dependent, Cross-Linking between Sublimits of Complex I from Escherichia Coli and Thermus Thermophilus.” <i>Biochemistry</i>, vol. 47, no. 39, ACS, 2008, pp. 10262–70, doi:<a href=\"https://doi.org/10.1021/bi801160u\">10.1021/bi801160u</a>.","ieee":"J. Berrisford, C. Thompson, and L. A. Sazanov, “Chemical and NADH-induced, ROS-dependent, cross-linking between sublimits of complex I from Escherichia coli and Thermus thermophilus,” <i>Biochemistry</i>, vol. 47, no. 39. ACS, pp. 10262–10270, 2008.","ista":"Berrisford J, Thompson C, Sazanov LA. 2008. Chemical and NADH-induced, ROS-dependent, cross-linking between sublimits of complex I from Escherichia coli and Thermus thermophilus. Biochemistry. 47(39), 10262–10270."},"publication_status":"published","abstract":[{"lang":"eng","text":"Complex I of respiratory chains transfers electrons from NADH to ubiquinone, coupled to the translocation of protons across the membrane. Two alternative coupling mechanisms are being discussed, redox-driven or conformation-driven. Using &quot;zero-length&quot; cross-linking reagent and isolated hydrophilic domains of complex I from Escherichia coli and Thermus thermophilus, we show that the pattern of cross-links between subunits changes significantly in the presence of NADH. Similar observations were made previously with intact purified E. coli and bovine complex I. This indicates that, upon reduction with NADH, similar conformational changes are likely to occur in the intact enzyme and in the isolated hydrophilic domain (which can be used for crystallographic studies). Within intact E. coli complex I, the cross-link between the hydrophobic subunits NuoA and NuoJ was abolished in the presence of NADH, indicating that conformational changes extend into the membrane domain, possibly as part of a coupling mechanism. Unexpectedly, in the absence of any chemical cross-linker, incubation of complex I with NADH resulted in covalent cross-links between subunits Nqo4 (NuoCD) and Nqo6 (NuoB), as well as between Nqo6 and Nqo9. Their formation depends on the presence of oxygen and so is likely a result of oxidative damage via reactive oxygen species (ROS) induced cross-linking. In addition, ROS- and metal ion-dependent proteolysis of these subunits (as well as Nqo3) is observed. Fe-S cluster N2 is coordinated between subunits Nqo4 and Nqo6 and could be involved in these processes. Our observations suggest that oxidative damage to complex I in vivo may include not only side-chain modifications but also protein cross-linking and degradation."}],"page":"10262 - 10270","type":"journal_article","publication":"Biochemistry","date_created":"2018-12-11T11:54:57Z","_id":"1967","year":"2008","date_updated":"2021-01-12T06:54:24Z"},{"acknowledgement":"This work was supported by the Medical Research Council.","author":[{"first_name":"David","full_name":"Morgan, David J","last_name":"Morgan"},{"orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Leonid Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"      1777","publist_id":"5116","title":"Three-dimensional structure of respiratory complex I from Escherichia coli in ice in the presence of nucleotides","publisher":"Elsevier","volume":1777,"day":"01","month":"07","date_published":"2008-07-01T00:00:00Z","extern":1,"quality_controlled":0,"status":"public","doi":"10.1016/j.bbabio.2008.03.023","publication":"Biochimica et Biophysica Acta - Bioenergetics","date_created":"2018-12-11T11:54:58Z","_id":"1968","year":"2008","date_updated":"2021-01-12T06:54:24Z","issue":"7-8","citation":{"chicago":"Morgan, David, and Leonid A Sazanov. “Three-Dimensional Structure of Respiratory Complex I from Escherichia Coli in Ice in the Presence of Nucleotides.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.bbabio.2008.03.023\">https://doi.org/10.1016/j.bbabio.2008.03.023</a>.","ama":"Morgan D, Sazanov LA. Three-dimensional structure of respiratory complex I from Escherichia coli in ice in the presence of nucleotides. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. 2008;1777(7-8):711-718. doi:<a href=\"https://doi.org/10.1016/j.bbabio.2008.03.023\">10.1016/j.bbabio.2008.03.023</a>","short":"D. Morgan, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1777 (2008) 711–718.","apa":"Morgan, D., &#38; Sazanov, L. A. (2008). Three-dimensional structure of respiratory complex I from Escherichia coli in ice in the presence of nucleotides. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbabio.2008.03.023\">https://doi.org/10.1016/j.bbabio.2008.03.023</a>","ieee":"D. Morgan and L. A. Sazanov, “Three-dimensional structure of respiratory complex I from Escherichia coli in ice in the presence of nucleotides,” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1777, no. 7–8. Elsevier, pp. 711–718, 2008.","mla":"Morgan, David, and Leonid A. Sazanov. “Three-Dimensional Structure of Respiratory Complex I from Escherichia Coli in Ice in the Presence of Nucleotides.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1777, no. 7–8, Elsevier, 2008, pp. 711–18, doi:<a href=\"https://doi.org/10.1016/j.bbabio.2008.03.023\">10.1016/j.bbabio.2008.03.023</a>.","ista":"Morgan D, Sazanov LA. 2008. Three-dimensional structure of respiratory complex I from Escherichia coli in ice in the presence of nucleotides. Biochimica et Biophysica Acta - Bioenergetics. 1777(7–8), 711–718."},"page":"711 - 718","abstract":[{"text":"\n\nComplex I (NADH:ubiquinone oxidoreductase) is the largest protein complex of bacterial and mitochondrial respiratory chains. The first three-dimensional structure of bacterial complex I in vitrified ice was determined by electron cryo-microscopy and single particle analysis. The structure of the Escherichia coli enzyme incubated with either NAD+ (as a reference) or NADH was calculated to 35 and 39 Å resolution, respectively. The X-ray structure of the peripheral arm of Thermus thermophilus complex I was docked into the reference EM structure. The model obtained indicates that Fe-S cluster N2 is close to the membrane domain interface, allowing for effective electron transfer to membrane-embedded quinone. At the current resolution, the structures in the presence of NAD+ or NADH are similar. Additionally, side-view class averages were calculated for the negatively stained bovine enzyme. The structures of bovine complex I in the presence of either NAD+ or NADH also appeared to be similar. These observations indicate that conformational changes upon reduction with NADH, suggested to occur by a range of studies, are smaller than had been thought previously. The model of the entire bacterial complex I could be built from the crystal structures of subcomplexes using the EM envelope described here.","lang":"eng"}],"publication_status":"published","type":"journal_article"},{"date_created":"2018-12-11T11:55:02Z","publication":"Science","date_updated":"2021-01-12T06:54:30Z","_id":"1982","year":"2008","citation":{"ama":"Loose M, Fischer Friedrich E, Ries J, Kruse K, Schwille P. Spatial regulators for bacterial cell division self-organize into surface waves in vitro. <i>Science</i>. 2008;320(5877):789-792. doi:<a href=\"https://doi.org/10.1126/science.1154413\">10.1126/science.1154413</a>","chicago":"Loose, Martin, Elisabeth Fischer Friedrich, Jonas Ries, Karsten Kruse, and Petra Schwille. “Spatial Regulators for Bacterial Cell Division Self-Organize into Surface Waves in Vitro.” <i>Science</i>. American Association for the Advancement of Science, 2008. <a href=\"https://doi.org/10.1126/science.1154413\">https://doi.org/10.1126/science.1154413</a>.","short":"M. Loose, E. Fischer Friedrich, J. Ries, K. Kruse, P. Schwille, Science 320 (2008) 789–792.","apa":"Loose, M., Fischer Friedrich, E., Ries, J., Kruse, K., &#38; Schwille, P. (2008). Spatial regulators for bacterial cell division self-organize into surface waves in vitro. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1154413\">https://doi.org/10.1126/science.1154413</a>","ieee":"M. Loose, E. Fischer Friedrich, J. Ries, K. Kruse, and P. Schwille, “Spatial regulators for bacterial cell division self-organize into surface waves in vitro,” <i>Science</i>, vol. 320, no. 5877. American Association for the Advancement of Science, pp. 789–792, 2008.","mla":"Loose, Martin, et al. “Spatial Regulators for Bacterial Cell Division Self-Organize into Surface Waves in Vitro.” <i>Science</i>, vol. 320, no. 5877, American Association for the Advancement of Science, 2008, pp. 789–92, doi:<a href=\"https://doi.org/10.1126/science.1154413\">10.1126/science.1154413</a>.","ista":"Loose M, Fischer Friedrich E, Ries J, Kruse K, Schwille P. 2008. Spatial regulators for bacterial cell division self-organize into surface waves in vitro. Science. 320(5877), 789–792."},"issue":"5877","type":"journal_article","publication_status":"published","abstract":[{"lang":"eng","text":"In the bacterium Escherichia coli, the Min proteins oscillate between the cell poles to select the cell center as division site. This dynamic pattern has been proposed to arise by self-organization of these proteins, and several models have suggested a reaction-diffusion type mechanism. Here, we found that the Min proteins spontaneously formed planar surface waves on a flat membrane in vitro. The formation and maintenance of these patterns, which extended for hundreds of micrometers, required adenosine 5′-triphosphate (ATP), and they persisted for hours. We present a reaction-diffusion model of the MinD and MinE dynamics that accounts for our experimental observations and also captures the in vivo oscillations."}],"page":"789 - 792","title":"Spatial regulators for bacterial cell division self-organize into surface waves in vitro","intvolume":"       320","publist_id":"5101","author":[{"last_name":"Loose","full_name":"Martin Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724"},{"first_name":"Elisabeth","full_name":"Fischer-Friedrich, Elisabeth","last_name":"Fischer Friedrich"},{"last_name":"Ries","full_name":"Ries, Jonas ","first_name":"Jonas"},{"last_name":"Kruse","full_name":"Kruse, Karsten","first_name":"Karsten"},{"first_name":"Petra","last_name":"Schwille","full_name":"Schwille, Petra "}],"acknowledgement":"This work was supported by the Max-Planck-Society (M.L., P.S., E.F.). ","month":"05","date_published":"2008-05-09T00:00:00Z","publisher":"American Association for the Advancement of Science","day":"09","volume":320,"quality_controlled":0,"extern":1,"status":"public","doi":"10.1126/science.1154413"},{"publication":"Genetical Research","date_created":"2018-12-11T11:55:30Z","year":"2008","_id":"2065","date_updated":"2021-01-12T06:55:05Z","issue":"5","citation":{"ista":"Vicoso B, Haddrill P, Charlesworth B. 2008. A multispecies approach for comparing sequence evolution of X-linked and autosomal sites in Drosophila. Genetical Research. 90(5), 421–431.","short":"B. Vicoso, P. Haddrill, B. Charlesworth, Genetical Research 90 (2008) 421–431.","apa":"Vicoso, B., Haddrill, P., &#38; Charlesworth, B. (2008). A multispecies approach for comparing sequence evolution of X-linked and autosomal sites in Drosophila. <i>Genetical Research</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0016672308009804\">https://doi.org/10.1017/S0016672308009804</a>","ama":"Vicoso B, Haddrill P, Charlesworth B. A multispecies approach for comparing sequence evolution of X-linked and autosomal sites in Drosophila. <i>Genetical Research</i>. 2008;90(5):421-431. doi:<a href=\"https://doi.org/10.1017/S0016672308009804\">10.1017/S0016672308009804</a>","chicago":"Vicoso, Beatriz, Penelope Haddrill, and Brian Charlesworth. “A Multispecies Approach for Comparing Sequence Evolution of X-Linked and Autosomal Sites in Drosophila.” <i>Genetical Research</i>. Cambridge University Press, 2008. <a href=\"https://doi.org/10.1017/S0016672308009804\">https://doi.org/10.1017/S0016672308009804</a>.","mla":"Vicoso, Beatriz, et al. “A Multispecies Approach for Comparing Sequence Evolution of X-Linked and Autosomal Sites in Drosophila.” <i>Genetical Research</i>, vol. 90, no. 5, Cambridge University Press, 2008, pp. 421–31, doi:<a href=\"https://doi.org/10.1017/S0016672308009804\">10.1017/S0016672308009804</a>.","ieee":"B. Vicoso, P. Haddrill, and B. Charlesworth, “A multispecies approach for comparing sequence evolution of X-linked and autosomal sites in Drosophila,” <i>Genetical Research</i>, vol. 90, no. 5. Cambridge University Press, pp. 421–431, 2008."},"publication_status":"published","abstract":[{"text":"Population genetics models show that, under certain conditions, the X chromosome is expected to be under more efficient selection than the autosomes. This could lead to 'faster-X evolution', if a large proportion of mutations are fixed by positive selection, as suggested by recent studies in Drosophila. We used a multispecies approach to test this: Muller's element D, an autosomal arm, is fused to the ancestral X chromosome in Drosophila pseudoobscura and its sister species, Drosophila affinis. We tested whether the same set of genes had higher rates of non-synonymous evolution when they were X-linked (in the D. pseudoobscura/D. affinis comparison) than when they were autosomal (in Drosophila melanogaster/Drosophila yakuba). Although not significant, our results suggest this may be the case, but only for genes under particularly strong positive selection/weak purifying selection. They also suggest that genes that have become X-linked have higher levels of codon bias and slower synonymous site evolution, consistent with more effective selection on codon usage at X-linked sites.","lang":"eng"}],"page":"421 - 431","type":"journal_article","author":[{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Beatriz Vicoso","last_name":"Vicoso"},{"first_name":"Penelope","full_name":"Haddrill, Penelope R","last_name":"Haddrill"},{"full_name":"Charlesworth, Brian","last_name":"Charlesworth","first_name":"Brian"}],"acknowledgement":"B.V. was supported by the Portuguese Foundation for Science and Technology, P.R.H. is supported by the Natural Environmental Research Council (UK) and B.C. was supported by the Royal Society (UK)","title":"A multispecies approach for comparing sequence evolution of X-linked and autosomal sites in Drosophila","intvolume":"        90","publist_id":"4972","day":"01","volume":90,"publisher":"Cambridge University Press","month":"10","date_published":"2008-10-01T00:00:00Z","extern":1,"quality_controlled":0,"status":"public","doi":"10.1017/S0016672308009804"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"This paper presents a novel method for real-time animation of highly-detailed facial expressions based on a multi-scale decomposition of facial geometry into large-scale motion and fine-scale details, such as expression wrinkles. Our hybrid animation is tailored to the specific characteristics of large- and fine-scale facial deformations: Large-scale deformations are computed with a fast linear shell model, which is intuitively and accurately controlled through a sparse set of motion-capture markers or user-defined handle points. Fine-scale facial details are incorporated using a novel pose-space deformation technique, which learns the correspondence of sparse measurements of skin strain to wrinkle formation from a small set of example poses. Our hybrid method features real-time animation of highly-detailed faces with realistic wrinkle formation, and allows both large-scale deformations and fine-scale wrinkles to be edited intuitively. Furthermore, our pose-space representation enables the transfer of facial details to novel expressions or other facial models."}],"page":"57  - 66","type":"conference","language":[{"iso":"eng"}],"oa_version":"None","citation":{"ista":"Bickel B, Lang M, Botsch M, Otaduy M, Gross M. 2008. Pose-space animation and transfer of facial details. SIGGRAPH: Eurographics Symposium on Computer Animation, 57–66.","short":"B. Bickel, M. Lang, M. Botsch, M. Otaduy, M. Gross, in:, ACM, 2008, pp. 57–66.","apa":"Bickel, B., Lang, M., Botsch, M., Otaduy, M., &#38; Gross, M. (2008). Pose-space animation and transfer of facial details (pp. 57–66). Presented at the SIGGRAPH: Eurographics Symposium on Computer Animation, ACM. <a href=\"https://doi.org/10.2312/SCA/SCA08/057-066\">https://doi.org/10.2312/SCA/SCA08/057-066</a>","chicago":"Bickel, Bernd, Manuel Lang, Mario Botsch, Miguel Otaduy, and Markus Gross. “Pose-Space Animation and Transfer of Facial Details,” 57–66. ACM, 2008. <a href=\"https://doi.org/10.2312/SCA/SCA08/057-066\">https://doi.org/10.2312/SCA/SCA08/057-066</a>.","ama":"Bickel B, Lang M, Botsch M, Otaduy M, Gross M. Pose-space animation and transfer of facial details. In: ACM; 2008:57-66. doi:<a href=\"https://doi.org/10.2312/SCA/SCA08/057-066\">10.2312/SCA/SCA08/057-066</a>","mla":"Bickel, Bernd, et al. <i>Pose-Space Animation and Transfer of Facial Details</i>. ACM, 2008, pp. 57–66, doi:<a href=\"https://doi.org/10.2312/SCA/SCA08/057-066\">10.2312/SCA/SCA08/057-066</a>.","ieee":"B. Bickel, M. Lang, M. Botsch, M. Otaduy, and M. Gross, “Pose-space animation and transfer of facial details,” presented at the SIGGRAPH: Eurographics Symposium on Computer Animation, 2008, pp. 57–66."},"year":"2008","_id":"2078","date_updated":"2021-01-12T06:55:10Z","conference":{"name":"SIGGRAPH: Eurographics Symposium on Computer Animation"},"date_created":"2018-12-11T11:55:35Z","doi":"10.2312/SCA/SCA08/057-066","status":"public","extern":"1","publisher":"ACM","date_published":"2008-01-01T00:00:00Z","author":[{"orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd"},{"first_name":"Manuel","full_name":"Lang, Manuel","last_name":"Lang"},{"last_name":"Botsch","full_name":"Botsch, Mario","first_name":"Mario"},{"last_name":"Otaduy","full_name":"Otaduy, Miguel","first_name":"Miguel"},{"full_name":"Gross, Markus","last_name":"Gross","first_name":"Markus"}],"acknowledgement":"This research was supported by the NCCR Co-Me of the Swiss National Science Foundation.","title":"Pose-space animation and transfer of facial details","publist_id":"4960"}]