--- _id: '764' abstract: - lang: eng text: Set agreement is a fundamental problem in distributed computing in which processes collectively choose a small subset of values from a larger set of proposals. The impossibility of fault-tolerant set agreement in asynchronous networks is one of the seminal results in distributed computing. In synchronous networks, too, the complexity of set agreement has been a significant research challenge that has now been resolved. Real systems, however, are neither purely synchronous nor purely asynchronous. Rather, they tend to alternate between periods of synchrony and periods of asynchrony. Nothing specific is known about the complexity of set agreement in such a "partially synchronous" setting. In this paper, we address this challenge, presenting the first (asymptotically) tight bound on the complexity of set agreement in such systems. We introduce a novel technique for simulating, in a fault-prone asynchronous shared memory, executions of an asynchronous and failure-prone message-passing system in which some fragments appear synchronous to some processes. We use this simulation technique to derive a lower bound on the round complexity of set agreement in a partially synchronous system by a reduction from asynchronous wait-free set agreement. Specifically, we show that every set agreement protocol requires at least $\lfloor\frac t k \rfloor + 2$ synchronous rounds to decide. We present an (asymptotically) matching algorithm that relies on a distributed asynchrony detection mechanism to decide as soon as possible during periods of synchrony. From these two results, we derive the size of the minimal window of synchrony needed to solve set agreement. By relating synchronous, asynchronous and partially synchronous environments, our simulation technique is of independent interest. In particular, it allows us to obtain a new lower bound on the complexity of early deciding k-set agreement complementary to that of Gafni et al. (in SIAM J. Comput. 40(1):63-78, 2011), and to re-derive the combinatorial topology lower bound of Guerraoui et al. (in Theor. Comput. Sci. 410(6-7):570-580, 2009) in an algorithmic way. acknowledgement: "We would like to thank Hagit Attiya, Keren Censor-Hillel, and the anonymous\r\nreviewers for their feedback on drafts of this paper.\r\nPart of the work was performed as C. Travers was a Post-Doctoral Fellow at the Technion, Haifa,\r\nsupported by the “Sam & Cecilia Neaman” Fellowship. Part of the work was performed as S. Gilbert was\r\na Post-Doctoral Fellow at the Swiss Federal Institute of Technology, Lausanne, Switzerland." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Seth full_name: Gilbert, Seth last_name: Gilbert - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Corentin full_name: Travers, Corentin last_name: Travers citation: ama: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). 2012;62(1-2):595-629. doi:10.1007/s00453-011-9581-7' apa: 'Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2012). Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). Springer. https://doi.org/10.1007/s00453-011-9581-7' chicago: 'Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement.” Algorithmica (New York). Springer, 2012. https://doi.org/10.1007/s00453-011-9581-7.' ieee: 'D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Of choices, failures and asynchrony: the many faces of set agreement,” Algorithmica (New York), vol. 62, no. 1–2. Springer, pp. 595–629, 2012.' ista: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). 62(1–2), 595–629.' mla: 'Alistarh, Dan-Adrian, et al. “Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement.” Algorithmica (New York), vol. 62, no. 1–2, Springer, 2012, pp. 595–629, doi:10.1007/s00453-011-9581-7.' short: D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Algorithmica (New York) 62 (2012) 595–629. date_created: 2018-12-11T11:48:23Z date_published: 2012-02-01T00:00:00Z date_updated: 2023-02-23T13:13:02Z day: '01' doi: 10.1007/s00453-011-9581-7 extern: '1' intvolume: ' 62' issue: 1-2 language: - iso: eng month: '02' oa_version: None page: 595 - 629 publication: Algorithmica (New York) publication_status: published publisher: Springer publist_id: '6894' status: public title: 'Of choices, failures and asynchrony: the many faces of set agreement' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2012' ... --- _id: '766' 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.' article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Michael full_name: Bender, Michael last_name: Bender - first_name: Seth full_name: Gilbert, Seth last_name: Gilbert - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui citation: ama: 'Alistarh D-A, Bender M, Gilbert S, Guerraoui R. How to allocate tasks asynchronously. In: IEEE; 2012:331-340. doi:10.1109/FOCS.2012.41' apa: 'Alistarh, D.-A., Bender, M., Gilbert, S., & Guerraoui, R. (2012). How to allocate tasks asynchronously (pp. 331–340). Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2012.41' chicago: Alistarh, Dan-Adrian, Michael Bender, Seth Gilbert, and Rachid Guerraoui. “How to Allocate Tasks Asynchronously,” 331–40. IEEE, 2012. https://doi.org/10.1109/FOCS.2012.41. 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.' mla: Alistarh, Dan-Adrian, et al. How to Allocate Tasks Asynchronously. IEEE, 2012, pp. 331–40, doi:10.1109/FOCS.2012.41. short: D.-A. Alistarh, M. Bender, S. Gilbert, R. Guerraoui, in:, IEEE, 2012, pp. 331–340. conference: name: 'FOCS: Foundations of Computer Science' date_created: 2018-12-11T11:48:23Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T13:13:27Z day: '01' doi: 10.1109/FOCS.2012.41 extern: '1' language: - iso: eng month: '01' oa_version: None page: 331 - 340 publication_status: published publisher: IEEE publist_id: '6890' status: public title: How to allocate tasks asynchronously type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '767' abstract: - lang: eng 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. 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." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Seth full_name: Gilbert, Seth last_name: Gilbert - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Corentin full_name: Travers, Corentin last_name: Travers citation: ama: Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Generating Fast Indulgent Algorithms. Theory of Computing Systems. 2012;51(4):404-424. doi:10.1007/s00224-012-9407-2 apa: Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2012). Generating Fast Indulgent Algorithms. Theory of Computing Systems. Elsevier. https://doi.org/10.1007/s00224-012-9407-2 chicago: Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Generating Fast Indulgent Algorithms.” Theory of Computing Systems. Elsevier, 2012. https://doi.org/10.1007/s00224-012-9407-2. ieee: D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Generating Fast Indulgent Algorithms,” Theory of Computing Systems, vol. 51, no. 4. Elsevier, pp. 404–424, 2012. ista: Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Generating Fast Indulgent Algorithms. Theory of Computing Systems. 51(4), 404–424. mla: Alistarh, Dan-Adrian, et al. “Generating Fast Indulgent Algorithms.” Theory of Computing Systems, vol. 51, no. 4, Elsevier, 2012, pp. 404–24, doi:10.1007/s00224-012-9407-2. short: D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Theory of Computing Systems 51 (2012) 404–424. date_created: 2018-12-11T11:48:23Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T13:13:40Z day: '01' doi: 10.1007/s00224-012-9407-2 extern: '1' intvolume: ' 51' issue: '4' language: - iso: eng month: '01' oa_version: None page: 404 - 424 publication: Theory of Computing Systems publication_status: published publisher: Elsevier publist_id: '6891' status: public title: Generating Fast Indulgent Algorithms type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2012' ... --- _id: '7749' 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. article_processing_charge: No article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Khyne U full_name: Mar, Khyne U last_name: Mar - first_name: Virpi full_name: Lummaa, Virpi last_name: Lummaa citation: ama: Robinson MR, Mar KU, Lummaa V. Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. 2012;15(3):260-266. doi:10.1111/j.1461-0248.2011.01735.x apa: Robinson, M. R., Mar, K. U., & Lummaa, V. (2012). Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. Wiley. https://doi.org/10.1111/j.1461-0248.2011.01735.x chicago: Robinson, Matthew Richard, Khyne U Mar, and Virpi Lummaa. “Senescence and Age-Specific Trade-Offs between Reproduction and Survival in Female Asian Elephants.” Ecology Letters. Wiley, 2012. https://doi.org/10.1111/j.1461-0248.2011.01735.x. ieee: M. R. Robinson, K. U. Mar, and V. Lummaa, “Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants,” Ecology Letters, vol. 15, no. 3. Wiley, pp. 260–266, 2012. 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. mla: Robinson, Matthew Richard, et al. “Senescence and Age-Specific Trade-Offs between Reproduction and Survival in Female Asian Elephants.” Ecology Letters, vol. 15, no. 3, Wiley, 2012, pp. 260–66, doi:10.1111/j.1461-0248.2011.01735.x. short: M.R. Robinson, K.U. Mar, V. Lummaa, Ecology Letters 15 (2012) 260–266. date_created: 2020-04-30T11:01:26Z date_published: 2012-03-01T00:00:00Z date_updated: 2021-01-12T08:15:16Z day: '01' doi: 10.1111/j.1461-0248.2011.01735.x extern: '1' intvolume: ' 15' issue: '3' language: - iso: eng month: '03' oa_version: None page: 260-266 publication: Ecology Letters publication_identifier: issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2012' ... --- _id: '7748' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: G. full_name: Sander van Doorn, G. last_name: Sander van Doorn - first_name: Lars full_name: Gustafsson, Lars last_name: Gustafsson - first_name: Anna full_name: Qvarnström, Anna last_name: Qvarnström citation: ama: Robinson MR, Sander van Doorn G, Gustafsson L, Qvarnström A. Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. 2012;15(6):611-618. doi:10.1111/j.1461-0248.2012.01780.x apa: Robinson, M. R., Sander van Doorn, G., Gustafsson, L., & Qvarnström, A. (2012). Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. Wiley. https://doi.org/10.1111/j.1461-0248.2012.01780.x 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.” Ecology Letters. Wiley, 2012. https://doi.org/10.1111/j.1461-0248.2012.01780.x. 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,” Ecology Letters, vol. 15, no. 6. Wiley, pp. 611–618, 2012. 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. mla: Robinson, Matthew Richard, et al. “Environment-Dependent Selection on Mate Choice in a Natural Population of Birds.” Ecology Letters, vol. 15, no. 6, Wiley, 2012, pp. 611–18, doi:10.1111/j.1461-0248.2012.01780.x. short: M.R. Robinson, G. Sander van Doorn, L. Gustafsson, A. Qvarnström, Ecology Letters 15 (2012) 611–618. date_created: 2020-04-30T11:01:07Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T08:15:15Z day: '01' doi: 10.1111/j.1461-0248.2012.01780.x extern: '1' intvolume: ' 15' issue: '6' language: - iso: eng month: '06' oa_version: None page: 611-618 publication: Ecology Letters publication_identifier: issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Environment-dependent selection on mate choice in a natural population of birds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2012' ... --- _id: '7776' 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. article_number: '095704' article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: Goodrich CP, Liu AJ, Nagel SR. Finite-size scaling at the jamming transition. Physical Review Letters. 2012;109(9). doi:10.1103/physrevlett.109.095704 apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2012). Finite-size scaling at the jamming transition. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.109.095704 chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Finite-Size Scaling at the Jamming Transition.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/physrevlett.109.095704. ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Finite-size scaling at the jamming transition,” Physical Review Letters, vol. 109, no. 9. American Physical Society, 2012. ista: Goodrich CP, Liu AJ, Nagel SR. 2012. Finite-size scaling at the jamming transition. Physical Review Letters. 109(9), 095704. mla: Goodrich, Carl Peter, et al. “Finite-Size Scaling at the Jamming Transition.” Physical Review Letters, vol. 109, no. 9, 095704, American Physical Society, 2012, doi:10.1103/physrevlett.109.095704. short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 109 (2012). date_created: 2020-04-30T11:44:12Z date_published: 2012-08-27T00:00:00Z date_updated: 2021-01-12T08:15:27Z day: '27' doi: 10.1103/physrevlett.109.095704 extern: '1' intvolume: ' 109' issue: '9' language: - iso: eng month: '08' oa_version: None publication: Physical Review Letters publication_identifier: issn: - 0031-9007 - 1079-7114 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Finite-size scaling at the jamming transition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2012' ... --- _id: '801' abstract: - lang: eng 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. acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft. article_processing_charge: No article_type: original author: - first_name: Jakob full_name: Engel, Jakob last_name: Engel - first_name: Philipp S full_name: Schmalhorst, Philipp S id: 309D50DA-F248-11E8-B48F-1D18A9856A87 last_name: Schmalhorst orcid: 0000-0002-5795-0133 - first_name: Françoise full_name: Routier, Françoise last_name: Routier citation: ama: Engel J, Schmalhorst PS, Routier F. Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. 2012;287(53):44418-44424. doi:10.1074/jbc.M112.398321 apa: Engel, J., Schmalhorst, P. S., & Routier, F. (2012). Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M112.398321 chicago: Engel, Jakob, Philipp S Schmalhorst, and Françoise Routier. “Biosynthesis of the Fungal Cell Wall Polysaccharide Galactomannan Requires Intraluminal GDP-Mannose.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2012. https://doi.org/10.1074/jbc.M112.398321. ieee: J. Engel, P. S. Schmalhorst, and F. Routier, “Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose,” Journal of Biological Chemistry, vol. 287, no. 53. American Society for Biochemistry and Molecular Biology, pp. 44418–44424, 2012. 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. mla: Engel, Jakob, et al. “Biosynthesis of the Fungal Cell Wall Polysaccharide Galactomannan Requires Intraluminal GDP-Mannose.” Journal of Biological Chemistry, vol. 287, no. 53, American Society for Biochemistry and Molecular Biology, 2012, pp. 44418–24, doi:10.1074/jbc.M112.398321. short: J. Engel, P.S. Schmalhorst, F. Routier, Journal of Biological Chemistry 287 (2012) 44418–44424. date_created: 2018-12-11T11:48:34Z date_published: 2012-12-28T00:00:00Z date_updated: 2022-03-21T07:57:14Z day: '28' doi: 10.1074/jbc.M112.398321 extern: '1' external_id: pmid: - '23139423' intvolume: ' 287' issue: '53' language: - iso: eng month: '12' oa_version: None page: 44418 - 44424 pmid: 1 publication: Journal of Biological Chemistry publication_status: published publisher: American Society for Biochemistry and Molecular Biology publist_id: '6852' quality_controlled: '1' scopus_import: '1' status: public title: Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 287 year: '2012' ... --- _id: '8024' 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. article_number: '011909' article_processing_charge: No article_type: original author: - first_name: Guillaume full_name: Hennequin, Guillaume last_name: Hennequin - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Wulfram full_name: Gerstner, Wulfram last_name: Gerstner citation: ama: Hennequin G, Vogels TP, Gerstner W. Non-normal amplification in random balanced neuronal networks. Physical Review E. 2012;86(1). doi:10.1103/physreve.86.011909 apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2012). Non-normal amplification in random balanced neuronal networks. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.86.011909 chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Non-Normal Amplification in Random Balanced Neuronal Networks.” Physical Review E. American Physical Society, 2012. https://doi.org/10.1103/physreve.86.011909. ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Non-normal amplification in random balanced neuronal networks,” Physical Review E, vol. 86, no. 1. American Physical Society, 2012. ista: Hennequin G, Vogels TP, Gerstner W. 2012. Non-normal amplification in random balanced neuronal networks. Physical Review E. 86(1), 011909. mla: Hennequin, Guillaume, et al. “Non-Normal Amplification in Random Balanced Neuronal Networks.” Physical Review E, vol. 86, no. 1, 011909, American Physical Society, 2012, doi:10.1103/physreve.86.011909. short: G. Hennequin, T.P. Vogels, W. Gerstner, Physical Review E 86 (2012). date_created: 2020-06-25T13:09:06Z date_published: 2012-06-11T00:00:00Z date_updated: 2021-01-12T08:16:35Z day: '11' doi: 10.1103/physreve.86.011909 extern: '1' external_id: pmid: - '23005454' intvolume: ' 86' issue: '1' language: - iso: eng month: '06' oa_version: None pmid: 1 publication: Physical Review E publication_identifier: eisbn: - 1550-2376 issn: - 1539-3755 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Non-normal amplification in random balanced neuronal networks type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 86 year: '2012' ... --- _id: '808' abstract: - lang: eng 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. 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. author: - first_name: Marlene full_name: Vinzenz, Marlene last_name: Vinzenz - first_name: Maria full_name: Nemethova, Maria id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Florian full_name: Schur, Florian id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Jan full_name: Mueller, Jan last_name: Mueller - first_name: Akihiro full_name: Narita, Akihiro last_name: Narita - first_name: Edit full_name: Urban, Edit last_name: Urban - first_name: Christoph full_name: Winkler, Christoph last_name: Winkler - first_name: Christian full_name: Schmeiser, Christian last_name: Schmeiser - first_name: Stefan full_name: Koestler, Stefan last_name: Koestler - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner - first_name: Guenter full_name: Resch, Guenter last_name: Resch - first_name: Yuichiro full_name: Maéda, Yuichiro last_name: Maéda - first_name: John full_name: Small, John last_name: Small citation: ama: Vinzenz M, Nemethova M, Schur FK, et al. Actin branching in the initiation and maintenance of lamellipodia. Journal of Cell Science. 2012;125(11):2775-2785. doi:10.1242/jcs.107623 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. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.107623 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.” Journal of Cell Science. Company of Biologists, 2012. https://doi.org/10.1242/jcs.107623. ieee: M. Vinzenz et al., “Actin branching in the initiation and maintenance of lamellipodia,” Journal of Cell Science, vol. 125, no. 11. Company of Biologists, pp. 2775–2785, 2012. 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. mla: Vinzenz, Marlene, et al. “Actin Branching in the Initiation and Maintenance of Lamellipodia.” Journal of Cell Science, vol. 125, no. 11, Company of Biologists, 2012, pp. 2775–85, doi:10.1242/jcs.107623. 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. date_created: 2018-12-11T11:48:37Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T08:16:47Z day: '01' ddc: - '570' doi: 10.1242/jcs.107623 extern: '1' file: - access_level: open_access checksum: 2f59e15cc3a85bb500a9887cef2aab67 content_type: application/pdf creator: kschuh date_created: 2019-02-12T08:54:51Z date_updated: 2020-07-14T12:48:09Z file_id: '5956' file_name: 2012_Biologists_Vinzenz.pdf file_size: 3326073 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' intvolume: ' 125' issue: '11' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '06' oa: 1 oa_version: None page: 2775 - 2785 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '6842' quality_controlled: '1' status: public title: Actin branching in the initiation and maintenance of lamellipodia tmp: image: /images/cc_by_nc_sa.png 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) short: CC BY-NC-SA (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 125 year: '2012' ... --- _id: '8246' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Vanina full_name: Dengler, Vanina last_name: Dengler - first_name: Patricia Stutzmann full_name: Meier, Patricia Stutzmann last_name: Meier - first_name: Ronald full_name: Heusser, Ronald last_name: Heusser - first_name: Peter full_name: Kupferschmied, Peter last_name: Kupferschmied - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: Sarah full_name: Friebe, Sarah last_name: Friebe - first_name: Sibylle Burger full_name: Staufer, Sibylle Burger last_name: Staufer - first_name: Paul A. full_name: Majcherczyk, Paul A. last_name: Majcherczyk - first_name: Philippe full_name: Moreillon, Philippe last_name: Moreillon - first_name: Brigitte full_name: Berger-Bächi, Brigitte last_name: Berger-Bächi - first_name: Nadine full_name: McCallum, Nadine last_name: McCallum citation: 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. FEMS Microbiology Letters. 2012;333(2):109-120. doi:10.1111/j.1574-6968.2012.02603.x 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. FEMS Microbiology Letters. Oxford University Press. https://doi.org/10.1111/j.1574-6968.2012.02603.x 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.” FEMS Microbiology Letters. Oxford University Press, 2012. https://doi.org/10.1111/j.1574-6968.2012.02603.x. ieee: V. Dengler et al., “Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response,” FEMS Microbiology Letters, vol. 333, no. 2. Oxford University Press, pp. 109–120, 2012. 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. mla: Dengler, Vanina, et al. “Deletion of Hypothetical Wall Teichoic Acid Ligases in Staphylococcus Aureus Activates the Cell Wall Stress Response.” FEMS Microbiology Letters, vol. 333, no. 2, Oxford University Press, 2012, pp. 109–20, doi:10.1111/j.1574-6968.2012.02603.x. 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. date_created: 2020-08-10T11:54:47Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T08:17:43Z day: '01' doi: 10.1111/j.1574-6968.2012.02603.x extern: '1' external_id: pmid: - '22640011' intvolume: ' 333' issue: '2' language: - iso: eng month: '08' oa_version: None page: 109-120 pmid: 1 publication: FEMS Microbiology Letters publication_identifier: issn: - 0378-1097 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 333 year: '2012' ... --- _id: '826' 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. 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. author: - first_name: Marleen full_name: Vanstraelen, Marleen last_name: Vanstraelen - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Vanstraelen M, Benková E. Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. 2012;28:463-487. doi:10.1146/annurev-cellbio-101011-155741 apa: Vanstraelen, M., & Benková, E. (2012). Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-101011-155741 chicago: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation of Plant Development.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2012. https://doi.org/10.1146/annurev-cellbio-101011-155741. ieee: M. Vanstraelen and E. Benková, “Hormonal interactions in the regulation of plant development,” Annual Review of Cell and Developmental Biology, vol. 28. Annual Reviews, pp. 463–487, 2012. ista: Vanstraelen M, Benková E. 2012. Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. 28, 463–487. mla: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation of Plant Development.” Annual Review of Cell and Developmental Biology, vol. 28, Annual Reviews, 2012, pp. 463–87, doi:10.1146/annurev-cellbio-101011-155741. short: M. Vanstraelen, E. Benková, Annual Review of Cell and Developmental Biology 28 (2012) 463–487. date_created: 2018-12-11T11:48:43Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T08:17:46Z day: '01' doi: 10.1146/annurev-cellbio-101011-155741 extern: 1 intvolume: ' 28' month: '11' page: 463 - 487 publication: Annual Review of Cell and Developmental Biology publication_status: published publisher: Annual Reviews publist_id: '6822' quality_controlled: 0 status: public title: Hormonal interactions in the regulation of plant development type: journal_article volume: 28 year: '2012' ... --- _id: '829' abstract: - lang: eng 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. 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. author: - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Katerina full_name: Podlesakova, Katerina last_name: Podlesakova - first_name: Peter full_name: Peter Marhavy id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Jérôme full_name: Duclercq, Jérôme last_name: Duclercq - first_name: Candela full_name: Candela Cuesta id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Bruno full_name: Muller, Bruno last_name: Muller - first_name: Wim full_name: Grunewald, Wim last_name: Grunewald - first_name: Petr full_name: Tarkowski, Petr last_name: Tarkowski - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Bielach A, Podlesakova K, Marhavý P, et al. Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. The Plant Cell. 2012;24(10):3967-3981. doi:10.1105/tpc.112.103044 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. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.112.103044 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.” The Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.103044. ieee: A. Bielach et al., “Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin,” The Plant Cell, vol. 24, no. 10. American Society of Plant Biologists, pp. 3967–3981, 2012. 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. mla: Bielach, Agnieszka, et al. “Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.” The Plant Cell, vol. 24, no. 10, American Society of Plant Biologists, 2012, pp. 3967–81, doi:10.1105/tpc.112.103044. 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. date_created: 2018-12-11T11:48:43Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T08:17:55Z day: '01' doi: 10.1105/tpc.112.103044 extern: 1 intvolume: ' 24' issue: '10' month: '10' page: 3967 - 3981 publication: The Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '6819' quality_controlled: 0 status: public title: Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin type: journal_article volume: 24 year: '2012' ... --- _id: '846' 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. 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. author: - first_name: Onuralp full_name: Soylemez, Onuralp last_name: Soylemez - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Soylemez O, Kondrashov F. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 2012;4(12):1213-1222. doi:10.1093/gbe/evs096 apa: Soylemez, O., & Kondrashov, F. (2012). Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evs096 chicago: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution. Oxford University Press, 2012. https://doi.org/10.1093/gbe/evs096. ieee: O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in protein evolution,” Genome Biology and Evolution, vol. 4, no. 12. Oxford University Press, pp. 1213–1222, 2012. ista: Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 4(12), 1213–1222. mla: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096. short: O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222. date_created: 2018-12-11T11:48:49Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:19:25Z day: '01' doi: 10.1093/gbe/evs096 extern: 1 intvolume: ' 4' issue: '12' license: https://creativecommons.org/licenses/by-nc/4.0/ month: '01' page: 1213 - 1222 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6802' quality_controlled: 0 status: public title: Estimating the rate of irreversibility in protein evolution tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article volume: 4 year: '2012' ... --- _id: '8463' 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. article_processing_charge: No article_type: original author: - first_name: Sam full_name: Asami, Sam last_name: Asami - first_name: Kathrin full_name: Szekely, Kathrin last_name: Szekely - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier - first_name: Bernd full_name: Reif, Bernd last_name: Reif citation: 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. Journal of Biomolecular NMR. 2012;54(2):155-168. doi:10.1007/s10858-012-9659-9 apa: Asami, S., Szekely, K., Schanda, P., Meier, B. H., & 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. Springer Nature. https://doi.org/10.1007/s10858-012-9659-9 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.” Journal of Biomolecular NMR. Springer Nature, 2012. https://doi.org/10.1007/s10858-012-9659-9. 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,” Journal of Biomolecular NMR, vol. 54, no. 2. Springer Nature, pp. 155–168, 2012. 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. 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.” Journal of Biomolecular NMR, vol. 54, no. 2, Springer Nature, 2012, pp. 155–68, doi:10.1007/s10858-012-9659-9. short: S. Asami, K. Szekely, P. Schanda, B.H. Meier, B. Reif, Journal of Biomolecular NMR 54 (2012) 155–168. date_created: 2020-09-18T10:09:18Z date_published: 2012-08-23T00:00:00Z date_updated: 2021-01-12T08:19:27Z day: '23' doi: 10.1007/s10858-012-9659-9 extern: '1' intvolume: ' 54' issue: '2' language: - iso: eng month: '08' oa_version: None page: 155-168 publication: Journal of Biomolecular NMR publication_identifier: issn: - 0925-2738 - 1573-5001 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2012' ... --- _id: '8465' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Martin full_name: Tollinger, Martin last_name: Tollinger - first_name: Astrid C. full_name: Sivertsen, Astrid C. last_name: Sivertsen - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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. Journal of the American Chemical Society. 2012;134(36):14800-14807. doi:10.1021/ja303591y apa: Tollinger, M., Sivertsen, A. C., Meier, B. H., 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. American Chemical Society. https://doi.org/10.1021/ja303591y 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.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja303591y. 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,” Journal of the American Chemical Society, vol. 134, no. 36. American Chemical Society, pp. 14800–14807, 2012. 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. mla: Tollinger, Martin, et al. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.” Journal of the American Chemical Society, vol. 134, no. 36, American Chemical Society, 2012, pp. 14800–07, doi:10.1021/ja303591y. short: M. Tollinger, A.C. Sivertsen, B.H. Meier, M. Ernst, P. Schanda, Journal of the American Chemical Society 134 (2012) 14800–14807. date_created: 2020-09-18T10:10:20Z date_published: 2012-08-21T00:00:00Z date_updated: 2021-01-12T08:19:27Z day: '21' doi: 10.1021/ja303591y extern: '1' intvolume: ' 134' issue: '36' language: - iso: eng month: '08' oa_version: None page: 14800-14807 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '8466' 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. article_processing_charge: No article_type: original author: - first_name: Enrico full_name: Rennella, Enrico last_name: Rennella - first_name: Thomas full_name: Cutuil, Thomas last_name: Cutuil - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Vincent full_name: Forge, Vincent last_name: Forge - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher citation: 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. Journal of the American Chemical Society. 2012;134(19):8066-8069. doi:10.1021/ja302598j apa: 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. American Chemical Society. https://doi.org/10.1021/ja302598j 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.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja302598j. 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,” Journal of the American Chemical Society, vol. 134, no. 19. American Chemical Society, pp. 8066–8069, 2012. 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. mla: Rennella, Enrico, et al. “Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate.” Journal of the American Chemical Society, vol. 134, no. 19, American Chemical Society, 2012, pp. 8066–69, doi:10.1021/ja302598j. short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, B. Brutscher, Journal of the American Chemical Society 134 (2012) 8066–8069. date_created: 2020-09-18T10:10:28Z date_published: 2012-05-03T00:00:00Z date_updated: 2021-01-12T08:19:28Z day: '03' doi: 10.1021/ja302598j extern: '1' intvolume: ' 134' issue: '19' language: - iso: eng month: '05' oa_version: None page: 8066-8069 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '8467' 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. article_processing_charge: No article_type: original author: - first_name: Matthias full_name: Huber, Matthias last_name: Huber - first_name: Oliver full_name: With, Oliver last_name: With - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: René full_name: Verel, René last_name: Verel - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier citation: ama: Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. 2012;214:76-80. doi:10.1016/j.jmr.2011.10.010 apa: Huber, M., With, O., Schanda, P., Verel, R., Ernst, M., & Meier, B. H. (2012). A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2011.10.010 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.” Journal of Magnetic Resonance. Elsevier, 2012. https://doi.org/10.1016/j.jmr.2011.10.010. 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,” Journal of Magnetic Resonance, vol. 214. Elsevier, pp. 76–80, 2012. 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. mla: Huber, Matthias, et al. “A Supplementary Coil for 2H Decoupling with Commercial HCN MAS Probes.” Journal of Magnetic Resonance, vol. 214, Elsevier, 2012, pp. 76–80, doi:10.1016/j.jmr.2011.10.010. short: M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, B.H. Meier, Journal of Magnetic Resonance 214 (2012) 76–80. date_created: 2020-09-18T10:10:36Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:19:28Z day: '01' doi: 10.1016/j.jmr.2011.10.010 extern: '1' intvolume: ' 214' language: - iso: eng month: '01' oa_version: None page: 76-80 publication: Journal of Magnetic Resonance publication_identifier: issn: - 1090-7807 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: A supplementary coil for 2H decoupling with commercial HCN MAS probes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 214 year: '2012' ... --- _id: '8502' 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.' article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Maria full_name: Saprykina, Maria last_name: Saprykina citation: ama: Kaloshin V, Saprykina M. An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. 2012;315(3):643-697. doi:10.1007/s00220-012-1532-x apa: 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. Springer Nature. https://doi.org/10.1007/s00220-012-1532-x 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.” Communications in Mathematical Physics. Springer Nature, 2012. https://doi.org/10.1007/s00220-012-1532-x. 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,” Communications in Mathematical Physics, 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. 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.” Communications in Mathematical Physics, vol. 315, no. 3, Springer Nature, 2012, pp. 643–97, doi:10.1007/s00220-012-1532-x. short: V. Kaloshin, M. Saprykina, Communications in Mathematical Physics 315 (2012) 643–697. date_created: 2020-09-18T10:47:16Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T08:19:44Z day: '01' doi: 10.1007/s00220-012-1532-x extern: '1' intvolume: ' 315' issue: '3' keyword: - Mathematical Physics - Statistical and Nonlinear Physics language: - iso: eng month: '11' oa_version: None page: 643-697 publication: Communications in Mathematical Physics publication_identifier: issn: - 0010-3616 - 1432-0916 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 315 year: '2012' ... --- _id: '858' 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.' 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. author: - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alice full_name: Ledda, Alice last_name: Ledda - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov citation: ama: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. Stop codons in bacteria are not selectively equivalent. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-30 apa: Povolotskaya, I., Kondrashov, F., Ledda, A., & Vlasov, P. (2012). Stop codons in bacteria are not selectively equivalent. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-30 chicago: Povolotskaya, Inna, Fyodor Kondrashov, Alice Ledda, and Peter Vlasov. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-30. ieee: I. Povolotskaya, F. Kondrashov, A. Ledda, and P. Vlasov, “Stop codons in bacteria are not selectively equivalent,” Biology Direct, vol. 7. BioMed Central, 2012. ista: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria are not selectively equivalent. Biology Direct. 7. mla: Povolotskaya, Inna, et al. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct, vol. 7, BioMed Central, 2012, doi:10.1186/1745-6150-7-30. short: I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012). date_created: 2018-12-11T11:48:52Z date_published: 2012-09-01T00:00:00Z date_updated: 2021-01-12T08:20:08Z day: '01' doi: 10.1186/1745-6150-7-30 extern: 1 intvolume: ' 7' license: https://creativecommons.org/licenses/by/4.0/ month: '09' publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '6792' quality_controlled: 0 status: public title: Stop codons in bacteria are not selectively equivalent tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 7 year: '2012' ... --- _id: '900' abstract: - lang: eng text: 'The main forces directing long-term molecular evolution remain obscure. A sizable fraction of amino-acid substitutions seem to be fixed by positive selection, but it is unclear to what degree long-term protein evolution is constrained by epistasis, that is, instances when substitutions that are accepted in one genotype are deleterious in another. Here we obtain a quantitative estimate of the prevalence of epistasis in long-term protein evolution by relating data on amino-acid usage in 14 organelle proteins and 2 nuclear-encoded proteins to their rates of short-term evolution. We studied multiple alignments of at least 1,000 orthologues for each of these 16 proteins from species from a diverse phylogenetic background and found that an average site contained approximately eight different amino acids. Thus, without epistasis an average site should accept two-fifths of all possible amino acids, and the average rate of amino-acid substitutions should therefore be about three-fifths lower than the rate of neutral evolution. However, we found that the measured rate of amino-acid substitution in recent evolution is 20 times lower than the rate of neutral evolution and an order of magnitude lower than that expected in the absence of epistasis. These data indicate that epistasis is pervasive throughout protein evolution: about 90 per cent of all amino-acid substitutions have a neutral or beneficial impact only in the genetic backgrounds in which they occur, and must therefore be deleterious in a different background of other species. Our findings show that most amino-acid substitutions have different fitness effects in different species and that epistasis provides the primary conceptual framework to describe the tempo and mode of long-term protein evolution.' acknowledgement: | The work was supported by Plan Nacional grants from the Spanish Ministry of Science and Innovation, to F.A.K. and C.N. C.K. was supported by the European Union FP7 project Quantomics (KBBE2A222664). F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. We thank B. Lehner and T. Warnecke for input and a critical reading of the manuscript. author: - first_name: Michael full_name: Breen, Michael S last_name: Breen - first_name: Carsten full_name: Kemena, Carsten last_name: Kemena - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Cédric full_name: Notredame, Cédric last_name: Notredame - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Epistasis as the primary factor in molecular evolution. Nature. 2012;490(7421):535-538. doi:10.1038/nature11510 apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2012). Epistasis as the primary factor in molecular evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11510 chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Epistasis as the Primary Factor in Molecular Evolution.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11510. ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Epistasis as the primary factor in molecular evolution,” Nature, vol. 490, no. 7421. Nature Publishing Group, pp. 535–538, 2012. ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2012. Epistasis as the primary factor in molecular evolution. Nature. 490(7421), 535–538. mla: Breen, Michael, et al. “Epistasis as the Primary Factor in Molecular Evolution.” Nature, vol. 490, no. 7421, Nature Publishing Group, 2012, pp. 535–38, doi:10.1038/nature11510. short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 490 (2012) 535–538. date_created: 2018-12-11T11:49:06Z date_published: 2012-10-25T00:00:00Z date_updated: 2021-01-12T08:21:45Z day: '25' doi: 10.1038/nature11510 extern: 1 intvolume: ' 490' issue: '7421' month: '10' page: 535 - 538 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6748' quality_controlled: 0 status: public title: Epistasis as the primary factor in molecular evolution type: journal_article volume: 490 year: '2012' ... --- _id: '9014' abstract: - lang: eng text: In this Letter, we explore experimentally the phase behavior of a dense active suspension of self-propelled colloids. In addition to a solidlike and gaslike phase observed for high and low densities, a novel cluster phase is reported at intermediate densities. This takes the form of a stationary assembly of dense aggregates—resulting from a permanent dynamical merging and separation of active colloids—whose average size grows with activity as a linear function of the self-propelling velocity. While different possible scenarios can be considered to account for these observations—such as a generic velocity weakening instability recently put forward—we show that the experimental results are reproduced mathematically by a chemotactic aggregation mechanism, originally introduced to account for bacterial aggregation and accounting here for diffusiophoretic chemical interaction between colloidal swimmers. article_number: '268303' article_processing_charge: No article_type: letter_note author: - first_name: I. full_name: Theurkauff, I. last_name: Theurkauff - first_name: C. full_name: Cottin-Bizonne, C. last_name: Cottin-Bizonne - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: C. full_name: Ybert, C. last_name: Ybert - first_name: L. full_name: Bocquet, L. last_name: Bocquet citation: ama: Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 2012;108(26). doi:10.1103/physrevlett.108.268303 apa: Theurkauff, I., Cottin-Bizonne, C., Palacci, J. A., Ybert, C., & Bocquet, L. (2012). Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. American Physical Society . https://doi.org/10.1103/physrevlett.108.268303 chicago: Theurkauff, I., C. Cottin-Bizonne, Jérémie A Palacci, C. Ybert, and L. Bocquet. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” Physical Review Letters. American Physical Society , 2012. https://doi.org/10.1103/physrevlett.108.268303. ieee: I. Theurkauff, C. Cottin-Bizonne, J. A. Palacci, C. Ybert, and L. Bocquet, “Dynamic clustering in active colloidal suspensions with chemical signaling,” Physical Review Letters, vol. 108, no. 26. American Physical Society , 2012. ista: Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. 2012. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 108(26), 268303. mla: Theurkauff, I., et al. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” Physical Review Letters, vol. 108, no. 26, 268303, American Physical Society , 2012, doi:10.1103/physrevlett.108.268303. short: I. Theurkauff, C. Cottin-Bizonne, J.A. Palacci, C. Ybert, L. Bocquet, Physical Review Letters 108 (2012). date_created: 2021-01-19T10:26:59Z date_published: 2012-06-29T00:00:00Z date_updated: 2023-02-23T13:46:45Z day: '29' doi: 10.1103/physrevlett.108.268303 extern: '1' external_id: arxiv: - '1202.6264' pmid: - '23005020' intvolume: ' 108' issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1202.6264 month: '06' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - '10797114' issn: - '00319007' publication_status: published publisher: 'American Physical Society ' quality_controlled: '1' scopus_import: '1' status: public title: Dynamic clustering in active colloidal suspensions with chemical signaling type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 108 year: '2012' ... --- _id: '91' abstract: - lang: eng text: 'We demonstrate how to appropriately estimate the zero-frequency (static) hyperpolarizability of an organic molecule from its charge distribution, and we explore applications of these estimates for identifying and evaluating new organic nonlinear optical (NLO) materials. First, we calculate hyperpolarizabilities from Hartree-Fock-derived charge distributions and find order-of-magnitude agreement with experimental values. We show that these simple arithmetic calculations will enable systematic searches for new organic NLO molecules. Second, we derive hyperpolarizabilities from crystallographic data using a multipolar charge-density analysis and find good agreement with empirical calculations. This demonstrates an experimental determination of the full static hyperpolarizability tensor in a solid-state sample. ' acknowledgement: This work was supported by The Winston Churchill Foundation of the United States (A.P.H., M.A.B.F., D.D.H.), The Royal Society via a University Research Fellowship (J.M.C.), and the University of New Brunswick via The Vice-Chancellor’s Research Chair (J.M.C.). article_number: '033512' author: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Jacqueline full_name: Cole, Jacqueline last_name: Cole - first_name: Martin full_name: Blood Forsythe, Martin last_name: Blood Forsythe - first_name: Daniel full_name: Hickstein, Daniel last_name: Hickstein citation: ama: Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. 2012;111(3). doi:10.1063/1.3678593 apa: Higginbotham, A. P., Cole, J., Blood Forsythe, M., & Hickstein, D. (2012). Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. American Institute of Physics. https://doi.org/10.1063/1.3678593 chicago: Higginbotham, Andrew P, Jacqueline Cole, Martin Blood Forsythe, and Daniel Hickstein. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” Journal of Applied Physics. American Institute of Physics, 2012. https://doi.org/10.1063/1.3678593. ieee: A. P. Higginbotham, J. Cole, M. Blood Forsythe, and D. Hickstein, “Identifying and evaluating organic nonlinear optical materials via molecular moments,” Journal of Applied Physics, vol. 111, no. 3. American Institute of Physics, 2012. ista: Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. 2012. Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. 111(3), 033512. mla: Higginbotham, Andrew P., et al. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” Journal of Applied Physics, vol. 111, no. 3, 033512, American Institute of Physics, 2012, doi:10.1063/1.3678593. short: A.P. Higginbotham, J. Cole, M. Blood Forsythe, D. Hickstein, Journal of Applied Physics 111 (2012). date_created: 2018-12-11T11:44:35Z date_published: 2012-02-07T00:00:00Z date_updated: 2021-01-12T08:21:50Z day: '07' doi: 10.1063/1.3678593 extern: '1' intvolume: ' 111' issue: '3' language: - iso: eng month: '02' oa_version: None publication: Journal of Applied Physics publication_status: published publisher: American Institute of Physics publist_id: '7963' quality_controlled: '1' status: public title: Identifying and evaluating organic nonlinear optical materials via molecular moments type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2012' ... --- _id: '9142' abstract: - lang: eng text: "In models of radiative–convective equilibrium it is known that convection can spontaneously aggregate into one single localized moist region if the domain is large enough. The large changes in the mean climate state and radiative fluxes accompanying this self-aggregation raise questions as to what simulations at lower resolutions with parameterized convection, in similar homogeneous geometries, should be expected to produce to be considered successful in mimicking a cloud-resolving model.\r\nThe authors investigate this self-aggregation in a nonrotating, three-dimensional cloud-resolving model on a square domain without large-scale forcing. It is found that self-aggregation is sensitive not only to the domain size, but also to the horizontal resolution. With horizontally homogeneous initial conditions, convective aggregation only occurs on domains larger than about 200km and with resolutions coarser than about 2km in the model examined. The system exhibits hysteresis, so that with aggregated initial conditions, convection remains aggregated even at our finest resolution, 500m, as long as the domain is greater than 200–300km.\r\nThe sensitivity of self-aggregation to resolution and domain size in this model is due to the sensitivity of the distribution of low clouds to these two parameters. Indeed, the mechanism responsible for the aggregation of convection is the dynamical response to the longwave radiative cooling from low clouds. Strong longwave cooling near cloud top in dry regions forces downward motion, which by continuity generates inflow near cloud top and near-surface outflow from dry regions. This circulation results in the net export of moist static energy from regions with low moist static energy, yielding a positive feedback." article_processing_charge: No article_type: original author: - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Isaac M. full_name: Held, Isaac M. last_name: Held citation: ama: Muller CJ, Held IM. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 2012;69(8):2551-2565. doi:10.1175/jas-d-11-0257.1 apa: Muller, C. J., & Held, I. M. (2012). Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. American Meteorological Society. https://doi.org/10.1175/jas-d-11-0257.1 chicago: Muller, Caroline J, and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences. American Meteorological Society, 2012. https://doi.org/10.1175/jas-d-11-0257.1. ieee: C. J. Muller and I. M. Held, “Detailed investigation of the self-aggregation of convection in cloud-resolving simulations,” Journal of the Atmospheric Sciences, vol. 69, no. 8. American Meteorological Society, pp. 2551–2565, 2012. ista: Muller CJ, Held IM. 2012. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 69(8), 2551–2565. mla: Muller, Caroline J., and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences, vol. 69, no. 8, American Meteorological Society, 2012, pp. 2551–65, doi:10.1175/jas-d-11-0257.1. short: C.J. Muller, I.M. Held, Journal of the Atmospheric Sciences 69 (2012) 2551–2565. date_created: 2021-02-15T14:39:03Z date_published: 2012-08-01T00:00:00Z date_updated: 2022-01-24T13:49:41Z day: '01' doi: 10.1175/jas-d-11-0257.1 extern: '1' intvolume: ' 69' issue: '8' keyword: - Atmospheric Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1175/JAS-D-11-0257.1 month: '08' oa: 1 oa_version: Published Version page: 2551-2565 publication: Journal of the Atmospheric Sciences publication_identifier: issn: - 0022-4928 - 1520-0469 publication_status: published publisher: American Meteorological Society quality_controlled: '1' status: public title: Detailed investigation of the self-aggregation of convection in cloud-resolving simulations type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 69 year: '2012' ... --- _id: '9451' abstract: - lang: eng text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations. article_processing_charge: No article_type: original author: - first_name: Christian A. full_name: Ibarra, Christian A. last_name: Ibarra - first_name: Xiaoqi full_name: Feng, Xiaoqi last_name: Feng - first_name: Vera K. full_name: Schoft, Vera K. last_name: Schoft - first_name: Tzung-Fu full_name: Hsieh, Tzung-Fu last_name: Hsieh - first_name: Rie full_name: Uzawa, Rie last_name: Uzawa - first_name: Jessica A. full_name: Rodrigues, Jessica A. last_name: Rodrigues - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach - first_name: Nina full_name: Chumak, Nina last_name: Chumak - first_name: Adriana full_name: Machlicova, Adriana last_name: Machlicova - first_name: Toshiro full_name: Nishimura, Toshiro last_name: Nishimura - first_name: Denisse full_name: Rojas, Denisse last_name: Rojas - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer - first_name: Hisashi full_name: Tamaru, Hisashi last_name: Tamaru - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364. doi:10.1126/science.1224839 apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224839 chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839. ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012. ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364. mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839. short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364. date_created: 2021-06-04T07:51:31Z date_published: 2012-09-14T00:00:00Z date_updated: 2021-12-14T08:28:51Z day: '14' ddc: - '580' department: - _id: DaZi doi: 10.1126/science.1224839 extern: '1' external_id: pmid: - '22984074' has_accepted_license: '1' intvolume: ' 337' issue: '6100' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/ month: '09' oa: 1 oa_version: Published Version page: 1360-1364 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 337 year: '2012' ... --- _id: '9535' abstract: - lang: eng text: The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies. article_processing_charge: No article_type: review author: - first_name: D. full_name: Coleman-Derr, D. last_name: Coleman-Derr - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 2012;77:147-154. doi:10.1101/sqb.2012.77.014944 apa: Coleman-Derr, D., & Zilberman, D. (2012). DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2012.77.014944 chicago: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press, 2012. https://doi.org/10.1101/sqb.2012.77.014944. ieee: D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation of constitutive expression,” Cold Spring Harbor Symposia on Quantitative Biology, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012. ista: Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 77, 147–154. mla: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology, vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:10.1101/sqb.2012.77.014944. short: D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154. date_created: 2021-06-08T13:01:23Z date_published: 2012-12-18T00:00:00Z date_updated: 2021-12-14T08:33:09Z day: '18' department: - _id: DaZi doi: 10.1101/sqb.2012.77.014944 extern: '1' external_id: pmid: - '23250988' intvolume: ' 77' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/sqb.2012.77.014944 month: '12' oa: 1 oa_version: Published Version page: 147-154 pmid: 1 publication: Cold Spring Harbor Symposia on Quantitative Biology publication_identifier: eissn: - 1943-4456 issn: - 0091-7451 publication_status: published publisher: Cold Spring Harbor Laboratory Press quality_controlled: '1' scopus_import: '1' status: public title: DNA methylation, H2A.Z, and the regulation of constitutive expression type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 77 year: '2012' ... --- _id: '3242' abstract: - lang: eng text: Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”). acknowledgement: Funding for this project was obtained by the German Research Foundation DFG (http://www.dfg.de/en/index.jsp) as an Individual Research Grant (CR118/2-1 to SC) and the European Research Council (http://erc.europa.eu/) in form of two ERC Starting Grants (ERC-2009-StG240371-SocialVaccines to SC and ERC-2010-StG259294-LatentCauses to FJT). In addition, the Junge Akademie (Young Academy of the Berlin-Brandenburg Academy of Sciences and Humanities and the National Academy of Sciences Leopoldina (http://www.diejungeakademie.de/english/i​ndex.html) funded this joint Antnet project of SC and FJT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. article_number: e1001300 author: - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Meghan full_name: Vyleta, Meghan id: 418901AA-F248-11E8-B48F-1D18A9856A87 last_name: Vyleta - first_name: Fabian full_name: Theis, Fabian last_name: Theis - first_name: Miriam full_name: Stock, Miriam id: 42462816-F248-11E8-B48F-1D18A9856A87 last_name: Stock - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Martina full_name: Klatt, Martina id: E60F29C6-E9AE-11E9-AF6E-D190C7302F38 last_name: Klatt - first_name: Verena full_name: Drescher, Verena last_name: Drescher - first_name: Carsten full_name: Marr, Carsten last_name: Marr - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Konrad M, Vyleta M, Theis F, et al. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. 2012;10(4). doi:10.1371/journal.pbio.1001300 apa: Konrad, M., Vyleta, M., Theis, F., Stock, M., Tragust, S., Klatt, M., … Cremer, S. (2012). Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001300 chicago: Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Simon Tragust, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001300. ieee: M. Konrad et al., “Social transfer of pathogenic fungus promotes active immunisation in ant colonies,” PLoS Biology, vol. 10, no. 4. Public Library of Science, 2012. ista: Konrad M, Vyleta M, Theis F, Stock M, Tragust S, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. 10(4), e1001300. mla: Konrad, Matthias, et al. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” PLoS Biology, vol. 10, no. 4, e1001300, Public Library of Science, 2012, doi:10.1371/journal.pbio.1001300. short: M. Konrad, M. Vyleta, F. Theis, M. Stock, S. Tragust, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, PLoS Biology 10 (2012). date_created: 2018-12-11T12:02:13Z date_published: 2012-04-03T00:00:00Z date_updated: 2023-02-23T14:07:11Z day: '03' ddc: - '570' - '579' department: - _id: SyCr doi: 10.1371/journal.pbio.1001300 ec_funded: 1 file: - access_level: open_access checksum: 4ebacefd9fbab5c68adf829124115fd1 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:28Z date_updated: 2020-07-14T12:46:04Z file_id: '4689' file_name: IST-2012-96-v1+1_journal.pbio.1001300.pdf file_size: 674228 relation: main_file file_date_updated: 2020-07-14T12:46:04Z has_accepted_license: '1' intvolume: ' 10' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 25DAF0B2-B435-11E9-9278-68D0E5697425 grant_number: CR-118/3-1 name: Host-Parasite Coevolution - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' - _id: 25E0E184-B435-11E9-9278-68D0E5697425 name: Antnet publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '3434' pubrep_id: '96' quality_controlled: '1' related_material: record: - id: '9755' relation: research_data status: public scopus_import: 1 status: public title: Social transfer of pathogenic fungus promotes active immunisation in ant colonies tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2012' ... --- _id: '9755' abstract: - lang: eng text: Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”). article_processing_charge: No author: - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Meghan full_name: Vyleta, Meghan id: 418901AA-F248-11E8-B48F-1D18A9856A87 last_name: Vyleta - first_name: Fabian full_name: Theis, Fabian last_name: Theis - first_name: Miriam full_name: Stock, Miriam id: 42462816-F248-11E8-B48F-1D18A9856A87 last_name: Stock - first_name: Martina full_name: Klatt, Martina id: E60F29C6-E9AE-11E9-AF6E-D190C7302F38 last_name: Klatt - first_name: Verena full_name: Drescher, Verena last_name: Drescher - first_name: Carsten full_name: Marr, Carsten last_name: Marr - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Konrad M, Vyleta M, Theis F, et al. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. 2012. doi:10.5061/dryad.sv37s' apa: 'Konrad, M., Vyleta, M., Theis, F., Stock, M., Klatt, M., Drescher, V., … Cremer, S. (2012). Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. Dryad. https://doi.org/10.5061/dryad.sv37s' chicago: 'Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” Dryad, 2012. https://doi.org/10.5061/dryad.sv37s.' ieee: 'M. Konrad et al., “Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies.” Dryad, 2012.' ista: 'Konrad M, Vyleta M, Theis F, Stock M, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies, Dryad, 10.5061/dryad.sv37s.' mla: 'Konrad, Matthias, et al. Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies. Dryad, 2012, doi:10.5061/dryad.sv37s.' short: M. Konrad, M. Vyleta, F. Theis, M. Stock, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, (2012). date_created: 2021-07-30T08:39:13Z date_published: 2012-09-27T00:00:00Z date_updated: 2023-02-23T11:18:41Z day: '27' department: - _id: SyCr doi: 10.5061/dryad.sv37s main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.sv37s month: '09' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '3242' relation: used_in_publication status: public status: public title: 'Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2012' ... --- _id: '9758' abstract: - lang: eng text: 'We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.' article_processing_charge: No author: - first_name: Simon full_name: Aeschbacher, Simon id: 2D35326E-F248-11E8-B48F-1D18A9856A87 last_name: Aeschbacher - first_name: Andreas full_name: Futschik, Andreas last_name: Futschik - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont citation: ama: 'Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. 2012. doi:10.5061/dryad.274b1' apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2012). Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. Dryad. https://doi.org/10.5061/dryad.274b1' chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates.” Dryad, 2012. https://doi.org/10.5061/dryad.274b1.' ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates.” Dryad, 2012.' ista: 'Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates, Dryad, 10.5061/dryad.274b1.' mla: 'Aeschbacher, Simon, et al. Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. Dryad, 2012, doi:10.5061/dryad.274b1.' short: S. Aeschbacher, A. Futschik, M. Beaumont, (2012). date_created: 2021-07-30T12:36:39Z date_published: 2012-11-14T00:00:00Z date_updated: 2023-02-23T11:05:19Z day: '14' department: - _id: NiBa doi: 10.5061/dryad.274b1 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.274b1 month: '11' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2944' relation: used_in_publication status: public status: public title: 'Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2012' ... --- _id: '9757' abstract: - lang: eng text: To fight infectious diseases, host immune defences are employed at multiple levels. Sanitary behaviour, such as pathogen avoidance and removal, acts as a first line of defence to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care towards pathogen-exposed group members [2]. One of the most common behaviours is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores as it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behaviour extends current understanding of grooming and the establishment of social immunity in insect societies. article_processing_charge: No author: - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Barbara full_name: Mitteregger, Barbara id: 479DDAAC-E9CD-11E9-9B5F-82450873F7A1 last_name: Mitteregger - first_name: Vanessa full_name: Barone, Vanessa id: 419EECCC-F248-11E8-B48F-1D18A9856A87 last_name: Barone orcid: 0000-0003-2676-3367 - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. 2012. doi:10.5061/dryad.61649' apa: 'Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., & Cremer, S. (2012). Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Dryad. https://doi.org/10.5061/dryad.61649' chicago: 'Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” Dryad, 2012. https://doi.org/10.5061/dryad.61649.' ieee: 'S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison.” Dryad, 2012.' ista: 'Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2012. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison, Dryad, 10.5061/dryad.61649.' mla: 'Tragust, Simon, et al. Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison. Dryad, 2012, doi:10.5061/dryad.61649.' short: S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, (2012). date_created: 2021-07-30T12:31:31Z date_published: 2012-12-14T00:00:00Z date_updated: 2023-02-23T11:04:28Z day: '14' department: - _id: SyCr doi: 10.5061/dryad.61649 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.61649 month: '12' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2926' relation: used_in_publication status: public status: public title: 'Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2012' ... --- _id: '8504' 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. article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: O. S. full_name: KOZLOVSKI, O. S. last_name: KOZLOVSKI citation: ama: Kaloshin V, KOZLOVSKI OS. A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. 2012;32(1):159-165. doi:10.1017/s0143385710000817 apa: Kaloshin, V., & KOZLOVSKI, O. S. (2012). A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/s0143385710000817 chicago: Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2012. https://doi.org/10.1017/s0143385710000817. ieee: V. Kaloshin and O. S. KOZLOVSKI, “A Cr unimodal map with an arbitrary fast growth of the number of periodic points,” Ergodic Theory and Dynamical Systems, vol. 32, no. 1. Cambridge University Press, pp. 159–165, 2012. 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. mla: Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical Systems, vol. 32, no. 1, Cambridge University Press, 2012, pp. 159–65, doi:10.1017/s0143385710000817. short: V. Kaloshin, O.S. KOZLOVSKI, Ergodic Theory and Dynamical Systems 32 (2012) 159–165. date_created: 2020-09-18T10:47:33Z date_published: 2012-02-01T00:00:00Z date_updated: 2021-01-12T08:19:44Z day: '01' doi: 10.1017/s0143385710000817 extern: '1' intvolume: ' 32' issue: '1' keyword: - Applied Mathematics - General Mathematics language: - iso: eng month: '02' oa_version: None page: 159-165 publication: Ergodic Theory and Dynamical Systems publication_identifier: issn: - 0143-3857 - 1469-4417 publication_status: published publisher: Cambridge University Press quality_controlled: '1' status: public title: A Cr unimodal map with an arbitrary fast growth of the number of periodic points type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2012' ... --- _id: '8503' 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. article_processing_charge: No article_type: original author: - first_name: Alain full_name: Albouy, Alain last_name: Albouy - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Albouy A, Kaloshin V. Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. 2012;176(1):535-588. doi:10.4007/annals.2012.176.1.10 apa: Albouy, A., & Kaloshin, V. (2012). Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. Princeton University Press. https://doi.org/10.4007/annals.2012.176.1.10 chicago: Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of Five Bodies in the Plane.” Annals of Mathematics. Princeton University Press, 2012. https://doi.org/10.4007/annals.2012.176.1.10. ieee: A. Albouy and V. Kaloshin, “Finiteness of central configurations of five bodies in the plane,” Annals of Mathematics, vol. 176, no. 1. Princeton University Press, pp. 535–588, 2012. ista: Albouy A, Kaloshin V. 2012. Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. 176(1), 535–588. mla: Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of Five Bodies in the Plane.” Annals of Mathematics, vol. 176, no. 1, Princeton University Press, 2012, pp. 535–88, doi:10.4007/annals.2012.176.1.10. short: A. Albouy, V. Kaloshin, Annals of Mathematics 176 (2012) 535–588. date_created: 2020-09-18T10:47:24Z date_published: 2012-07-01T00:00:00Z date_updated: 2021-01-12T08:19:44Z day: '01' doi: 10.4007/annals.2012.176.1.10 extern: '1' intvolume: ' 176' issue: '1' language: - iso: eng month: '07' oa_version: None page: 535-588 publication: Annals of Mathematics publication_identifier: issn: - 0003-486X publication_status: published publisher: Princeton University Press quality_controlled: '1' status: public title: Finiteness of central configurations of five bodies in the plane type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 176 year: '2012' ... --- _id: '887' abstract: - lang: eng text: A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications. acknowledgement: The work was supported by a Plan Nacional grant no. BFU2009-09271 from the Spanish Ministry of Science and Innovation. The author is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov F. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 2012;279(1749):5048-5057. doi:10.1098/rspb.2012.1108 apa: Kondrashov, F. (2012). Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.1108 chicago: Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2012. https://doi.org/10.1098/rspb.2012.1108. ieee: F. Kondrashov, “Gene duplication as a mechanism of genomic adaptation to a changing environment,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749. Royal Society, The, pp. 5048–5057, 2012. ista: Kondrashov F. 2012. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 279(1749), 5048–5057. mla: Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749, Royal Society, The, 2012, pp. 5048–57, doi:10.1098/rspb.2012.1108. short: F. Kondrashov, Proceedings of the Royal Society of London Series B Biological Sciences 279 (2012) 5048–5057. date_created: 2018-12-11T11:49:01Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:21:16Z day: '01' doi: 10.1098/rspb.2012.1108 extern: 1 intvolume: ' 279' issue: '1749' month: '01' page: 5048 - 5057 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '6765' quality_controlled: 0 status: public title: Gene duplication as a mechanism of genomic adaptation to a changing environment tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 279 year: '2012' ... --- _id: '9049' abstract: - lang: eng text: 'Diffusiophoretic motion of colloids and macromolecules under salt gradients exhibits a logarithmic-sensing, i.e. the particle velocity is proportional to the spatial gradient of the logarithm of the salt concentration, as VDP = DDP∇logc. Here we explore experimentally the implications of this log-sensing behavior, on the basis of a hydrogel microfluidic device allowing to build spatially and temporally controlled gradients. We first demonstrate that the non-linearity of the salt-taxis leads to a trapping of particles under concentration gradient oscillations via a rectification of the motion. As an alternative, we make use of the high sensitivity of diffusiophoretic migration to vanishing salt concentration due to the log-sensing: in a counter-intuitive way, a vanishing gradient can lead to measurable velocity provided that the solute concentration is low enough, thus keeping ∇c/c finite. We show that this leads to a strong segregation of particles in osmotic shock configuration, resulting from a step change of the salt concentration at the boundaries. These various phenomena are rationalized on the basis of a theoretical description for the time-dependent Smoluchowski equation for the colloidal density.' article_processing_charge: No article_type: original author: - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Cécile full_name: Cottin-Bizonne, Cécile last_name: Cottin-Bizonne - first_name: Christophe full_name: Ybert, Christophe last_name: Ybert - first_name: Lydéric full_name: Bocquet, Lydéric last_name: Bocquet citation: ama: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 2012;8(4):980-994. doi:10.1039/c1sm06395b apa: Palacci, J. A., Cottin-Bizonne, C., Ybert, C., & Bocquet, L. (2012). Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c1sm06395b chicago: Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter. Royal Society of Chemistry, 2012. https://doi.org/10.1039/c1sm06395b. ieee: J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis,” Soft Matter, vol. 8, no. 4. Royal Society of Chemistry, pp. 980–994, 2012. ista: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2012. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 8(4), 980–994. mla: Palacci, Jérémie A., et al. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter, vol. 8, no. 4, Royal Society of Chemistry, 2012, pp. 980–94, doi:10.1039/c1sm06395b. short: J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Soft Matter 8 (2012) 980–994. date_created: 2021-02-01T13:43:10Z date_published: 2012-01-28T00:00:00Z date_updated: 2023-02-23T13:47:31Z day: '28' doi: 10.1039/c1sm06395b extern: '1' intvolume: ' 8' issue: '4' language: - iso: eng month: '01' oa_version: None page: 980-994 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 8 year: '2012' ... --- _id: '922' abstract: - lang: eng text: 'We study theoretically the morphologies of biological tubes affected by various pathologies. When epithelial cells grow, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated: varicose, dilated, sinuous, or sausagelike. They are all found in pathologies of tracheal, renal tubes, or arteries. The final shape depends crucially on the mechanical parameters of the tissues: Young''s modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation.' article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jacques full_name: Prost, Jacques last_name: Prost - first_name: Jean full_name: Joanny, Jean last_name: Joanny citation: ama: Hannezo EB, Prost J, Joanny J. Mechanical instabilities of biological tubes. Physical Review Letters. 2012;109(1). doi:10.1103/PhysRevLett.109.018101 apa: Hannezo, E. B., Prost, J., & Joanny, J. (2012). Mechanical instabilities of biological tubes. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.018101 chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Mechanical Instabilities of Biological Tubes.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.018101. ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Mechanical instabilities of biological tubes,” Physical Review Letters, vol. 109, no. 1. American Physical Society, 2012. ista: Hannezo EB, Prost J, Joanny J. 2012. Mechanical instabilities of biological tubes. Physical Review Letters. 109(1). mla: Hannezo, Edouard B., et al. “Mechanical Instabilities of Biological Tubes.” Physical Review Letters, vol. 109, no. 1, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.018101. short: E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 109 (2012). date_created: 2018-12-11T11:49:13Z date_published: 2012-07-03T00:00:00Z date_updated: 2021-01-12T08:21:56Z day: '03' doi: 10.1103/PhysRevLett.109.018101 extern: '1' external_id: arxiv: - '1207.1516' intvolume: ' 109' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1207.1516 month: '07' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6519' status: public title: Mechanical instabilities of biological tubes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2012' ... --- _id: '9499' abstract: - lang: eng text: EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism. article_number: e1002512 article_processing_charge: No article_type: original author: - first_name: Sang Yeol full_name: Kim, Sang Yeol last_name: Kim - first_name: Jungeun full_name: Lee, Jungeun last_name: Lee - first_name: Leor full_name: Eshed-Williams, Leor last_name: Eshed-Williams - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Z. Renee full_name: Sung, Z. Renee last_name: Sung citation: ama: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3). doi:10.1371/journal.pgen.1002512 apa: Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., & Sung, Z. R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002512 chicago: Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512. ieee: S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development,” PLoS Genetics, vol. 8, no. 3. Public Library of Science, 2012. ista: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 8(3), e1002512. mla: Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics, vol. 8, no. 3, e1002512, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002512. short: S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012). date_created: 2021-06-07T11:07:56Z date_published: 2012-03-22T00:00:00Z date_updated: 2021-12-14T08:31:14Z day: '22' department: - _id: DaZi doi: 10.1371/journal.pgen.1002512 extern: '1' external_id: pmid: - '22457632' intvolume: ' 8' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pgen.1002512 month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: eissn: - 1553-7404 issn: - 1553-7390 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 8 year: '2012' ... --- _id: '9497' abstract: - lang: eng text: The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes. article_number: e1002988 article_processing_charge: No article_type: original author: - first_name: Devin full_name: Coleman-Derr, Devin last_name: Coleman-Derr - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988 apa: Coleman-Derr, D., & Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002988 chicago: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988. ieee: D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” PLoS Genetics, vol. 8, no. 10. Public Library of Science, 2012. ista: Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988. mla: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002988. short: D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012). date_created: 2021-06-07T10:55:27Z date_published: 2012-10-11T00:00:00Z date_updated: 2021-12-14T08:29:57Z day: '11' department: - _id: DaZi doi: 10.1371/journal.pgen.1002988 extern: '1' external_id: pmid: - '23071449' intvolume: ' 8' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pgen.1002988 month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: eissn: - 1553-7404 issn: - 1553-7390 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Deposition of histone variant H2A.Z within gene bodies regulates responsive genes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 8 year: '2012' ... --- _id: '9528' abstract: - lang: eng text: Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory. article_processing_charge: No article_type: review author: - first_name: Jason T. full_name: Huff, Jason T. last_name: Huff - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007 apa: Huff, J. T., & Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2012.01.007 chicago: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007. ieee: J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” Current Opinion in Genetics and Development, vol. 22, no. 2. Elsevier, pp. 132–138, 2012. ista: Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 22(2), 132–138. mla: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:10.1016/j.gde.2012.01.007. short: J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138. date_created: 2021-06-08T08:58:52Z date_published: 2012-04-01T00:00:00Z date_updated: 2021-12-14T08:32:38Z department: - _id: DaZi doi: 10.1016/j.gde.2012.01.007 extern: '1' external_id: pmid: - '22336527' intvolume: ' 22' issue: '2' language: - iso: eng month: '04' oa_version: None page: 132-138 pmid: 1 publication: Current Opinion in Genetics and Development publication_identifier: issn: - 0959-437X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Regulation of biological accuracy, precision, and memory by plant chromatin organization type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 22 year: '2012' ... --- _id: '966' abstract: - lang: eng text: Motivated by recent experiments on Ba3NiSb2O 9, we investigate possible quantum spin liquid ground states for spin S=1 Heisenberg models on the triangular lattice. We use variational Monte Carlo techniques to calculate the energies of microscopic spin liquid wave functions where spin is represented by three flavors of fermionic spinon operators. These energies are compared with the energies of various competing three-sublattice ordered states. Our approach shows that the antiferromagnetic Heisenberg model with biquadratic term and single-ion anisotropy does not have a low-temperature spin liquid phase. However, for an SU(3)-invariant model with sufficiently strong ring-exchange terms, we find a paired chiral quantum spin liquid with a Fermi surface of deconfined spinons that is stable against all types of ordering patterns we considered. We discuss the physics of this exotic spin liquid state in relation to the recent experiment and suggest new ways to test this scenario. acknowledgement: We thank Kuang-Ting Chen, Rebecca Flint, Dmitri Ivanov, Z.-X. Liu, Tai-Kai Ng, Lara Thompson, Tamás Tóth, and Fa Wang for helpful discussions. T.S. is supported by NSF DMR 1005434. P.A.L. is supported by NSF DMR 1104498. S.B. acknowledges support from the Swiss National Science Foundation (SNSF). author: - first_name: Samuel full_name: Bieri, Samuel last_name: Bieri - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Todadri full_name: Senthil, Todadri S last_name: Senthil - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: ama: Bieri S, Serbyn M, Senthil T, Lee P. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 2012;86(22). doi:10.1103/PhysRevB.86.224409 apa: Bieri, S., Serbyn, M., Senthil, T., & Lee, P. (2012). Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.86.224409 chicago: Bieri, Samuel, Maksym Serbyn, Todadri Senthil, and Patrick Lee. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2012. https://doi.org/10.1103/PhysRevB.86.224409. ieee: S. Bieri, M. Serbyn, T. Senthil, and P. Lee, “Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice,” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22. American Physical Society, 2012. ista: Bieri S, Serbyn M, Senthil T, Lee P. 2012. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 86(22). mla: Bieri, Samuel, et al. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22, American Physical Society, 2012, doi:10.1103/PhysRevB.86.224409. short: S. Bieri, M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 86 (2012). date_created: 2018-12-11T11:49:27Z date_published: 2012-12-13T00:00:00Z date_updated: 2021-01-12T08:22:18Z day: '13' doi: 10.1103/PhysRevB.86.224409 extern: 1 intvolume: ' 86' issue: '22' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1208.3231 month: '12' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6431' quality_controlled: 0 status: public title: Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice type: journal_article volume: 86 year: '2012' ... --- _id: '2968' abstract: - lang: eng text: Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and-using triplet alignments of intronic loci-quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. © 2012 Blackwell Publishing Ltd. acknowledgement: "This work was supported by funding from the UK Natural Environment Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1, NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on earlier versions of the manuscript. " author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: George full_name: Melika, George last_name: Melika - first_name: Graham full_name: Stone, Graham last_name: Stone citation: ama: Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 2012;21(18):4605-4617. doi:10.1111/j.1365-294X.2012.05700.x apa: Lohse, K., Barton, N. H., Melika, G., & Stone, G. (2012). A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05700.x chicago: Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05700.x. ieee: K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison of population histories in a parasitoid guild,” Molecular Ecology, vol. 21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012. ista: Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617. mla: Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology, vol. 21, no. 18, Wiley-Blackwell, 2012, pp. 4605–17, doi:10.1111/j.1365-294X.2012.05700.x. short: K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617. date_created: 2018-12-11T12:00:36Z date_published: 2012-09-01T00:00:00Z date_updated: 2023-05-30T13:07:47Z day: '01' ddc: - '570' - '579' department: - _id: NiBa doi: 10.1111/j.1365-294X.2012.05700.x ec_funded: 1 file: - access_level: open_access checksum: c14ee4cb2a8ba9575bfd8a9bb7a883bb content_type: application/pdf creator: system date_created: 2018-12-12T10:17:47Z date_updated: 2020-07-14T12:45:57Z file_id: '5304' file_name: IST-2014-296-v1+1_4_wasps_revised3.pdf file_size: 235820 relation: main_file - access_level: open_access checksum: f00afc5b887c8222014b57375b8caece content_type: application/pdf creator: system date_created: 2018-12-12T10:17:48Z date_updated: 2020-07-14T12:45:57Z file_id: '5305' file_name: IST-2014-296-v1+2_4_wasps_Supporting2.pdf file_size: 41975 relation: main_file file_date_updated: 2020-07-14T12:45:57Z has_accepted_license: '1' intvolume: ' 21' issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 4605 - 4617 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3746' pubrep_id: '296' quality_controlled: '1' related_material: record: - id: '13075' relation: research_data status: public scopus_import: 1 status: public title: A likelihood based comparison of population histories in a parasitoid guild type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2012' ... --- _id: '13075' abstract: - lang: eng text: Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. article_processing_charge: No author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Graham full_name: Stone, Graham last_name: Stone - first_name: George full_name: Melika, George last_name: Melika citation: ama: 'Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:10.5061/DRYAD.0G0FS' apa: 'Lohse, K., Barton, N. H., Stone, G., & Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. https://doi.org/10.5061/DRYAD.0G0FS' chicago: 'Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. https://doi.org/10.5061/DRYAD.0G0FS.' ieee: 'K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012.' ista: 'Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, 10.5061/DRYAD.0G0FS.' mla: 'Lohse, Konrad, et al. Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild. Dryad, 2012, doi:10.5061/DRYAD.0G0FS.' short: K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012). date_created: 2023-05-23T17:01:02Z date_published: 2012-06-08T00:00:00Z date_updated: 2023-05-30T13:07:48Z day: '08' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.0G0FS license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.0g0fs month: '06' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2968' relation: used_in_publication status: public status: public title: 'Data from: A likelihood-based comparison of population histories in a parasitoid guild' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '13407' abstract: - lang: eng text: We show that diamagnetic particles can be remotely manipulated by a magnet by the reversible adsorption of dual-responsive, light-switchable/superparamagnetic nanoparticles down to their surface. Adsorption occurs upon exposure to UV light, and can be reversed thermally or by ambient light. The dynamic self-assembly of thin films of the dual-responsive nanoparticles induces attractive interactions between diamagnetic particles. We demonstrate that catalytic amounts of the dual-responsive nanoparticles are sufficient to magnetically guide and deliver the diamagnetic particles to desired locations, where they can then be released by disassembling the dynamic layers of superparamagnetic nanoparticles with visible light. article_processing_charge: No article_type: original author: - first_name: Olga full_name: Chovnik, Olga last_name: Chovnik - first_name: Renata full_name: Balgley, Renata last_name: Balgley - first_name: Joel R. full_name: Goldman, Joel R. last_name: Goldman - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Chovnik O, Balgley R, Goldman JR, Klajn R. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. 2012;134(48):19564-19567. doi:10.1021/ja309633v apa: Chovnik, O., Balgley, R., Goldman, J. R., & Klajn, R. (2012). Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja309633v chicago: Chovnik, Olga, Renata Balgley, Joel R. Goldman, and Rafal Klajn. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja309633v. ieee: O. Chovnik, R. Balgley, J. R. Goldman, and R. Klajn, “Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets,” Journal of the American Chemical Society, vol. 134, no. 48. American Chemical Society, pp. 19564–19567, 2012. ista: Chovnik O, Balgley R, Goldman JR, Klajn R. 2012. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. 134(48), 19564–19567. mla: Chovnik, Olga, et al. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” Journal of the American Chemical Society, vol. 134, no. 48, American Chemical Society, 2012, pp. 19564–67, doi:10.1021/ja309633v. short: O. Chovnik, R. Balgley, J.R. Goldman, R. Klajn, Journal of the American Chemical Society 134 (2012) 19564–19567. date_created: 2023-08-01T09:47:42Z date_published: 2012-11-26T00:00:00Z date_updated: 2023-08-08T07:51:10Z day: '26' doi: 10.1021/ja309633v extern: '1' external_id: pmid: - '23181449' intvolume: ' 134' issue: '48' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '11' oa_version: Published Version page: 19564-19567 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '13408' abstract: - lang: eng text: Well-defined metallic nanobowls can be prepared by extending the concept of a protecting group to colloidal synthesis. Magnetic nanoparticles are employed as “protecting groups” during the galvanic replacement of silver with gold. The replacement reaction is accompanied by spontantous dissociation of the protecting groups, leaving behind metallic nanobowls. article_processing_charge: No article_type: original author: - first_name: Yonatan full_name: Ridelman, Yonatan last_name: Ridelman - first_name: Gurvinder full_name: Singh, Gurvinder last_name: Singh - first_name: Ronit full_name: Popovitz-Biro, Ronit last_name: Popovitz-Biro - first_name: Sharon G. full_name: Wolf, Sharon G. last_name: Wolf - first_name: Sanjib full_name: Das, Sanjib last_name: Das - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 2012;8(5):654-660. doi:10.1002/smll.201101882 apa: Ridelman, Y., Singh, G., Popovitz-Biro, R., Wolf, S. G., Das, S., & Klajn, R. (2012). Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. Wiley. https://doi.org/10.1002/smll.201101882 chicago: Ridelman, Yonatan, Gurvinder Singh, Ronit Popovitz-Biro, Sharon G. Wolf, Sanjib Das, and Rafal Klajn. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small. Wiley, 2012. https://doi.org/10.1002/smll.201101882. ieee: Y. Ridelman, G. Singh, R. Popovitz-Biro, S. G. Wolf, S. Das, and R. Klajn, “Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles,” Small, vol. 8, no. 5. Wiley, pp. 654–660, 2012. ista: Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. 2012. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 8(5), 654–660. mla: Ridelman, Yonatan, et al. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small, vol. 8, no. 5, Wiley, 2012, pp. 654–60, doi:10.1002/smll.201101882. short: Y. Ridelman, G. Singh, R. Popovitz-Biro, S.G. Wolf, S. Das, R. Klajn, Small 8 (2012) 654–660. date_created: 2023-08-01T09:47:55Z date_published: 2012-03-12T00:00:00Z date_updated: 2023-08-08T07:55:10Z day: '12' doi: 10.1002/smll.201101882 extern: '1' external_id: pmid: - '22392681' intvolume: ' 8' issue: '5' keyword: - Biomaterials - Biotechnology - General Materials Science - General Chemistry language: - iso: eng month: '03' oa_version: None page: 654-660 pmid: 1 publication: Small publication_identifier: eissn: - 1613-6829 issn: - 1613-6810 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2012' ... --- _id: '10903' abstract: - lang: eng text: We propose a logic-based framework for automated reasoning about sequential programs manipulating singly-linked lists and arrays with unbounded data. We introduce the logic SLAD, which allows combining shape constraints, written in a fragment of Separation Logic, with data and size constraints. We address the problem of checking the entailment between SLAD formulas, which is crucial in performing pre-post condition reasoning. Although this problem is undecidable in general for SLAD, we propose a sound and powerful procedure that is able to solve this problem for a large class of formulas, beyond the capabilities of existing techniques and tools. We prove that this procedure is complete, i.e., it is actually a decision procedure for this problem, for an important fragment of SLAD including known decidable logics. We implemented this procedure and shown its preciseness and its efficiency on a significant benchmark of formulas. acknowledgement: This work has been partially supported by the French ANR project Veridyc alternative_title: - LNCS article_processing_charge: No author: - first_name: Ahmed full_name: Bouajjani, Ahmed last_name: Bouajjani - first_name: Cezara full_name: Dragoi, Cezara id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87 last_name: Dragoi - first_name: Constantin full_name: Enea, Constantin last_name: Enea - first_name: Mihaela full_name: Sighireanu, Mihaela last_name: Sighireanu citation: ama: 'Bouajjani A, Dragoi C, Enea C, Sighireanu M. Accurate invariant checking for programs manipulating lists and arrays with infinite data. In: Automated Technology for Verification and Analysis. Vol 7561. LNCS. Berlin, Heidelberg: Springer; 2012:167-182. doi:10.1007/978-3-642-33386-6_14' apa: 'Bouajjani, A., Dragoi, C., Enea, C., & Sighireanu, M. (2012). Accurate invariant checking for programs manipulating lists and arrays with infinite data. In Automated Technology for Verification and Analysis (Vol. 7561, pp. 167–182). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-33386-6_14' chicago: 'Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” In Automated Technology for Verification and Analysis, 7561:167–82. LNCS. Berlin, Heidelberg: Springer, 2012. https://doi.org/10.1007/978-3-642-33386-6_14.' ieee: A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Accurate invariant checking for programs manipulating lists and arrays with infinite data,” in Automated Technology for Verification and Analysis, Thiruvananthapuram, India, 2012, vol. 7561, pp. 167–182. ista: 'Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Accurate invariant checking for programs manipulating lists and arrays with infinite data. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and AnalysisLNCS, LNCS, vol. 7561, 167–182.' mla: Bouajjani, Ahmed, et al. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” Automated Technology for Verification and Analysis, vol. 7561, Springer, 2012, pp. 167–82, doi:10.1007/978-3-642-33386-6_14. short: A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Automated Technology for Verification and Analysis, Springer, Berlin, Heidelberg, 2012, pp. 167–182. conference: end_date: 2012-10-06 location: Thiruvananthapuram, India name: 'ATVA: Automated Technology for Verification and Analysis' start_date: 2012-10-03 date_created: 2022-03-21T07:58:39Z date_published: 2012-10-15T00:00:00Z date_updated: 2023-09-05T14:07:24Z day: '15' department: - _id: ToHe doi: 10.1007/978-3-642-33386-6_14 intvolume: ' 7561' language: - iso: eng month: '10' oa_version: None page: 167-182 place: Berlin, Heidelberg publication: Automated Technology for Verification and Analysis publication_identifier: eisbn: - '9783642333866' eissn: - 1611-3349 isbn: - '9783642333859' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: Accurate invariant checking for programs manipulating lists and arrays with infinite data type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7561 year: '2012' ... --- _id: '10905' abstract: - lang: eng text: "Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP ∩ co−NP, but are not known to be in P. While the existence of polynomial-time algorithms has been a major open problem for decades, there is no algorithm that solves any non-trivial subclass in polynomial time.\r\nIn this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several counter examples that show that many previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting graph structures need not help." acknowledgement: 'Supported by the Austrian Science Fund (FWF): P23499-N23, the Austrian Science Fund (FWF): S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft Faculty Fellows Award' alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. In: Algorithms – ESA 2012. Vol 7501. Springer; 2012:301-312. doi:10.1007/978-3-642-33090-2_27' apa: 'Chatterjee, K., Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2012). Polynomial-time algorithms for energy games with special weight structures. In Algorithms – ESA 2012 (Vol. 7501, pp. 301–312). Ljubljana, Slovenia: Springer. https://doi.org/10.1007/978-3-642-33090-2_27' chicago: Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” In Algorithms – ESA 2012, 7501:301–12. Springer, 2012. https://doi.org/10.1007/978-3-642-33090-2_27. ieee: K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” in Algorithms – ESA 2012, Ljubljana, Slovenia, 2012, vol. 7501, pp. 301–312. ista: 'Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2012. Polynomial-time algorithms for energy games with special weight structures. Algorithms – ESA 2012. ESA: European Symposium on Algorithms, LNCS, vol. 7501, 301–312.' mla: Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithms – ESA 2012, vol. 7501, Springer, 2012, pp. 301–12, doi:10.1007/978-3-642-33090-2_27. short: K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, Algorithms – ESA 2012, Springer, 2012, pp. 301–312. conference: end_date: 2012-09-12 location: Ljubljana, Slovenia name: 'ESA: European Symposium on Algorithms' start_date: 2012-09-10 date_created: 2022-03-21T08:01:45Z date_published: 2012-10-01T00:00:00Z date_updated: 2023-09-05T14:09:30Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-33090-2_27 ec_funded: 1 external_id: arxiv: - '1604.08234' intvolume: ' 7501' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.08234 month: '10' oa: 1 oa_version: Preprint page: 301-312 project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Algorithms – ESA 2012 publication_identifier: eisbn: - '9783642330902' eissn: - 1611-3349 isbn: - '9783642330896' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' related_material: record: - id: '535' relation: later_version status: public scopus_import: '1' status: public title: Polynomial-time algorithms for energy games with special weight structures type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7501 year: '2012' ... --- _id: '10906' abstract: - lang: eng text: HSF(C) is a tool that automates verification of safety and liveness properties for C programs. This paper describes the verification approach taken by HSF(C) and provides instructions on how to install and use the tool. alternative_title: - LNCS article_processing_charge: No author: - first_name: Sergey full_name: Grebenshchikov, Sergey last_name: Grebenshchikov - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Nuno P. full_name: Lopes, Nuno P. last_name: Lopes - first_name: Corneliu full_name: Popeea, Corneliu last_name: Popeea - first_name: Andrey full_name: Rybalchenko, Andrey last_name: Rybalchenko citation: ama: 'Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. HSF(C): A software verifier based on Horn clauses. In: Flanagan C, König B, eds. Tools and Algorithms for the Construction and Analysis of Systems. Vol 7214. LNCS. Berlin, Heidelberg: Springer; 2012:549-551. doi:10.1007/978-3-642-28756-5_46' apa: 'Grebenshchikov, S., Gupta, A., Lopes, N. P., Popeea, C., & Rybalchenko, A. (2012). HSF(C): A software verifier based on Horn clauses. In C. Flanagan & B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems (Vol. 7214, pp. 549–551). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-28756-5_46' chicago: 'Grebenshchikov, Sergey, Ashutosh Gupta, Nuno P. Lopes, Corneliu Popeea, and Andrey Rybalchenko. “HSF(C): A Software Verifier Based on Horn Clauses.” In Tools and Algorithms for the Construction and Analysis of Systems, edited by Cormac Flanagan and Barbara König, 7214:549–51. LNCS. Berlin, Heidelberg: Springer, 2012. https://doi.org/10.1007/978-3-642-28756-5_46.' ieee: 'S. Grebenshchikov, A. Gupta, N. P. Lopes, C. Popeea, and A. Rybalchenko, “HSF(C): A software verifier based on Horn clauses,” in Tools and Algorithms for the Construction and Analysis of Systems, Tallinn, Estonia, 2012, vol. 7214, pp. 549–551.' ista: 'Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. 2012. HSF(C): A software verifier based on Horn clauses. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of SystemsLNCS, LNCS, vol. 7214, 549–551.' mla: 'Grebenshchikov, Sergey, et al. “HSF(C): A Software Verifier Based on Horn Clauses.” Tools and Algorithms for the Construction and Analysis of Systems, edited by Cormac Flanagan and Barbara König, vol. 7214, Springer, 2012, pp. 549–51, doi:10.1007/978-3-642-28756-5_46.' short: S. Grebenshchikov, A. Gupta, N.P. Lopes, C. Popeea, A. Rybalchenko, in:, C. Flanagan, B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems, Springer, Berlin, Heidelberg, 2012, pp. 549–551. conference: end_date: 2012-04-01 location: Tallinn, Estonia name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2012-03-24 date_created: 2022-03-21T08:03:30Z date_published: 2012-04-01T00:00:00Z date_updated: 2023-09-05T14:09:54Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-642-28756-5_46 editor: - first_name: Cormac full_name: Flanagan, Cormac last_name: Flanagan - first_name: Barbara full_name: König, Barbara last_name: König intvolume: ' 7214' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/978-3-642-28756-5_46 month: '04' oa: 1 oa_version: Published Version page: 549-551 place: Berlin, Heidelberg publication: Tools and Algorithms for the Construction and Analysis of Systems publication_identifier: eisbn: - '9783642287565' eissn: - 1611-3349 isbn: - '9783642287558' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: 'HSF(C): A software verifier based on Horn clauses' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7214 year: '2012' ... --- _id: '5745' article_processing_charge: No author: - first_name: Ashutosh full_name: Gupta, Ashutosh last_name: Gupta citation: ama: 'Gupta A. Improved Single Pass Algorithms for Resolution Proof Reduction. In: Automated Technology for Verification and Analysis. Vol 7561. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2012:107-121. doi:10.1007/978-3-642-33386-6_10' apa: 'Gupta, A. (2012). Improved Single Pass Algorithms for Resolution Proof Reduction. In Automated Technology for Verification and Analysis (Vol. 7561, pp. 107–121). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-33386-6_10' chicago: 'Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” In Automated Technology for Verification and Analysis, 7561:107–21. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. https://doi.org/10.1007/978-3-642-33386-6_10.' ieee: 'A. Gupta, “Improved Single Pass Algorithms for Resolution Proof Reduction,” in Automated Technology for Verification and Analysis, vol. 7561, Berlin, Heidelberg: Springer Berlin Heidelberg, 2012, pp. 107–121.' ista: 'Gupta A. 2012.Improved Single Pass Algorithms for Resolution Proof Reduction. In: Automated Technology for Verification and Analysis. vol. 7561, 107–121.' mla: Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” Automated Technology for Verification and Analysis, vol. 7561, Springer Berlin Heidelberg, 2012, pp. 107–21, doi:10.1007/978-3-642-33386-6_10. short: A. Gupta, in:, Automated Technology for Verification and Analysis, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 107–121. conference: end_date: 2012-10-06 location: Thiruvananthapuram, Kerala, India name: ATVA 2012 start_date: 2012-10-03 date_created: 2018-12-18T13:01:46Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-09-05T14:15:29Z ddc: - '005' department: - _id: ToHe doi: 10.1007/978-3-642-33386-6_10 ec_funded: 1 file: - access_level: open_access checksum: 68415837a315de3cc4d120f6019d752c content_type: application/pdf creator: dernst date_created: 2018-12-18T13:07:35Z date_updated: 2020-07-14T12:47:10Z file_id: '5746' file_name: 2012_ATVA_Gupta.pdf file_size: 465502 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 7561' language: - iso: eng oa: 1 oa_version: None page: 107-121 place: Berlin, Heidelberg project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Automated Technology for Verification and Analysis publication_identifier: eissn: - 1611-3349 isbn: - '9783642333859' - '9783642333866' issn: - 0302-9743 publication_status: published publisher: Springer Berlin Heidelberg pubrep_id: '180' quality_controlled: '1' series_title: LNCS status: public title: Improved Single Pass Algorithms for Resolution Proof Reduction type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7561 year: '2012' ... --- _id: '3251' abstract: - lang: eng text: Many infinite state systems can be seen as well-structured transition systems (WSTS), i.e., systems equipped with a well-quasi-ordering on states that is also a simulation relation. WSTS are an attractive target for formal analysis because there exist generic algorithms that decide interesting verification problems for this class. Among the most popular algorithms are acceleration-based forward analyses for computing the covering set. Termination of these algorithms can only be guaranteed for flattable WSTS. Yet, many WSTS of practical interest are not flattable and the question whether any given WSTS is flattable is itself undecidable. We therefore propose an analysis that computes the covering set and captures the essence of acceleration-based algorithms, but sacrifices precision for guaranteed termination. Our analysis is an abstract interpretation whose abstract domain builds on the ideal completion of the well-quasi-ordered state space, and a widening operator that mimics acceleration and controls the loss of precision of the analysis. We present instances of our framework for various classes of WSTS. Our experience with a prototype implementation indicates that, despite the inherent precision loss, our analysis often computes the precise covering set of the analyzed system. acknowledgement: This research was supported in part by the European Research Council (ERC) Advanced Investigator Grant QUAREM and by the Austrian Science Fund (FWF) project S11402-N23. alternative_title: - LNCS author: - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 - first_name: Thomas full_name: Wies, Thomas id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Zufferey D, Wies T, Henzinger TA. Ideal abstractions for well structured transition systems. In: Vol 7148. Springer; 2012:445-460. doi:10.1007/978-3-642-27940-9_29' apa: 'Zufferey, D., Wies, T., & Henzinger, T. A. (2012). Ideal abstractions for well structured transition systems (Vol. 7148, pp. 445–460). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_29' chicago: Zufferey, Damien, Thomas Wies, and Thomas A Henzinger. “Ideal Abstractions for Well Structured Transition Systems,” 7148:445–60. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_29. ieee: 'D. Zufferey, T. Wies, and T. A. Henzinger, “Ideal abstractions for well structured transition systems,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 445–460.' ista: 'Zufferey D, Wies T, Henzinger TA. 2012. Ideal abstractions for well structured transition systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 445–460.' mla: Zufferey, Damien, et al. Ideal Abstractions for Well Structured Transition Systems. Vol. 7148, Springer, 2012, pp. 445–60, doi:10.1007/978-3-642-27940-9_29. short: D. Zufferey, T. Wies, T.A. Henzinger, in:, Springer, 2012, pp. 445–460. conference: end_date: 2012-01-24 location: Philadelphia, PA, USA name: 'VMCAI: Verification, Model Checking and Abstract Interpretation' start_date: 2012-01-22 date_created: 2018-12-11T12:02:16Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-09-07T11:36:36Z day: '01' ddc: - '000' - '005' department: - _id: ToHe doi: 10.1007/978-3-642-27940-9_29 ec_funded: 1 file: - access_level: open_access checksum: f2f0d55efa32309ad1fe65a5fcaad90c content_type: application/pdf creator: system date_created: 2018-12-12T10:09:35Z date_updated: 2020-07-14T12:46:05Z file_id: '4759' file_name: IST-2012-100-v1+1_Ideal_abstractions_for_well-structured_transition_systems.pdf file_size: 217104 relation: main_file file_date_updated: 2020-07-14T12:46:05Z has_accepted_license: '1' intvolume: ' 7148' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 445 - 460 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '3406' pubrep_id: '100' quality_controlled: '1' related_material: record: - id: '1405' relation: dissertation_contains status: public status: public title: Ideal abstractions for well structured transition systems type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7148 year: '2012' ... --- _id: '3157' abstract: - lang: eng text: Colorectal tumours that are wild type for KRAS are often sensitive to EGFR blockade, but almost always develop resistance within several months of initiating therapy. The mechanisms underlying this acquired resistance to anti-EGFR antibodies are largely unknown. This situation is in marked contrast to that of small-molecule targeted agents, such as inhibitors of ABL, EGFR, BRAF and MEK, in which mutations in the genes encoding the protein targets render the tumours resistant to the effects of the drugs. The simplest hypothesis to account for the development of resistance to EGFR blockade is that rare cells with KRAS mutations pre-exist at low levels in tumours with ostensibly wild-type KRAS genes. Although this hypothesis would seem readily testable, there is no evidence in pre-clinical models to support it, nor is there data from patients. To test this hypothesis, we determined whether mutant KRAS DNA could be detected in the circulation of 28 patients receiving monotherapy with panitumumab, a therapeutic anti-EGFR antibody. We found that 9 out of 24 (38%) patients whose tumours were initially KRAS wild type developed detectable mutations in KRAS in their sera, three of which developed multiple different KRAS mutations. The appearance of these mutations was very consistent, generally occurring between 5 and 6months following treatment. Mathematical modelling indicated that the mutations were present in expanded subclones before the initiation of panitumumab treatment. These results suggest that the emergence of KRAS mutations is a mediator of acquired resistance to EGFR blockade and that these mutations can be detected in a non-invasive manner. They explain why solid tumours develop resistance to targeted therapies in a highly reproducible fashion. author: - first_name: Luis full_name: Diaz Jr, Luis last_name: Diaz Jr - first_name: Richard full_name: Williams, Richard last_name: Williams - first_name: Jian full_name: Wu, Jian last_name: Wu - first_name: Isaac full_name: Kinde, Isaac last_name: Kinde - first_name: Joel full_name: Hecht, Joel last_name: Hecht - first_name: Jordan full_name: Berlin, Jordan last_name: Berlin - first_name: Benjamin full_name: Allen, Benjamin last_name: Allen - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Martin full_name: Nowak, Martin last_name: Nowak - first_name: Kenneth full_name: Kinzler, Kenneth last_name: Kinzler - first_name: Kelly full_name: Oliner, Kelly last_name: Oliner - first_name: Bert full_name: Vogelstein, Bert last_name: Vogelstein citation: ama: Diaz Jr L, Williams R, Wu J, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 2012;486(7404):537-540. doi:10.1038/nature11219 apa: Diaz Jr, L., Williams, R., Wu, J., Kinde, I., Hecht, J., Berlin, J., … Vogelstein, B. (2012). The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11219 chicago: Diaz Jr, Luis, Richard Williams, Jian Wu, Isaac Kinde, Joel Hecht, Jordan Berlin, Benjamin Allen, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11219. ieee: L. Diaz Jr et al., “The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers,” Nature, vol. 486, no. 7404. Nature Publishing Group, pp. 537–540, 2012. ista: Diaz Jr L, Williams R, Wu J, Kinde I, Hecht J, Berlin J, Allen B, Božić I, Reiter J, Nowak M, Kinzler K, Oliner K, Vogelstein B. 2012. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 486(7404), 537–540. mla: Diaz Jr, Luis, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” Nature, vol. 486, no. 7404, Nature Publishing Group, 2012, pp. 537–40, doi:10.1038/nature11219. short: L. Diaz Jr, R. Williams, J. Wu, I. Kinde, J. Hecht, J. Berlin, B. Allen, I. Božić, J. Reiter, M. Nowak, K. Kinzler, K. Oliner, B. Vogelstein, Nature 486 (2012) 537–540. date_created: 2018-12-11T12:01:43Z date_published: 2012-06-28T00:00:00Z date_updated: 2023-09-07T11:40:43Z day: '28' department: - _id: KrCh doi: 10.1038/nature11219 ec_funded: 1 external_id: pmid: - '22722843' intvolume: ' 486' issue: '7404' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436069/ month: '06' oa: 1 oa_version: Submitted Version page: 537 - 540 pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3537' quality_controlled: '1' related_material: record: - id: '1400' relation: dissertation_contains status: public scopus_import: 1 status: public title: The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 486 year: '2012' ... --- _id: '3260' abstract: - lang: eng text: "Many scenarios in the living world, where individual organisms compete for winning positions (or resources), have properties of auctions. Here we study the evolution of bids in biological auctions. For each auction, n individuals are drawn at random from a population of size N. Each individual makes a bid which entails a cost. The winner obtains a benefit of a certain value. Costs and benefits are translated into reproductive success (fitness). Therefore, successful bidding strategies spread in the population. We compare two types of auctions. In “biological all-pay auctions”, the costs are the bid for every participating individual. In “biological second price all-pay auctions”, the cost for everyone other than the winner is the bid, but the cost for the winner is the second highest bid. Second price all-pay auctions are generalizations of the “war of attrition” introduced by Maynard Smith. We study evolutionary dynamics in both types of auctions. We calculate pairwise invasion plots and evolutionarily stable distributions over the continuous strategy space. We find that the average bid in second price all-pay auctions is higher than in all-pay auctions, but the average cost for the winner is similar in both auctions. In both cases, the average bid is a declining function of the number of participants, n. The more individuals participate in an auction the smaller is the chance of winning, and thus expensive bids must be avoided.\r\n" author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Chatterjee K, Reiter J, Nowak M. Evolutionary dynamics of biological auctions. Theoretical Population Biology. 2012;81(1):69-80. doi:10.1016/j.tpb.2011.11.003 apa: Chatterjee, K., Reiter, J., & Nowak, M. (2012). Evolutionary dynamics of biological auctions. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2011.11.003 chicago: Chatterjee, Krishnendu, Johannes Reiter, and Martin Nowak. “Evolutionary Dynamics of Biological Auctions.” Theoretical Population Biology. Academic Press, 2012. https://doi.org/10.1016/j.tpb.2011.11.003. ieee: K. Chatterjee, J. Reiter, and M. Nowak, “Evolutionary dynamics of biological auctions,” Theoretical Population Biology, vol. 81, no. 1. Academic Press, pp. 69–80, 2012. ista: Chatterjee K, Reiter J, Nowak M. 2012. Evolutionary dynamics of biological auctions. Theoretical Population Biology. 81(1), 69–80. mla: Chatterjee, Krishnendu, et al. “Evolutionary Dynamics of Biological Auctions.” Theoretical Population Biology, vol. 81, no. 1, Academic Press, 2012, pp. 69–80, doi:10.1016/j.tpb.2011.11.003. short: K. Chatterjee, J. Reiter, M. Nowak, Theoretical Population Biology 81 (2012) 69–80. date_created: 2018-12-11T12:02:19Z date_published: 2012-02-01T00:00:00Z date_updated: 2023-09-07T11:40:43Z day: '01' department: - _id: KrCh doi: 10.1016/j.tpb.2011.11.003 ec_funded: 1 external_id: pmid: - '22120126' intvolume: ' 81' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279759/ ' month: '02' oa: 1 oa_version: Submitted Version page: 69 - 80 pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '3388' quality_controlled: '1' related_material: record: - id: '1400' relation: dissertation_contains status: public scopus_import: 1 status: public title: Evolutionary dynamics of biological auctions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 81 year: '2012' ... --- _id: '3258' abstract: - lang: eng text: CA3 pyramidal neurons are important for memory formation and pattern completion in the hippocampal network. It is generally thought that proximal synapses from the mossy fibers activate these neurons most efficiently, whereas distal inputs from the perforant path have a weaker modulatory influence. We used confocally targeted patch-clamp recording from dendrites and axons to map the activation of rat CA3 pyramidal neurons at the subcellular level. Our results reveal two distinct dendritic domains. In the proximal domain, action potentials initiated in the axon backpropagate actively with large amplitude and fast time course. In the distal domain, Na+ channel–mediated dendritic spikes are efficiently initiated by waveforms mimicking synaptic events. CA3 pyramidal neuron dendrites showed a high Na+-to-K+ conductance density ratio, providing ideal conditions for active backpropagation and dendritic spike initiation. Dendritic spikes may enhance the computational power of CA3 pyramidal neurons in the hippocampal network. acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft (TR 3/B10) and the European Union (European Research Council Advanced grant to P.J.). article_processing_charge: No article_type: original author: - first_name: Sooyun full_name: Kim, Sooyun id: 394AB1C8-F248-11E8-B48F-1D18A9856A87 last_name: Kim - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán orcid: 0000-0003-2209-5242 - first_name: Hua full_name: Hu, Hua id: 4AC0145C-F248-11E8-B48F-1D18A9856A87 last_name: Hu - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Kim S, Guzmán J, Hu H, Jonas PM. Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons. Nature Neuroscience. 2012;15(4):600-606. doi:10.1038/nn.3060 apa: Kim, S., Guzmán, J., Hu, H., & Jonas, P. M. (2012). Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3060 chicago: Kim, Sooyun, José Guzmán, Hua Hu, and Peter M Jonas. “Active Dendrites Support Efficient Initiation of Dendritic Spikes in Hippocampal CA3 Pyramidal Neurons.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3060. ieee: S. Kim, J. Guzmán, H. Hu, and P. M. Jonas, “Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons,” Nature Neuroscience, vol. 15, no. 4. Nature Publishing Group, pp. 600–606, 2012. ista: Kim S, Guzmán J, Hu H, Jonas PM. 2012. Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons. Nature Neuroscience. 15(4), 600–606. mla: Kim, Sooyun, et al. “Active Dendrites Support Efficient Initiation of Dendritic Spikes in Hippocampal CA3 Pyramidal Neurons.” Nature Neuroscience, vol. 15, no. 4, Nature Publishing Group, 2012, pp. 600–06, doi:10.1038/nn.3060. short: S. Kim, J. Guzmán, H. Hu, P.M. Jonas, Nature Neuroscience 15 (2012) 600–606. date_created: 2018-12-11T12:02:18Z date_published: 2012-04-01T00:00:00Z date_updated: 2023-09-07T11:43:52Z day: '01' department: - _id: PeJo doi: 10.1038/nn.3060 external_id: pmid: - '22388958' intvolume: ' 15' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617474/ month: '04' oa: 1 oa_version: Published Version page: 600 - 606 pmid: 1 project: - _id: 25BDE9A4-B435-11E9-9278-68D0E5697425 grant_number: SFB-TR3-TP10B name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen publication: Nature Neuroscience publication_identifier: issn: - 1546-1726 publication_status: published publisher: Nature Publishing Group publist_id: '3390' quality_controlled: '1' related_material: record: - id: '2964' relation: dissertation_contains status: public scopus_import: '1' status: public title: Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 15 year: '2012' ...