[{"month":"01","type":"journal_article","abstract":[{"text":"Axon-axon interactions have been implicated in neural circuit assembly, but the underlying mechanisms are poorly understood. Here, we show that in the Drosophila antennal lobe, early-arriving axons of olfactory receptor neurons (ORNs) from the antenna are required for the proper targeting of late-arriving ORN axons from the maxillary palp (MP). Semaphorin-1a is required for targeting of all MP but only half of the antennal ORN classes examined. Sema-1a acts nonautonomously to control ORN axon-axon interactions, in contrast to its cell-autonomous function in olfactory projection neurons. Phenotypic and genetic interaction analyses implicate PlexinA as the Sema-1a receptor in ORN targeting. Sema-1a on antennal ORN axons is required for correct targeting of MP axons within the antennal lobe, while interactions amongst MP axons facilitate their entry into the antennal lobe. We propose that Sema-1a/PlexinA-mediated repulsion provides a mechanism by which early-arriving ORN axons constrain the target choices of late-arriving axons.","lang":"eng"}],"citation":{"short":"L.B. Sweeney, A. Couto, Y.-H. Chou, D. Berdnik, B.J. Dickson, L. Luo, T. Komiyama, Neuron 53 (2007) 185–200.","mla":"Sweeney, Lora B., et al. “Temporal Target Restriction of Olfactory Receptor Neurons by Semaphorin-1a/PlexinA-Mediated Axon-Axon Interactions.” <i>Neuron</i>, vol. 53, no. 2, Elsevier, 2007, pp. 185–200, doi:<a href=\"https://doi.org/10.1016/j.neuron.2006.12.022\">10.1016/j.neuron.2006.12.022</a>.","ista":"Sweeney LB, Couto A, Chou Y-H, Berdnik D, Dickson BJ, Luo L, Komiyama T. 2007. Temporal target restriction of olfactory receptor neurons by semaphorin-1a/plexinA-mediated axon-axon interactions. Neuron. 53(2), 185–200.","apa":"Sweeney, L. B., Couto, A., Chou, Y.-H., Berdnik, D., Dickson, B. J., Luo, L., &#38; Komiyama, T. (2007). Temporal target restriction of olfactory receptor neurons by semaphorin-1a/plexinA-mediated axon-axon interactions. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2006.12.022\">https://doi.org/10.1016/j.neuron.2006.12.022</a>","chicago":"Sweeney, Lora B., Africa Couto, Ya-Hui Chou, Daniela Berdnik, Barry J. Dickson, Liqun Luo, and Takaki Komiyama. “Temporal Target Restriction of Olfactory Receptor Neurons by Semaphorin-1a/PlexinA-Mediated Axon-Axon Interactions.” <i>Neuron</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.neuron.2006.12.022\">https://doi.org/10.1016/j.neuron.2006.12.022</a>.","ieee":"L. B. Sweeney <i>et al.</i>, “Temporal target restriction of olfactory receptor neurons by semaphorin-1a/plexinA-mediated axon-axon interactions,” <i>Neuron</i>, vol. 53, no. 2. Elsevier, pp. 185–200, 2007.","ama":"Sweeney LB, Couto A, Chou Y-H, et al. Temporal target restriction of olfactory receptor neurons by semaphorin-1a/plexinA-mediated axon-axon interactions. <i>Neuron</i>. 2007;53(2):185-200. doi:<a href=\"https://doi.org/10.1016/j.neuron.2006.12.022\">10.1016/j.neuron.2006.12.022</a>"},"publication":"Neuron","oa_version":"None","page":"185-200","year":"2007","issue":"2","doi":"10.1016/j.neuron.2006.12.022","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2020-04-30T10:37:24Z","publication_status":"published","day":"18","status":"public","extern":"1","_id":"7705","author":[{"full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","last_name":"Sweeney"},{"last_name":"Couto","full_name":"Couto, Africa","first_name":"Africa"},{"last_name":"Chou","first_name":"Ya-Hui","full_name":"Chou, Ya-Hui"},{"last_name":"Berdnik","full_name":"Berdnik, Daniela","first_name":"Daniela"},{"last_name":"Dickson","first_name":"Barry J.","full_name":"Dickson, Barry J."},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"},{"last_name":"Komiyama","full_name":"Komiyama, Takaki","first_name":"Takaki"}],"intvolume":"        53","article_processing_charge":"No","publisher":"Elsevier","title":"Temporal target restriction of olfactory receptor neurons by semaphorin-1a/plexinA-mediated axon-axon interactions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2007-01-18T00:00:00Z","article_type":"original","publication_identifier":{"issn":["0896-6273"]},"date_updated":"2024-01-31T10:14:39Z","volume":53},{"_id":"7753","author":[{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson"},{"last_name":"Kruuk","first_name":"Loeske E.B","full_name":"Kruuk, Loeske E.B"}],"date_published":"2007-08-21T00:00:00Z","publication_identifier":{"issn":["1744-9561","1744-957X"]},"volume":3,"external_id":{"pmid":["17711817"]},"month":"08","main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2007.0278","open_access":"1"}],"citation":{"ama":"Robinson MR, Kruuk LE. Function of weaponry in females: The use of horns in intrasexual competition for resources in female Soay sheep. <i>Biology Letters</i>. 2007;3(6):651-654. doi:<a href=\"https://doi.org/10.1098/rsbl.2007.0278\">10.1098/rsbl.2007.0278</a>","ieee":"M. R. Robinson and L. E. . Kruuk, “Function of weaponry in females: The use of horns in intrasexual competition for resources in female Soay sheep,” <i>Biology Letters</i>, vol. 3, no. 6. The Royal Society, pp. 651–654, 2007.","mla":"Robinson, Matthew Richard, and Loeske E. .. Kruuk. “Function of Weaponry in Females: The Use of Horns in Intrasexual Competition for Resources in Female Soay Sheep.” <i>Biology Letters</i>, vol. 3, no. 6, The Royal Society, 2007, pp. 651–54, doi:<a href=\"https://doi.org/10.1098/rsbl.2007.0278\">10.1098/rsbl.2007.0278</a>.","ista":"Robinson MR, Kruuk LE. 2007. Function of weaponry in females: The use of horns in intrasexual competition for resources in female Soay sheep. Biology Letters. 3(6), 651–654.","apa":"Robinson, M. R., &#38; Kruuk, L. E. . (2007). Function of weaponry in females: The use of horns in intrasexual competition for resources in female Soay sheep. <i>Biology Letters</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsbl.2007.0278\">https://doi.org/10.1098/rsbl.2007.0278</a>","chicago":"Robinson, Matthew Richard, and Loeske E.B Kruuk. “Function of Weaponry in Females: The Use of Horns in Intrasexual Competition for Resources in Female Soay Sheep.” <i>Biology Letters</i>. The Royal Society, 2007. <a href=\"https://doi.org/10.1098/rsbl.2007.0278\">https://doi.org/10.1098/rsbl.2007.0278</a>.","short":"M.R. Robinson, L.E.. Kruuk, Biology Letters 3 (2007) 651–654."},"abstract":[{"text":"In many species, females show reduced expression of a trait that is under sexual selection in males, and this expression is thought to be maintained through genetic associations with the male phenotype. However, there is also the potential for the female trait to convey an advantage in intrasexual conflicts over resources. We tested this hypothesis in a feral population of Soay sheep, in which males and females have a polymorphism for horn development, producing either full (normal horned), reduced (scurred) or no (polled, females only) horns. During the lambing period, females who possessed horns were more likely to initiate and win aggressive interactions, independent of age, weight and birthing status. The occurrence of aggression was also context dependent, decreasing over the lambing period and associated with local density. Our results demonstrate that a trait that confers benefits to males during intrasexual competition for mates may also be used by females in intrasexual competition over resources: males use weaponry to gain mates, whereas females use weaponry to gain food.","lang":"eng"}],"oa_version":"Published Version","year":"2007","oa":1,"issue":"6","quality_controlled":"1","extern":"1","language":[{"iso":"eng"}],"date_created":"2020-04-30T11:02:28Z","pmid":1,"intvolume":"         3","article_processing_charge":"No","title":"Function of weaponry in females: The use of horns in intrasexual competition for resources in female Soay sheep","publisher":"The Royal Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","date_updated":"2021-01-12T08:15:18Z","type":"journal_article","publication":"Biology Letters","page":"651-654","doi":"10.1098/rsbl.2007.0278","day":"21","status":"public","publication_status":"published"},{"publication_identifier":{"issn":["1520-6106","1520-5207"]},"date_updated":"2021-01-12T08:15:29Z","article_type":"original","date_published":"2007-03-13T00:00:00Z","volume":111,"article_processing_charge":"No","intvolume":"       111","_id":"7780","author":[{"last_name":"Goodrich","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"first_name":"Serdal","full_name":"Kirmizialtin, Serdal","last_name":"Kirmizialtin"},{"last_name":"Huyghues-Despointes","full_name":"Huyghues-Despointes, Beatrice M.","first_name":"Beatrice M."},{"last_name":"Zhu","first_name":"Aiping","full_name":"Zhu, Aiping"},{"full_name":"Scholtz, J. Martin","first_name":"J. Martin","last_name":"Scholtz"},{"full_name":"Makarov, Dmitrii E.","first_name":"Dmitrii E.","last_name":"Makarov"},{"first_name":"Liviu","full_name":"Movileanu, Liviu","last_name":"Movileanu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations","publisher":"American Chemical Society","doi":"10.1021/jp071364h","issue":"13","year":"2007","extern":"1","day":"13","publication_status":"published","status":"public","date_created":"2020-04-30T12:19:15Z","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","month":"03","oa_version":"None","page":"3332-3335","publication":"The Journal of Physical Chemistry B","citation":{"ama":"Goodrich CP, Kirmizialtin S, Huyghues-Despointes BM, et al. Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations. <i>The Journal of Physical Chemistry B</i>. 2007;111(13):3332-3335. doi:<a href=\"https://doi.org/10.1021/jp071364h\">10.1021/jp071364h</a>","ieee":"C. P. Goodrich <i>et al.</i>, “Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations,” <i>The Journal of Physical Chemistry B</i>, vol. 111, no. 13. American Chemical Society, pp. 3332–3335, 2007.","apa":"Goodrich, C. P., Kirmizialtin, S., Huyghues-Despointes, B. M., Zhu, A., Scholtz, J. M., Makarov, D. E., &#38; Movileanu, L. (2007). Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jp071364h\">https://doi.org/10.1021/jp071364h</a>","mla":"Goodrich, Carl Peter, et al. “Single-Molecule Electrophoresis of β-Hairpin Peptides by Electrical Recordings and Langevin Dynamics Simulations.” <i>The Journal of Physical Chemistry B</i>, vol. 111, no. 13, American Chemical Society, 2007, pp. 3332–35, doi:<a href=\"https://doi.org/10.1021/jp071364h\">10.1021/jp071364h</a>.","ista":"Goodrich CP, Kirmizialtin S, Huyghues-Despointes BM, Zhu A, Scholtz JM, Makarov DE, Movileanu L. 2007. Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations. The Journal of Physical Chemistry B. 111(13), 3332–3335.","chicago":"Goodrich, Carl Peter, Serdal Kirmizialtin, Beatrice M. Huyghues-Despointes, Aiping Zhu, J. Martin Scholtz, Dmitrii E. Makarov, and Liviu Movileanu. “Single-Molecule Electrophoresis of β-Hairpin Peptides by Electrical Recordings and Langevin Dynamics Simulations.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2007. <a href=\"https://doi.org/10.1021/jp071364h\">https://doi.org/10.1021/jp071364h</a>.","short":"C.P. Goodrich, S. Kirmizialtin, B.M. Huyghues-Despointes, A. Zhu, J.M. Scholtz, D.E. Makarov, L. Movileanu, The Journal of Physical Chemistry B 111 (2007) 3332–3335."},"abstract":[{"text":"We used single-channel electrical recordings and Langevin molecular dynamics simulations to explore the electrophoretic translocation of various β-hairpin peptides across the staphylococcal α-hemolysin (αHL) protein pore at single-molecule resolution. The β-hairpin peptides, which varied in their folding properties, corresponded to the C terminal residues of the B1 domain of protein G. The translocation time was strongly dependent on the electric force and was correlated with the folding features of the β-hairpin peptides. Highly unfolded peptides entered the pore in an extended conformation, resulting in fast single-file translocation events. In contrast, the translocation of the folded β-hairpin peptides occurred more slowly. In this case, the β-hairpin peptides traversed the αHL pore in a misfolded or fully folded conformation. This study demonstrates that the interaction between a polypeptide and a β-barrel protein pore is dependent on the folding features of the polypeptide. ","lang":"eng"}]},{"date_published":"2007-05-08T00:00:00Z","article_type":"original","publication_identifier":{"issn":["0014-3820"]},"date_updated":"2021-01-12T08:15:30Z","volume":60,"_id":"7781","author":[{"orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"},{"full_name":"Pilkington, Jill G.","first_name":"Jill G.","last_name":"Pilkington"},{"last_name":"Clutton-Brock","full_name":"Clutton-Brock, Tim H.","first_name":"Tim H."},{"first_name":"Josephine M.","full_name":"Pemberton, Josephine M.","last_name":"Pemberton"},{"last_name":"Kruuk","first_name":"Loeske E.B.","full_name":"Kruuk, Loeske E.B."}],"intvolume":"        60","article_processing_charge":"No","publisher":"Wiley","title":"Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2007","issue":"10","doi":"10.1111/j.0014-3820.2006.tb01854.x","quality_controlled":"1","status":"public","publication_status":"published","language":[{"iso":"eng"}],"date_created":"2020-04-30T13:01:47Z","day":"08","extern":"1","month":"05","type":"journal_article","abstract":[{"text":"Males are predicted to compete for reproductive opportunities, with sexual selection driving the evolution of large body size and weaponry through the advantage they confer for access to females. Few studies have explored potential trade‐offs of investment in secondary sexual traits between different components of fitness or tested for sexually antagonistic selection pressures. These factors may provide explanations for observed polymorphisms in both form and quality of secondary sexual traits. We report here an analysis of selection on horn phenotype in a feral population of Soay sheep (Ovis aries) on the island of Hirta, St. Kilda, Scotland. Soay sheep display a phenotypic polymorphism for horn type with males growing either normal or reduced (scurred) horns, and females growing either normal, scurred, or no (polled) horns; further variation in size exists within horn morphs. We show that horn phenotype and the size of the trait displayed is subject to different selection pressures in males and females, generating sexually antagonistic selection. Furthermore, there was evidence of a trade‐off between breeding success and longevity in normal‐horned males, with both the normal horn type and larger horn size being associated with greater annual breeding success but reduced longevity. Therefore, selection through lifetime breeding success was not found to act upon horn phenotype in males. In females, a negative association of annual breeding success within the normal‐horned phenotype did not result in a significant difference in lifetime fitness when compared to scurred individuals, as no significant difference in longevity was found. However, increased horn size within this group was negatively associated with breeding success and longevity. Females without horns (polled) suffered reduced longevity and thus reduced lifetime breeding success relative the other horn morphs. Our results therefore suggest that trade‐offs between different components of fitness and antagonistic selection between the sexes may maintain genetic variation for secondary sexual traits within a population.","lang":"eng"}],"citation":{"ama":"Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep. <i>Evolution</i>. 2007;60(10):2168-2181. doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2006.tb01854.x\">10.1111/j.0014-3820.2006.tb01854.x</a>","ieee":"M. R. Robinson, J. G. Pilkington, T. H. Clutton-Brock, J. M. Pemberton, and L. E. B. Kruuk, “Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep,” <i>Evolution</i>, vol. 60, no. 10. Wiley, pp. 2168–2181, 2007.","chicago":"Robinson, Matthew Richard, Jill G. Pilkington, Tim H. Clutton-Brock, Josephine M. Pemberton, and Loeske E.B. Kruuk. “Live Fast, Die Young: Trade-Offs between Fitness Components and Sexually Antagonistic Selection on Weaponry in Soay Sheep.” <i>Evolution</i>. Wiley, 2007. <a href=\"https://doi.org/10.1111/j.0014-3820.2006.tb01854.x\">https://doi.org/10.1111/j.0014-3820.2006.tb01854.x</a>.","mla":"Robinson, Matthew Richard, et al. “Live Fast, Die Young: Trade-Offs between Fitness Components and Sexually Antagonistic Selection on Weaponry in Soay Sheep.” <i>Evolution</i>, vol. 60, no. 10, Wiley, 2007, pp. 2168–81, doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2006.tb01854.x\">10.1111/j.0014-3820.2006.tb01854.x</a>.","apa":"Robinson, M. R., Pilkington, J. G., Clutton-Brock, T. H., Pemberton, J. M., &#38; Kruuk, L. E. B. (2007). Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/j.0014-3820.2006.tb01854.x\">https://doi.org/10.1111/j.0014-3820.2006.tb01854.x</a>","ista":"Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. 2007. Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep. Evolution. 60(10), 2168–2181.","short":"M.R. Robinson, J.G. Pilkington, T.H. Clutton-Brock, J.M. Pemberton, L.E.B. Kruuk, Evolution 60 (2007) 2168–2181."},"publication":"Evolution","oa_version":"None","page":"2168-2181"},{"month":"12","citation":{"ieee":"T. P. Vogels and L. Abbott, “Gating deficits in model networks: A path to schizophrenia?,” <i>Pharmacopsychiatry</i>, vol. 40, no. S 1. Thieme, pp. S73–S77, 2007.","ama":"Vogels TP, Abbott L. Gating deficits in model networks: A path to schizophrenia? <i>Pharmacopsychiatry</i>. 2007;40(S 1):S73-S77. doi:<a href=\"https://doi.org/10.1055/s-2007-992130\">10.1055/s-2007-992130</a>","short":"T.P. Vogels, L. Abbott, Pharmacopsychiatry 40 (2007) S73–S77.","chicago":"Vogels, Tim P, and L. Abbott. “Gating Deficits in Model Networks: A Path to Schizophrenia?” <i>Pharmacopsychiatry</i>. Thieme, 2007. <a href=\"https://doi.org/10.1055/s-2007-992130\">https://doi.org/10.1055/s-2007-992130</a>.","mla":"Vogels, Tim P., and L. Abbott. “Gating Deficits in Model Networks: A Path to Schizophrenia?” <i>Pharmacopsychiatry</i>, vol. 40, no. S 1, Thieme, 2007, pp. S73–77, doi:<a href=\"https://doi.org/10.1055/s-2007-992130\">10.1055/s-2007-992130</a>.","ista":"Vogels TP, Abbott L. 2007. Gating deficits in model networks: A path to schizophrenia? Pharmacopsychiatry. 40(S 1), S73–S77.","apa":"Vogels, T. P., &#38; Abbott, L. (2007). Gating deficits in model networks: A path to schizophrenia? <i>Pharmacopsychiatry</i>. Thieme. <a href=\"https://doi.org/10.1055/s-2007-992130\">https://doi.org/10.1055/s-2007-992130</a>"},"abstract":[{"text":"Gating deficits and hallucinatory sensations are prominent symptoms of schizophrenia. Comparing these abnormalities with the failure modes of network models is an interesting way to explore how they arise. We present a network model that can both propagate and gate signals. The model exhibits effects reminiscent of clinically observed pathologies when the balance between excitation and inhibition that it requires is not properly maintained.","lang":"eng"}],"oa_version":"None","year":"2007","issue":"S 1","quality_controlled":"1","extern":"1","date_created":"2020-06-25T13:11:37Z","language":[{"iso":"eng"}],"author":[{"last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"last_name":"Abbott","first_name":"L.","full_name":"Abbott, L."}],"_id":"8027","date_published":"2007-12-01T00:00:00Z","publication_identifier":{"issn":["0176-3679","1439-0795"]},"volume":40,"external_id":{"pmid":["18080946"]},"type":"journal_article","publication":"Pharmacopsychiatry","page":"S73-S77","doi":"10.1055/s-2007-992130","status":"public","publication_status":"published","day":"01","intvolume":"        40","pmid":1,"article_processing_charge":"No","title":"Gating deficits in model networks: A path to schizophrenia?","publisher":"Thieme","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","article_type":"original","date_updated":"2021-01-12T08:16:36Z"},{"author":[{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"last_name":"Forge","first_name":"V.","full_name":"Forge, V."},{"full_name":"Brutscher, B.","first_name":"B.","last_name":"Brutscher"}],"_id":"8483","intvolume":"       104","article_processing_charge":"No","publisher":"National Academy of Sciences","title":"Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2007-07-03T00:00:00Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_updated":"2021-01-12T08:19:35Z","article_type":"original","volume":104,"keyword":["Multidisciplinary"],"month":"07","type":"journal_article","abstract":[{"lang":"eng","text":"Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of α-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of α-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes."}],"citation":{"ieee":"P. Schanda, V. Forge, and B. Brutscher, “Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy,” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 27. National Academy of Sciences, pp. 11257–11262, 2007.","ama":"Schanda P, Forge V, Brutscher B. Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. <i>Proceedings of the National Academy of Sciences</i>. 2007;104(27):11257-11262. doi:<a href=\"https://doi.org/10.1073/pnas.0702069104\">10.1073/pnas.0702069104</a>","short":"P. Schanda, V. Forge, B. Brutscher, Proceedings of the National Academy of Sciences 104 (2007) 11257–11262.","chicago":"Schanda, Paul, V. Forge, and B. Brutscher. “Protein Folding and Unfolding Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0702069104\">https://doi.org/10.1073/pnas.0702069104</a>.","apa":"Schanda, P., Forge, V., &#38; Brutscher, B. (2007). Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0702069104\">https://doi.org/10.1073/pnas.0702069104</a>","ista":"Schanda P, Forge V, Brutscher B. 2007. Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. Proceedings of the National Academy of Sciences. 104(27), 11257–11262.","mla":"Schanda, Paul, et al. “Protein Folding and Unfolding Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 27, National Academy of Sciences, 2007, pp. 11257–62, doi:<a href=\"https://doi.org/10.1073/pnas.0702069104\">10.1073/pnas.0702069104</a>."},"publication":"Proceedings of the National Academy of Sciences","oa_version":"None","page":"11257-11262","year":"2007","issue":"27","doi":"10.1073/pnas.0702069104","quality_controlled":"1","day":"03","publication_status":"published","date_created":"2020-09-18T10:12:54Z","status":"public","language":[{"iso":"eng"}],"extern":"1"},{"month":"07","type":"journal_article","publication":"Journal of Magnetic Resonance","abstract":[{"text":"A series of sequential, intra-residue, and bi-directional BEST H–N–CA, H–N–CO, and H–N–CB pulse sequences is presented that extends the BEST concept introduced recently for fast multidimensional protein NMR [Schanda et al., J. Am. Chem. Soc. 128 (2006) 9042] to the complete set of experiments required for sequential resonance assignment. We demonstrate for the protein ubiquitin that 3D BEST H–N–C correlation spectra can be recorded on a 600 MHz NMR spectrometer equipped with a cryogenic probe in only a few minutes of acquisition time with sufficient sensitivity to detect all expected cross peaks.","lang":"eng"}],"citation":{"apa":"Lescop, E., Schanda, P., &#38; Brutscher, B. (2007). A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">https://doi.org/10.1016/j.jmr.2007.04.002</a>","ista":"Lescop E, Schanda P, Brutscher B. 2007. A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. Journal of Magnetic Resonance. 187(1), 163–169.","mla":"Lescop, Ewen, et al. “A Set of BEST Triple-Resonance Experiments for Time-Optimized Protein Resonance Assignment.” <i>Journal of Magnetic Resonance</i>, vol. 187, no. 1, Elsevier, 2007, pp. 163–69, doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">10.1016/j.jmr.2007.04.002</a>.","chicago":"Lescop, Ewen, Paul Schanda, and Bernhard Brutscher. “A Set of BEST Triple-Resonance Experiments for Time-Optimized Protein Resonance Assignment.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">https://doi.org/10.1016/j.jmr.2007.04.002</a>.","short":"E. Lescop, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 187 (2007) 163–169.","ama":"Lescop E, Schanda P, Brutscher B. A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. <i>Journal of Magnetic Resonance</i>. 2007;187(1):163-169. doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">10.1016/j.jmr.2007.04.002</a>","ieee":"E. Lescop, P. Schanda, and B. Brutscher, “A set of BEST triple-resonance experiments for time-optimized protein resonance assignment,” <i>Journal of Magnetic Resonance</i>, vol. 187, no. 1. Elsevier, pp. 163–169, 2007."},"oa_version":"None","page":"163-169","year":"2007","doi":"10.1016/j.jmr.2007.04.002","issue":"1","quality_controlled":"1","extern":"1","day":"01","publication_status":"published","status":"public","language":[{"iso":"eng"}],"date_created":"2020-09-18T10:13:02Z","intvolume":"       187","_id":"8484","author":[{"full_name":"Lescop, Ewen","first_name":"Ewen","last_name":"Lescop"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"}],"article_processing_charge":"No","title":"A set of BEST triple-resonance experiments for time-optimized protein resonance assignment","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2007-07-01T00:00:00Z","publication_identifier":{"issn":["1090-7807"]},"article_type":"letter_note","date_updated":"2021-01-12T08:19:35Z","volume":187},{"article_processing_charge":"No","author":[{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"full_name":"Lescop, Ewen","first_name":"Ewen","last_name":"Lescop"},{"last_name":"Falge","full_name":"Falge, Mirjam","first_name":"Mirjam"},{"last_name":"Sounier","first_name":"Rémy","full_name":"Sounier, Rémy"},{"last_name":"Boisbouvier","full_name":"Boisbouvier, Jérôme","first_name":"Jérôme"},{"last_name":"Brutscher","full_name":"Brutscher, Bernhard","first_name":"Bernhard"}],"_id":"8485","intvolume":"        38","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","title":"Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons","publication_identifier":{"issn":["0925-2738","1573-5001"]},"date_updated":"2021-01-12T08:19:36Z","article_type":"original","date_published":"2007-03-08T00:00:00Z","volume":38,"keyword":["Spectroscopy","Biochemistry"],"type":"journal_article","month":"03","oa_version":"None","page":"47-55","citation":{"ieee":"P. Schanda, E. Lescop, M. Falge, R. Sounier, J. Boisbouvier, and B. Brutscher, “Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons,” <i>Journal of Biomolecular NMR</i>, vol. 38. Springer Nature, pp. 47–55, 2007.","ama":"Schanda P, Lescop E, Falge M, Sounier R, Boisbouvier J, Brutscher B. Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons. <i>Journal of Biomolecular NMR</i>. 2007;38:47-55. doi:<a href=\"https://doi.org/10.1007/s10858-006-9138-2\">10.1007/s10858-006-9138-2</a>","short":"P. Schanda, E. Lescop, M. Falge, R. Sounier, J. Boisbouvier, B. Brutscher, Journal of Biomolecular NMR 38 (2007) 47–55.","ista":"Schanda P, Lescop E, Falge M, Sounier R, Boisbouvier J, Brutscher B. 2007. Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons. Journal of Biomolecular NMR. 38, 47–55.","apa":"Schanda, P., Lescop, E., Falge, M., Sounier, R., Boisbouvier, J., &#38; Brutscher, B. (2007). Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-006-9138-2\">https://doi.org/10.1007/s10858-006-9138-2</a>","mla":"Schanda, Paul, et al. “Sensitivity-Optimized Experiment for the Measurement of Residual Dipolar Couplings between Amide Protons.” <i>Journal of Biomolecular NMR</i>, vol. 38, Springer Nature, 2007, pp. 47–55, doi:<a href=\"https://doi.org/10.1007/s10858-006-9138-2\">10.1007/s10858-006-9138-2</a>.","chicago":"Schanda, Paul, Ewen Lescop, Mirjam Falge, Rémy Sounier, Jérôme Boisbouvier, and Bernhard Brutscher. “Sensitivity-Optimized Experiment for the Measurement of Residual Dipolar Couplings between Amide Protons.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2007. <a href=\"https://doi.org/10.1007/s10858-006-9138-2\">https://doi.org/10.1007/s10858-006-9138-2</a>."},"abstract":[{"lang":"eng","text":"High signal to noise is a necessity for the quantification of NMR spectral parameters to be translated into accurate and precise restraints on protein structure and dynamics. An important source of long-range structural information is obtained from 1H–1H residual dipolar couplings (RDCs) measured for weakly aligned molecules. For sensitivity reasons, such measurements are generally performed on highly deuterated protein samples. Here we show that high sensitivity is also obtained for protonated protein samples if the pulse schemes are optimized in terms of longitudinal relaxation efficiency and J-mismatch compensated coherence transfer. The new sensitivity-optimized quantitative J-correlation experiment yields important signal gains reaching factors of 1.5 to 8 for individual correlation peaks when compared to previously proposed pulse schemes."}],"publication":"Journal of Biomolecular NMR","doi":"10.1007/s10858-006-9138-2","year":"2007","publication_status":"published","date_created":"2020-09-18T10:13:12Z","day":"08","language":[{"iso":"eng"}],"status":"public","extern":"1","quality_controlled":"1"},{"oa_version":"None","page":"2756-2757","publication":"Journal of the American Chemical Society","abstract":[{"text":"A technique is described that allows reducing acquisition times of multidimensional NMR experiments by extensive spectral folding. The method is simple and has many interesting applications for NMR studies of molecular structure, dynamics, and kinetics.","lang":"eng"}],"citation":{"ieee":"E. Lescop, P. Schanda, R. Rasia, and B. Brutscher, “Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy,” <i>Journal of the American Chemical Society</i>, vol. 129, no. 10. American Chemical Society, pp. 2756–2757, 2007.","ama":"Lescop E, Schanda P, Rasia R, Brutscher B. Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. <i>Journal of the American Chemical Society</i>. 2007;129(10):2756-2757. doi:<a href=\"https://doi.org/10.1021/ja068949u\">10.1021/ja068949u</a>","short":"E. Lescop, P. Schanda, R. Rasia, B. Brutscher, Journal of the American Chemical Society 129 (2007) 2756–2757.","chicago":"Lescop, Ewen, Paul Schanda, Rodolfo Rasia, and Bernhard Brutscher. “Automated Spectral Compression for Fast Multidimensional NMR and Increased Time Resolution in Real-Time NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2007. <a href=\"https://doi.org/10.1021/ja068949u\">https://doi.org/10.1021/ja068949u</a>.","ista":"Lescop E, Schanda P, Rasia R, Brutscher B. 2007. Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. Journal of the American Chemical Society. 129(10), 2756–2757.","apa":"Lescop, E., Schanda, P., Rasia, R., &#38; Brutscher, B. (2007). Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja068949u\">https://doi.org/10.1021/ja068949u</a>","mla":"Lescop, Ewen, et al. “Automated Spectral Compression for Fast Multidimensional NMR and Increased Time Resolution in Real-Time NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>, vol. 129, no. 10, American Chemical Society, 2007, pp. 2756–57, doi:<a href=\"https://doi.org/10.1021/ja068949u\">10.1021/ja068949u</a>."},"type":"journal_article","month":"02","extern":"1","publication_status":"published","day":"17","status":"public","date_created":"2020-09-18T10:13:21Z","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1021/ja068949u","issue":"10","year":"2007","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy","publisher":"American Chemical Society","article_processing_charge":"No","intvolume":"       129","author":[{"first_name":"Ewen","full_name":"Lescop, Ewen","last_name":"Lescop"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"last_name":"Rasia","full_name":"Rasia, Rodolfo","first_name":"Rodolfo"},{"last_name":"Brutscher","full_name":"Brutscher, Bernhard","first_name":"Bernhard"}],"_id":"8486","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"volume":129,"publication_identifier":{"issn":["0002-7863","1520-5126"]},"article_type":"original","date_updated":"2021-01-12T08:19:36Z","date_published":"2007-02-17T00:00:00Z"},{"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"volume":129,"date_published":"2007-01-10T00:00:00Z","publication_identifier":{"issn":["0002-7863","1520-5126"]},"article_type":"original","date_updated":"2021-01-12T08:19:37Z","title":"UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates","publisher":"American Chemical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       129","_id":"8487","author":[{"last_name":"Gal","first_name":"Maayan","full_name":"Gal, Maayan"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"},{"last_name":"Brutscher","full_name":"Brutscher, Bernhard","first_name":"Bernhard"},{"last_name":"Frydman","first_name":"Lucio","full_name":"Frydman, Lucio"}],"article_processing_charge":"No","quality_controlled":"1","extern":"1","day":"10","date_created":"2020-09-18T10:13:27Z","publication_status":"published","status":"public","language":[{"iso":"eng"}],"year":"2007","doi":"10.1021/ja066915g","issue":"5","publication":"Journal of the American Chemical Society","abstract":[{"text":"Following unidirectional biophysical events such as the folding of proteins or the equilibration of binding interactions, requires experimental methods that yield information at both atomic-level resolution and at high repetition rates. Toward this end a number of different approaches enabling the rapid acquisition of 2D NMR spectra have been recently introduced, including spatially encoded “ultrafast” 2D NMR spectroscopy and SOFAST HMQC NMR. Whereas the former accelerates acquisitions by reducing the number of scans that are necessary for completing arbitrary 2D NMR experiments, the latter operates by reducing the delay between consecutive scans while preserving sensitivity. Given the complementarities between these two approaches it seems natural to combine them into a single tool, enabling the acquisition of full 2D protein NMR spectra at high repetition rates. We demonstrate here this capability with the introduction of “ultraSOFAST” HMQC NMR, a spatially encoded and relaxation-optimized approach that can provide 2D protein correlation spectra at ∼1 s repetition rates for samples in the ∼2 mM concentration range. The principles, relative advantages, and current limitations of this new approach are discussed, and its application is exemplified with a study of the fast hydrogen−deuterium exchange characterizing amide sites in Ubiquitin.","lang":"eng"}],"citation":{"ieee":"M. Gal, P. Schanda, B. Brutscher, and L. Frydman, “UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates,” <i>Journal of the American Chemical Society</i>, vol. 129, no. 5. American Chemical Society, pp. 1372–1377, 2007.","ama":"Gal M, Schanda P, Brutscher B, Frydman L. UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. <i>Journal of the American Chemical Society</i>. 2007;129(5):1372-1377. doi:<a href=\"https://doi.org/10.1021/ja066915g\">10.1021/ja066915g</a>","short":"M. Gal, P. Schanda, B. Brutscher, L. Frydman, Journal of the American Chemical Society 129 (2007) 1372–1377.","chicago":"Gal, Maayan, Paul Schanda, Bernhard Brutscher, and Lucio Frydman. “UltraSOFAST HMQC NMR and the Repetitive Acquisition of 2D Protein Spectra at Hz Rates.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2007. <a href=\"https://doi.org/10.1021/ja066915g\">https://doi.org/10.1021/ja066915g</a>.","ista":"Gal M, Schanda P, Brutscher B, Frydman L. 2007. UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. Journal of the American Chemical Society. 129(5), 1372–1377.","mla":"Gal, Maayan, et al. “UltraSOFAST HMQC NMR and the Repetitive Acquisition of 2D Protein Spectra at Hz Rates.” <i>Journal of the American Chemical Society</i>, vol. 129, no. 5, American Chemical Society, 2007, pp. 1372–77, doi:<a href=\"https://doi.org/10.1021/ja066915g\">10.1021/ja066915g</a>.","apa":"Gal, M., Schanda, P., Brutscher, B., &#38; Frydman, L. (2007). UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja066915g\">https://doi.org/10.1021/ja066915g</a>"},"page":"1372-1377","oa_version":"None","month":"01","type":"journal_article"},{"type":"journal_article","month":"01","page":"710-797","oa_version":"None","publication":"Advances in Mathematics","abstract":[{"text":"Here we study an amazing phenomenon discovered by Newhouse [S. Newhouse, Non-density of Axiom A(a) on S2, in: Proc. Sympos. Pure Math., vol. 14, Amer. Math. Soc., 1970, pp. 191–202; S. Newhouse,\r\nDiffeomorphisms with infinitely many sinks, Topology 13 (1974) 9–18; S. Newhouse, The abundance of\r\nwild hyperbolic sets and nonsmooth stable sets of diffeomorphisms, Publ. Math. Inst. Hautes Études Sci.\r\n50 (1979) 101–151]. It turns out that in the space of Cr smooth diffeomorphisms Diffr(M) of a compact\r\nsurface M there is an open set U such that a Baire generic diffeomorphism f ∈ U has infinitely many coexisting sinks. In this paper we make a step towards understanding “how often does a surface diffeomorphism\r\nhave infinitely many sinks.” Our main result roughly says that with probability one for any positive D a\r\nsurface diffeomorphism has only finitely many localized sinks either of cyclicity bounded by D or those\r\nwhose period is relatively large compared to its cyclicity. It verifies a particular case of Palis’ Conjecture\r\nsaying that even though diffeomorphisms with infinitely many coexisting sinks are Baire generic, they have\r\nprobability zero.\r\nOne of the key points of the proof is an application of Newton Interpolation Polynomials to study the dynamics initiated in [V. Kaloshin, B. Hunt, A stretched exponential bound on the rate of growth of the number\r\nof periodic points for prevalent diffeomorphisms I, Ann. of Math., in press, 92 pp.; V. Kaloshin, A stretched\r\nexponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II,\r\npreprint, 85 pp.].","lang":"eng"}],"citation":{"ama":"Gorodetski A, Kaloshin V. How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency. <i>Advances in Mathematics</i>. 2007;208(2):710-797. doi:<a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">10.1016/j.aim.2006.03.012</a>","ieee":"A. Gorodetski and V. Kaloshin, “How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency,” <i>Advances in Mathematics</i>, vol. 208, no. 2. Elsevier, pp. 710–797, 2007.","chicago":"Gorodetski, A., and Vadim Kaloshin. “How Often Surface Diffeomorphisms Have Infinitely Many Sinks and Hyperbolicity of Periodic Points near a Homoclinic Tangency.” <i>Advances in Mathematics</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">https://doi.org/10.1016/j.aim.2006.03.012</a>.","apa":"Gorodetski, A., &#38; Kaloshin, V. (2007). How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">https://doi.org/10.1016/j.aim.2006.03.012</a>","ista":"Gorodetski A, Kaloshin V. 2007. How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency. Advances in Mathematics. 208(2), 710–797.","mla":"Gorodetski, A., and Vadim Kaloshin. “How Often Surface Diffeomorphisms Have Infinitely Many Sinks and Hyperbolicity of Periodic Points near a Homoclinic Tangency.” <i>Advances in Mathematics</i>, vol. 208, no. 2, Elsevier, 2007, pp. 710–97, doi:<a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">10.1016/j.aim.2006.03.012</a>.","short":"A. Gorodetski, V. Kaloshin, Advances in Mathematics 208 (2007) 710–797."},"doi":"10.1016/j.aim.2006.03.012","issue":"2","year":"2007","extern":"1","publication_status":"published","date_created":"2020-09-18T10:48:27Z","day":"30","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","intvolume":"       208","_id":"8511","author":[{"full_name":"Gorodetski, A.","first_name":"A.","last_name":"Gorodetski"},{"orcid":"0000-0002-6051-2628","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency","publisher":"Elsevier","date_updated":"2021-01-12T08:19:47Z","publication_identifier":{"issn":["0001-8708"]},"article_type":"original","date_published":"2007-01-30T00:00:00Z","keyword":["General Mathematics"],"volume":208},{"volume":165,"date_published":"2007-01-01T00:00:00Z","article_type":"original","date_updated":"2021-01-12T08:19:48Z","publication_identifier":{"issn":["0003-486X"]},"title":"Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I","publisher":"Princeton University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       165","author":[{"first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628"},{"first_name":"Brian","full_name":"Hunt, Brian","last_name":"Hunt"}],"_id":"8512","article_processing_charge":"No","quality_controlled":"1","extern":"1","date_created":"2020-09-18T10:48:33Z","status":"public","day":"01","language":[{"iso":"eng"}],"publication_status":"published","year":"2007","doi":"10.4007/annals.2007.165.89","issue":"1","publication":"Annals of Mathematics","abstract":[{"text":"For diffeomorphisms of smooth compact finite-dimensional manifolds, we consider the problem of how fast the number of periodic points with period n grows as a function of n. In many familiar cases (e.g., Anosov systems) the growth is exponential, but arbitrarily fast growth is possible; in fact, the first author has shown that arbitrarily fast growth is topologically (Baire) generic for C2 or smoother diffeomorphisms. In the present work we show that, by contrast, for a measure-theoretic notion of genericity we call “prevalence”, the growth is not much faster than exponential. Specifically, we show that for each ρ,δ>0, there is a prevalent set of C1+ρ (or smoother) diffeomorphisms for which the number of periodic n points is bounded above by exp(Cn1+δ) for some C independent of n. We also obtain a related bound on the decay of hyperbolicity of the periodic points as a function of n, and obtain the same results for 1-dimensional endomorphisms. The contrast between topologically generic and measure-theoretically generic behavior for the growth of the number of periodic points and the decay of their hyperbolicity show this to be a subtle and complex phenomenon, reminiscent of KAM theory. Here in Part I we state our results and describe the methods we use. We complete most of the proof in the 1-dimensional C2-smooth case and outline the remaining steps, deferred to Part II, that are needed to establish the general case.\r\n\r\nThe novel feature of the approach we develop in this paper is the introduction of Newton Interpolation Polynomials as a tool for perturbing trajectories of iterated maps.","lang":"eng"}],"citation":{"ieee":"V. Kaloshin and B. Hunt, “Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I,” <i>Annals of Mathematics</i>, vol. 165, no. 1. Princeton University Press, pp. 89–170, 2007.","ama":"Kaloshin V, Hunt B. Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I. <i>Annals of Mathematics</i>. 2007;165(1):89-170. doi:<a href=\"https://doi.org/10.4007/annals.2007.165.89\">10.4007/annals.2007.165.89</a>","short":"V. Kaloshin, B. Hunt, Annals of Mathematics 165 (2007) 89–170.","mla":"Kaloshin, Vadim, and Brian Hunt. “Stretched Exponential Estimates on Growth of the Number of Periodic Points for Prevalent Diffeomorphisms I.” <i>Annals of Mathematics</i>, vol. 165, no. 1, Princeton University Press, 2007, pp. 89–170, doi:<a href=\"https://doi.org/10.4007/annals.2007.165.89\">10.4007/annals.2007.165.89</a>.","apa":"Kaloshin, V., &#38; Hunt, B. (2007). Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I. <i>Annals of Mathematics</i>. Princeton University Press. <a href=\"https://doi.org/10.4007/annals.2007.165.89\">https://doi.org/10.4007/annals.2007.165.89</a>","ista":"Kaloshin V, Hunt B. 2007. Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I. Annals of Mathematics. 165(1), 89–170.","chicago":"Kaloshin, Vadim, and Brian Hunt. “Stretched Exponential Estimates on Growth of the Number of Periodic Points for Prevalent Diffeomorphisms I.” <i>Annals of Mathematics</i>. Princeton University Press, 2007. <a href=\"https://doi.org/10.4007/annals.2007.165.89\">https://doi.org/10.4007/annals.2007.165.89</a>."},"oa_version":"None","page":"89-170","month":"01","type":"journal_article"},{"year":"2007","issue":"1","doi":"10.1086/518616","quality_controlled":0,"date_created":"2018-12-11T11:48:53Z","status":"public","day":"01","publication_status":"published","extern":1,"month":"07","acknowledgement":"This study was supported by the Biodiversity and Dynamics of Gene Pools program of the Presidium of the Russian Academy of Sciences (support to E.I.R.). E.I.R. is also supported in part by the National Institute of Diabetes and Digestive and Kidney Diseases and National Institute of Neurological Disorders and Stroke (National Institutes of Health), and F.A.K. is supported by a National Science Foundation graduate research fellowship.","type":"journal_article","citation":{"ieee":"O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, and E. Rogaev, “Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state,” <i>American Journal of Human Genetics</i>, vol. 81, no. 1. Cell Press, pp. 32–43, 2007.","ama":"Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. <i>American Journal of Human Genetics</i>. 2007;81(1):32-43. doi:<a href=\"https://doi.org/10.1086/518616\">10.1086/518616</a>","short":"O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, E. Rogaev, American Journal of Human Genetics 81 (2007) 32–43.","chicago":"Plotnikova, Olga, Fyodor Kondrashov, Peter Vlasov, Anastasia Grigorenko, Evgeny Ginter, and Evgeny Rogaev. “Conversion and Compensatory Evolution of the γ-Crystallin Genes and Identification of a Cataractogenic Mutation That Reverses the Sequence of the Human CRYGD Gene to an Ancestral State.” <i>American Journal of Human Genetics</i>. Cell Press, 2007. <a href=\"https://doi.org/10.1086/518616\">https://doi.org/10.1086/518616</a>.","mla":"Plotnikova, Olga, et al. “Conversion and Compensatory Evolution of the γ-Crystallin Genes and Identification of a Cataractogenic Mutation That Reverses the Sequence of the Human CRYGD Gene to an Ancestral State.” <i>American Journal of Human Genetics</i>, vol. 81, no. 1, Cell Press, 2007, pp. 32–43, doi:<a href=\"https://doi.org/10.1086/518616\">10.1086/518616</a>.","apa":"Plotnikova, O., Kondrashov, F., Vlasov, P., Grigorenko, A., Ginter, E., &#38; Rogaev, E. (2007). Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. <i>American Journal of Human Genetics</i>. Cell Press. <a href=\"https://doi.org/10.1086/518616\">https://doi.org/10.1086/518616</a>","ista":"Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. 2007. Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. American Journal of Human Genetics. 81(1), 32–43."},"abstract":[{"lang":"eng","text":"We identified a mutation in the CRYGD gene (P23S) of the γ-crystallin gene cluster that is associated with a polymorphic congenital cataract that occurs with frequency of ∼0.3% in a human population. To gain insight into the molecular mechanism of the pathogenesis of γ-crystallin isoforms, we undertook an evolutionary analysis of the available mammalian and newly obtained primate sequences of the γ-crystallin genes. The cataract-associated serine at site 23 corresponds to the ancestral state, since it was found in CRYGD of a lower primate and all the surveyed nonprimate mammals. Crystallin proteins include two structurally similar domains, and substitutions in mammalian CRYGD protein at site 23 of the first domain were always associated with substitutions in the structurally reciprocal sites 109 and 136 of the second domain. These data suggest that the cataractogenic effect of serine at site 23 in the N-terminal domain of CRYGD may be compensated indirectly by amino acid changes in a distal domain. We also found that gene conversion was a factor in the evolution of the γ-crystallin gene cluster throughout different mammalian clades. The high rate of gene conversion observed between the functional CRYGD gene and two primate γ-crystallin pseudogenes (CRYGEP1 and CRYGFP1) coupled with a surprising finding of apparent negative selection in primate pseudogenes suggest a deleterious impact of recently derived pseudogenes involved in gene conversion in the γ-crystallin gene cluster."}],"publication":"American Journal of Human Genetics","page":"32 - 43","date_published":"2007-07-01T00:00:00Z","date_updated":"2021-01-12T08:20:14Z","volume":81,"_id":"860","author":[{"last_name":"Plotnikova","first_name":"Olga","full_name":"Plotnikova, Olga V"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vlasov","first_name":"Peter","full_name":"Vlasov, Peter K"},{"first_name":"Anastasia","full_name":"Grigorenko, Anastasia P","last_name":"Grigorenko"},{"last_name":"Ginter","first_name":"Evgeny","full_name":"Ginter, Evgeny K"},{"first_name":"Evgeny","full_name":"Rogaev, Evgeny I","last_name":"Rogaev"}],"intvolume":"        81","publisher":"Cell Press","title":"Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state","publist_id":"6788"},{"type":"journal_article","month":"11","acknowledgement":"KYuP and LAM were supported by the Molecular and Cellular Biology Program of the Russian Academy of Science. KYuP was supported by the Russian Fund of Basic Research (grant 04-04-49623). LAM was partially supported by grants from the Howard Hughes Medical Institute (55005610), INTAS (05-1000008-8028). FAK is a National Science Foundation Graduate Research Fellow.","license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"text":"Background: Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. Description: We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. Conclusion: We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.","lang":"eng"}],"citation":{"ieee":"K. Popadin, L. Mamirova, and F. Kondrashov, “A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures,” <i>BMC Bioinformatics</i>, vol. 8. BioMed Central, 2007.","ama":"Popadin K, Mamirova L, Kondrashov F. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. <i>BMC Bioinformatics</i>. 2007;8. doi:<a href=\"https://doi.org/10.1186/1471-2105-8-441\">10.1186/1471-2105-8-441</a>","short":"K. Popadin, L. Mamirova, F. Kondrashov, BMC Bioinformatics 8 (2007).","mla":"Popadin, Konstantin, et al. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” <i>BMC Bioinformatics</i>, vol. 8, BioMed Central, 2007, doi:<a href=\"https://doi.org/10.1186/1471-2105-8-441\">10.1186/1471-2105-8-441</a>.","ista":"Popadin K, Mamirova L, Kondrashov F. 2007. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. 8.","apa":"Popadin, K., Mamirova, L., &#38; Kondrashov, F. (2007). A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. <i>BMC Bioinformatics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2105-8-441\">https://doi.org/10.1186/1471-2105-8-441</a>","chicago":"Popadin, Konstantin, Leila Mamirova, and Fyodor Kondrashov. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” <i>BMC Bioinformatics</i>. BioMed Central, 2007. <a href=\"https://doi.org/10.1186/1471-2105-8-441\">https://doi.org/10.1186/1471-2105-8-441</a>."},"publication":"BMC Bioinformatics","doi":"10.1186/1471-2105-8-441","year":"2007","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","day":"14","date_created":"2018-12-11T11:48:54Z","status":"public","extern":1,"quality_controlled":0,"author":[{"last_name":"Popadin","full_name":"Popadin, Konstantin Yu","first_name":"Konstantin"},{"last_name":"Mamirova","first_name":"Leila","full_name":"Mamirova, Leila A"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"_id":"861","intvolume":"         8","publist_id":"6789","publisher":"BioMed Central","title":"A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures","date_updated":"2021-01-12T08:20:18Z","date_published":"2007-11-14T00:00:00Z","volume":8},{"intvolume":"        23","_id":"879","author":[{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"last_name":"Gurbich","full_name":"Gurbich, Tatiana A","first_name":"Tatiana"},{"first_name":"Peter","full_name":"Vlasov, Peter K","last_name":"Vlasov"}],"publist_id":"6771","title":"Selection for functional uniformity of tuf duplicates in γ-proteobacteria","publisher":"Elsevier","date_updated":"2021-01-12T08:21:04Z","date_published":"2007-05-01T00:00:00Z","volume":23,"type":"journal_article","month":"05","acknowledgement":"We thank Peter Andolfatto, Doris Bachtrog, Robert Cutler, Hideki Innan, Eugene Koonin, Alexey Kondrashov and Martin Lercher for comments on the manuscript and for discussions on the interplay between gene conversion and selection. This work was supported by a National Science Foundation Graduate Research Fellowship (F.A.K.) and a Molecular and Cellular Biology RAS (Program No 10) grant (P.K.V.).","page":"215 - 218","publication":"Trends in Genetics","citation":{"ama":"Kondrashov F, Gurbich T, Vlasov P. Selection for functional uniformity of tuf duplicates in γ-proteobacteria. <i>Trends in Genetics</i>. 2007;23(5):215-218. doi:<a href=\"https://doi.org/10.1016/j.tig.2007.03.002\">10.1016/j.tig.2007.03.002</a>","ieee":"F. Kondrashov, T. Gurbich, and P. Vlasov, “Selection for functional uniformity of tuf duplicates in γ-proteobacteria,” <i>Trends in Genetics</i>, vol. 23, no. 5. Elsevier, pp. 215–218, 2007.","apa":"Kondrashov, F., Gurbich, T., &#38; Vlasov, P. (2007). Selection for functional uniformity of tuf duplicates in γ-proteobacteria. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2007.03.002\">https://doi.org/10.1016/j.tig.2007.03.002</a>","mla":"Kondrashov, Fyodor, et al. “Selection for Functional Uniformity of Tuf Duplicates in γ-Proteobacteria.” <i>Trends in Genetics</i>, vol. 23, no. 5, Elsevier, 2007, pp. 215–18, doi:<a href=\"https://doi.org/10.1016/j.tig.2007.03.002\">10.1016/j.tig.2007.03.002</a>.","ista":"Kondrashov F, Gurbich T, Vlasov P. 2007. Selection for functional uniformity of tuf duplicates in γ-proteobacteria. Trends in Genetics. 23(5), 215–218.","chicago":"Kondrashov, Fyodor, Tatiana Gurbich, and Peter Vlasov. “Selection for Functional Uniformity of Tuf Duplicates in γ-Proteobacteria.” <i>Trends in Genetics</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.tig.2007.03.002\">https://doi.org/10.1016/j.tig.2007.03.002</a>.","short":"F. Kondrashov, T. Gurbich, P. Vlasov, Trends in Genetics 23 (2007) 215–218."},"abstract":[{"lang":"eng","text":"Having an extra copy of a gene is thought to provide some functional redundancy, which results in a higher rate of evolution in duplicated genes. In this article, we estimate the impact of gene duplication on the selection of tuf paralogs, and we find that in the absence of gene conversion, tuf paralogs have evolved significantly slower than when gene conversion has been a factor in their evolution. Thus, tuf gene copies evolve under a selective pressure that ensures their functional uniformity, and gene conversion reduces selection against amino acid substitutions that affect the function of the encoded protein, EF-Tu."}],"doi":"10.1016/j.tig.2007.03.002","issue":"5","year":"2007","extern":1,"date_created":"2018-12-11T11:48:59Z","status":"public","day":"01","publication_status":"published","quality_controlled":0},{"volume":2,"date_updated":"2021-01-12T08:21:47Z","date_published":"2007-08-16T00:00:00Z","publist_id":"6745","publisher":"BioMed Central","title":"Extensive parallelism in protein evolution","_id":"904","author":[{"full_name":"Bazykin, Georgii A","first_name":"Georgii","last_name":"Bazykin"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov"},{"first_name":"Michael","full_name":"Brudno, Michael","last_name":"Brudno"},{"last_name":"Poliakov","first_name":"Alexander","full_name":"Poliakov, Alexander V"},{"last_name":"Dubchak","first_name":"Inna","full_name":"Dubchak, Inna L"},{"full_name":"Kondrashov, Alexey S","first_name":"Alexey","last_name":"Kondrashov"}],"intvolume":"         2","publication_status":"published","day":"16","status":"public","date_created":"2018-12-11T11:49:07Z","extern":1,"quality_controlled":0,"doi":"10.1186/1745-6150-2-20","year":"2007","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"abstract":[{"text":"Background: Independently evolving lineages mostly accumulate different changes, which leads to their gradual divergence. However, parallel accumulation of identical changes is also common, especially in traits with only a small number of possible states. Results: We characterize parallelism in evolution of coding sequences in three four-species sets of genomes of mammals, Drosophila, and yeasts. Each such set contains two independent evolutionary paths, which we call paths I and II. An amino acid replacement which occurred along path I also occurs along path II with the probability 50-8211;80% of that expected under selective neutrality. Thus, the per site rate of parallel evolution of proteins is several times higher than their average rate of evolution, but still lower than the rate of evolution of neutral sequences. This deficit may be caused by changes in the fitness landscape, leading to a replacement being possible along path I but not along path II. However, constant, weak selection assumed by the nearly neutral model of evolution appears to be a more likely explanation. Then, the average coefficient of selection associated with an amino acid replacement, in the units of the effective population size, must exceed ∼0.4, and the fraction of effectively neutral replacements must be below ∼30%. At a majority of evolvable amino acid sites, only a relatively small number of different amino acids is permitted. Conclusion: High, but below-neutral, rates of parallel amino acid replacements suggest that a majority of amino acid replacements that occur in evolution are subject to weak, but non-trivial, selection, as predicted by Ohta's nearly-neutral theory.","lang":"eng"}],"citation":{"ama":"Bazykin G, Kondrashov F, Brudno M, Poliakov A, Dubchak I, Kondrashov A. Extensive parallelism in protein evolution. <i>Biology Direct</i>. 2007;2. doi:<a href=\"https://doi.org/10.1186/1745-6150-2-20\">10.1186/1745-6150-2-20</a>","ieee":"G. Bazykin, F. Kondrashov, M. Brudno, A. Poliakov, I. Dubchak, and A. Kondrashov, “Extensive parallelism in protein evolution,” <i>Biology Direct</i>, vol. 2. BioMed Central, 2007.","apa":"Bazykin, G., Kondrashov, F., Brudno, M., Poliakov, A., Dubchak, I., &#38; Kondrashov, A. (2007). Extensive parallelism in protein evolution. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-2-20\">https://doi.org/10.1186/1745-6150-2-20</a>","ista":"Bazykin G, Kondrashov F, Brudno M, Poliakov A, Dubchak I, Kondrashov A. 2007. Extensive parallelism in protein evolution. Biology Direct. 2.","mla":"Bazykin, Georgii, et al. “Extensive Parallelism in Protein Evolution.” <i>Biology Direct</i>, vol. 2, BioMed Central, 2007, doi:<a href=\"https://doi.org/10.1186/1745-6150-2-20\">10.1186/1745-6150-2-20</a>.","chicago":"Bazykin, Georgii, Fyodor Kondrashov, Michael Brudno, Alexander Poliakov, Inna Dubchak, and Alexey Kondrashov. “Extensive Parallelism in Protein Evolution.” <i>Biology Direct</i>. BioMed Central, 2007. <a href=\"https://doi.org/10.1186/1745-6150-2-20\">https://doi.org/10.1186/1745-6150-2-20</a>.","short":"G. Bazykin, F. Kondrashov, M. Brudno, A. Poliakov, I. Dubchak, A. Kondrashov, Biology Direct 2 (2007)."},"publication":"Biology Direct","type":"journal_article","month":"08","acknowledgement":"G.A.B. gratefully acknowledges fellowships from the Pew Charitable Trusts award 2000-002558 and the Burroughs Wellcome Fund award 1001782, both to Princeton University. F.A.K. is a National Science Foundation Graduate Fellow. M.B.'s work is partially supported by the NSERC Discovery grant. I.D. and A.P. were partially supported by grant HL066681 (L.A.P., I.D. and S.M.), Berkeley-PGA, under the Programs for Genomic Applications, funded by National Heart, Lung, & Blood Institute and Department of Energy Contract DE-AC02-05CH11231, University of California. This work was partially supported through the Molecular and Cellular Biology Program of the Russian Academy of Sciences."},{"keyword":["mechanical engineering","mechanics of materials","condensed matter physics"],"volume":588,"publication_identifier":{"issn":["0022-1120","1469-7645"]},"date_published":"2007-10-10T00:00:00Z","_id":"9149","author":[{"last_name":"Bühler","full_name":"Bühler, Oliver","first_name":"Oliver"},{"orcid":"0000-0001-5836-5350","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","full_name":"Muller, Caroline J"}],"extern":"1","language":[{"iso":"eng"}],"date_created":"2021-02-15T14:41:45Z","quality_controlled":"1","year":"2007","oa":1,"oa_version":"None","abstract":[{"text":"The interaction of tidal currents with sea-floor topography results in the radiation of internal gravity waves into the ocean interior. These waves are called internal tides and their dissipation due to nonlinear wave breaking and concomitant three-dimensional turbulence could play an important role in the mixing of the abyssal ocean, and hence in controlling the large-scale ocean circulation.\r\nAs part of on-going work aimed at providing a theory for the vertical distribution of wave breaking over sea-floor topography, in this paper we investigate the instability of internal tides in a very simple linear model that helps us to relate the formation of unstable regions to simple features in the sea-floor topography. For two-dimensional tides over one-dimensional topography we find that the formation of overturning instabilities is closely linked to the singularities in the topography shape and that it is possible to have stable waves at the sea floor and unstable waves in the ocean interior above.\r\nFor three-dimensional tides over two-dimensional topography there is in addition an effect of geometric focusing of wave energy into localized regions of high wave amplitude, and we investigate this focusing effect in simple examples. Overall, we find that the distribution of unstable wave breaking regions can be highly non-uniform even for very simple idealized topography shapes.","lang":"eng"}],"citation":{"ieee":"O. Bühler and C. J. Muller, “Instability and focusing of internal tides in the deep ocean,” <i>Journal of Fluid Mechanics</i>, vol. 588. Cambridge University Press, pp. 1–28, 2007.","ama":"Bühler O, Muller CJ. Instability and focusing of internal tides in the deep ocean. <i>Journal of Fluid Mechanics</i>. 2007;588:1-28. doi:<a href=\"https://doi.org/10.1017/s0022112007007410\">10.1017/s0022112007007410</a>","short":"O. Bühler, C.J. Muller, Journal of Fluid Mechanics 588 (2007) 1–28.","apa":"Bühler, O., &#38; Muller, C. J. (2007). Instability and focusing of internal tides in the deep ocean. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/s0022112007007410\">https://doi.org/10.1017/s0022112007007410</a>","ista":"Bühler O, Muller CJ. 2007. Instability and focusing of internal tides in the deep ocean. Journal of Fluid Mechanics. 588, 1–28.","mla":"Bühler, Oliver, and Caroline J. Muller. “Instability and Focusing of Internal Tides in the Deep Ocean.” <i>Journal of Fluid Mechanics</i>, vol. 588, Cambridge University Press, 2007, pp. 1–28, doi:<a href=\"https://doi.org/10.1017/s0022112007007410\">10.1017/s0022112007007410</a>.","chicago":"Bühler, Oliver, and Caroline J Muller. “Instability and Focusing of Internal Tides in the Deep Ocean.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2007. <a href=\"https://doi.org/10.1017/s0022112007007410\">https://doi.org/10.1017/s0022112007007410</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/S0022112007007410"}],"month":"10","date_updated":"2022-01-24T13:43:36Z","article_type":"original","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Instability and focusing of internal tides in the deep ocean","publisher":"Cambridge University Press","article_processing_charge":"No","intvolume":"       588","status":"public","publication_status":"published","day":"10","doi":"10.1017/s0022112007007410","page":"1-28","publication":"Journal of Fluid Mechanics","type":"journal_article"},{"scopus_import":"1","type":"journal_article","publication":"Proceedings of the National Academy of Sciences","page":"6752-6757","doi":"10.1073/pnas.0701861104","day":"17","publication_status":"published","status":"public","pmid":1,"intvolume":"       104","article_processing_charge":"No","publisher":"National Academy of Sciences","title":"DNA demethylation in the Arabidopsis genome","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_type":"original","date_updated":"2021-12-14T08:55:12Z","month":"04","main_file_link":[{"url":"https://doi.org/10.1073/pnas.0701861104","open_access":"1"}],"abstract":[{"lang":"eng","text":"Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals. In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic background. However, the extent and function of demethylation by DEMETER-LIKE (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA hypermethylation. Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist. Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the overall distribution of WT DNA methylation. Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation."}],"citation":{"ama":"Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA demethylation in the Arabidopsis genome. <i>Proceedings of the National Academy of Sciences</i>. 2007;104(16):6752-6757. doi:<a href=\"https://doi.org/10.1073/pnas.0701861104\">10.1073/pnas.0701861104</a>","ieee":"J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L. Fischer, “DNA demethylation in the Arabidopsis genome,” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 16. National Academy of Sciences, pp. 6752–6757, 2007.","chicago":"Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0701861104\">https://doi.org/10.1073/pnas.0701861104</a>.","mla":"Penterman, Jon, et al. “DNA Demethylation in the Arabidopsis Genome.” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 16, National Academy of Sciences, 2007, pp. 6752–57, doi:<a href=\"https://doi.org/10.1073/pnas.0701861104\">10.1073/pnas.0701861104</a>.","ista":"Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007. DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. 104(16), 6752–6757.","apa":"Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., &#38; Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0701861104\">https://doi.org/10.1073/pnas.0701861104</a>","short":"J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer, Proceedings of the National Academy of Sciences 104 (2007) 6752–6757."},"oa_version":"Published Version","year":"2007","oa":1,"issue":"16","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2021-06-07T09:38:21Z","extern":"1","author":[{"full_name":"Penterman, Jon","first_name":"Jon","last_name":"Penterman"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"},{"first_name":"Jin Hoe","full_name":"Huh, Jin Hoe","last_name":"Huh"},{"full_name":"Ballinger, Tracy","first_name":"Tracy","last_name":"Ballinger"},{"last_name":"Henikoff","first_name":"Steven","full_name":"Henikoff, Steven"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"}],"_id":"9487","date_published":"2007-04-17T00:00:00Z","department":[{"_id":"DaZi"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"external_id":{"pmid":["17409185"]},"volume":104},{"citation":{"ieee":"D. Zilberman, <i>The human promoter methylome</i>, vol. 39, no. 4. Nature Publishing Group, 2007, pp. 442–443.","ama":"Zilberman D. <i>The Human Promoter Methylome</i>. Vol 39. Nature Publishing Group; 2007:442-443. doi:<a href=\"https://doi.org/10.1038/ng0407-442\">10.1038/ng0407-442</a>","short":"D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.","chicago":"Zilberman, Daniel. <i>The Human Promoter Methylome</i>. <i>Nature Genetics</i>. Vol. 39. Nature Publishing Group, 2007. <a href=\"https://doi.org/10.1038/ng0407-442\">https://doi.org/10.1038/ng0407-442</a>.","apa":"Zilberman, D. (2007). <i>The human promoter methylome</i>. <i>Nature Genetics</i> (Vol. 39, pp. 442–443). Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng0407-442\">https://doi.org/10.1038/ng0407-442</a>","mla":"Zilberman, Daniel. “The Human Promoter Methylome.” <i>Nature Genetics</i>, vol. 39, no. 4, Nature Publishing Group, 2007, pp. 442–43, doi:<a href=\"https://doi.org/10.1038/ng0407-442\">10.1038/ng0407-442</a>.","ista":"Zilberman D. 2007. The human promoter methylome, Nature Publishing Group,p."},"publication":"Nature Genetics","page":"442-443","oa_version":"None","month":"04","type":"other_academic_publication","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","date_created":"2021-06-07T12:08:24Z","publication_status":"published","day":"01","extern":"1","year":"2007","issue":"4","doi":"10.1038/ng0407-442","publisher":"Nature Publishing Group","title":"The human promoter methylome","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"_id":"9504","pmid":1,"intvolume":"        39","article_processing_charge":"No","external_id":{"pmid":["17392803"]},"volume":39,"date_published":"2007-04-01T00:00:00Z","department":[{"_id":"DaZi"}],"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"date_updated":"2021-12-14T08:55:46Z"},{"issue":"22","year":"2007","oa":1,"extern":"1","language":[{"iso":"eng"}],"date_created":"2021-06-08T06:29:50Z","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.001131"}],"month":"11","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA methylation has an important role in many aspects of biology, including development and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies. Combining these techniques with DNA microarrays and high-throughput sequencing has made the mapping of DNA methylation feasible on a genome-wide scale. Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests."}],"citation":{"ieee":"D. Zilberman and S. Henikoff, “Genome-wide analysis of DNA methylation patterns,” <i>Development</i>, vol. 134, no. 22. The Company of Biologists, pp. 3959–3965, 2007.","ama":"Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns. <i>Development</i>. 2007;134(22):3959-3965. doi:<a href=\"https://doi.org/10.1242/dev.001131\">10.1242/dev.001131</a>","short":"D. Zilberman, S. Henikoff, Development 134 (2007) 3959–3965.","chicago":"Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.” <i>Development</i>. The Company of Biologists, 2007. <a href=\"https://doi.org/10.1242/dev.001131\">https://doi.org/10.1242/dev.001131</a>.","ista":"Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns. Development. 134(22), 3959–3965.","mla":"Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.” <i>Development</i>, vol. 134, no. 22, The Company of Biologists, 2007, pp. 3959–65, doi:<a href=\"https://doi.org/10.1242/dev.001131\">10.1242/dev.001131</a>.","apa":"Zilberman, D., &#38; Henikoff, S. (2007). Genome-wide analysis of DNA methylation patterns. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.001131\">https://doi.org/10.1242/dev.001131</a>"},"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"department":[{"_id":"DaZi"}],"date_published":"2007-11-15T00:00:00Z","volume":134,"external_id":{"pmid":["17928417"]},"_id":"9524","author":[{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel"},{"full_name":"Henikoff, Steven","first_name":"Steven","last_name":"Henikoff"}],"doi":"10.1242/dev.001131","publication_status":"published","day":"15","status":"public","type":"journal_article","scopus_import":"1","page":"3959-3965","publication":"Development","date_updated":"2021-12-14T08:57:58Z","article_type":"review","article_processing_charge":"No","intvolume":"       134","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Genome-wide analysis of DNA methylation patterns","publisher":"The Company of Biologists"}]