[{"article_processing_charge":"No","conference":{"name":"FOCS: Foundations of Computer Science"},"year":"2012","abstract":[{"lang":"eng","text":"Asynchronous task allocation is a fundamental problem in distributed computing in which p asynchronous processes must execute a set of m tasks. Also known as write-all or do-all, this problem been studied extensively, both independently and as a key building block for various distributed algorithms. In this paper, we break new ground on this classic problem: we introduce the To-Do Tree concurrent data structure, which improves on the best known randomized and deterministic upper bounds. In the presence of an adaptive adversary, the randomized To-Do Tree algorithm has O(m + p log p log2 m) work complexity. We then show that there exists a deterministic variant of the To-Do Tree algorithm with work complexity O(m + p log5 m log2 max(m, p)). For all values of m and p, our algorithms are within log factors of the Ω(m + p log p) lower bound for this problem. The key technical ingredient in our results is a new approach for analyzing concurrent executions against a strong adaptive scheduler. This technique allows us to handle the complex dependencies between the processes' coin flips and their scheduling, and to tightly bound the work needed to perform subsets of the tasks."}],"page":"331 - 340","oa_version":"None","status":"public","language":[{"iso":"eng"}],"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Bender","full_name":"Bender, Michael","first_name":"Michael"},{"first_name":"Seth","last_name":"Gilbert","full_name":"Gilbert, Seth"},{"first_name":"Rachid","last_name":"Guerraoui","full_name":"Guerraoui, Rachid"}],"citation":{"ama":"Alistarh D-A, Bender M, Gilbert S, Guerraoui R. How to allocate tasks asynchronously. In: IEEE; 2012:331-340. doi:<a href=\"https://doi.org/10.1109/FOCS.2012.41\">10.1109/FOCS.2012.41</a>","chicago":"Alistarh, Dan-Adrian, Michael Bender, Seth Gilbert, and Rachid Guerraoui. “How to Allocate Tasks Asynchronously,” 331–40. IEEE, 2012. <a href=\"https://doi.org/10.1109/FOCS.2012.41\">https://doi.org/10.1109/FOCS.2012.41</a>.","mla":"Alistarh, Dan-Adrian, et al. <i>How to Allocate Tasks Asynchronously</i>. IEEE, 2012, pp. 331–40, doi:<a href=\"https://doi.org/10.1109/FOCS.2012.41\">10.1109/FOCS.2012.41</a>.","short":"D.-A. Alistarh, M. Bender, S. Gilbert, R. Guerraoui, in:, IEEE, 2012, pp. 331–340.","ieee":"D.-A. Alistarh, M. Bender, S. Gilbert, and R. Guerraoui, “How to allocate tasks asynchronously,” presented at the FOCS: Foundations of Computer Science, 2012, pp. 331–340.","ista":"Alistarh D-A, Bender M, Gilbert S, Guerraoui R. 2012. How to allocate tasks asynchronously. FOCS: Foundations of Computer Science, 331–340.","apa":"Alistarh, D.-A., Bender, M., Gilbert, S., &#38; Guerraoui, R. (2012). How to allocate tasks asynchronously (pp. 331–340). Presented at the FOCS: Foundations of Computer Science, IEEE. <a href=\"https://doi.org/10.1109/FOCS.2012.41\">https://doi.org/10.1109/FOCS.2012.41</a>"},"publication_status":"published","day":"01","title":"How to allocate tasks asynchronously","publist_id":"6890","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","doi":"10.1109/FOCS.2012.41","date_published":"2012-01-01T00:00:00Z","date_created":"2018-12-11T11:48:23Z","publisher":"IEEE","_id":"766","date_updated":"2023-02-23T13:13:27Z","type":"conference"},{"title":"Generating Fast Indulgent Algorithms","intvolume":"        51","doi":"10.1007/s00224-012-9407-2","month":"01","extern":"1","volume":51,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6891","publisher":"Elsevier","date_created":"2018-12-11T11:48:23Z","acknowledgement":"Dan Alistarh was supported by the NCCR MICS Project. Corentin Travers had additional support from INRIA team REGAL and ANR project SPREADS.\r\nThe authors would like to thank Hagit Attiya and Nikola Kneževi\r\n ́\r\nc for their feed-\r\nback on previous drafts of this paper, and the anonymous reviewers for their useful comments.","date_published":"2012-01-01T00:00:00Z","type":"journal_article","issue":"4","date_updated":"2023-02-23T13:13:40Z","_id":"767","year":"2012","article_processing_charge":"No","status":"public","oa_version":"None","abstract":[{"text":"Synchronous distributed algorithms are easier to design and prove correct than algorithms that tolerate asynchrony. Yet, in the real world, networks experience asynchrony and other timing anomalies. In this paper, we address the question of how to efficiently transform an algorithm that relies on synchronous timing into an algorithm that tolerates asynchronous executions. We introduce a transformation technique from synchronous algorithms to indulgent algorithms (Guerraoui, in PODC, pp. 289-297, 2000), which induces only a constant overhead in terms of time complexity in well-behaved executions. Our technique is based on a new abstraction we call an asynchrony detector, which the participating processes implement collectively. The resulting transformation works for the class of colorless distributed tasks, including consensus and set agreement. Interestingly, we also show that our technique is relevant for colored tasks, by applying it to the renaming problem, to obtain the first indulgent renaming algorithm.","lang":"eng"}],"page":"404 - 424","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gilbert","full_name":"Gilbert, Seth","first_name":"Seth"},{"full_name":"Guerraoui, Rachid","last_name":"Guerraoui","first_name":"Rachid"},{"first_name":"Corentin","full_name":"Travers, Corentin","last_name":"Travers"}],"language":[{"iso":"eng"}],"publication":"Theory of Computing Systems","day":"01","publication_status":"published","citation":{"ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Generating Fast Indulgent Algorithms,” <i>Theory of Computing Systems</i>, vol. 51, no. 4. Elsevier, pp. 404–424, 2012.","short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Theory of Computing Systems 51 (2012) 404–424.","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Generating Fast Indulgent Algorithms. Theory of Computing Systems. 51(4), 404–424.","apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., &#38; Travers, C. (2012). Generating Fast Indulgent Algorithms. <i>Theory of Computing Systems</i>. Elsevier. <a href=\"https://doi.org/10.1007/s00224-012-9407-2\">https://doi.org/10.1007/s00224-012-9407-2</a>","ama":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Generating Fast Indulgent Algorithms. <i>Theory of Computing Systems</i>. 2012;51(4):404-424. doi:<a href=\"https://doi.org/10.1007/s00224-012-9407-2\">10.1007/s00224-012-9407-2</a>","chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Generating Fast Indulgent Algorithms.” <i>Theory of Computing Systems</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1007/s00224-012-9407-2\">https://doi.org/10.1007/s00224-012-9407-2</a>.","mla":"Alistarh, Dan-Adrian, et al. “Generating Fast Indulgent Algorithms.” <i>Theory of Computing Systems</i>, vol. 51, no. 4, Elsevier, 2012, pp. 404–24, doi:<a href=\"https://doi.org/10.1007/s00224-012-9407-2\">10.1007/s00224-012-9407-2</a>."}},{"_id":"7748","issue":"6","date_updated":"2021-01-12T08:15:15Z","type":"journal_article","quality_controlled":"1","date_published":"2012-06-01T00:00:00Z","publisher":"Wiley","date_created":"2020-04-30T11:01:07Z","article_type":"original","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","volume":15,"doi":"10.1111/j.1461-0248.2012.01780.x","intvolume":"        15","title":"Environment-dependent selection on mate choice in a natural population of birds","citation":{"ama":"Robinson MR, Sander van Doorn G, Gustafsson L, Qvarnström A. Environment-dependent selection on mate choice in a natural population of birds. <i>Ecology Letters</i>. 2012;15(6):611-618. doi:<a href=\"https://doi.org/10.1111/j.1461-0248.2012.01780.x\">10.1111/j.1461-0248.2012.01780.x</a>","chicago":"Robinson, Matthew Richard, G. Sander van Doorn, Lars Gustafsson, and Anna Qvarnström. “Environment-Dependent Selection on Mate Choice in a Natural Population of Birds.” <i>Ecology Letters</i>. Wiley, 2012. <a href=\"https://doi.org/10.1111/j.1461-0248.2012.01780.x\">https://doi.org/10.1111/j.1461-0248.2012.01780.x</a>.","mla":"Robinson, Matthew Richard, et al. “Environment-Dependent Selection on Mate Choice in a Natural Population of Birds.” <i>Ecology Letters</i>, vol. 15, no. 6, Wiley, 2012, pp. 611–18, doi:<a href=\"https://doi.org/10.1111/j.1461-0248.2012.01780.x\">10.1111/j.1461-0248.2012.01780.x</a>.","short":"M.R. Robinson, G. Sander van Doorn, L. Gustafsson, A. Qvarnström, Ecology Letters 15 (2012) 611–618.","ieee":"M. R. Robinson, G. Sander van Doorn, L. Gustafsson, and A. Qvarnström, “Environment-dependent selection on mate choice in a natural population of birds,” <i>Ecology Letters</i>, vol. 15, no. 6. Wiley, pp. 611–618, 2012.","apa":"Robinson, M. R., Sander van Doorn, G., Gustafsson, L., &#38; Qvarnström, A. (2012). Environment-dependent selection on mate choice in a natural population of birds. <i>Ecology Letters</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1461-0248.2012.01780.x\">https://doi.org/10.1111/j.1461-0248.2012.01780.x</a>","ista":"Robinson MR, Sander van Doorn G, Gustafsson L, Qvarnström A. 2012. Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. 15(6), 611–618."},"publication_status":"published","day":"01","publication":"Ecology Letters","publication_identifier":{"issn":["1461-023X"]},"language":[{"iso":"eng"}],"author":[{"last_name":"Robinson","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813"},{"first_name":"G.","full_name":"Sander van Doorn, G.","last_name":"Sander van Doorn"},{"last_name":"Gustafsson","full_name":"Gustafsson, Lars","first_name":"Lars"},{"last_name":"Qvarnström","full_name":"Qvarnström, Anna","first_name":"Anna"}],"abstract":[{"text":"Female mate choice acts as an important evolutionary force, yet the influence of the environment on both its expression and the selective pressures acting upon it remains unknown. We found consistent heritable differences between females in their choice of mate based on ornament size during a 25‐year study of a population of collared flycatchers. However, the fitness consequences of mate choice were dependent on environmental conditions experienced whilst breeding. Females breeding with highly ornamented males experienced high relative fitness during dry summer conditions, but low relative fitness during wetter years. Our results imply that sexual selection within a population can be highly variable and dependent upon the prevailing weather conditions experienced by individuals.","lang":"eng"}],"page":"611-618","oa_version":"None","status":"public","article_processing_charge":"No","year":"2012"},{"publication_status":"published","citation":{"mla":"Robinson, Matthew Richard, et al. “Senescence and Age-Specific Trade-Offs between Reproduction and Survival in Female Asian Elephants.” <i>Ecology Letters</i>, vol. 15, no. 3, Wiley, 2012, pp. 260–66, doi:<a href=\"https://doi.org/10.1111/j.1461-0248.2011.01735.x\">10.1111/j.1461-0248.2011.01735.x</a>.","chicago":"Robinson, Matthew Richard, Khyne U Mar, and Virpi Lummaa. “Senescence and Age-Specific Trade-Offs between Reproduction and Survival in Female Asian Elephants.” <i>Ecology Letters</i>. Wiley, 2012. <a href=\"https://doi.org/10.1111/j.1461-0248.2011.01735.x\">https://doi.org/10.1111/j.1461-0248.2011.01735.x</a>.","ama":"Robinson MR, Mar KU, Lummaa V. Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. <i>Ecology Letters</i>. 2012;15(3):260-266. doi:<a href=\"https://doi.org/10.1111/j.1461-0248.2011.01735.x\">10.1111/j.1461-0248.2011.01735.x</a>","ista":"Robinson MR, Mar KU, Lummaa V. 2012. Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. 15(3), 260–266.","apa":"Robinson, M. R., Mar, K. U., &#38; Lummaa, V. (2012). Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. <i>Ecology Letters</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1461-0248.2011.01735.x\">https://doi.org/10.1111/j.1461-0248.2011.01735.x</a>","ieee":"M. R. Robinson, K. U. Mar, and V. Lummaa, “Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants,” <i>Ecology Letters</i>, vol. 15, no. 3. Wiley, pp. 260–266, 2012.","short":"M.R. Robinson, K.U. Mar, V. Lummaa, Ecology Letters 15 (2012) 260–266."},"day":"01","publication":"Ecology Letters","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1461-023X"]},"author":[{"full_name":"Robinson, Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Khyne U","last_name":"Mar","full_name":"Mar, Khyne U"},{"first_name":"Virpi","full_name":"Lummaa, Virpi","last_name":"Lummaa"}],"abstract":[{"lang":"eng","text":"Although studies on laboratory species and natural populations of vertebrates have shown reproduction to impair later performance, little is known of the age‐specific associations between reproduction and survival, and how such findings apply to the ageing of large, long‐lived species. Herein we develop a framework to examine population‐level patterns of reproduction and survival across lifespan in long‐lived organisms, and decompose those changes into individual‐level effects, and the effects of age‐specific trade‐offs between fitness components. We apply this to an extensive longitudinal dataset on female semi‐captive Asian timber elephants (Elephas maximus) and report the first evidence of age‐specific fitness declines that are driven by age‐specific associations between fitness components in a long‐lived mammal. Associations between reproduction and survival are positive in early life, but negative in later life with up to 71% of later‐life survival declines associated with investing in the production of offspring within this population of this critically endangered species."}],"page":"260-266","status":"public","oa_version":"None","article_processing_charge":"No","year":"2012","_id":"7749","type":"journal_article","issue":"3","date_updated":"2021-01-12T08:15:16Z","date_published":"2012-03-01T00:00:00Z","quality_controlled":"1","date_created":"2020-04-30T11:01:26Z","publisher":"Wiley","article_type":"original","doi":"10.1111/j.1461-0248.2011.01735.x","month":"03","extern":"1","volume":15,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants","intvolume":"        15"},{"publisher":"American Physical Society","date_created":"2020-04-30T11:44:12Z","date_published":"2012-08-27T00:00:00Z","quality_controlled":"1","type":"journal_article","date_updated":"2021-01-12T08:15:27Z","issue":"9","_id":"7776","title":"Finite-size scaling at the jamming transition","intvolume":"       109","doi":"10.1103/physrevlett.109.095704","month":"08","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":109,"article_type":"original","author":[{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"Liu","full_name":"Liu, Andrea J.","first_name":"Andrea J."},{"full_name":"Nagel, Sidney R.","last_name":"Nagel","first_name":"Sidney R."}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007","1079-7114"]},"publication":"Physical Review Letters","day":"27","publication_status":"published","article_number":"095704","citation":{"ista":"Goodrich CP, Liu AJ, Nagel SR. 2012. Finite-size scaling at the jamming transition. Physical Review Letters. 109(9), 095704.","apa":"Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2012). Finite-size scaling at the jamming transition. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.109.095704\">https://doi.org/10.1103/physrevlett.109.095704</a>","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 109 (2012).","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Finite-size scaling at the jamming transition,” <i>Physical Review Letters</i>, vol. 109, no. 9. American Physical Society, 2012.","mla":"Goodrich, Carl Peter, et al. “Finite-Size Scaling at the Jamming Transition.” <i>Physical Review Letters</i>, vol. 109, no. 9, 095704, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/physrevlett.109.095704\">10.1103/physrevlett.109.095704</a>.","ama":"Goodrich CP, Liu AJ, Nagel SR. Finite-size scaling at the jamming transition. <i>Physical Review Letters</i>. 2012;109(9). doi:<a href=\"https://doi.org/10.1103/physrevlett.109.095704\">10.1103/physrevlett.109.095704</a>","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Finite-Size Scaling at the Jamming Transition.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/physrevlett.109.095704\">https://doi.org/10.1103/physrevlett.109.095704</a>."},"year":"2012","article_processing_charge":"No","status":"public","oa_version":"None","abstract":[{"lang":"eng","text":"We present an analysis of finite-size effects in jammed packings of N soft, frictionless spheres at zero temperature. There is a 1/N correction to the discrete jump in the contact number at the transition so that jammed packings exist only above isostaticity. As a result, the canonical power-law scalings of the contact number and elastic moduli break down at low pressure. These quantities exhibit scaling collapse with a nontrivial scaling function, demonstrating that the jamming transition can be considered a phase transition. Scaling is achieved as a function of N in both two and three dimensions, indicating an upper critical dimension of 2."}]},{"type":"journal_article","issue":"53","date_published":"2012-12-28T00:00:00Z","quality_controlled":"1","date_created":"2018-12-11T11:48:34Z","publisher":"American Society for Biochemistry and Molecular Biology","scopus_import":"1","article_type":"original","publist_id":"6852","doi":"10.1074/jbc.M112.398321","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"28","abstract":[{"text":"Fungal cell walls frequently contain a polymer of mannose and galactose called galactomannan. In the pathogenic filamentous fungus Aspergillus fumigatus, this polysaccharide is made of a linear mannan backbone with side chains of galactofuran and is anchored to the plasma membrane via a glycosylphosphatidylinositol or is covalently linked to the cell wall. To date, the biosynthesis and significance of this polysaccharide are unknown. The present data demonstrate that deletion of the Golgi UDP-galactofuranose transporter GlfB or the GDP-mannose transporter GmtA leads to the absence of galactofuran or galactomannan, respectively. This indicates that the biosynthesis of galactomannan probably occurs in the lumen of the Golgi apparatus and thus contrasts with the biosynthesis of other fungal cell wall polysaccharides studied to date that takes place at the plasma membrane. Transglycosylation of galactomannan from the membrane to the cell wall is hypothesized because both the cell wall-bound and membrane-bound polysaccharide forms are affected in the generated mutants. Considering the severe growth defect of the A. fumigatus GmtA-deficient mutant, proving this paradigm might provide new targets for antifungal therapy.","lang":"eng"}],"status":"public","_id":"801","date_updated":"2022-03-21T07:57:14Z","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft.","pmid":1,"external_id":{"pmid":["23139423"]},"month":"12","volume":287,"title":"Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose","intvolume":"       287","publication_status":"published","citation":{"chicago":"Engel, Jakob, Philipp S Schmalhorst, and Françoise Routier. “Biosynthesis of the Fungal Cell Wall Polysaccharide Galactomannan Requires Intraluminal GDP-Mannose.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2012. <a href=\"https://doi.org/10.1074/jbc.M112.398321\">https://doi.org/10.1074/jbc.M112.398321</a>.","ama":"Engel J, Schmalhorst PS, Routier F. Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. <i>Journal of Biological Chemistry</i>. 2012;287(53):44418-44424. doi:<a href=\"https://doi.org/10.1074/jbc.M112.398321\">10.1074/jbc.M112.398321</a>","mla":"Engel, Jakob, et al. “Biosynthesis of the Fungal Cell Wall Polysaccharide Galactomannan Requires Intraluminal GDP-Mannose.” <i>Journal of Biological Chemistry</i>, vol. 287, no. 53, American Society for Biochemistry and Molecular Biology, 2012, pp. 44418–24, doi:<a href=\"https://doi.org/10.1074/jbc.M112.398321\">10.1074/jbc.M112.398321</a>.","ieee":"J. Engel, P. S. Schmalhorst, and F. Routier, “Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose,” <i>Journal of Biological Chemistry</i>, vol. 287, no. 53. American Society for Biochemistry and Molecular Biology, pp. 44418–44424, 2012.","short":"J. Engel, P.S. Schmalhorst, F. Routier, Journal of Biological Chemistry 287 (2012) 44418–44424.","ista":"Engel J, Schmalhorst PS, Routier F. 2012. Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. 287(53), 44418–44424.","apa":"Engel, J., Schmalhorst, P. S., &#38; Routier, F. (2012). Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M112.398321\">https://doi.org/10.1074/jbc.M112.398321</a>"},"publication":"Journal of Biological Chemistry","language":[{"iso":"eng"}],"author":[{"full_name":"Engel, Jakob","last_name":"Engel","first_name":"Jakob"},{"full_name":"Schmalhorst, Philipp S","last_name":"Schmalhorst","first_name":"Philipp S","orcid":"0000-0002-5795-0133","id":"309D50DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Routier, Françoise","last_name":"Routier","first_name":"Françoise"}],"page":"44418 - 44424","oa_version":"None","article_processing_charge":"No","year":"2012"},{"oa_version":"None","year":"2012","article_processing_charge":"No","publication":"Physical Review E","citation":{"ama":"Hennequin G, Vogels TP, Gerstner W. Non-normal amplification in random balanced neuronal networks. <i>Physical Review E</i>. 2012;86(1). doi:<a href=\"https://doi.org/10.1103/physreve.86.011909\">10.1103/physreve.86.011909</a>","chicago":"Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Non-Normal Amplification in Random Balanced Neuronal Networks.” <i>Physical Review E</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/physreve.86.011909\">https://doi.org/10.1103/physreve.86.011909</a>.","mla":"Hennequin, Guillaume, et al. “Non-Normal Amplification in Random Balanced Neuronal Networks.” <i>Physical Review E</i>, vol. 86, no. 1, 011909, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/physreve.86.011909\">10.1103/physreve.86.011909</a>.","ieee":"G. Hennequin, T. P. Vogels, and W. Gerstner, “Non-normal amplification in random balanced neuronal networks,” <i>Physical Review E</i>, vol. 86, no. 1. American Physical Society, 2012.","short":"G. Hennequin, T.P. Vogels, W. Gerstner, Physical Review E 86 (2012).","ista":"Hennequin G, Vogels TP, Gerstner W. 2012. Non-normal amplification in random balanced neuronal networks. Physical Review E. 86(1), 011909.","apa":"Hennequin, G., Vogels, T. P., &#38; Gerstner, W. (2012). Non-normal amplification in random balanced neuronal networks. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.86.011909\">https://doi.org/10.1103/physreve.86.011909</a>"},"publication_status":"published","article_number":"011909","author":[{"full_name":"Hennequin, Guillaume","last_name":"Hennequin","first_name":"Guillaume"},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels","full_name":"Vogels, Tim P"},{"full_name":"Gerstner, Wulfram","last_name":"Gerstner","first_name":"Wulfram"}],"publication_identifier":{"eisbn":["1550-2376"],"issn":["1539-3755"]},"language":[{"iso":"eng"}],"volume":86,"month":"06","external_id":{"pmid":["23005454"]},"intvolume":"        86","title":"Non-normal amplification in random balanced neuronal networks","date_updated":"2021-01-12T08:16:35Z","_id":"8024","pmid":1,"status":"public","abstract":[{"lang":"eng","text":"In dynamical models of cortical networks, the recurrent connectivity can amplify the input given to the network in two distinct ways. One is induced by the presence of near-critical eigenvalues in the connectivity matrix W, producing large but slow activity fluctuations along the corresponding eigenvectors (dynamical slowing). The other relies on W not being normal, which allows the network activity to make large but fast excursions along specific directions. Here we investigate the trade-off between non-normal amplification and dynamical slowing in the spontaneous activity of large random neuronal networks composed of excitatory and inhibitory neurons. We use a Schur decomposition of W to separate the two amplification mechanisms. Assuming linear stochastic dynamics, we derive an exact expression for the expected amount of purely non-normal amplification. We find that amplification is very limited if dynamical slowing must be kept weak. We conclude that, to achieve strong transient amplification with little slowing, the connectivity must be structured. We show that unidirectional connections between neurons of the same type together with reciprocal connections between neurons of different types, allow for amplification already in the fast dynamical regime. Finally, our results also shed light on the differences between balanced networks in which inhibition exactly cancels excitation and those where inhibition dominates."}],"day":"11","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","extern":"1","doi":"10.1103/physreve.86.011909","article_type":"original","issue":"1","type":"journal_article","publisher":"American Physical Society","date_created":"2020-06-25T13:09:06Z","quality_controlled":"1","date_published":"2012-06-11T00:00:00Z"},{"status":"public","abstract":[{"text":"Using correlated live-cell imaging and electron tomography we found that actin branch junctions in protruding and treadmilling lamellipodia are not concentrated at the front as previously supposed, but link actin filament subsets in which there is a continuum of distances from a junction to the filament plus ends, for up to at least 1 mm. When branch sites were observed closely spaced on the same filament their separation was commonly a multiple of the actin helical repeat of 36 nm. Image averaging of branch junctions in the tomograms yielded a model for the in vivo branch at 2.9 nm resolution, which was comparable with that derived for the in vitro actin- Arp2/3 complex. Lamellipodium initiation was monitored in an intracellular wound-healing model and was found to involve branching from the sides of actin filaments oriented parallel to the plasmalemma. Many filament plus ends, presumably capped, terminated behind the lamellipodium tip and localized on the dorsal and ventral surfaces of the actin network. These findings reveal how branching events initiate and maintain a network of actin filaments of variable length, and provide the first structural model of the branch junction in vivo. A possible role of filament capping in generating the lamellipodium leaflet is discussed and a mathematical model of protrusion is also presented.","lang":"eng"}],"isi":1,"day":"01","doi":"10.1242/jcs.107623","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","extern":"1","has_accepted_license":"1","file":[{"access_level":"open_access","file_id":"5956","file_size":3326073,"file_name":"2012_Biologists_Vinzenz.pdf","checksum":"2f59e15cc3a85bb500a9887cef2aab67","creator":"kschuh","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:48:09Z","date_created":"2019-02-12T08:54:51Z"}],"publist_id":"6842","publisher":"Company of Biologists","date_created":"2018-12-11T11:48:37Z","quality_controlled":"1","date_published":"2012-06-01T00:00:00Z","type":"journal_article","issue":"11","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","year":"2012","article_processing_charge":"No","oa_version":"None","page":"2775 - 2785","file_date_updated":"2020-07-14T12:48:09Z","author":[{"full_name":"Vinzenz, Marlene","last_name":"Vinzenz","first_name":"Marlene"},{"first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria","last_name":"Nemethova"},{"full_name":"Schur, Florian","last_name":"Schur","first_name":"Florian","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mueller","full_name":"Mueller, Jan","first_name":"Jan"},{"first_name":"Akihiro","last_name":"Narita","full_name":"Narita, Akihiro"},{"first_name":"Edit","full_name":"Urban, Edit","last_name":"Urban"},{"last_name":"Winkler","full_name":"Winkler, Christoph","first_name":"Christoph"},{"first_name":"Christian","last_name":"Schmeiser","full_name":"Schmeiser, Christian"},{"full_name":"Koestler, Stefan","last_name":"Koestler","first_name":"Stefan"},{"last_name":"Rottner","full_name":"Rottner, Klemens","first_name":"Klemens"},{"full_name":"Resch, Guenter","last_name":"Resch","first_name":"Guenter"},{"last_name":"Maéda","full_name":"Maéda, Yuichiro","first_name":"Yuichiro"},{"last_name":"Small","full_name":"Small, John","first_name":"John"}],"language":[{"iso":"eng"}],"publication":"Journal of Cell Science","publication_status":"published","citation":{"chicago":"Vinzenz, Marlene, Maria Nemethova, Florian KM Schur, Jan Mueller, Akihiro Narita, Edit Urban, Christoph Winkler, et al. “Actin Branching in the Initiation and Maintenance of Lamellipodia.” <i>Journal of Cell Science</i>. Company of Biologists, 2012. <a href=\"https://doi.org/10.1242/jcs.107623\">https://doi.org/10.1242/jcs.107623</a>.","ama":"Vinzenz M, Nemethova M, Schur FK, et al. Actin branching in the initiation and maintenance of lamellipodia. <i>Journal of Cell Science</i>. 2012;125(11):2775-2785. doi:<a href=\"https://doi.org/10.1242/jcs.107623\">10.1242/jcs.107623</a>","mla":"Vinzenz, Marlene, et al. “Actin Branching in the Initiation and Maintenance of Lamellipodia.” <i>Journal of Cell Science</i>, vol. 125, no. 11, Company of Biologists, 2012, pp. 2775–85, doi:<a href=\"https://doi.org/10.1242/jcs.107623\">10.1242/jcs.107623</a>.","short":"M. Vinzenz, M. Nemethova, F.K. Schur, J. Mueller, A. Narita, E. Urban, C. Winkler, C. Schmeiser, S. Koestler, K. Rottner, G. Resch, Y. Maéda, J. Small, Journal of Cell Science 125 (2012) 2775–2785.","ieee":"M. Vinzenz <i>et al.</i>, “Actin branching in the initiation and maintenance of lamellipodia,” <i>Journal of Cell Science</i>, vol. 125, no. 11. Company of Biologists, pp. 2775–2785, 2012.","apa":"Vinzenz, M., Nemethova, M., Schur, F. K., Mueller, J., Narita, A., Urban, E., … Small, J. (2012). Actin branching in the initiation and maintenance of lamellipodia. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.107623\">https://doi.org/10.1242/jcs.107623</a>","ista":"Vinzenz M, Nemethova M, Schur FK, Mueller J, Narita A, Urban E, Winkler C, Schmeiser C, Koestler S, Rottner K, Resch G, Maéda Y, Small J. 2012. Actin branching in the initiation and maintenance of lamellipodia. Journal of Cell Science. 125(11), 2775–2785."},"title":"Actin branching in the initiation and maintenance of lamellipodia","intvolume":"       125","ddc":["570"],"tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"oa":1,"month":"06","volume":125,"external_id":{"isi":["000306705000022"]},"acknowledgement":"This work was supported by the Austrian Science Fund [projects FWF I516-B09 and FWF P21292-B09 to J.V.S.]; the Vienna Science and Technology Fund [WWTF-grant numbers MA 09-004 to J.V.S. and C.S], ZIT - The Technology Agency of the City of Vienna [VSOE, CMCN to J.V.S. and G.P.R.]; the Deutsche Forschungsgemeinschaft [grant number RO 2414/1-2 to K.R.]; the Daiko research foundation [grant number 9134 to A.N.]; and a Grant-in-Aid for Scientific Research [S, grant number 20227008 to Y.M.] and a Grant-in-Aid for Young Scientists [B, grant number 22770145 to A.N.] (B) from The Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government. Deposited in PMC for immediate release. We thank Tibor Kulcsar for assistance with graphics.","date_updated":"2025-09-30T08:23:31Z","_id":"808"},{"date_updated":"2021-01-12T08:17:43Z","_id":"8246","pmid":1,"volume":333,"month":"08","external_id":{"pmid":["22640011"]},"title":"Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response","intvolume":"       333","publication":"FEMS Microbiology Letters","publication_status":"published","citation":{"chicago":"Dengler, Vanina, Patricia Stutzmann Meier, Ronald Heusser, Peter Kupferschmied, Judit Singer, Sarah Friebe, Sibylle Burger Staufer, et al. “Deletion of Hypothetical Wall Teichoic Acid Ligases in Staphylococcus Aureus Activates the Cell Wall Stress Response.” <i>FEMS Microbiology Letters</i>. Oxford University Press, 2012. <a href=\"https://doi.org/10.1111/j.1574-6968.2012.02603.x\">https://doi.org/10.1111/j.1574-6968.2012.02603.x</a>.","ama":"Dengler V, Meier PS, Heusser R, et al. Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. <i>FEMS Microbiology Letters</i>. 2012;333(2):109-120. doi:<a href=\"https://doi.org/10.1111/j.1574-6968.2012.02603.x\">10.1111/j.1574-6968.2012.02603.x</a>","mla":"Dengler, Vanina, et al. “Deletion of Hypothetical Wall Teichoic Acid Ligases in Staphylococcus Aureus Activates the Cell Wall Stress Response.” <i>FEMS Microbiology Letters</i>, vol. 333, no. 2, Oxford University Press, 2012, pp. 109–20, doi:<a href=\"https://doi.org/10.1111/j.1574-6968.2012.02603.x\">10.1111/j.1574-6968.2012.02603.x</a>.","ieee":"V. Dengler <i>et al.</i>, “Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response,” <i>FEMS Microbiology Letters</i>, vol. 333, no. 2. Oxford University Press, pp. 109–120, 2012.","short":"V. Dengler, P.S. Meier, R. Heusser, P. Kupferschmied, J. Singer, S. Friebe, S.B. Staufer, P.A. Majcherczyk, P. Moreillon, B. Berger-Bächi, N. McCallum, FEMS Microbiology Letters 333 (2012) 109–120.","apa":"Dengler, V., Meier, P. S., Heusser, R., Kupferschmied, P., Singer, J., Friebe, S., … McCallum, N. (2012). Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. <i>FEMS Microbiology Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1111/j.1574-6968.2012.02603.x\">https://doi.org/10.1111/j.1574-6968.2012.02603.x</a>","ista":"Dengler V, Meier PS, Heusser R, Kupferschmied P, Singer J, Friebe S, Staufer SB, Majcherczyk PA, Moreillon P, Berger-Bächi B, McCallum N. 2012. Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology Letters. 333(2), 109–120."},"author":[{"full_name":"Dengler, Vanina","last_name":"Dengler","first_name":"Vanina"},{"last_name":"Meier","full_name":"Meier, Patricia Stutzmann","first_name":"Patricia Stutzmann"},{"first_name":"Ronald","last_name":"Heusser","full_name":"Heusser, Ronald"},{"first_name":"Peter","full_name":"Kupferschmied, Peter","last_name":"Kupferschmied"},{"last_name":"Fazekas","full_name":"Fazekas, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","orcid":"0000-0002-8777-3502"},{"first_name":"Sarah","full_name":"Friebe, Sarah","last_name":"Friebe"},{"last_name":"Staufer","full_name":"Staufer, Sibylle Burger","first_name":"Sibylle Burger"},{"full_name":"Majcherczyk, Paul A.","last_name":"Majcherczyk","first_name":"Paul A."},{"full_name":"Moreillon, Philippe","last_name":"Moreillon","first_name":"Philippe"},{"last_name":"Berger-Bächi","full_name":"Berger-Bächi, Brigitte","first_name":"Brigitte"},{"full_name":"McCallum, Nadine","last_name":"McCallum","first_name":"Nadine"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0378-1097"]},"oa_version":"None","page":"109-120","year":"2012","article_processing_charge":"No","type":"journal_article","issue":"2","date_created":"2020-08-10T11:54:47Z","publisher":"Oxford University Press","quality_controlled":"1","date_published":"2012-08-01T00:00:00Z","doi":"10.1111/j.1574-6968.2012.02603.x","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","day":"01","status":"public","abstract":[{"text":"The Staphylococcus aureus cell wall stress stimulon (CWSS) is activated by cell envelope-targeting antibiotics or depletion of essential cell wall biosynthesis enzymes. The functionally uncharacterized S. aureus LytR-CpsA-Psr (LCP) proteins, MsrR, SA0908 and SA2103, all belong to the CWSS. Although not essential, deletion of all three LCP proteins severely impairs cell division. We show here that VraSR-dependent CWSS expression was up to 250-fold higher in single, double and triple LCP mutants than in wild type S. aureus in the absence of external stress. The LCP triple mutant was virtually depleted of wall teichoic acids (WTA), which could be restored to different degrees by any of the single LCP proteins. Subinhibitory concentrations of tunicamycin, which inhibits the first WTA synthesis enzyme TarO (TagO), could partially complement the severe growth defect of the LCP triple mutant. Both of the latter findings support a role for S. aureus LCP proteins in late WTA synthesis, as in Bacillus subtilis where LCP proteins were recently proposed to transfer WTA from lipid carriers to the cell wall peptidoglycan. Intrinsic activation of the CWSS upon LCP deletion and the fact that LCP proteins were essential for WTA-loading of the cell wall, highlight their important role(s) in S. aureus cell envelope biogenesis.","lang":"eng"}]},{"intvolume":"        28","title":"Hormonal interactions in the regulation of plant development","publist_id":"6822","extern":1,"month":"11","volume":28,"doi":"10.1146/annurev-cellbio-101011-155741","date_published":"2012-11-01T00:00:00Z","quality_controlled":0,"acknowledgement":"We would like to thank Annick Bleys for help in preparing the manuscript. This work was supported by the European Research Council with a Starting Independent Research grant (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043 (to the Central European Institute of Technology, CEITEC) to E.B. M.V. is a postdoctoral fellow of the Research Foundation Flanders. We apologize that, because of space restrictions, the scientific contributions of only a limited number of original articles could be cited and discussed.","date_created":"2018-12-11T11:48:43Z","publisher":"Annual Reviews","_id":"826","date_updated":"2021-01-12T08:17:46Z","type":"journal_article","year":"2012","page":"463 - 487","abstract":[{"lang":"eng","text":"Plants exhibit a unique developmental flexibility to ever-changing environmental conditions. To achieve their profound adaptability, plants are able to maintain permanent stem cell populations and form new organs during the entire plant life cycle. Signaling substances, called plant hormones, such as auxin, cytokinin, abscisic acid, brassinosteroid, ethylene, gibberellin, jasmonic acid, and strigolactone, govern and coordinate these developmental processes. Physiological and genetic studies have dissected the molecular components of signal perception and transduction of the individual hormonal pathways. However, over recent years it has become evident that hormones do not act only in a linear pathway. Hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions. This raises questions about the molecular mechanisms underlying hormonal cross talk and about how these hormonal networks are established, maintained, and modulated throughout plant development."}],"status":"public","author":[{"first_name":"Marleen","full_name":"Vanstraelen, Marleen","last_name":"Vanstraelen"},{"last_name":"Benková","full_name":"Eva Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"citation":{"mla":"Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation of Plant Development.” <i>Annual Review of Cell and Developmental Biology</i>, vol. 28, Annual Reviews, 2012, pp. 463–87, doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-101011-155741\">10.1146/annurev-cellbio-101011-155741</a>.","chicago":"Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation of Plant Development.” <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews, 2012. <a href=\"https://doi.org/10.1146/annurev-cellbio-101011-155741\">https://doi.org/10.1146/annurev-cellbio-101011-155741</a>.","ama":"Vanstraelen M, Benková E. Hormonal interactions in the regulation of plant development. <i>Annual Review of Cell and Developmental Biology</i>. 2012;28:463-487. doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-101011-155741\">10.1146/annurev-cellbio-101011-155741</a>","ista":"Vanstraelen M, Benková E. 2012. Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. 28, 463–487.","apa":"Vanstraelen, M., &#38; Benková, E. (2012). Hormonal interactions in the regulation of plant development. <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-cellbio-101011-155741\">https://doi.org/10.1146/annurev-cellbio-101011-155741</a>","ieee":"M. Vanstraelen and E. Benková, “Hormonal interactions in the regulation of plant development,” <i>Annual Review of Cell and Developmental Biology</i>, vol. 28. Annual Reviews, pp. 463–487, 2012.","short":"M. Vanstraelen, E. Benková, Annual Review of Cell and Developmental Biology 28 (2012) 463–487."},"publication_status":"published","publication":"Annual Review of Cell and Developmental Biology","day":"01"},{"title":"Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin","intvolume":"        24","publist_id":"6819","doi":"10.1105/tpc.112.103044","month":"10","extern":1,"volume":24,"quality_controlled":0,"date_published":"2012-10-01T00:00:00Z","publisher":"American Society of Plant Biologists","acknowledgement":"We thank Jen Sheen, Dolf Weijers, Tatsuo Kakimoto, Stephen Depuydt, and Laurent Laplaze for sharing published material, Jiri Friml for discussions, and Martine De Cock and Annick Bleys for help in preparing the manuscript. This work was supported by a Starting Independent Research grant from the European Research Council (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043 to the Central European Institute of Technology to E.B. and grants from the Ministry of Education, Youth, and Sports of the Czech Republic (MSM 6198959216) and the Centre of the Region Haná for Biotechnological and Agricultural Research (ED0007/01/01) to P.T.","date_created":"2018-12-11T11:48:43Z","_id":"829","type":"journal_article","issue":"10","date_updated":"2021-01-12T08:17:55Z","year":"2012","abstract":[{"text":"The architecture of a plant's root system, established postembryonically, results from both coordinated root growth and lateral root branching. The plant hormones auxin and cytokinin are central endogenous signaling molecules that regulate lateral root organogenesis positively and negatively, respectively. Tight control and mutual balance of their antagonistic activities are particularly important during the early phases of lateral root organogenesis to ensure continuous lateral root initiation (LRI) and proper development of lateral root primordia (LRP). Here, we show that the early phases of lateral root organogenesis, including priming and initiation, take place in root zones with a repressed cytokinin response. Accordingly, ectopic overproduction of cytokinin in the root basal meristem most efficiently inhibits LRI. Enhanced cytokinin responses in pericycle cells between existing LRP might restrict LRI near existing LRP and, when compromised, ectopic LRI occurs. Furthermore, our results demonstrate that young LRP are more sensitive to perturbations in the cytokinin activity than are developmentally more advanced primordia. We hypothesize that the effect of cytokinin on the development of primordia possibly depends on the robustness and stability of the auxin gradient.","lang":"eng"}],"page":"3967 - 3981","status":"public","author":[{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"first_name":"Katerina","full_name":"Podlesakova, Katerina","last_name":"Podlesakova"},{"last_name":"Marhavy","full_name":"Peter Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","orcid":"0000-0001-5227-5741"},{"full_name":"Duclercq, Jérôme","last_name":"Duclercq","first_name":"Jérôme"},{"last_name":"Cuesta","full_name":"Candela Cuesta","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela","orcid":"0000-0003-1923-2410"},{"first_name":"Bruno","last_name":"Muller","full_name":"Muller, Bruno"},{"full_name":"Grunewald, Wim","last_name":"Grunewald","first_name":"Wim"},{"first_name":"Petr","full_name":"Tarkowski, Petr","last_name":"Tarkowski"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková","last_name":"Benková"}],"publication_status":"published","citation":{"ista":"Bielach A, Podlesakova K, Marhavý P, Duclercq J, Cuesta C, Muller B, Grunewald W, Tarkowski P, Benková E. 2012. Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. The Plant Cell. 24(10), 3967–3981.","apa":"Bielach, A., Podlesakova, K., Marhavý, P., Duclercq, J., Cuesta, C., Muller, B., … Benková, E. (2012). Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. <i>The Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.112.103044\">https://doi.org/10.1105/tpc.112.103044</a>","ieee":"A. Bielach <i>et al.</i>, “Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin,” <i>The Plant Cell</i>, vol. 24, no. 10. American Society of Plant Biologists, pp. 3967–3981, 2012.","short":"A. Bielach, K. Podlesakova, P. Marhavý, J. Duclercq, C. Cuesta, B. Muller, W. Grunewald, P. Tarkowski, E. Benková, The Plant Cell 24 (2012) 3967–3981.","mla":"Bielach, Agnieszka, et al. “Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.” <i>The Plant Cell</i>, vol. 24, no. 10, American Society of Plant Biologists, 2012, pp. 3967–81, doi:<a href=\"https://doi.org/10.1105/tpc.112.103044\">10.1105/tpc.112.103044</a>.","ama":"Bielach A, Podlesakova K, Marhavý P, et al. Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. <i>The Plant Cell</i>. 2012;24(10):3967-3981. doi:<a href=\"https://doi.org/10.1105/tpc.112.103044\">10.1105/tpc.112.103044</a>","chicago":"Bielach, Agnieszka, Katerina Podlesakova, Peter Marhavý, Jérôme Duclercq, Candela Cuesta, Bruno Muller, Wim Grunewald, Petr Tarkowski, and Eva Benková. “Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.” <i>The Plant Cell</i>. American Society of Plant Biologists, 2012. <a href=\"https://doi.org/10.1105/tpc.112.103044\">https://doi.org/10.1105/tpc.112.103044</a>."},"publication":"The Plant Cell","day":"01"},{"author":[{"first_name":"Onuralp","full_name":"Soylemez, Onuralp","last_name":"Soylemez"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","last_name":"Kondrashov"}],"citation":{"mla":"Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” <i>Genome Biology and Evolution</i>, vol. 4, no. 12, Oxford University Press, 2012, pp. 1213–22, doi:<a href=\"https://doi.org/10.1093/gbe/evs096\">10.1093/gbe/evs096</a>.","ama":"Soylemez O, Kondrashov F. Estimating the rate of irreversibility in protein evolution. <i>Genome Biology and Evolution</i>. 2012;4(12):1213-1222. doi:<a href=\"https://doi.org/10.1093/gbe/evs096\">10.1093/gbe/evs096</a>","chicago":"Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2012. <a href=\"https://doi.org/10.1093/gbe/evs096\">https://doi.org/10.1093/gbe/evs096</a>.","apa":"Soylemez, O., &#38; Kondrashov, F. (2012). Estimating the rate of irreversibility in protein evolution. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evs096\">https://doi.org/10.1093/gbe/evs096</a>","ista":"Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 4(12), 1213–1222.","ieee":"O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in protein evolution,” <i>Genome Biology and Evolution</i>, vol. 4, no. 12. Oxford University Press, pp. 1213–1222, 2012.","short":"O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222."},"publication_status":"published","day":"01","publication":"Genome Biology and Evolution","year":"2012","page":"1213 - 1222","abstract":[{"lang":"eng","text":"Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function."}],"status":"public","date_published":"2012-01-01T00:00:00Z","quality_controlled":0,"publisher":"Oxford University Press","acknowledgement":"This work was supported by Plan Nacional grant BFU2009-09271 from the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado Universitario) program grant AP2008-01888 from the Spanish Ministry of Education to O.S. F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist.","date_created":"2018-12-11T11:48:49Z","_id":"846","license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"12","date_updated":"2021-01-12T08:19:25Z","type":"journal_article","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"intvolume":"         4","title":"Estimating the rate of irreversibility in protein evolution","publist_id":"6802","volume":4,"extern":1,"month":"01","doi":"10.1093/gbe/evs096"},{"status":"public","oa_version":"None","abstract":[{"lang":"eng","text":"The 1H dipolar network, which is the major obstacle for applying proton detection in the solid-state, can be reduced by deuteration, employing the RAP (Reduced Adjoining Protonation) labeling scheme, which yields random protonation at non-exchangeable sites. We present here a systematic study on the optimal degree of random sidechain protonation in RAP samples as a function of the MAS (magic angle spinning) frequency. In particular, we compare 1H sensitivity and linewidth of a microcrystalline protein, the SH3 domain of chicken α-spectrin, for samples, prepared with 5–25 % H2O in the E. coli growth medium, in the MAS frequency range of 20–60 kHz. At an external field of 19.96 T (850 MHz), we find that using a proton concentration between 15 and 25 % in the M9 medium yields the best compromise in terms of sensitivity and resolution, with an achievable average 1H linewidth on the order of 40–50 Hz. Comparing sensitivities at a MAS frequency of 60 versus 20 kHz, a gain in sensitivity by a factor of 4–4.5 is observed in INEPT-based 1H detected 1D 1H,13C correlation experiments. In total, we find that spectra recorded with a 1.3 mm rotor at 60 kHz have almost the same sensitivity as spectra recorded with a fully packed 3.2 mm rotor at 20 kHz, even though ~20× less material is employed. The improved sensitivity is attributed to 1H line narrowing due to fast MAS and to the increased efficiency of the 1.3 mm coil."}],"page":"155-168","year":"2012","article_processing_charge":"No","publication":"Journal of Biomolecular NMR","day":"23","publication_status":"published","citation":{"mla":"Asami, Sam, et al. “Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” <i>Journal of Biomolecular NMR</i>, vol. 54, no. 2, Springer Nature, 2012, pp. 155–68, doi:<a href=\"https://doi.org/10.1007/s10858-012-9659-9\">10.1007/s10858-012-9659-9</a>.","ama":"Asami S, Szekely K, Schanda P, Meier BH, Reif B. Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. <i>Journal of Biomolecular NMR</i>. 2012;54(2):155-168. doi:<a href=\"https://doi.org/10.1007/s10858-012-9659-9\">10.1007/s10858-012-9659-9</a>","chicago":"Asami, Sam, Kathrin Szekely, Paul Schanda, Beat H. Meier, and Bernd Reif. “Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2012. <a href=\"https://doi.org/10.1007/s10858-012-9659-9\">https://doi.org/10.1007/s10858-012-9659-9</a>.","apa":"Asami, S., Szekely, K., Schanda, P., Meier, B. H., &#38; Reif, B. (2012). Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-012-9659-9\">https://doi.org/10.1007/s10858-012-9659-9</a>","ista":"Asami S, Szekely K, Schanda P, Meier BH, Reif B. 2012. Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. Journal of Biomolecular NMR. 54(2), 155–168.","short":"S. Asami, K. Szekely, P. Schanda, B.H. Meier, B. Reif, Journal of Biomolecular NMR 54 (2012) 155–168.","ieee":"S. Asami, K. Szekely, P. Schanda, B. H. Meier, and B. Reif, “Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency,” <i>Journal of Biomolecular NMR</i>, vol. 54, no. 2. Springer Nature, pp. 155–168, 2012."},"author":[{"first_name":"Sam","last_name":"Asami","full_name":"Asami, Sam"},{"first_name":"Kathrin","full_name":"Szekely, Kathrin","last_name":"Szekely"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"},{"first_name":"Beat H.","last_name":"Meier","full_name":"Meier, Beat H."},{"first_name":"Bernd","full_name":"Reif, Bernd","last_name":"Reif"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0925-2738","1573-5001"]},"doi":"10.1007/s10858-012-9659-9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","volume":54,"extern":"1","article_type":"original","title":"Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency","intvolume":"        54","type":"journal_article","date_updated":"2021-01-12T08:19:27Z","issue":"2","_id":"8463","date_created":"2020-09-18T10:09:18Z","publisher":"Springer Nature","quality_controlled":"1","date_published":"2012-08-23T00:00:00Z"},{"status":"public","oa_version":"None","page":"14800-14807","abstract":[{"text":"We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond time scales can be detected and quantified by solid-state NMR spectroscopy. We show two independent approaches that measure the effect of conformational exchange on transverse relaxation parameters, namely Carr–Purcell–Meiboom–Gill relaxation-dispersion experiments and measurement of differential multiple-quantum coherence decay. Long coherence lifetimes, as required for these experiments, are achieved by the use of highly deuterated samples and fast magic-angle spinning. The usefulness of the approaches is demonstrated by application to microcrystalline ubiquitin. We detect a conformational exchange process in a region of the protein for which dynamics have also been observed in solution. Interestingly, quantitative analysis of the data reveals that the exchange process is more than 1 order of magnitude slower than in solution, and this points to the impact of the crystalline environment on free energy barriers.","lang":"eng"}],"year":"2012","article_processing_charge":"No","day":"21","publication":"Journal of the American Chemical Society","publication_status":"published","citation":{"apa":"Tollinger, M., Sivertsen, A. C., Meier, B. H., Ernst, M., &#38; Schanda, P. (2012). Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja303591y\">https://doi.org/10.1021/ja303591y</a>","ista":"Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. 2012. Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society. 134(36), 14800–14807.","ieee":"M. Tollinger, A. C. Sivertsen, B. H. Meier, M. Ernst, and P. Schanda, “Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy,” <i>Journal of the American Chemical Society</i>, vol. 134, no. 36. American Chemical Society, pp. 14800–14807, 2012.","short":"M. Tollinger, A.C. Sivertsen, B.H. Meier, M. Ernst, P. Schanda, Journal of the American Chemical Society 134 (2012) 14800–14807.","mla":"Tollinger, Martin, et al. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>, vol. 134, no. 36, American Chemical Society, 2012, pp. 14800–07, doi:<a href=\"https://doi.org/10.1021/ja303591y\">10.1021/ja303591y</a>.","chicago":"Tollinger, Martin, Astrid C. Sivertsen, Beat H. Meier, Matthias Ernst, and Paul Schanda. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2012. <a href=\"https://doi.org/10.1021/ja303591y\">https://doi.org/10.1021/ja303591y</a>.","ama":"Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. <i>Journal of the American Chemical Society</i>. 2012;134(36):14800-14807. doi:<a href=\"https://doi.org/10.1021/ja303591y\">10.1021/ja303591y</a>"},"author":[{"first_name":"Martin","last_name":"Tollinger","full_name":"Tollinger, Martin"},{"full_name":"Sivertsen, Astrid C.","last_name":"Sivertsen","first_name":"Astrid C."},{"full_name":"Meier, Beat H.","last_name":"Meier","first_name":"Beat H."},{"full_name":"Ernst, Matthias","last_name":"Ernst","first_name":"Matthias"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0002-7863","1520-5126"]},"doi":"10.1021/ja303591y","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","month":"08","volume":134,"article_type":"original","title":"Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy","intvolume":"       134","type":"journal_article","issue":"36","date_updated":"2021-01-12T08:19:27Z","_id":"8465","publisher":"American Chemical Society","date_created":"2020-09-18T10:10:20Z","quality_controlled":"1","date_published":"2012-08-21T00:00:00Z"},{"_id":"8466","issue":"19","date_updated":"2021-01-12T08:19:28Z","type":"journal_article","date_published":"2012-05-03T00:00:00Z","quality_controlled":"1","date_created":"2020-09-18T10:10:28Z","publisher":"American Chemical Society","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":134,"month":"05","extern":"1","doi":"10.1021/ja302598j","intvolume":"       134","title":"Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate","citation":{"short":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, B. Brutscher, Journal of the American Chemical Society 134 (2012) 8066–8069.","ieee":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, and B. Brutscher, “Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate,” <i>Journal of the American Chemical Society</i>, vol. 134, no. 19. American Chemical Society, pp. 8066–8069, 2012.","apa":"Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Forge, V., &#38; Brutscher, B. (2012). Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja302598j\">https://doi.org/10.1021/ja302598j</a>","ista":"Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. 2012. Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. 134(19), 8066–8069.","ama":"Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. <i>Journal of the American Chemical Society</i>. 2012;134(19):8066-8069. doi:<a href=\"https://doi.org/10.1021/ja302598j\">10.1021/ja302598j</a>","chicago":"Rennella, Enrico, Thomas Cutuil, Paul Schanda, Isabel Ayala, Vincent Forge, and Bernhard Brutscher. “Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2012. <a href=\"https://doi.org/10.1021/ja302598j\">https://doi.org/10.1021/ja302598j</a>.","mla":"Rennella, Enrico, et al. “Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate.” <i>Journal of the American Chemical Society</i>, vol. 134, no. 19, American Chemical Society, 2012, pp. 8066–69, doi:<a href=\"https://doi.org/10.1021/ja302598j\">10.1021/ja302598j</a>."},"publication_status":"published","day":"03","publication":"Journal of the American Chemical Society","publication_identifier":{"issn":["0002-7863","1520-5126"]},"language":[{"iso":"eng"}],"author":[{"full_name":"Rennella, Enrico","last_name":"Rennella","first_name":"Enrico"},{"last_name":"Cutuil","full_name":"Cutuil, Thomas","first_name":"Thomas"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda"},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"last_name":"Forge","full_name":"Forge, Vincent","first_name":"Vincent"},{"last_name":"Brutscher","full_name":"Brutscher, Bernhard","first_name":"Bernhard"}],"abstract":[{"lang":"eng","text":"Recent advances in NMR spectroscopy and the availability of high magnetic field strengths now offer the possibility to record real-time 3D NMR spectra of short-lived protein states, e.g., states that become transiently populated during protein folding. Here we present a strategy for obtaining sequential NMR assignments as well as atom-resolved information on structural and dynamic features within a folding intermediate of the amyloidogenic protein β2-microglobulin that has a half-lifetime of only 20 min."}],"page":"8066-8069","oa_version":"None","status":"public","article_processing_charge":"No","year":"2012"},{"article_type":"original","doi":"10.1016/j.jmr.2011.10.010","volume":214,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","extern":"1","title":"A supplementary coil for 2H decoupling with commercial HCN MAS probes","intvolume":"       214","_id":"8467","type":"journal_article","date_updated":"2021-01-12T08:19:28Z","date_published":"2012-01-01T00:00:00Z","quality_controlled":"1","date_created":"2020-09-18T10:10:36Z","publisher":"Elsevier","page":"76-80","abstract":[{"lang":"eng","text":"Partial deuteration is a powerful tool to increase coherence life times and spectral resolution in proton solid-state NMR. The J coupling to deuterium needs, however, to be decoupled to maintain the good resolution in the (usually indirect) 13C dimension(s). We present a simple and reversible way to expand a commercial 1.3 mm HCN MAS probe with a 2H channel with sufficient field strength for J-decoupling of deuterium, namely 2–3 kHz. The coil is placed at the outside of the stator and requires no significant modifications to the probe. The performance and the realizable gains in sensitivity and resolution are demonstrated using perdeuterated ubiquitin, with selectively CHD2-labeled methyl groups."}],"status":"public","oa_version":"None","article_processing_charge":"No","year":"2012","publication_status":"published","citation":{"chicago":"Huber, Matthias, Oliver With, Paul Schanda, René Verel, Matthias Ernst, and Beat H. Meier. “A Supplementary Coil for 2H Decoupling with Commercial HCN MAS Probes.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.jmr.2011.10.010\">https://doi.org/10.1016/j.jmr.2011.10.010</a>.","ama":"Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. A supplementary coil for 2H decoupling with commercial HCN MAS probes. <i>Journal of Magnetic Resonance</i>. 2012;214:76-80. doi:<a href=\"https://doi.org/10.1016/j.jmr.2011.10.010\">10.1016/j.jmr.2011.10.010</a>","mla":"Huber, Matthias, et al. “A Supplementary Coil for 2H Decoupling with Commercial HCN MAS Probes.” <i>Journal of Magnetic Resonance</i>, vol. 214, Elsevier, 2012, pp. 76–80, doi:<a href=\"https://doi.org/10.1016/j.jmr.2011.10.010\">10.1016/j.jmr.2011.10.010</a>.","short":"M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, B.H. Meier, Journal of Magnetic Resonance 214 (2012) 76–80.","ieee":"M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, and B. H. Meier, “A supplementary coil for 2H decoupling with commercial HCN MAS probes,” <i>Journal of Magnetic Resonance</i>, vol. 214. Elsevier, pp. 76–80, 2012.","apa":"Huber, M., With, O., Schanda, P., Verel, R., Ernst, M., &#38; Meier, B. H. (2012). A supplementary coil for 2H decoupling with commercial HCN MAS probes. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2011.10.010\">https://doi.org/10.1016/j.jmr.2011.10.010</a>","ista":"Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. 2012. A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. 214, 76–80."},"publication":"Journal of Magnetic Resonance","day":"01","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1090-7807"]},"author":[{"first_name":"Matthias","full_name":"Huber, Matthias","last_name":"Huber"},{"last_name":"With","full_name":"With, Oliver","first_name":"Oliver"},{"last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606"},{"first_name":"René","full_name":"Verel, René","last_name":"Verel"},{"last_name":"Ernst","full_name":"Ernst, Matthias","first_name":"Matthias"},{"full_name":"Meier, Beat H.","last_name":"Meier","first_name":"Beat H."}]},{"intvolume":"       315","title":"An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","volume":315,"doi":"10.1007/s00220-012-1532-x","article_type":"original","date_created":"2020-09-18T10:47:16Z","publisher":"Springer Nature","quality_controlled":"1","date_published":"2012-11-01T00:00:00Z","date_updated":"2021-01-12T08:19:44Z","issue":"3","type":"journal_article","_id":"8502","year":"2012","article_processing_charge":"No","oa_version":"None","status":"public","page":"643-697","abstract":[{"lang":"eng","text":"The famous ergodic hypothesis suggests that for a typical Hamiltonian on a typical energy surface nearly all trajectories are dense. KAM theory disproves it. Ehrenfest (The Conceptual Foundations of the Statistical Approach in Mechanics. Ithaca, NY: Cornell University Press, 1959) and Birkhoff (Collected Math Papers. Vol 2, New York: Dover, pp 462–465, 1968) stated the quasi-ergodic hypothesis claiming that a typical Hamiltonian on a typical energy surface has a dense orbit. This question is wide open. Herman (Proceedings of the International Congress of Mathematicians, Vol II (Berlin, 1998). Doc Math 1998, Extra Vol II, Berlin: Int Math Union, pp 797–808, 1998) proposed to look for an example of a Hamiltonian near H0(I)=⟨I,I⟩2 with a dense orbit on the unit energy surface. In this paper we construct a Hamiltonian H0(I)+εH1(θ,I,ε) which has an orbit dense in a set of maximal Hausdorff dimension equal to 5 on the unit energy surface."}],"author":[{"full_name":"Kaloshin, Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"last_name":"Saprykina","full_name":"Saprykina, Maria","first_name":"Maria"}],"publication_identifier":{"issn":["0010-3616","1432-0916"]},"language":[{"iso":"eng"}],"keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"publication":"Communications in Mathematical Physics","day":"01","citation":{"short":"V. Kaloshin, M. Saprykina, Communications in Mathematical Physics 315 (2012) 643–697.","ieee":"V. Kaloshin and M. Saprykina, “An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension,” <i>Communications in Mathematical Physics</i>, vol. 315, no. 3. Springer Nature, pp. 643–697, 2012.","ista":"Kaloshin V, Saprykina M. 2012. An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. 315(3), 643–697.","apa":"Kaloshin, V., &#38; Saprykina, M. (2012). An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-012-1532-x\">https://doi.org/10.1007/s00220-012-1532-x</a>","chicago":"Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2012. <a href=\"https://doi.org/10.1007/s00220-012-1532-x\">https://doi.org/10.1007/s00220-012-1532-x</a>.","ama":"Kaloshin V, Saprykina M. An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. <i>Communications in Mathematical Physics</i>. 2012;315(3):643-697. doi:<a href=\"https://doi.org/10.1007/s00220-012-1532-x\">10.1007/s00220-012-1532-x</a>","mla":"Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” <i>Communications in Mathematical Physics</i>, vol. 315, no. 3, Springer Nature, 2012, pp. 643–97, doi:<a href=\"https://doi.org/10.1007/s00220-012-1532-x\">10.1007/s00220-012-1532-x</a>."},"publication_status":"published"},{"date_created":"2020-09-18T10:47:24Z","publisher":"Princeton University Press","date_published":"2012-07-01T00:00:00Z","quality_controlled":"1","issue":"1","date_updated":"2021-01-12T08:19:44Z","type":"journal_article","_id":"8503","intvolume":"       176","title":"Finiteness of central configurations of five bodies in the plane","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","volume":176,"month":"07","doi":"10.4007/annals.2012.176.1.10","article_type":"original","author":[{"last_name":"Albouy","full_name":"Albouy, Alain","first_name":"Alain"},{"last_name":"Kaloshin","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","orcid":"0000-0002-6051-2628"}],"publication_identifier":{"issn":["0003-486X"]},"language":[{"iso":"eng"}],"day":"01","publication":"Annals of Mathematics","citation":{"chicago":"Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of Five Bodies in the Plane.” <i>Annals of Mathematics</i>. Princeton University Press, 2012. <a href=\"https://doi.org/10.4007/annals.2012.176.1.10\">https://doi.org/10.4007/annals.2012.176.1.10</a>.","ama":"Albouy A, Kaloshin V. Finiteness of central configurations of five bodies in the plane. <i>Annals of Mathematics</i>. 2012;176(1):535-588. doi:<a href=\"https://doi.org/10.4007/annals.2012.176.1.10\">10.4007/annals.2012.176.1.10</a>","mla":"Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of Five Bodies in the Plane.” <i>Annals of Mathematics</i>, vol. 176, no. 1, Princeton University Press, 2012, pp. 535–88, doi:<a href=\"https://doi.org/10.4007/annals.2012.176.1.10\">10.4007/annals.2012.176.1.10</a>.","ieee":"A. Albouy and V. Kaloshin, “Finiteness of central configurations of five bodies in the plane,” <i>Annals of Mathematics</i>, vol. 176, no. 1. Princeton University Press, pp. 535–588, 2012.","short":"A. Albouy, V. Kaloshin, Annals of Mathematics 176 (2012) 535–588.","apa":"Albouy, A., &#38; Kaloshin, V. (2012). Finiteness of central configurations of five bodies in the plane. <i>Annals of Mathematics</i>. Princeton University Press. <a href=\"https://doi.org/10.4007/annals.2012.176.1.10\">https://doi.org/10.4007/annals.2012.176.1.10</a>","ista":"Albouy A, Kaloshin V. 2012. Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. 176(1), 535–588."},"publication_status":"published","year":"2012","article_processing_charge":"No","oa_version":"None","status":"public","page":"535-588","abstract":[{"lang":"eng","text":"We prove there are finitely many isometry classes of planar central configurations (also called relative equilibria) in the Newtonian 5-body problem, except perhaps if the 5-tuple of positive masses belongs to a given codimension 2 subvariety of the mass space."}]},{"title":"A Cr unimodal map with an arbitrary fast growth of the number of periodic points","intvolume":"        32","doi":"10.1017/s0143385710000817","volume":32,"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_type":"original","publisher":"Cambridge University Press","date_created":"2020-09-18T10:47:33Z","date_published":"2012-02-01T00:00:00Z","quality_controlled":"1","type":"journal_article","date_updated":"2021-01-12T08:19:44Z","issue":"1","_id":"8504","year":"2012","article_processing_charge":"No","status":"public","oa_version":"None","abstract":[{"lang":"eng","text":"In this paper we present a surprising example of a Cr unimodal map of an interval f:I→I whose number of periodic points Pn(f)=∣{x∈I:fnx=x}∣ grows faster than any ahead given sequence along a subsequence nk=3k. This example also shows that ‘non-flatness’ of critical points is necessary for the Martens–de Melo–van Strien theorem [M. Martens, W. de Melo and S. van Strien. Julia–Fatou–Sullivan theory for real one-dimensional dynamics. Acta Math.168(3–4) (1992), 273–318] to hold."}],"page":"159-165","author":[{"orcid":"0000-0002-6051-2628","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","last_name":"Kaloshin"},{"full_name":"KOZLOVSKI, O. S.","last_name":"KOZLOVSKI","first_name":"O. S."}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0143-3857","1469-4417"]},"day":"01","publication":"Ergodic Theory and Dynamical Systems","keyword":["Applied Mathematics","General Mathematics"],"publication_status":"published","citation":{"mla":"Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary Fast Growth of the Number of Periodic Points.” <i>Ergodic Theory and Dynamical Systems</i>, vol. 32, no. 1, Cambridge University Press, 2012, pp. 159–65, doi:<a href=\"https://doi.org/10.1017/s0143385710000817\">10.1017/s0143385710000817</a>.","ama":"Kaloshin V, KOZLOVSKI OS. A Cr unimodal map with an arbitrary fast growth of the number of periodic points. <i>Ergodic Theory and Dynamical Systems</i>. 2012;32(1):159-165. doi:<a href=\"https://doi.org/10.1017/s0143385710000817\">10.1017/s0143385710000817</a>","chicago":"Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary Fast Growth of the Number of Periodic Points.” <i>Ergodic Theory and Dynamical Systems</i>. Cambridge University Press, 2012. <a href=\"https://doi.org/10.1017/s0143385710000817\">https://doi.org/10.1017/s0143385710000817</a>.","apa":"Kaloshin, V., &#38; KOZLOVSKI, O. S. (2012). A Cr unimodal map with an arbitrary fast growth of the number of periodic points. <i>Ergodic Theory and Dynamical Systems</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/s0143385710000817\">https://doi.org/10.1017/s0143385710000817</a>","ista":"Kaloshin V, KOZLOVSKI OS. 2012. A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. 32(1), 159–165.","ieee":"V. Kaloshin and O. S. KOZLOVSKI, “A Cr unimodal map with an arbitrary fast growth of the number of periodic points,” <i>Ergodic Theory and Dynamical Systems</i>, vol. 32, no. 1. Cambridge University Press, pp. 159–165, 2012.","short":"V. Kaloshin, O.S. KOZLOVSKI, Ergodic Theory and Dynamical Systems 32 (2012) 159–165."}},{"status":"public","abstract":[{"lang":"eng","text":"ackground: The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes.Results: We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates the relationship between TAG and nucleotide content. For biologically plausible rates of mutations we show that, in bacteria, TAG stop codon is universally associated with lower fitness, with TAA being the optimal for G-content < 16% while for G-content > 16% TGA has a higher fitness than TAG.Conclusions: Our data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications.Reviewers: This article was reviewed by Michail Gelfand, Arcady Mushegian and Shamil Sunyaev. For the full reviews, please go to the Reviewers' Comments section."}],"year":"2012","day":"01","publication":"Biology Direct","citation":{"mla":"Povolotskaya, Inna, et al. “Stop Codons in Bacteria Are Not Selectively Equivalent.” <i>Biology Direct</i>, vol. 7, BioMed Central, 2012, doi:<a href=\"https://doi.org/10.1186/1745-6150-7-30\">10.1186/1745-6150-7-30</a>.","chicago":"Povolotskaya, Inna, Fyodor Kondrashov, Alice Ledda, and Peter Vlasov. “Stop Codons in Bacteria Are Not Selectively Equivalent.” <i>Biology Direct</i>. BioMed Central, 2012. <a href=\"https://doi.org/10.1186/1745-6150-7-30\">https://doi.org/10.1186/1745-6150-7-30</a>.","ama":"Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. Stop codons in bacteria are not selectively equivalent. <i>Biology Direct</i>. 2012;7. doi:<a href=\"https://doi.org/10.1186/1745-6150-7-30\">10.1186/1745-6150-7-30</a>","ista":"Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria are not selectively equivalent. Biology Direct. 7.","apa":"Povolotskaya, I., Kondrashov, F., Ledda, A., &#38; Vlasov, P. (2012). Stop codons in bacteria are not selectively equivalent. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-7-30\">https://doi.org/10.1186/1745-6150-7-30</a>","short":"I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012).","ieee":"I. Povolotskaya, F. Kondrashov, A. Ledda, and P. Vlasov, “Stop codons in bacteria are not selectively equivalent,” <i>Biology Direct</i>, vol. 7. BioMed Central, 2012."},"publication_status":"published","author":[{"first_name":"Inna","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna"},{"last_name":"Kondrashov","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor"},{"full_name":"Ledda, Alice","last_name":"Ledda","first_name":"Alice"},{"first_name":"Peter","full_name":"Vlasov, Peter K","last_name":"Vlasov"}],"month":"09","extern":1,"volume":7,"doi":"10.1186/1745-6150-7-30","publist_id":"6792","intvolume":"         7","title":"Stop codons in bacteria are not selectively equivalent","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)"},"date_updated":"2021-01-12T08:20:08Z","type":"journal_article","_id":"858","publisher":"BioMed Central","acknowledgement":"We thank Elena Alkalaeva and Peter Kolosov for insightful discussion and Brian Charlesworth for a critical reading of our manuscript. The work has been supported by a Plan Nacional grant from the Spanish Ministry of Science and Innovation, EMBO Young Investigator and Howard Hughes Medical Institute International Early Career Scientist awards.\n","date_created":"2018-12-11T11:48:52Z","date_published":"2012-09-01T00:00:00Z","quality_controlled":0}]