--- _id: '5407' abstract: - lang: eng text: This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the mandatory features, which need to be fulfilled to provide an institutional repository as a platform and also a service to the scientists at the institute. It also includes optional features, which would be of strong benefit for the scientists and would increase the usage of the repository, and hence the visibility of research at IST Austria. author: - first_name: Jana full_name: Porsche, Jana id: 3252EDC2-F248-11E8-B48F-1D18A9856A87 last_name: Porsche citation: ama: Porsche J. Technical Requirements and Features. IST Austria; 2013. apa: Porsche, J. (2013). Technical requirements and features. IST Austria. chicago: Porsche, Jana. Technical Requirements and Features. IST Austria, 2013. ieee: J. Porsche, Technical requirements and features. IST Austria, 2013. ista: Porsche J. 2013. Technical requirements and features, IST Austria,p. mla: Porsche, Jana. Technical Requirements and Features. IST Austria, 2013. short: J. Porsche, Technical Requirements and Features, IST Austria, 2013. date_created: 2018-12-12T11:39:09Z date_published: 2013-07-13T00:00:00Z date_updated: 2020-07-14T23:07:51Z day: '13' ddc: - '020' department: - _id: E-Lib file: - access_level: open_access checksum: 9e4f9abf79a56f651f0012a34909880f content_type: application/pdf creator: system date_created: 2018-12-12T11:53:02Z date_updated: 2020-07-14T12:46:46Z file_id: '5463' file_name: IST-2013-135-v1+1_Features.pdf file_size: 90311 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication_status: published publisher: IST Austria pubrep_id: '135' status: public title: Technical requirements and features type: report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5410' abstract: - lang: eng text: "Board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in development of mathematical and logical skills, but also in emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. \r\nOur approach generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. Also, the presence of such states for standard game variants like Tic-Tac-Toe on board size 4x4 opens up new games to be played that have not been played for ages since the default start state is heavily biased. " alternative_title: - IST Austria Technical Report author: - first_name: Umair full_name: Ahmed, Umair last_name: Ahmed - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Sumit full_name: Gulwani, Sumit last_name: Gulwani citation: ama: Ahmed U, Chatterjee K, Gulwani S. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-146-v1-1 apa: Ahmed, U., Chatterjee, K., & Gulwani, S. (2013). Automatic generation of alternative starting positions for traditional board games. IST Austria. https://doi.org/10.15479/AT:IST-2013-146-v1-1 chicago: Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-146-v1-1. ieee: U. Ahmed, K. Chatterjee, and S. Gulwani, Automatic generation of alternative starting positions for traditional board games. IST Austria, 2013. ista: Ahmed U, Chatterjee K, Gulwani S. 2013. Automatic generation of alternative starting positions for traditional board games, IST Austria, 13p. mla: Ahmed, Umair, et al. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-146-v1-1. short: U. Ahmed, K. Chatterjee, S. Gulwani, Automatic Generation of Alternative Starting Positions for Traditional Board Games, IST Austria, 2013. date_created: 2018-12-12T11:39:10Z date_published: 2013-12-03T00:00:00Z date_updated: 2023-02-23T10:00:50Z day: '03' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2013-146-v1-1 file: - access_level: open_access checksum: 409f3aaaf1184e4057b89cbb449dac80 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:06Z date_updated: 2020-07-14T12:46:46Z file_id: '5528' file_name: IST-2013-146-v1+1_main.pdf file_size: 818189 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '13' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '146' related_material: record: - id: '1481' relation: later_version status: public status: public title: Automatic generation of alternative starting positions for traditional board games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2327' abstract: - lang: eng text: 'We define the model-measuring problem: given a model M and specification φ, what is the maximal distance ρ such that all models M′ within distance ρ from M satisfy (or violate) φ. The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification. We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved. We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications.' alternative_title: - LNCS author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: Henzinger TA, Otop J. From model checking to model measuring. 2013;8052:273-287. doi:10.1007/978-3-642-40184-8_20 apa: 'Henzinger, T. A., & Otop, J. (2013). From model checking to model measuring. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-40184-8_20' chicago: Henzinger, Thomas A, and Jan Otop. “From Model Checking to Model Measuring.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40184-8_20. ieee: T. A. Henzinger and J. Otop, “From model checking to model measuring,” vol. 8052. Springer, pp. 273–287, 2013. ista: Henzinger TA, Otop J. 2013. From model checking to model measuring. 8052, 273–287. mla: Henzinger, Thomas A., and Jan Otop. From Model Checking to Model Measuring. Vol. 8052, Springer, 2013, pp. 273–87, doi:10.1007/978-3-642-40184-8_20. short: T.A. Henzinger, J. Otop, 8052 (2013) 273–287. conference: end_date: 2013-08-30 location: Buenos Aires, Argentina name: 'CONCUR: Concurrency Theory' start_date: 2013-08-27 date_created: 2018-12-11T11:57:00Z date_published: 2013-08-01T00:00:00Z date_updated: 2023-02-23T12:25:26Z day: '01' ddc: - '005' - '000' department: - _id: ToHe doi: 10.1007/978-3-642-40184-8_20 file: - access_level: open_access checksum: 4c04695c4bfdf2119cd4f5d1babc3e8a content_type: application/pdf creator: system date_created: 2018-12-12T10:17:45Z date_updated: 2020-07-14T12:45:38Z file_id: '5301' file_name: IST-2013-129-v1+1_concur.pdf file_size: 378587 relation: main_file file_date_updated: 2020-07-14T12:45:38Z has_accepted_license: '1' intvolume: ' 8052' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 273 - 287 publication_status: published publisher: Springer publist_id: '4599' pubrep_id: '129' quality_controlled: '1' related_material: record: - id: '5417' relation: earlier_version status: public series_title: Lecture Notes in Computer Science status: public title: From model checking to model measuring type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8052 year: '2013' ... --- _id: '590' abstract: - lang: eng text: We present two methods of creating two orthogonally-polarized focal points at customizable relative locations. These schemes may be critical for enhancing entanglement sources and other applications. alternative_title: - Optics InfoBase Conference Papers author: - first_name: David full_name: Schmid, David last_name: Schmid - first_name: Ting full_name: Huang, Ting-Yu last_name: Huang - first_name: Radhika full_name: Dirks, Radhika last_name: Dirks - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: 'Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. Polarization dependent focusing. In: OSA; 2013. doi:10.1364/QIM.2013.W6.23' apa: 'Schmid, D., Huang, T., Dirks, R., Hosten, O., & Kwiat, P. (2013). Polarization dependent focusing. Presented at the QIM: Quantum Information and Measurement, OSA. https://doi.org/10.1364/QIM.2013.W6.23' chicago: Schmid, David, Ting Huang, Radhika Dirks, Onur Hosten, and Paul Kwiat. “Polarization Dependent Focusing.” OSA, 2013. https://doi.org/10.1364/QIM.2013.W6.23. ieee: 'D. Schmid, T. Huang, R. Dirks, O. Hosten, and P. Kwiat, “Polarization dependent focusing,” presented at the QIM: Quantum Information and Measurement, 2013.' ista: 'Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. 2013. Polarization dependent focusing. QIM: Quantum Information and Measurement, Optics InfoBase Conference Papers, .' mla: Schmid, David, et al. Polarization Dependent Focusing. OSA, 2013, doi:10.1364/QIM.2013.W6.23. short: D. Schmid, T. Huang, R. Dirks, O. Hosten, P. Kwiat, in:, OSA, 2013. conference: name: 'QIM: Quantum Information and Measurement' date_created: 2018-12-11T11:47:22Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T08:05:10Z day: '01' doi: 10.1364/QIM.2013.W6.23 extern: 1 month: '01' publication_status: published publisher: OSA publist_id: '7217' quality_controlled: 0 status: public title: Polarization dependent focusing type: conference year: '2013' ... --- _id: '5920' abstract: - lang: eng text: We study chains of lattice ideals that are invariant under a symmetric group action. In our setting, the ambient rings for these ideals are polynomial rings which are increasing in (Krull) dimension. Thus, these chains will fail to stabilize in the traditional commutative algebra sense. However, we prove a theorem which says that “up to the action of the group”, these chains locally stabilize. We also give an algorithm, which we have implemented in software, for explicitly constructing these stabilization generators for a family of Laurent toric ideals involved in applications to algebraic statistics. We close with several open problems and conjectures arising from our theoretical and computational investigations. article_processing_charge: No article_type: original author: - first_name: Christopher J. full_name: Hillar, Christopher J. last_name: Hillar - first_name: Abraham full_name: Martin del Campo Sanchez, Abraham id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87 last_name: Martin del Campo Sanchez citation: ama: Hillar CJ, Martin del Campo Sanchez A. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. 2013;50:314-334. doi:10.1016/j.jsc.2012.06.006 apa: Hillar, C. J., & Martin del Campo Sanchez, A. (2013). Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2012.06.006 chicago: Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” Journal of Symbolic Computation. Elsevier, 2013. https://doi.org/10.1016/j.jsc.2012.06.006. ieee: C. J. Hillar and A. Martin del Campo Sanchez, “Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals,” Journal of Symbolic Computation, vol. 50. Elsevier, pp. 314–334, 2013. ista: Hillar CJ, Martin del Campo Sanchez A. 2013. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. 50, 314–334. mla: Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” Journal of Symbolic Computation, vol. 50, Elsevier, 2013, pp. 314–34, doi:10.1016/j.jsc.2012.06.006. short: C.J. Hillar, A. Martin del Campo Sanchez, Journal of Symbolic Computation 50 (2013) 314–334. date_created: 2019-02-05T08:48:24Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T08:05:15Z day: '01' doi: 10.1016/j.jsc.2012.06.006 extern: '1' intvolume: ' 50' language: - iso: eng month: '03' oa_version: None page: 314-334 publication: Journal of Symbolic Computation publication_identifier: issn: - 0747-7171 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1016/j.jsc.2015.09.002 status: public title: Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2013' ... --- _id: '591' abstract: - lang: eng text: We present two methods for the precise independent focusing of orthogonal linear polarizations of light at arbitrary relative locations. Our first scheme uses a displaced lens in a polarization Sagnac interferometer to provide adjustable longitudinal and lateral focal displacements via simple geometry; the second uses uniaxial crystals to achieve the same effect in a compact collinear setup. We develop the theoretical applications and limitations of our schemes, and provide experimental confirmation of our calculations. author: - first_name: David full_name: Schmid, David last_name: Schmid - first_name: Ting full_name: Huang, Ting-Yu last_name: Huang - first_name: Shiraz full_name: Hazrat, Shiraz last_name: Hazrat - first_name: Radhika full_name: Dirks, Radhika last_name: Dirks - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Stephan full_name: Quint, Stephan last_name: Quint - first_name: Dickson full_name: Thian, Dickson last_name: Thian - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: Schmid D, Huang T, Hazrat S, et al. Adjustable and robust methods for polarization-dependent focusing. Optics Express. 2013;21(13):15538-15552. doi:10.1364/OE.21.015538 apa: Schmid, D., Huang, T., Hazrat, S., Dirks, R., Hosten, O., Quint, S., … Kwiat, P. (2013). Adjustable and robust methods for polarization-dependent focusing. Optics Express. Optical Society of America. https://doi.org/10.1364/OE.21.015538 chicago: Schmid, David, Ting Huang, Shiraz Hazrat, Radhika Dirks, Onur Hosten, Stephan Quint, Dickson Thian, and Paul Kwiat. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” Optics Express. Optical Society of America, 2013. https://doi.org/10.1364/OE.21.015538. ieee: D. Schmid et al., “Adjustable and robust methods for polarization-dependent focusing,” Optics Express, vol. 21, no. 13. Optical Society of America, pp. 15538–15552, 2013. ista: Schmid D, Huang T, Hazrat S, Dirks R, Hosten O, Quint S, Thian D, Kwiat P. 2013. Adjustable and robust methods for polarization-dependent focusing. Optics Express. 21(13), 15538–15552. mla: Schmid, David, et al. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” Optics Express, vol. 21, no. 13, Optical Society of America, 2013, pp. 15538–52, doi:10.1364/OE.21.015538. short: D. Schmid, T. Huang, S. Hazrat, R. Dirks, O. Hosten, S. Quint, D. Thian, P. Kwiat, Optics Express 21 (2013) 15538–15552. date_created: 2018-12-11T11:47:22Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T08:05:12Z day: '01' doi: 10.1364/OE.21.015538 extern: 1 intvolume: ' 21' issue: '13' month: '07' page: 15538 - 15552 publication: Optics Express publication_status: published publisher: Optical Society of America publist_id: '7218' quality_controlled: 0 status: public title: Adjustable and robust methods for polarization-dependent focusing type: journal_article volume: 21 year: '2013' ... --- _id: '595' article_processing_charge: No author: - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Patrick full_name: Cramer, Patrick last_name: Cramer citation: ama: 'Bernecky C, Cramer P. Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. 2013;32(6):771-772. doi:10.1038/emboj.2013.36' apa: 'Bernecky, C., & Cramer, P. (2013). Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2013.36' chicago: 'Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2013.36.' ieee: 'C. Bernecky and P. Cramer, “Struggling to let go: A non-coding RNA directs its own extension and destruction,” EMBO Journal, vol. 32, no. 6. Wiley-Blackwell, pp. 771–772, 2013.' ista: 'Bernecky C, Cramer P. 2013. Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. 32(6), 771–772.' mla: 'Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” EMBO Journal, vol. 32, no. 6, Wiley-Blackwell, 2013, pp. 771–72, doi:10.1038/emboj.2013.36.' short: C. Bernecky, P. Cramer, EMBO Journal 32 (2013) 771–772. date_created: 2018-12-11T11:47:23Z date_published: 2013-03-20T00:00:00Z date_updated: 2021-01-12T08:05:20Z day: '20' doi: 10.1038/emboj.2013.36 extern: '1' intvolume: ' 32' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604726/ month: '03' oa: 1 oa_version: None page: 771 - 772 publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '7207' status: public title: 'Struggling to let go: A non-coding RNA directs its own extension and destruction' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '6128' abstract: - lang: eng text: Different interoceptive systems must be integrated to ensure that multiple homeostatic insults evoke appropriate behavioral and physiological responses. Little is known about how this is achieved. Using C. elegans, we dissect cross-modulation between systems that monitor temperature, O2 and CO2. CO2 is less aversive to animals acclimated to 15°C than those grown at 22°C. This difference requires the AFD neurons, which respond to both temperature and CO2 changes. CO2 evokes distinct AFD Ca2+ responses in animals acclimated at 15°C or 22°C. Mutants defective in synaptic transmission can reprogram AFD CO2 responses according to temperature experience, suggesting reprogramming occurs cell autonomously. AFD is exquisitely sensitive to CO2. Surprisingly, gradients of 0.01% CO2/second evoke very different Ca2+ responses from gradients of 0.04% CO2/second. Ambient O2 provides further contextual modulation of CO2 avoidance. At 21% O2 tonic signalling from the O2-sensing neuron URX inhibits CO2 avoidance. This inhibition can be graded according to O2 levels. In a natural wild isolate, a switch from 21% to 19% O2 is sufficient to convert CO2 from a neutral to an aversive cue. This sharp tuning is conferred partly by the neuroglobin GLB-5. The modulatory effects of O2 on CO2 avoidance involve the RIA interneurons, which are post-synaptic to URX and exhibit CO2-evoked Ca2+ responses. Ambient O2 and acclimation temperature act combinatorially to modulate CO2 responsiveness. Our work highlights the integrated architecture of homeostatic responses in C. elegans. article_number: e1004011 author: - first_name: Eiji full_name: Kodama-Namba, Eiji last_name: Kodama-Namba - first_name: Lorenz A. full_name: Fenk, Lorenz A. last_name: Fenk - first_name: Andrew J. full_name: Bretscher, Andrew J. last_name: Bretscher - first_name: Einav full_name: Gross, Einav last_name: Gross - first_name: K. Emanuel full_name: Busch, K. Emanuel last_name: Busch - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. 2013;9(12). doi:10.1371/journal.pgen.1004011 apa: Kodama-Namba, E., Fenk, L. A., Bretscher, A. J., Gross, E., Busch, K. E., & de Bono, M. (2013). Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1004011 chicago: Kodama-Namba, Eiji, Lorenz A. Fenk, Andrew J. Bretscher, Einav Gross, K. Emanuel Busch, and Mario de Bono. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” PLoS Genetics. Public Library of Science (PLoS), 2013. https://doi.org/10.1371/journal.pgen.1004011. ieee: E. Kodama-Namba, L. A. Fenk, A. J. Bretscher, E. Gross, K. E. Busch, and M. de Bono, “Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans,” PLoS Genetics, vol. 9, no. 12. Public Library of Science (PLoS), 2013. ista: Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. 2013. Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. 9(12), e1004011. mla: Kodama-Namba, Eiji, et al. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” PLoS Genetics, vol. 9, no. 12, e1004011, Public Library of Science (PLoS), 2013, doi:10.1371/journal.pgen.1004011. short: E. Kodama-Namba, L.A. Fenk, A.J. Bretscher, E. Gross, K.E. Busch, M. de Bono, PLoS Genetics 9 (2013). date_created: 2019-03-19T14:58:51Z date_published: 2013-12-19T00:00:00Z date_updated: 2021-01-12T08:06:15Z day: '19' ddc: - '570' doi: 10.1371/journal.pgen.1004011 extern: '1' external_id: pmid: - '24385919' file: - access_level: open_access checksum: 299b6321be79931c7c17c5db6e69c711 content_type: application/pdf creator: kschuh date_created: 2019-03-19T15:14:51Z date_updated: 2020-07-14T12:47:20Z file_id: '6129' file_name: 2013_PLOS_Kodama-Namba.PDF file_size: 4499039 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 9' issue: '12' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: issn: - 1553-7404 publication_status: published publisher: Public Library of Science (PLoS) quality_controlled: '1' status: public title: Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '6130' abstract: - lang: eng text: 'Cas9 is an RNA-guided double-stranded DNA nuclease that participates in clustered regularly interspaced short palindromic repeats (CRISPR)-mediated adaptive immunity in prokaryotes. CRISPR–Cas9 has recently been used to generate insertion and deletion mutations in Caenorhabditis elegans, but not to create tailored changes (knock-ins). We show that the CRISPR–CRISPR-associated (Cas) system can be adapted for efficient and precise editing of the C. elegans genome. The targeted double-strand breaks generated by CRISPR are substrates for transgene-instructed gene conversion. This allows customized changes in the C. elegans genome by homologous recombination: sequences contained in the repair template (the transgene) are copied by gene conversion into the genome. The possibility to edit the C. elegans genome at selected locations will facilitate the systematic study of gene function in this widely used model organism.' article_number: e193 author: - first_name: Changchun full_name: Chen, Changchun last_name: Chen - first_name: Lorenz A. full_name: Fenk, Lorenz A. last_name: Fenk - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Chen C, Fenk LA, de Bono M. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. 2013;41(20). doi:10.1093/nar/gkt805 apa: Chen, C., Fenk, L. A., & de Bono, M. (2013). Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkt805 chicago: Chen, Changchun, Lorenz A. Fenk, and Mario de Bono. “Efficient Genome Editing in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” Nucleic Acids Research. Oxford University Press, 2013. https://doi.org/10.1093/nar/gkt805. ieee: C. Chen, L. A. Fenk, and M. de Bono, “Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination,” Nucleic Acids Research, vol. 41, no. 20. Oxford University Press, 2013. ista: Chen C, Fenk LA, de Bono M. 2013. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. 41(20), e193. mla: Chen, Changchun, et al. “Efficient Genome Editing in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” Nucleic Acids Research, vol. 41, no. 20, e193, Oxford University Press, 2013, doi:10.1093/nar/gkt805. short: C. Chen, L.A. Fenk, M. de Bono, Nucleic Acids Research 41 (2013). date_created: 2019-03-19T15:17:40Z date_published: 2013-11-01T00:00:00Z date_updated: 2021-01-12T08:06:16Z day: '01' ddc: - '570' doi: 10.1093/nar/gkt805 extern: '1' external_id: pmid: - '24013562' file: - access_level: open_access checksum: 0f1f127cefd043cb922b292e1cd16f02 content_type: application/pdf creator: kschuh date_created: 2019-03-19T15:25:42Z date_updated: 2020-07-14T12:47:20Z file_id: '6131' file_name: 2013_OUP_Chen.pdf file_size: 340225 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 41' issue: '20' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Nucleic Acids Research publication_identifier: issn: - 1362-4962 - 0305-1048 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination 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: 41 year: '2013' ... --- _id: '6133' abstract: - lang: eng text: cGMP signaling is widespread in the nervous system. However, it has proved difficult to visualize and genetically probe endogenously evoked cGMP dynamics in neurons in vivo. Here, we combine cGMP and Ca2+ biosensors to image and dissect a cGMP signaling network in a Caenorhabditis elegans oxygen-sensing neuron. We show that a rise in O2 can evoke a tonic increase in cGMP that requires an atypical O2-binding soluble guanylate cyclase and that is sustained until oxygen levels fall. Increased cGMP leads to a sustained Ca2+ response in the neuron that depends on cGMP-gated ion channels. Elevated levels of cGMP and Ca2+ stimulate competing negative feedback loops that shape cGMP dynamics. Ca2+-dependent negative feedback loops, including activation of phosphodiesterase-1 (PDE-1), dampen the rise of cGMP. A different negative feedback loop, mediated by phosphodiesterase-2 (PDE-2) and stimulated by cGMP-dependent kinase (PKG), unexpectedly promotes cGMP accumulation following a rise in O2, apparently by keeping in check gating of cGMP channels and limiting activation of Ca2+-dependent negative feedback loops. Simultaneous imaging of Ca2+ and cGMP suggests that cGMP levels can rise close to cGMP channels while falling elsewhere. O2-evoked cGMP and Ca2+ responses are highly reproducible when the same neuron in an individual animal is stimulated repeatedly, suggesting that cGMP transduction has high intrinsic reliability. However, responses vary substantially across individuals, despite animals being genetically identical and similarly reared. This variability may reflect stochastic differences in expression of cGMP signaling components. Our work provides in vivo insights into the architecture of neuronal cGMP signaling. author: - first_name: A. full_name: Couto, A. last_name: Couto - first_name: S. full_name: Oda, S. last_name: Oda - first_name: V. O. full_name: Nikolaev, V. O. last_name: Nikolaev - first_name: Z. full_name: Soltesz, Z. last_name: Soltesz - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings of the National Academy of Sciences. 2013;110(35):E3301-E3310. doi:10.1073/pnas.1217428110 apa: Couto, A., Oda, S., Nikolaev, V. O., Soltesz, Z., & de Bono, M. (2013). In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1217428110 chicago: Couto, A., S. Oda, V. O. Nikolaev, Z. Soltesz, and Mario de Bono. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1217428110. ieee: A. Couto, S. Oda, V. O. Nikolaev, Z. Soltesz, and M. de Bono, “In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor,” Proceedings of the National Academy of Sciences, vol. 110, no. 35. Proceedings of the National Academy of Sciences, pp. E3301–E3310, 2013. ista: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. 2013. In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings of the National Academy of Sciences. 110(35), E3301–E3310. mla: Couto, A., et al. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” Proceedings of the National Academy of Sciences, vol. 110, no. 35, Proceedings of the National Academy of Sciences, 2013, pp. E3301–10, doi:10.1073/pnas.1217428110. short: A. Couto, S. Oda, V.O. Nikolaev, Z. Soltesz, M. de Bono, Proceedings of the National Academy of Sciences 110 (2013) E3301–E3310. date_created: 2019-03-20T14:05:06Z date_published: 2013-08-27T00:00:00Z date_updated: 2021-01-12T08:06:16Z day: '27' ddc: - '570' doi: 10.1073/pnas.1217428110 extern: '1' external_id: pmid: - '23940325' file: - access_level: open_access checksum: 3ee28a694f74a49f0d098970ae391a91 content_type: application/pdf creator: kschuh date_created: 2019-03-20T14:07:53Z date_updated: 2020-07-14T12:47:20Z file_id: '6134' file_name: 2013_PNAS_Couto.pdf file_size: 2198763 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 110' issue: '35' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: E3301-E3310 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '6135' abstract: - lang: eng text: Many organisms have stress response pathways, components of which share homology with players in complex human disease pathways. Research on stress response in the nematode worm Caenorhabditis elegans has provided detailed insights into the genetic and molecular mechanisms underlying complex human diseases. In this review we focus on four different types of environmental stress responses – heat shock, oxidative stress, hypoxia, and osmotic stress – and on how these can be used to study the genetics of complex human diseases. All four types of responses involve the genetic machineries that underlie a number of complex human diseases such as cancer and neurodegenerative diseases, including Alzheimer's and Parkinson's. We highlight the types of stress response experiments required to detect the genes and pathways underlying human disease and suggest that studying stress biology in worms can be translated to understanding human disease and provide potential targets for drug discovery. author: - first_name: Miriam full_name: Rodriguez, Miriam last_name: Rodriguez - first_name: L. Basten full_name: Snoek, L. Basten last_name: Snoek - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: Jan E. full_name: Kammenga, Jan E. last_name: Kammenga citation: ama: 'Rodriguez M, Snoek LB, de Bono M, Kammenga JE. Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. 2013;29(6):367-374. doi:10.1016/j.tig.2013.01.010' apa: 'Rodriguez, M., Snoek, L. B., de Bono, M., & Kammenga, J. E. (2013). Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2013.01.010' chicago: 'Rodriguez, Miriam, L. Basten Snoek, Mario de Bono, and Jan E. Kammenga. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” Trends in Genetics. Elsevier, 2013. https://doi.org/10.1016/j.tig.2013.01.010.' ieee: 'M. Rodriguez, L. B. Snoek, M. de Bono, and J. E. Kammenga, “Worms under stress: C. elegans stress response and its relevance to complex human disease and aging,” Trends in Genetics, vol. 29, no. 6. Elsevier, pp. 367–374, 2013.' ista: 'Rodriguez M, Snoek LB, de Bono M, Kammenga JE. 2013. Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. 29(6), 367–374.' mla: 'Rodriguez, Miriam, et al. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” Trends in Genetics, vol. 29, no. 6, Elsevier, 2013, pp. 367–74, doi:10.1016/j.tig.2013.01.010.' short: M. Rodriguez, L.B. Snoek, M. de Bono, J.E. Kammenga, Trends in Genetics 29 (2013) 367–374. date_created: 2019-03-20T14:17:42Z date_published: 2013-06-01T00:00:00Z date_updated: 2021-01-12T08:06:17Z day: '01' doi: 10.1016/j.tig.2013.01.010 extern: '1' intvolume: ' 29' issue: '6' language: - iso: eng month: '06' oa_version: None page: 367-374 publication: Trends in Genetics publication_identifier: issn: - 0168-9525 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Worms under stress: C. elegans stress response and its relevance to complex human disease and aging' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2013' ... --- _id: '6132' author: - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: W.R. full_name: Schafer, W.R. last_name: Schafer - first_name: A. full_name: Gottschalk, A. last_name: Gottschalk citation: ama: 'de Bono M, Schafer WR, Gottschalk A. Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In: Hegemann P, Sigrist S, eds. Optogenetics. Walter de Gruyter; 2013:61-78.' apa: de Bono, M., Schafer, W. R., & Gottschalk, A. (2013). Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In P. Hegemann & S. Sigrist (Eds.), Optogenetics (pp. 61–78). Walter de Gruyter. chicago: Bono, Mario de, W.R. Schafer, and A. Gottschalk. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” In Optogenetics, edited by Peter Hegemann and Stephan Sigrist, 61–78. Walter de Gruyter, 2013. ieee: M. de Bono, W. R. Schafer, and A. Gottschalk, “Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans,” in Optogenetics, P. Hegemann and S. Sigrist, Eds. Walter de Gruyter, 2013, pp. 61–78. ista: 'de Bono M, Schafer WR, Gottschalk A. 2013.Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In: Optogenetics. , 61–78.' mla: de Bono, Mario, et al. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” Optogenetics, edited by Peter Hegemann and Stephan Sigrist, Walter de Gruyter, 2013, pp. 61–78. short: M. de Bono, W.R. Schafer, A. Gottschalk, in:, P. Hegemann, S. Sigrist (Eds.), Optogenetics, Walter de Gruyter, 2013, pp. 61–78. date_created: 2019-03-20T13:54:05Z date_published: 2013-08-28T00:00:00Z date_updated: 2021-01-12T08:06:16Z day: '28' editor: - first_name: Peter full_name: Hegemann, Peter last_name: Hegemann - first_name: Stephan full_name: Sigrist, Stephan last_name: Sigrist extern: '1' language: - iso: eng month: '08' oa_version: None page: 61-78 publication: Optogenetics publication_identifier: isbn: - 9783110270723; 9783110270716 publication_status: published publisher: Walter de Gruyter quality_controlled: '1' status: public title: Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '6370' abstract: - lang: eng text: 'The molecular and supramolecular origins of the superior nonlinear optical (NLO) properties observed in the organic phenolic triene material, OH1 (2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene)malononitrile), are presented. The molecular charge-transfer distribution is topographically mapped, demonstrating that a uniformly delocalized passive electronic medium facilitates the charge-transfer between the phenolic electron donor and the cyano electron acceptors which lie at opposite ends of the molecule. Its ability to act as a “push–pull” π-conjugated molecule is quantified, relative to similar materials, by supporting empirical calculations; these include bond-length alternation and harmonic-oscillator stabilization energy (HOSE) tests. Such tests, together with frontier molecular orbital considerations, reveal that OH1 can exist readily in its aromatic (neutral) or quinoidal (charge-separated) state, thereby overcoming the “nonlinearity-thermal stability trade-off”. The HOSE calculation also reveals a correlation between the quinoidal resonance contribution to the overall structure of OH1 and the UV–vis absorption peak wavelength in the wider family of configurationally locked polyene framework materials. Solid-state tensorial coefficients of the molecular dipole, polarizability, and the first hyperpolarizability for OH1 are derived from the first-, second-, and third-order electronic moments of the experimental charge-density distribution. The overall solid-state molecular dipole moment is compared with those from gas-phase calculations, revealing that crystal field effects are very significant in OH1. The solid-state hyperpolarizability derived from this charge-density study affords good agreement with gas-phase calculations as well as optical measurements based on hyper-Rayleigh scattering (HRS) and electric-field-induced second harmonic (EFISH) generation. This lends support to the further use of charge-density studies to calculate solid-state hyperpolarizability coefficients in other organic NLO materials. Finally, this charge-density study is also employed to provide an advanced classification of hydrogen bonds in OH1, which requires more stringent criteria than those from conventional structure analysis. As a result, only the strongest OH···NC interaction is so classified as a true hydrogen bond. Indeed, it is this electrostatic interaction that influences the molecular charge transfer: the other four, weaker, nonbonded contacts nonetheless affect the crystal packing. Overall, the establishment of these structure–property relationships lays a blueprint for designing further, more NLO efficient, materials in this industrially leading organic family of compounds.' author: - first_name: Tze-Chia full_name: Lin, Tze-Chia last_name: Lin - first_name: Jacqueline M. full_name: Cole, Jacqueline M. last_name: Cole - 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: Alison J. full_name: Edwards, Alison J. last_name: Edwards - first_name: Ross O. full_name: Piltz, Ross O. last_name: Piltz - first_name: Javier full_name: Pérez-Moreno, Javier last_name: Pérez-Moreno - first_name: Ji-Youn full_name: Seo, Ji-Youn last_name: Seo - first_name: Seung-Chul full_name: Lee, Seung-Chul last_name: Lee - first_name: Koen full_name: Clays, Koen last_name: Clays - first_name: O-Pil full_name: Kwon, O-Pil last_name: Kwon citation: ama: 'Lin T-C, Cole JM, Higginbotham AP, et al. Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical Chemistry C. 2013;117(18):9416-9430. doi:10.1021/jp400648q' apa: 'Lin, T.-C., Cole, J. M., Higginbotham, A. P., Edwards, A. J., Piltz, R. O., Pérez-Moreno, J., … Kwon, O.-P. (2013). Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical Chemistry C. American Chemical Society (ACS). https://doi.org/10.1021/jp400648q' chicago: 'Lin, Tze-Chia, Jacqueline M. Cole, Andrew P Higginbotham, Alison J. Edwards, Ross O. Piltz, Javier Pérez-Moreno, Ji-Youn Seo, Seung-Chul Lee, Koen Clays, and O-Pil Kwon. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding, and Ab Initio Calculations.” The Journal of Physical Chemistry C. American Chemical Society (ACS), 2013. https://doi.org/10.1021/jp400648q.' ieee: 'T.-C. Lin et al., “Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations,” The Journal of Physical Chemistry C, vol. 117, no. 18. American Chemical Society (ACS), pp. 9416–9430, 2013.' ista: 'Lin T-C, Cole JM, Higginbotham AP, Edwards AJ, Piltz RO, Pérez-Moreno J, Seo J-Y, Lee S-C, Clays K, Kwon O-P. 2013. Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical Chemistry C. 117(18), 9416–9430.' mla: 'Lin, Tze-Chia, et al. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding, and Ab Initio Calculations.” The Journal of Physical Chemistry C, vol. 117, no. 18, American Chemical Society (ACS), 2013, pp. 9416–30, doi:10.1021/jp400648q.' short: T.-C. Lin, J.M. Cole, A.P. Higginbotham, A.J. Edwards, R.O. Piltz, J. Pérez-Moreno, J.-Y. Seo, S.-C. Lee, K. Clays, O.-P. Kwon, The Journal of Physical Chemistry C 117 (2013) 9416–9430. date_created: 2019-05-03T09:40:31Z date_published: 2013-05-09T00:00:00Z date_updated: 2021-01-12T08:07:17Z day: '09' doi: 10.1021/jp400648q extern: '1' intvolume: ' 117' issue: '18' language: - iso: eng month: '05' oa_version: None page: 9416-9430 publication: The Journal of Physical Chemistry C publication_identifier: issn: - 1932-7447 - 1932-7455 publication_status: published publisher: American Chemical Society (ACS) quality_controlled: '1' status: public title: 'Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2013' ... --- _id: '6440' abstract: - lang: eng text: In order to guarantee that each method of a data structure updates the logical state exactly once, al-most all non-blocking implementations employ Compare-And-Swap (CAS) based synchronization. For FIFO queue implementations this translates into concurrent enqueue or dequeue methods competing among themselves to update the same variable, the tail or the head, respectively, leading to high contention and poor scalability. Recent non-blocking queue implementations try to alleviate high contentionby increasing the number of contention points, all the while using CAS-based synchronization. Furthermore, obtaining a wait-free implementation with competition is achieved by additional synchronization which leads to further degradation of performance.In this paper we formalize the notion of competitiveness of a synchronizing statement which can beused as a measure for the scalability of concurrent implementations. We present a new queue implementation, the Speculative Pairing (SP) queue, which, as we show, decreases competitiveness by using Fetch-And-Increment (FAI) instead of CAS. We prove that the SP queue is linearizable and lock-free.We also show that replacing CAS with FAI leads to wait-freedom for dequeue methods without an adverse effect on performance. In fact, our experiments suggest that the SP queue can perform and scale better than the state-of-the-art queue implementations. alternative_title: - IST Austria Technical Report author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Hannes full_name: Payer, Hannes last_name: Payer - first_name: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin citation: ama: Henzinger TA, Payer H, Sezgin A. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria; 2013. doi:10.15479/AT:IST-2013-124-v1-1 apa: Henzinger, T. A., Payer, H., & Sezgin, A. (2013). Replacing competition with cooperation to achieve scalable lock-free FIFO queues . IST Austria. https://doi.org/10.15479/AT:IST-2013-124-v1-1 chicago: Henzinger, Thomas A, Hannes Payer, and Ali Sezgin. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-124-v1-1. ieee: T. A. Henzinger, H. Payer, and A. Sezgin, Replacing competition with cooperation to achieve scalable lock-free FIFO queues . IST Austria, 2013. ista: Henzinger TA, Payer H, Sezgin A. 2013. Replacing competition with cooperation to achieve scalable lock-free FIFO queues , IST Austria, 23p. mla: Henzinger, Thomas A., et al. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria, 2013, doi:10.15479/AT:IST-2013-124-v1-1. short: T.A. Henzinger, H. Payer, A. Sezgin, Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues , IST Austria, 2013. date_created: 2019-05-13T14:13:27Z date_published: 2013-06-13T00:00:00Z date_updated: 2020-07-14T23:06:19Z day: '13' ddc: - '000' - '005' department: - _id: ToHe doi: 10.15479/AT:IST-2013-124-v1-1 file: - access_level: open_access checksum: a219ba4eada6cd62befed52262ee15d4 content_type: application/pdf creator: dernst date_created: 2019-05-13T14:11:39Z date_updated: 2020-07-14T12:47:30Z file_id: '6441' file_name: 2013_TechRep_Henzinger.pdf file_size: 549684 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '23' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '124' status: public title: 'Replacing competition with cooperation to achieve scalable lock-free FIFO queues ' type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '6768' abstract: - lang: eng text: The paper presents an algorithm that applies a stack filter simulating the Mean Curvature Motion equation via a finite difference scheme. article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: Mondelli M. A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. 2013;3:68-111. doi:10.5201/ipol.2013.53 apa: Mondelli, M. (2013). A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. Image Processing On Line. https://doi.org/10.5201/ipol.2013.53 chicago: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” Image Processing On Line. Image Processing On Line, 2013. https://doi.org/10.5201/ipol.2013.53. ieee: M. Mondelli, “A finite difference scheme for the stack filter simulating the MCM,” Image Processing On Line, vol. 3. Image Processing On Line, pp. 68–111, 2013. ista: Mondelli M. 2013. A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. 3, 68–111. mla: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” Image Processing On Line, vol. 3, Image Processing On Line, 2013, pp. 68–111, doi:10.5201/ipol.2013.53. short: M. Mondelli, Image Processing On Line 3 (2013) 68–111. date_created: 2019-08-05T12:30:38Z date_published: 2013-07-11T00:00:00Z date_updated: 2021-01-12T08:08:56Z day: '11' ddc: - '510' doi: 10.5201/ipol.2013.53 extern: '1' file: - access_level: open_access checksum: 83b7d429bc248c6c461229d3504fb139 content_type: application/pdf creator: dernst date_created: 2019-08-05T12:33:40Z date_updated: 2020-07-14T12:47:40Z file_id: '6769' file_name: 2013_IPOL_Mondelli.pdf file_size: 4306158 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '07' oa: 1 oa_version: Published Version page: 68-111 publication: Image Processing On Line publication_identifier: issn: - 2105-1232 publication_status: published publisher: Image Processing On Line quality_controlled: '1' status: public title: A finite difference scheme for the stack filter simulating the MCM 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2013' ... --- _id: '2329' abstract: - lang: eng text: 'Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work, we consider both finite-state game graphs, and recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion. The objectives we study are multidimensional mean-payoff objectives, where the goal of player 1 is to ensure that the mean-payoff is non-negative in all dimensions. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation. Our main contributions are as follows: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of the weights are fixed; whereas if the number of dimensions is arbitrary, then the problem is known to be coNP-complete. (2) We show that pushdown graphs with multidimensional mean-payoff objectives can be solved in polynomial time. For both (1) and (2) our algorithms are based on hyperplane separation technique. (3) For pushdown games under global strategies both one and multidimensional mean-payoff objectives problems are known to be undecidable, and we show that under modular strategies the multidimensional problem is also undecidable; under modular strategies the one-dimensional problem is NP-complete. We show that if the number of modules, the number of exits, and the maximal absolute value of the weights are fixed, then pushdown games under modular strategies with one-dimensional mean-payoff objectives can be solved in polynomial time, and if either the number of exits or the number of modules is unbounded, then the problem is NP-hard. (4) Finally we show that a fixed parameter tractable algorithm for finite-state multidimensional mean-payoff games or pushdown games under modular strategies with one-dimensional mean-payoff objectives would imply the fixed parameter tractability of parity games.' alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. 2013;8052:500-515. doi:10.1007/978-3-642-40184-8_35 apa: 'Chatterjee, K., & Velner, Y. (2013). Hyperplane separation technique for multidimensional mean-payoff games. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentinia: Springer. https://doi.org/10.1007/978-3-642-40184-8_35' chicago: Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40184-8_35. ieee: K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” vol. 8052. Springer, pp. 500–515, 2013. ista: Chatterjee K, Velner Y. 2013. Hyperplane separation technique for multidimensional mean-payoff games. 8052, 500–515. mla: Chatterjee, Krishnendu, and Yaron Velner. Hyperplane Separation Technique for Multidimensional Mean-Payoff Games. Vol. 8052, Springer, 2013, pp. 500–15, doi:10.1007/978-3-642-40184-8_35. short: K. Chatterjee, Y. Velner, 8052 (2013) 500–515. conference: end_date: 2013-08-30 location: Buenos Aires, Argentinia name: 'CONCUR: Concurrency Theory' start_date: 2013-08-27 date_created: 2018-12-11T11:57:01Z date_published: 2013-08-01T00:00:00Z date_updated: 2023-02-23T13:00:42Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-40184-8_35 ec_funded: 1 external_id: arxiv: - '1210.3141' intvolume: ' 8052' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1210.3141 month: '08' oa: 1 oa_version: Preprint page: 500 - 515 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _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_status: published publisher: Springer publist_id: '4597' quality_controlled: '1' related_material: record: - id: '717' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Hyperplane separation technique for multidimensional mean-payoff games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8052 year: '2013' ... --- _id: '7306' abstract: - lang: eng text: Rechargeable lithium–air (O2) batteries are receiving intense interest because their high theoretical specific energy exceeds that of lithium-ion batteries. If the Li–O2 battery is ever to succeed, highly reversible formation/decomposition of Li2O2 must take place at the cathode on cycling. However, carbon, used ubiquitously as the basis of the cathode, decomposes during Li2O2 oxidation on charge and actively promotes electrolyte decomposition on cycling. Replacing carbon with a nanoporous gold cathode, when in contact with a dimethyl sulphoxide-based electrolyte, does seem to demonstrate better stability. However, nanoporous gold is not a suitable cathode; its high mass destroys the key advantage of Li–O2 over Li ion (specific energy), it is too expensive and too difficult to fabricate. Identifying a suitable cathode material for the Li–O2 cell is one of the greatest challenges at present. Here we show that a TiC-based cathode reduces greatly side reactions (arising from the electrolyte and electrode degradation) compared with carbon and exhibits better reversible formation/decomposition of Li2O2 even than nanoporous gold (>98% capacity retention after 100 cycles, compared with 95% for nanoporous gold); it is also four times lighter, of lower cost and easier to fabricate. The stability may originate from the presence of TiO2 (along with some TiOC) on the surface of TiC. In contrast to carbon or nanoporous gold, TiC seems to represent a more viable, stable, cathode for aprotic Li–O2 cells. article_processing_charge: No article_type: original author: - first_name: Muhammed M. full_name: Ottakam Thotiyl, Muhammed M. last_name: Ottakam Thotiyl - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Zhangquan full_name: Peng, Zhangquan last_name: Peng - first_name: Yuhui full_name: Chen, Yuhui last_name: Chen - first_name: Zheng full_name: Liu, Zheng last_name: Liu - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. A stable cathode for the aprotic Li–O2 battery. Nature Materials. 2013;12(11):1050-1056. doi:10.1038/nmat3737 apa: Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., Chen, Y., Liu, Z., & Bruce, P. G. (2013). A stable cathode for the aprotic Li–O2 battery. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat3737 chicago: Ottakam Thotiyl, Muhammed M., Stefan Alexander Freunberger, Zhangquan Peng, Yuhui Chen, Zheng Liu, and Peter G. Bruce. “A Stable Cathode for the Aprotic Li–O2 Battery.” Nature Materials. Springer Nature, 2013. https://doi.org/10.1038/nmat3737. ieee: M. M. Ottakam Thotiyl, S. A. Freunberger, Z. Peng, Y. Chen, Z. Liu, and P. G. Bruce, “A stable cathode for the aprotic Li–O2 battery,” Nature Materials, vol. 12, no. 11. Springer Nature, pp. 1050–1056, 2013. ista: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. 2013. A stable cathode for the aprotic Li–O2 battery. Nature Materials. 12(11), 1050–1056. mla: Ottakam Thotiyl, Muhammed M., et al. “A Stable Cathode for the Aprotic Li–O2 Battery.” Nature Materials, vol. 12, no. 11, Springer Nature, 2013, pp. 1050–56, doi:10.1038/nmat3737. short: M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, Y. Chen, Z. Liu, P.G. Bruce, Nature Materials 12 (2013) 1050–1056. date_created: 2020-01-15T12:18:29Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T08:12:55Z day: '01' doi: 10.1038/nmat3737 extern: '1' intvolume: ' 12' issue: '11' language: - iso: eng month: '09' oa_version: None page: 1050-1056 publication: Nature Materials publication_identifier: issn: - 1476-1122 - 1476-4660 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: A stable cathode for the aprotic Li–O2 battery type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2013' ... --- _id: '7307' abstract: - lang: eng text: The non-aqueous Li–air (O2) battery is receiving intense interest because its theoretical specific energy exceeds that of Li-ion batteries. Recharging the Li–O2 battery depends on oxidizing solid lithium peroxide (Li2O2), which is formed on discharge within the porous cathode. However, transporting charge between Li2O2 particles and the solid electrode surface is at best very difficult and leads to voltage polarization on charging, even at modest rates. This is a significant problem facing the non-aqueous Li–O2 battery. Here we show that incorporation of a redox mediator, tetrathiafulvalene (TTF), enables recharging at rates that are impossible for the cell in the absence of the mediator. On charging, TTF is oxidized to TTF+ at the cathode surface; TTF+ in turn oxidizes the solid Li2O2, which results in the regeneration of TTF. The mediator acts as an electron–hole transfer agent that permits efficient oxidation of solid Li2O2. The cell with the mediator demonstrated 100 charge/discharge cycles. article_processing_charge: No article_type: original author: - first_name: Yuhui full_name: Chen, Yuhui last_name: Chen - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Zhangquan full_name: Peng, Zhangquan last_name: Peng - first_name: Olivier full_name: Fontaine, Olivier last_name: Fontaine - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. Charging a Li–O2 battery using a redox mediator. Nature Chemistry. 2013;5(6):489-494. doi:10.1038/nchem.1646 apa: Chen, Y., Freunberger, S. A., Peng, Z., Fontaine, O., & Bruce, P. G. (2013). Charging a Li–O2 battery using a redox mediator. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.1646 chicago: Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Olivier Fontaine, and Peter G. Bruce. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature Chemistry. Springer Nature, 2013. https://doi.org/10.1038/nchem.1646. ieee: Y. Chen, S. A. Freunberger, Z. Peng, O. Fontaine, and P. G. Bruce, “Charging a Li–O2 battery using a redox mediator,” Nature Chemistry, vol. 5, no. 6. Springer Nature, pp. 489–494, 2013. ista: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. 2013. Charging a Li–O2 battery using a redox mediator. Nature Chemistry. 5(6), 489–494. mla: Chen, Yuhui, et al. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature Chemistry, vol. 5, no. 6, Springer Nature, 2013, pp. 489–94, doi:10.1038/nchem.1646. short: Y. Chen, S.A. Freunberger, Z. Peng, O. Fontaine, P.G. Bruce, Nature Chemistry 5 (2013) 489–494. date_created: 2020-01-15T12:18:43Z date_published: 2013-05-12T00:00:00Z date_updated: 2021-01-12T08:12:56Z day: '12' doi: 10.1038/nchem.1646 extern: '1' intvolume: ' 5' issue: '6' language: - iso: eng month: '05' oa_version: None page: 489-494 publication: Nature Chemistry publication_identifier: issn: - 1755-4330 - 1755-4349 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Charging a Li–O2 battery using a redox mediator type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2013' ... --- _id: '7596' abstract: - lang: eng text: Casein kinase1 (CK1) plays crucial roles in regulating growth and development via phosphorylating various substrates throughout the eukaryote kingdom. Blue light is crucial for normal growth of both plants and animals, and blue light receptor cryptochrome2 (CRY2) undergoes blue light–dependent phosphorylation and degradation in planta. To study the function of plant CK1s, systematic genetic analysis showed that deficiency of two paralogous Arabidopsis thaliana CK1s, CK1.3 and CK1.4, caused shortened hypocotyls, especially under blue light, while overexpression of either CK1.3 or CK1.4 resulted in the insensitive response to blue light and delayed flowering under long-day conditions. CK1.3 or CK1.4 act dependently on CRY2, and overexpression of CK1.3 or CK1.4 significantly suppresses the hypersensitive response to blue light by CRY2 overexpression. Biochemical studies showed that CK1.3 and CK1.4 directly phosphorylate CRY2 at Ser-587 and Thr-603 in vitro and negatively regulate CRY2 stability in planta, which are stimulated by blue light, further confirming the crucial roles of CK1.3 and CK1.4 in blue light responses through phosphorylating CRY2. Interestingly, expression of CK1.3 and CK1.4 is stimulated by blue light and feedback regulated by CRY2-mediated signaling. These results provide direct evidence for CRY2 phosphorylation and informative clues on the mechanisms of CRY2-mediated light responses. article_processing_charge: No article_type: original author: - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: C. full_name: Dai, C. last_name: Dai - first_name: H.-T. full_name: Liu, H.-T. last_name: Liu - first_name: H.-W. full_name: Xue, H.-W. last_name: Xue citation: ama: Tan S, Dai C, Liu H-T, Xue H-W. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. 2013;25(7):2618-2632. doi:10.1105/tpc.113.114322 apa: Tan, S., Dai, C., Liu, H.-T., & Xue, H.-W. (2013). Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114322 chicago: Tan, Shutang, C. Dai, H.-T. Liu, and H.-W. Xue. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” The Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114322. ieee: S. Tan, C. Dai, H.-T. Liu, and H.-W. Xue, “Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling,” The Plant Cell, vol. 25, no. 7. American Society of Plant Biologists, pp. 2618–2632, 2013. ista: Tan S, Dai C, Liu H-T, Xue H-W. 2013. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. 25(7), 2618–2632. mla: Tan, Shutang, et al. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” The Plant Cell, vol. 25, no. 7, American Society of Plant Biologists, 2013, pp. 2618–32, doi:10.1105/tpc.113.114322. short: S. Tan, C. Dai, H.-T. Liu, H.-W. Xue, The Plant Cell 25 (2013) 2618–2632. date_created: 2020-03-21T16:06:55Z date_published: 2013-08-26T00:00:00Z date_updated: 2021-01-12T08:14:24Z day: '26' doi: 10.1105/tpc.113.114322 extern: '1' external_id: pmid: - '23897926' intvolume: ' 25' issue: '7' language: - iso: eng month: '08' oa_version: None page: 2618-2632 pmid: 1 publication: The Plant Cell publication_identifier: issn: - 1040-4651 - 1532-298X publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' status: public title: Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '7595' abstract: - lang: eng text: Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK) phosphorylates inositol 1,3,4-trisphosphate to form inositol 1,3,4,5-tetrakisphosphate and inositol 1,3,4,6-tetrakisphosphate which can be finally transferred to inositol hexaphosphate (IP6) and play important roles during plant growth and development. There are 4 putative ITPK members in Arabidopsis. Expression pattern analysis showed that ITPK2 is constitutively expressed in various tissues. A T-DNA knockout mutant of ITPK2 was identified and scanning electron microscopy (SEM) analysis showed that the epidermis structure of seed coat was irregularly formed in seeds of itpk2-1 mutant, resulting in the increased permeability of seed coat to tetrazolium salts. Further analysis by gas chromatography coupled with mass spectrometry of lipid polyester monomers in cell wall confirmed a dramatic decrease in composition of suberin and cutin, which relate to the permeability of seed coat and the formation of which is accompanied with seed coat development. These results indicate that ITPK2 plays an essential role in seed coat development and lipid polyester barrier formation. article_processing_charge: No article_type: original author: - first_name: Yong full_name: Tang, Yong last_name: Tang - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Hongwei full_name: Xue, Hongwei last_name: Xue citation: ama: Tang Y, Tan S, Xue H. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 2013;45(7):549-560. doi:10.1093/abbs/gmt039 apa: Tang, Y., Tan, S., & Xue, H. (2013). Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. Oxford University Press. https://doi.org/10.1093/abbs/gmt039 chicago: Tang, Yong, Shutang Tan, and Hongwei Xue. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica. Oxford University Press, 2013. https://doi.org/10.1093/abbs/gmt039. ieee: Y. Tang, S. Tan, and H. Xue, “Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development,” Acta Biochimica et Biophysica Sinica, vol. 45, no. 7. Oxford University Press, pp. 549–560, 2013. ista: Tang Y, Tan S, Xue H. 2013. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 45(7), 549–560. mla: Tang, Yong, et al. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica, vol. 45, no. 7, Oxford University Press, 2013, pp. 549–60, doi:10.1093/abbs/gmt039. short: Y. Tang, S. Tan, H. Xue, Acta Biochimica et Biophysica Sinica 45 (2013) 549–560. date_created: 2020-03-21T16:06:36Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T08:14:23Z day: '01' doi: 10.1093/abbs/gmt039 extern: '1' external_id: pmid: - '23595027' intvolume: ' 45' issue: '7' language: - iso: eng month: '07' oa_version: None page: 549-560 pmid: 1 publication: Acta Biochimica et Biophysica Sinica publication_identifier: issn: - 1745-7270 - 1672-9145 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2013' ... --- _id: '765' abstract: - lang: eng text: Renaming is a classic distributed coordination task in which a set of processes must pick distinct identifiers from a small namespace. In this paper, we consider the time complexity of this problem when the namespace is linear in the number of participants, a variant known as loose renaming. We give a non-adaptive algorithm with O(log log n) (individual) step complexity, where n is a known upper bound on contention, and an adaptive algorithm with step complexity O((log log k)2), where k is the actual contention in the execution. We also present a variant of the adaptive algorithm which requires O(k log log k) total process steps. All upper bounds hold with high probability against a strong adaptive adversary. We complement the algorithms with an ω(log log n) expected time lower bound on the complexity of randomized renaming using test-and-set operations and linear space. The result is based on a new coupling technique, and is the first to apply to non-adaptive randomized renaming. Since our algorithms use O(n) test-and-set objects, our results provide matching bounds on the cost of loose renaming in this setting. acknowledgement: "Dan Alistarh - This author was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant\r\nER26116/DE-SC0008923, \ and by grants from the Oracle\r\nand Intel corporations.\r\nJames Aspnes - Supported in part by NSF grant CCF-0916389.\r\nGeorge Giakkoupis - This work was funded in part by INRIA Associate Team\r\nRADCON, and ERC Starting Grant GOSSPLE 204742.\r\nPhilipp Woelfel - This research was undertaken, in part, thanks to funding\r\nfrom the Canada Research Chairs program and the HP Labs\r\nInnovation Research Program." 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: James full_name: Aspnes, James last_name: Aspnes - first_name: George full_name: Giakkoupis, George last_name: Giakkoupis - first_name: Philipp full_name: Woelfel, Philipp last_name: Woelfel citation: ama: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. Randomized loose renaming in O(loglogn) time. In: ACM; 2013:200-209. doi:10.1145/2484239.2484240' apa: 'Alistarh, D.-A., Aspnes, J., Giakkoupis, G., & Woelfel, P. (2013). Randomized loose renaming in O(loglogn) time (pp. 200–209). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2484239.2484240' chicago: Alistarh, Dan-Adrian, James Aspnes, George Giakkoupis, and Philipp Woelfel. “Randomized Loose Renaming in O(Loglogn) Time,” 200–209. ACM, 2013. https://doi.org/10.1145/2484239.2484240. ieee: 'D.-A. Alistarh, J. Aspnes, G. Giakkoupis, and P. Woelfel, “Randomized loose renaming in O(loglogn) time,” presented at the PODC: Principles of Distributed Computing, 2013, pp. 200–209.' ista: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. 2013. Randomized loose renaming in O(loglogn) time. PODC: Principles of Distributed Computing, 200–209.' mla: Alistarh, Dan-Adrian, et al. Randomized Loose Renaming in O(Loglogn) Time. ACM, 2013, pp. 200–09, doi:10.1145/2484239.2484240. short: D.-A. Alistarh, J. Aspnes, G. Giakkoupis, P. Woelfel, in:, ACM, 2013, pp. 200–209. conference: name: 'PODC: Principles of Distributed Computing' date_created: 2018-12-11T11:48:23Z date_published: 2013-01-01T00:00:00Z date_updated: 2023-02-23T13:13:14Z day: '01' doi: 10.1145/2484239.2484240 extern: '1' language: - iso: eng month: '01' oa_version: None page: 200 - 209 publication_status: published publisher: ACM publist_id: '6889' status: public title: Randomized loose renaming in O(loglogn) time type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '7745' abstract: - lang: eng text: The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high‐density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex‐, age‐ and environment‐specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems. 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: Anna W. full_name: Santure, Anna W. last_name: Santure - first_name: Isabelle full_name: DeCauwer, Isabelle last_name: DeCauwer - first_name: Ben C. full_name: Sheldon, Ben C. last_name: Sheldon - first_name: Jon full_name: Slate, Jon last_name: Slate citation: ama: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 2013;22(15):3963-3980. doi:10.1111/mec.12375 apa: Robinson, M. R., Santure, A. W., DeCauwer, I., Sheldon, B. C., & Slate, J. (2013). Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12375 chicago: Robinson, Matthew Richard, Anna W. Santure, Isabelle DeCauwer, Ben C. Sheldon, and Jon Slate. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12375. ieee: M. R. Robinson, A. W. Santure, I. DeCauwer, B. C. Sheldon, and J. Slate, “Partitioning of genetic variation across the genome using multimarker methods in a wild bird population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3963–3980, 2013. ista: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. 2013. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 22(15), 3963–3980. mla: Robinson, Matthew Richard, et al. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3963–80, doi:10.1111/mec.12375. short: M.R. Robinson, A.W. Santure, I. DeCauwer, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3963–3980. date_created: 2020-04-30T11:00:15Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T08:15:14Z day: '01' doi: 10.1111/mec.12375 extern: '1' intvolume: ' 22' issue: '15' language: - iso: eng month: '08' oa_version: None page: 3963-3980 publication: Molecular Ecology publication_identifier: issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Partitioning of genetic variation across the genome using multimarker methods in a wild bird population type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2013' ... --- _id: '7746' abstract: - lang: eng text: Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade‐off between them, either at the phenotypic or at the genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker‐based approaches – chromosome partitioning, quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome‐wide significant QTL, and no individual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, nonsignificant negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait. article_processing_charge: No article_type: original author: - first_name: Anna W. full_name: Santure, Anna W. last_name: Santure - first_name: Isabelle full_name: De Cauwer, Isabelle last_name: De Cauwer - 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: Jocelyn full_name: Poissant, Jocelyn last_name: Poissant - first_name: Ben C. full_name: Sheldon, Ben C. last_name: Sheldon - first_name: Jon full_name: Slate, Jon last_name: Slate citation: ama: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. 2013;22(15):3949-3962. doi:10.1111/mec.12376 apa: Santure, A. W., De Cauwer, I., Robinson, M. R., Poissant, J., Sheldon, B. C., & Slate, J. (2013). Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12376 chicago: Santure, Anna W., Isabelle De Cauwer, Matthew Richard Robinson, Jocelyn Poissant, Ben C. Sheldon, and Jon Slate. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12376. ieee: A. W. Santure, I. De Cauwer, M. R. Robinson, J. Poissant, B. C. Sheldon, and J. Slate, “Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3949–3962, 2013. ista: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. 2013. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. 22(15), 3949–3962. mla: Santure, Anna W., et al. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3949–62, doi:10.1111/mec.12376. short: A.W. Santure, I. De Cauwer, M.R. Robinson, J. Poissant, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3949–3962. date_created: 2020-04-30T11:00:32Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T08:15:14Z day: '01' doi: 10.1111/mec.12376 extern: '1' intvolume: ' 22' issue: '15' language: - iso: eng month: '08' oa_version: None page: 3949-3962 publication: Molecular Ecology publication_identifier: issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2013' ... --- _id: '7747' abstract: - lang: eng text: Acquisition and allocation of resources are central to life‐history theory. However, empirical work typically focuses only on allocation despite the fact that relationships between fitness components may be governed by differences in the ability of individuals to acquire resources across environments. Here, we outline a statistical framework to partition the genetic basis of multivariate plasticity into independent axes of genetic variation, and quantify for the first time, the extent to which specific traits drive multitrait genotype–environment interactions. Our framework generalises to analyses of plasticity, growth and ageing. We apply this approach to a unique, large‐scale, multivariate study of acquisition, allocation and plasticity in the life history of the cricket, Gryllus firmus. We demonstrate that resource acquisition and allocation are genetically correlated, and that plasticity in trade‐offs between allocation to components of fitness is 90% dependent on genetic variance for total resource acquisition. These results suggest that genotype–environment effects for resource acquisition can maintain variation in life‐history components that are typically observed in the wild. 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: Andrew P. full_name: Beckerman, Andrew P. last_name: Beckerman citation: ama: 'Robinson MR, Beckerman AP. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. 2013;16(3):281-290. doi:10.1111/ele.12047' apa: 'Robinson, M. R., & Beckerman, A. P. (2013). Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. Wiley. https://doi.org/10.1111/ele.12047' chicago: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” Ecology Letters. Wiley, 2013. https://doi.org/10.1111/ele.12047.' ieee: 'M. R. Robinson and A. P. Beckerman, “Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history,” Ecology Letters, vol. 16, no. 3. Wiley, pp. 281–290, 2013.' ista: 'Robinson MR, Beckerman AP. 2013. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. 16(3), 281–290.' mla: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” Ecology Letters, vol. 16, no. 3, Wiley, 2013, pp. 281–90, doi:10.1111/ele.12047.' short: M.R. Robinson, A.P. Beckerman, Ecology Letters 16 (2013) 281–290. date_created: 2020-04-30T11:00:49Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T08:15:15Z day: '01' doi: 10.1111/ele.12047 extern: '1' intvolume: ' 16' issue: '3' language: - iso: eng month: '03' oa_version: None page: 281-290 publication: Ecology Letters publication_identifier: issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2013' ... --- _id: '7775' abstract: - lang: eng text: As a function of packing fraction at zero temperature and applied stress, an amorphous packing of spheres exhibits a jamming transition where the system is sensitive to boundary conditions even in the thermodynamic limit. Upon further compression, the system should become insensitive to boundary conditions provided it is sufficiently large. Here we explore the linear response to a large class of boundary perturbations in 2 and 3 dimensions. We consider each finite packing with periodic-boundary conditions as the basis of an infinite square or cubic lattice and study properties of vibrational modes at arbitrary wave vector. We find that the stability of such modes can be understood in terms of a competition between plane waves and the anomalous vibrational modes associated with the jamming transition; infinitesimal boundary perturbations become irrelevant for systems that are larger than a length scale that characterizes the transverse excitations. This previously identified length diverges at the jamming transition. article_number: '11000' article_processing_charge: No article_type: original author: - first_name: Samuel S. full_name: Schoenholz, Samuel S. last_name: Schoenholz - 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: Oleg full_name: Kogan, Oleg last_name: Kogan - 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: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed packings II: The transverse length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51096d' apa: 'Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., & Nagel, S. R. (2013). Stability of jammed packings II: The transverse length scale. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51096d' chicago: 'Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu, and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51096d.' ieee: 'S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability of jammed packings II: The transverse length scale,” Soft Matter, vol. 9, no. 46. Royal Society of Chemistry, 2013.' ista: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.' mla: 'Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse Length Scale.” Soft Matter, vol. 9, no. 46, 11000, Royal Society of Chemistry, 2013, doi:10.1039/c3sm51096d.' short: S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter 9 (2013). date_created: 2020-04-30T11:43:58Z date_published: 2013-10-08T00:00:00Z date_updated: 2021-01-12T08:15:27Z day: '08' doi: 10.1039/c3sm51096d extern: '1' intvolume: ' 9' issue: '46' language: - iso: eng month: '10' oa_version: None publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Stability of jammed packings II: The transverse length scale' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '7774' abstract: - lang: eng text: In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low frequency vibrational properties of jammed amorphous sphere packings can be understood in terms of a length scale, called l*, that diverges as the system becomes marginally unstable. Despite the tremendous success of this theory, it has been difficult to connect the counting argument that defines l* to other length scales that diverge near the jamming transition. We present an alternate derivation of l* based on the onset of rigidity. This phenomenological approach reveals the physical mechanism underlying the length scale and is relevant to a range of systems for which the original argument breaks down. It also allows us to present the first direct numerical measurement of l*. article_number: '10993' 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: Wouter G. full_name: Ellenbroek, Wouter G. last_name: Ellenbroek - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu citation: ama: 'Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51095f' apa: 'Goodrich, C. P., Ellenbroek, W. G., & Liu, A. J. (2013). Stability of jammed packings I: The rigidity length scale. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51095f' chicago: 'Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability of Jammed Packings I: The Rigidity Length Scale.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51095f.' ieee: 'C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings I: The rigidity length scale,” Soft Matter, vol. 9, no. 46. Royal Society of Chemistry, 2013.' ista: 'Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I: The rigidity length scale. Soft Matter. 9(46), 10993.' mla: 'Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity Length Scale.” Soft Matter, vol. 9, no. 46, 10993, Royal Society of Chemistry, 2013, doi:10.1039/c3sm51095f.' short: C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013). date_created: 2020-04-30T11:43:42Z date_published: 2013-10-08T00:00:00Z date_updated: 2021-01-12T08:15:27Z day: '08' doi: 10.1039/c3sm51095f extern: '1' intvolume: ' 9' issue: '46' language: - iso: eng month: '10' oa_version: None publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Stability of jammed packings I: The rigidity length scale' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '8030' abstract: - lang: eng text: While the plasticity of excitatory synaptic connections in the brain has been widely studied, the plasticity of inhibitory connections is much less understood. Here, we present recent experimental and theoretical findings concerning the rules of spike timing-dependent inhibitory plasticity and their putative network function. This is a summary of a workshop at the COSYNE conference 2012. article_number: '119' article_processing_charge: No article_type: original author: - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: R. C. full_name: Froemke, R. C. last_name: Froemke - first_name: N. full_name: Doyon, N. last_name: Doyon - first_name: M. full_name: Gilson, M. last_name: Gilson - first_name: J. S. full_name: Haas, J. S. last_name: Haas - first_name: R. full_name: Liu, R. last_name: Liu - first_name: A. full_name: Maffei, A. last_name: Maffei - first_name: P. full_name: Miller, P. last_name: Miller - first_name: C. J. full_name: Wierenga, C. J. last_name: Wierenga - first_name: M. A. full_name: Woodin, M. A. last_name: Woodin - first_name: F. full_name: Zenke, F. last_name: Zenke - first_name: H. full_name: Sprekeler, H. last_name: Sprekeler citation: ama: 'Vogels TP, Froemke RC, Doyon N, et al. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. 2013;7. doi:10.3389/fncir.2013.00119' apa: 'Vogels, T. P., Froemke, R. C., Doyon, N., Gilson, M., Haas, J. S., Liu, R., … Sprekeler, H. (2013). Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. Frontiers Media. https://doi.org/10.3389/fncir.2013.00119' chicago: 'Vogels, Tim P, R. C. Froemke, N. Doyon, M. Gilson, J. S. Haas, R. Liu, A. Maffei, et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” Frontiers in Neural Circuits. Frontiers Media, 2013. https://doi.org/10.3389/fncir.2013.00119.' ieee: 'T. P. Vogels et al., “Inhibitory synaptic plasticity: Spike timing-dependence and putative network function,” Frontiers in Neural Circuits, vol. 7. Frontiers Media, 2013.' ista: 'Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. 2013. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. 7, 119.' mla: 'Vogels, Tim P., et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” Frontiers in Neural Circuits, vol. 7, 119, Frontiers Media, 2013, doi:10.3389/fncir.2013.00119.' short: T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei, P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, Frontiers in Neural Circuits 7 (2013). date_created: 2020-06-25T13:23:50Z date_published: 2013-07-18T00:00:00Z date_updated: 2021-01-12T08:16:38Z day: '18' ddc: - '570' doi: 10.3389/fncir.2013.00119 extern: '1' external_id: pmid: - '23882186' file: - access_level: open_access checksum: 9c321cb12977d84048712eefa7f0c497 content_type: application/pdf creator: cziletti date_created: 2020-07-16T11:23:40Z date_updated: 2020-07-16T11:23:40Z file_id: '8123' file_name: 2013_FrontNeurCirc_Vogels.pdf file_size: 1530469 relation: main_file success: 1 file_date_updated: 2020-07-16T11:23:40Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Neural Circuits publication_identifier: eissn: - 1662-5110 publication_status: published publisher: Frontiers Media quality_controlled: '1' status: public title: 'Inhibitory synaptic plasticity: Spike timing-dependence and putative network function' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2013' ... --- _id: '811' abstract: - lang: eng text: Cell migration is commonly accompanied by protrusion of membrane ruffles and lamellipodia. In two-dimensional migration, protrusion of these thin sheets of cytoplasm is considered relevant to both exploration of new space and initiation of nascent adhesion to the substratum. Lamellipodium formation can be potently stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent lamellipodia, but these structures were restored by expression of either Rac subfamily member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction in wound closure and random cell migration and a notable loss of sensitivity to a chemotactic gradient. Despite these defects, Rac-deficient cells were able to spread, formed filopodia and established focal adhesions. Spreading in these cells was achieved by the extension of filopodia followed by the advancement of cytoplasmic veils between them. The number and size of focal adhesions as well as their intensity were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased the mobility of different components in focal adhesions, potentially explaining how Rac - although not essential - can contribute to focal adhesion assembly. Together, our data demonstrate that Rac signaling is essential for lamellipodium protrusion and for efficient cell migration, but not for spreading or filopodium formation. Our findings also suggest that Rac GTPases are crucial to the establishment or maintenance of polarity in chemotactic migration. acknowledgement: |- This work was supported in part by the Deutsche Forschungsgemeinschaft [grants within programs SFB621 to K.R., and FOR629 and SFB629 to T.E.B.S.]. Deposited in PMC for immediate release. We thank Brigitte Denker and Gerd Landsberg for excellent technical assistance. We are grateful to Robert Geffers (HZI Braunschweig, Germany) for microarray analyses and to Mirko Himmel (UKE Hamburg, Germany) for valuable advice on FRAP analysis. author: - first_name: Anika full_name: Steffen, Anika last_name: Steffen - first_name: Markus full_name: Ladwein, Markus last_name: Ladwein - first_name: Georgi A full_name: Georgi Dimchev id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev - first_name: Anke full_name: Hein, Anke last_name: Hein - first_name: Lisa full_name: Schwenkmezger, Lisa last_name: Schwenkmezger - first_name: Stefan full_name: Arens, Stefan last_name: Arens - first_name: Kathrin full_name: Ladwein, Kathrin I last_name: Ladwein - first_name: J. full_name: Holleboom, J. Margit last_name: Holleboom - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: John full_name: Small, John V last_name: Small - first_name: Janett full_name: Schwarz, Janett last_name: Schwarz - first_name: Ralf full_name: Gerhard, Ralf last_name: Gerhard - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Theresia full_name: Stradal, Theresia E last_name: Stradal - first_name: Cord full_name: Brakebusch, Cord H last_name: Brakebusch - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner citation: ama: Steffen A, Ladwein M, Dimchev GA, et al. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. 2013;126(20):4572-4588. doi:10.1242/jcs.118232 apa: Steffen, A., Ladwein, M., Dimchev, G. A., Hein, A., Schwenkmezger, L., Arens, S., … Rottner, K. (2013). Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.118232 chicago: Steffen, Anika, Markus Ladwein, Georgi A Dimchev, Anke Hein, Lisa Schwenkmezger, Stefan Arens, Kathrin Ladwein, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.118232. ieee: A. Steffen et al., “Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation,” Journal of Cell Science, vol. 126, no. 20. Company of Biologists, pp. 4572–4588, 2013. ista: Steffen A, Ladwein M, Dimchev GA, Hein A, Schwenkmezger L, Arens S, Ladwein K, Holleboom J, Schur FK, Small J, Schwarz J, Gerhard R, Faix J, Stradal T, Brakebusch C, Rottner K. 2013. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. 126(20), 4572–4588. mla: Steffen, Anika, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science, vol. 126, no. 20, Company of Biologists, 2013, pp. 4572–88, doi:10.1242/jcs.118232. short: A. Steffen, M. Ladwein, G.A. Dimchev, A. Hein, L. Schwenkmezger, S. Arens, K. Ladwein, J. Holleboom, F.K. Schur, J. Small, J. Schwarz, R. Gerhard, J. Faix, T. Stradal, C. Brakebusch, K. Rottner, Journal of Cell Science 126 (2013) 4572–4588. date_created: 2018-12-11T11:48:38Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T08:16:57Z day: '01' doi: 10.1242/jcs.118232 extern: 1 intvolume: ' 126' issue: '20' month: '01' page: 4572 - 4588 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '6840' quality_controlled: 0 status: public title: Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation 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: 126 year: '2013' ... --- _id: '812' abstract: - lang: eng text: Lamellipodia are sheet-like protrusions formed during migration or phagocytosis and comprise a network of actin filaments. Filament formation in this network is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3) complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching versus actin filament elongation is unknown. Here we use instantaneous interference with Arp2/3 complex function in live fibroblasts with established lamellipodia. This allows direct examination of both the fate of elongating filaments upon instantaneous suppression of Arp2/3 complex activity and the consequences of this treatment on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex is an essential organizer of treadmilling actin filament arrays but has little effect on the net rate of actin filament turnover at the cell periphery. In addition, Arp2/3 complex serves as key upstream factor for the recruitment of modulators of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is thus decisive for filament organization and geometry within the network not only by generating branches and novel filament ends, but also by directing capping or severing activities to the lamellipodium. Arp2/3 complex is also crucial to lamellipodia-based migration of keratocytes. acknowledgement: "This work was supported in part by Deutsche Forschungsgemeinschaft Grants RO2414/3-1 (to K.R.) and FA330/6-1 (to J.F.), Austrian \nScience Fund Projects FWF 1516-B09 and FWF P21292-B09 (to J.V.S.), the Vienna Science and Technology \ Fund (WWTF, to \nJ.V.S. and C.S.), and Australian National Health and \ Medical \nResearch Council Grant APP1004175 (to P.W.G.). We thank J. Adams, \nR. Chisholm, A. Hall, L. Machesky, H. G. Mannherz, D. Schafer, and \nR. Wedlich-Söldner \ for expression constructs and B. Denker, \nP. Hagendorff, and G. Landsberg for technical assistance." author: - first_name: Stefan full_name: Koestler, Stefan A last_name: Koestler - first_name: Anika full_name: Steffen, Anika last_name: Steffen - first_name: Maria full_name: Maria Nemethova id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Moritz full_name: Winterhoff, Moritz last_name: Winterhoff - first_name: Ningning full_name: Luo, Ningning last_name: Luo - first_name: J. full_name: Holleboom, J. Margit last_name: Holleboom - first_name: Jessica full_name: Krupp, Jessica last_name: Krupp - first_name: Sonja full_name: Jacob, Sonja last_name: Jacob - first_name: Marlene full_name: Vinzenz, Marlene last_name: Vinzenz - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Kai full_name: Schlüter, Kai last_name: Schlüter - first_name: Peter full_name: Gunning, Peter W last_name: Gunning - first_name: Christoph full_name: Winkler, Christoph last_name: Winkler - first_name: Christian full_name: Schmeiser, Christian last_name: Schmeiser - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Theresia full_name: Stradal, Theresia E last_name: Stradal - first_name: John full_name: Small, John V last_name: Small - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner citation: ama: Koestler S, Steffen A, Nemethova M, et al. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. 2013;24(18):2861-2875. doi:10.1091/mbc.E12-12-0857 apa: Koestler, S., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom, J., … Rottner, K. (2013). Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. American Society for Biology. https://doi.org/10.1091/mbc.E12-12-0857 chicago: Koestler, Stefan, Anika Steffen, Maria Nemethova, Moritz Winterhoff, Ningning Luo, J. Holleboom, Jessica Krupp, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology of the Cell. American Society for Biology, 2013. https://doi.org/10.1091/mbc.E12-12-0857. ieee: S. Koestler et al., “Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin,” Molecular Biology of the Cell, vol. 24, no. 18. American Society for Biology, pp. 2861–2875, 2013. ista: Koestler S, Steffen A, Nemethova M, Winterhoff M, Luo N, Holleboom J, Krupp J, Jacob S, Vinzenz M, Schur FK, Schlüter K, Gunning P, Winkler C, Schmeiser C, Faix J, Stradal T, Small J, Rottner K. 2013. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. 24(18), 2861–2875. mla: Koestler, Stefan, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology of the Cell, vol. 24, no. 18, American Society for Biology, 2013, pp. 2861–75, doi:10.1091/mbc.E12-12-0857. short: S. Koestler, A. Steffen, M. Nemethova, M. Winterhoff, N. Luo, J. Holleboom, J. Krupp, S. Jacob, M. Vinzenz, F.K. Schur, K. Schlüter, P. Gunning, C. Winkler, C. Schmeiser, J. Faix, T. Stradal, J. Small, K. Rottner, Molecular Biology of the Cell 24 (2013) 2861–2875. date_created: 2018-12-11T11:48:38Z date_published: 2013-09-15T00:00:00Z date_updated: 2021-01-12T08:17:00Z day: '15' doi: 10.1091/mbc.E12-12-0857 extern: 1 intvolume: ' 24' issue: '18' month: '09' page: 2861 - 2875 publication: Molecular Biology of the Cell publication_status: published publisher: American Society for Biology publist_id: '6841' quality_controlled: 0 status: public title: Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin type: journal_article volume: 24 year: '2013' ... --- _id: '810' abstract: - lang: eng text: Cryo-electron tomography combined with image processing by sub-tomogram averaging is unique in its power to resolve the structures of proteins and macromolecular complexes in situ. Limitations of the method, including the low signal to noise ratio within individual images from cryo-tomographic datasets and difficulties in determining the defocus at which the data was collected, mean that to date the very best structures obtained by sub-tomogram averaging are limited to a resolution of approximately 15. Å. Here, by optimizing data collection and defocus determination steps, we have determined the structure of assembled Mason-Pfizer monkey virus Gag protein using sub-tomogram averaging to a resolution of 8.5. Å. At this resolution alpha-helices can be directly and clearly visualized. These data demonstrate for the first time that high-resolution structural information can be obtained from cryo-electron tomograms using sub-tomogram averaging. Sub-tomogram averaging has the potential to allow detailed studies of unsolved and biologically relevant structures under biologically relevant conditions. acknowledgement: The M-PMV ΔPro CANC tubes imaged in this study were a kind gift from Pavel Ulbrich and Tomas Ruml, Institute of Chemical Technology, Prague. The cryo-EM grids were prepared by Tanmay Bharat. This study was technically supported by EMBL’s IT services unit and by Frank Thommen. We thank Martin Schorb and Svetlana Dodonova for discussions and advice; Khanh Huy Bui for advice and scripts to streamline tomogram reconstruction; and Giulia Zanetti, Tanmay Bharat, and Martin Beck for comments on the manuscript. This study was supported by Deutsche Forschungsgemeinschaft grant BR 3635/2-1 to JAGB. author: - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Wim full_name: Hagen, Wim J last_name: Hagen - first_name: Alex full_name: De Marco, Alex last_name: De Marco - first_name: John full_name: Briggs, John A last_name: Briggs citation: ama: Schur FK, Hagen W, De Marco A, Briggs J. Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology. 2013;184(3):394-400. doi:10.1016/j.jsb.2013.10.015 apa: Schur, F. K., Hagen, W., De Marco, A., & Briggs, J. (2013). Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2013.10.015 chicago: Schur, Florian KM, Wim Hagen, Alex De Marco, and John Briggs. “Determination of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” Journal of Structural Biology. Academic Press, 2013. https://doi.org/10.1016/j.jsb.2013.10.015. ieee: F. K. Schur, W. Hagen, A. De Marco, and J. Briggs, “Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging,” Journal of Structural Biology, vol. 184, no. 3. Academic Press, pp. 394–400, 2013. ista: Schur FK, Hagen W, De Marco A, Briggs J. 2013. Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology. 184(3), 394–400. mla: Schur, Florian KM, et al. “Determination of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” Journal of Structural Biology, vol. 184, no. 3, Academic Press, 2013, pp. 394–400, doi:10.1016/j.jsb.2013.10.015. short: F.K. Schur, W. Hagen, A. De Marco, J. Briggs, Journal of Structural Biology 184 (2013) 394–400. date_created: 2018-12-11T11:48:37Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T08:16:54Z day: '01' doi: 10.1016/j.jsb.2013.10.015 extern: 1 intvolume: ' 184' issue: '3' month: '12' page: 394 - 400 publication: Journal of Structural Biology publication_status: published publisher: Academic Press publist_id: '6839' quality_controlled: 0 status: public title: Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging type: journal_article volume: 184 year: '2013' ... --- _id: '8245' abstract: - lang: eng text: "Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable addition to breast cancer therapy.\r\nData obtained from neoadjuvant settings revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a\r\nmajor mechanism of action for the mAb trastuzumab. Conflicting results still call into question whether disease\r\nprogression, prolonged treatment or concomitant chemotherapy influences ADCC and related immunological\r\nphenomena.\r\nMethods: We analyzed the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP) of\r\nperipheral blood mononuclear cells (PBMCs) from human epidermal growth factor receptor 2 (HER2/neu) positive\r\nbreast cancer patients receiving trastuzumab therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as\r\nwell as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n = 15). PBMCs from healthy volunteers\r\n(n = 24) were used as controls. ADCC and ADCP activity was correlated with the expression of antibody binding\r\nFc-gamma receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes) and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients, markers were correlated with progression-free survival (PFS).\r\nResults: ADCC activity was significantly down regulated in metastatic, adjuvant and t-naive patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely correlated with the expression of CD107a on CD56+\r\ncells in adjuvant patients. ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment duration\r\nor additional chemotherapy. PFS in metastatic patients inversely correlated with the number of peripheral Treg cells.\r\nConclusion: The reduction of ADCC in patients as compared to healthy controls calls for adjuvant strategies, such as\r\nimmune-enhancing agents, to improve the activity of trastuzumab. However, efficacy of trastuzumab-specific ADCC\r\nand ADCP appears not to be affected by treatment duration, disease progression or concomitant chemotherapy. This\r\nfinding supports the application of trastuzumab at any stage of the disease." article_number: '307' article_processing_charge: No author: - first_name: Branka full_name: Petricevic, Branka last_name: Petricevic - first_name: Johannes full_name: Laengle, Johannes last_name: Laengle - first_name: Josef full_name: Singer, Josef last_name: Singer - first_name: Monika full_name: Sachet, Monika last_name: Sachet - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: Guenther full_name: Steger, Guenther last_name: Steger - first_name: Rupert full_name: Bartsch, Rupert last_name: Bartsch - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim - first_name: Michael full_name: Bergmann, Michael last_name: Bergmann citation: ama: Petricevic B, Laengle J, Singer J, et al. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. 2013;11. doi:10.1186/1479-5876-11-307 apa: Petricevic, B., Laengle, J., Singer, J., Sachet, M., Singer, J., Steger, G., … Bergmann, M. (2013). Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. Springer Nature. https://doi.org/10.1186/1479-5876-11-307 chicago: Petricevic, Branka, Johannes Laengle, Josef Singer, Monika Sachet, Judit Singer, Guenther Steger, Rupert Bartsch, Erika Jensen-Jarolim, and Michael Bergmann. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” Journal of Translational Medicine. Springer Nature, 2013. https://doi.org/10.1186/1479-5876-11-307. ieee: B. Petricevic et al., “Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients,” Journal of Translational Medicine, vol. 11. Springer Nature, 2013. ista: Petricevic B, Laengle J, Singer J, Sachet M, Singer J, Steger G, Bartsch R, Jensen-Jarolim E, Bergmann M. 2013. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. 11, 307. mla: Petricevic, Branka, et al. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” Journal of Translational Medicine, vol. 11, 307, Springer Nature, 2013, doi:10.1186/1479-5876-11-307. short: B. Petricevic, J. Laengle, J. Singer, M. Sachet, J. Singer, G. Steger, R. Bartsch, E. Jensen-Jarolim, M. Bergmann, Journal of Translational Medicine 11 (2013). date_created: 2020-08-10T11:54:34Z date_published: 2013-12-12T00:00:00Z date_updated: 2022-08-25T14:52:39Z day: '12' ddc: - '570' doi: 10.1186/1479-5876-11-307 extern: '1' external_id: pmid: - '24330813' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-08-10T13:45:19Z date_updated: 2020-08-10T13:45:19Z file_id: '8247' file_name: 2013_JoTM_Petricevic.pdf file_size: 777311 relation: main_file success: 1 file_date_updated: 2020-08-10T13:45:19Z has_accepted_license: '1' intvolume: ' 11' language: - iso: eng month: '12' oa: 1 oa_version: None pmid: 1 publication: Journal of Translational Medicine publication_identifier: issn: - 1479-5876 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2013' ... --- _id: '827' abstract: - lang: eng text: As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed. article_number: '451' author: - first_name: José full_name: O'Brien, José last_name: O'Brien - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00451 apa: O’Brien, J., & Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00451 chicago: O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00451. ieee: J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” Frontiers in Plant Science, vol. 4. Frontiers Research Foundation, 2013. ista: O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451. mla: O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” Frontiers in Plant Science, vol. 4, 451, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00451. short: J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013). date_created: 2018-12-11T11:48:43Z date_published: 2013-11-19T00:00:00Z date_updated: 2021-01-12T08:17:50Z day: '19' ddc: - '580' department: - _id: EvBe doi: 10.3389/fpls.2013.00451 ec_funded: 1 file: - access_level: open_access checksum: fdc25ddd1bf9a99b99f662cdbafeddd4 content_type: application/pdf creator: dernst date_created: 2019-01-31T10:40:38Z date_updated: 2020-07-14T12:48:11Z file_id: '5903' file_name: 2013_FrontiersPlant_OBrien.pdf file_size: 953299 relation: main_file file_date_updated: 2020-07-14T12:48:11Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: Frontiers in Plant Science publication_status: published publisher: Frontiers Research Foundation publist_id: '6821' quality_controlled: '1' scopus_import: 1 status: public title: Cytokinin cross talking during biotic and abiotic stress responses 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: 4 year: '2013' ... --- _id: '828' abstract: - lang: eng text: The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed. article_number: '537' author: - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00537 apa: Cuesta, C., Wabnik, K. T., & Benková, E. (2013). Systems approaches to study root architecture dynamics. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00537 chicago: Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00537. ieee: C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” Frontiers in Plant Science, vol. 4. Frontiers Research Foundation, 2013. ista: Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537. mla: Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” Frontiers in Plant Science, vol. 4, 537, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00537. short: C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013). date_created: 2018-12-11T11:48:43Z date_published: 2013-12-26T00:00:00Z date_updated: 2021-01-12T08:17:52Z day: '26' ddc: - '580' department: - _id: EvBe doi: 10.3389/fpls.2013.00537 ec_funded: 1 file: - access_level: open_access checksum: 0185b3c4d7df9a94bd3ce5a66d213506 content_type: application/pdf creator: dernst date_created: 2019-01-31T10:36:43Z date_updated: 2020-07-14T12:48:11Z file_id: '5902' file_name: 2013_FrontiersPlant_Cuesta.pdf file_size: 710835 relation: main_file file_date_updated: 2020-07-14T12:48:11Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: Frontiers in Plant Science publication_status: published publisher: Frontiers Research Foundation publist_id: '6820' quality_controlled: '1' scopus_import: 1 status: public title: Systems approaches to study root architecture dynamics 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: 4 year: '2013' ... --- _id: '830' abstract: - lang: eng text: Upon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development. acknowledgement: The project and F.G. were supported by the CARIPLO Foundation (project 2009-2990) and COST (European Cooperation in Science and Technology) action HAPRECI (Harnessing Plant Reproduction for Crop Improvement). E.B. and C.C. were supported by the European Research Council through a ‘Starting Independent Research’ grant (ERC-2007-Stg-207362-HCPO). We thank A.P. MacCabe (Consejo Superior de Investigaciones Científicas, Valencia, Spain) for critical reading of the manuscript. article_processing_charge: No article_type: original author: - first_name: Francesca full_name: Galbiati, Francesca last_name: Galbiati - first_name: Dola full_name: Sinha Roy, Dola last_name: Sinha Roy - first_name: Sara full_name: Simonini, Sara last_name: Simonini - first_name: Mara full_name: Cucinotta, Mara last_name: Cucinotta - first_name: Luca full_name: Ceccato, Luca last_name: Ceccato - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Mária full_name: Šimášková, Mária last_name: Šimášková - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Yuri full_name: Kamiuchi, Yuri last_name: Kamiuchi - first_name: Mitsuhiro full_name: Aida, Mitsuhiro last_name: Aida - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Rüdiger full_name: Simon, Rüdiger last_name: Simon - first_name: Simona full_name: Masiero, Simona last_name: Masiero - first_name: Lucia full_name: Colombo, Lucia last_name: Colombo citation: ama: Galbiati F, Sinha Roy D, Simonini S, et al. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 2013;76(3):446-455. doi:10.1111/tpj.12309 apa: Galbiati, F., Sinha Roy, D., Simonini, S., Cucinotta, M., Ceccato, L., Cuesta, C., … Colombo, L. (2013). An integrative model of the control of ovule primordia formation. The Plant Journal for Cell and Molecular Biology. Wiley-Blackwell. https://doi.org/10.1111/tpj.12309 chicago: Galbiati, Francesca, Dola Sinha Roy, Sara Simonini, Mara Cucinotta, Luca Ceccato, Candela Cuesta, Mária Šimášková, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” The Plant Journal for Cell and Molecular Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/tpj.12309. ieee: F. Galbiati et al., “An integrative model of the control of ovule primordia formation,” The Plant journal for cell and molecular biology, vol. 76, no. 3. Wiley-Blackwell, pp. 446–455, 2013. ista: Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L, Cuesta C, Šimášková M, Benková E, Kamiuchi Y, Aida M, Weijers D, Simon R, Masiero S, Colombo L. 2013. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 76(3), 446–455. mla: Galbiati, Francesca, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” The Plant Journal for Cell and Molecular Biology, vol. 76, no. 3, Wiley-Blackwell, 2013, pp. 446–55, doi:10.1111/tpj.12309. short: F. Galbiati, D. Sinha Roy, S. Simonini, M. Cucinotta, L. Ceccato, C. Cuesta, M. Šimášková, E. Benková, Y. Kamiuchi, M. Aida, D. Weijers, R. Simon, S. Masiero, L. Colombo, The Plant Journal for Cell and Molecular Biology 76 (2013) 446–455. date_created: 2018-12-11T11:48:44Z date_published: 2013-09-19T00:00:00Z date_updated: 2022-03-21T07:17:26Z day: '19' doi: 10.1111/tpj.12309 extern: '1' external_id: pmid: - '23941199' intvolume: ' 76' issue: '3' language: - iso: eng month: '09' oa_version: None page: 446 - 455 pmid: 1 publication: The Plant journal for cell and molecular biology publication_status: published publisher: Wiley-Blackwell publist_id: '6818' quality_controlled: '1' scopus_import: '1' status: public title: An integrative model of the control of ovule primordia formation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 76 year: '2013' ... --- _id: '831' abstract: - lang: eng text: In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that auxin produced in new LRP is transported towards the outer tissues where it triggers cell separation by inducing both the auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two cell files overlaying new LRP. To understand how this striking pattern of LAX3 expression is regulated, we developed a mathematical model that captures the network regulating its expression and auxin transport within realistic three-dimensional cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression to be robust to natural variations in root tissue geometry, an efflux carrier is required--later identified to be PIN3. To prevent LAX3 from being transiently expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively, which we later demonstrated to be the case. Our study exemplifies how mathematical models can be used to direct experiments to elucidate complex developmental processes. acknowledgement: This work was supported by an FEBS Long‐Term Fellowship (BP), an Intra‐European Fellowship for Career Development under the 7th framework of the European Commission (IEF‐2008‐220506 to BP), an EMBO Long‐Term Fellowship (BP), an European Reintegration Grant under the 7th framework of the European Commission (ERG‐2010‐276662 to BP) and the Swedish Research Council (VR 621‐2010‐5720 to IS, GS and KL). AMM, APF, AL, LRB, SP, NM, DMW, MO, JRK and MJB acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative Biology (CPIB); BBSRC Professorial Research Fellowship funding to DMW and MJB; Belgian Scientific policy (BELSPO contract MARS) to TB and MJB. We thank Bert de Rybel for his help in Multisite Gateway cloning. author: - first_name: Benjamin full_name: Péret, Benjamin last_name: Péret - first_name: Alistair full_name: Middleton, Alistair M last_name: Middleton - first_name: Andrew full_name: French, Andrew P last_name: French - first_name: Antoine full_name: Larrieu, Antoine last_name: Larrieu - first_name: Anthony full_name: Bishopp, Anthony last_name: Bishopp - first_name: Maria full_name: Njo, Maria last_name: Njo - first_name: Darren full_name: Wells, Darren M last_name: Wells - first_name: Silvana full_name: Porco, Silvana last_name: Porco - first_name: Nathan full_name: Mellor, Nathan last_name: Mellor - first_name: Leah full_name: Band, Leah R last_name: Band - first_name: Ilda full_name: Casimiro, Ilda last_name: Casimiro - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Ilkka full_name: Sairanen, Ilkka last_name: Sairanen - first_name: Romain full_name: Mallet, Romain last_name: Mallet - first_name: Göran full_name: Sandberg, Göran last_name: Sandberg - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eric full_name: Kramer, Eric last_name: Kramer - first_name: John full_name: King, John R last_name: King - first_name: Ive full_name: De Smet, Ive last_name: De Smet - first_name: Tony full_name: Pridmore, Tony last_name: Pridmore - first_name: Markus full_name: Owen, Markus last_name: Owen - first_name: Malcolm full_name: Bennett, Malcolm J last_name: Bennett citation: ama: Péret B, Middleton A, French A, et al. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 2013;9. doi:10.1038/msb.2013.43 apa: Péret, B., Middleton, A., French, A., Larrieu, A., Bishopp, A., Njo, M., … Bennett, M. (2013). Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2013.43 chicago: Péret, Benjamin, Alistair Middleton, Andrew French, Antoine Larrieu, Anthony Bishopp, Maria Njo, Darren Wells, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” Molecular Systems Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/msb.2013.43. ieee: B. Péret et al., “Sequential induction of auxin efflux and influx carriers regulates lateral root emergence,” Molecular Systems Biology, vol. 9. Nature Publishing Group, 2013. ista: Péret B, Middleton A, French A, Larrieu A, Bishopp A, Njo M, Wells D, Porco S, Mellor N, Band L, Casimiro I, Kleine Vehn J, Vanneste S, Sairanen I, Mallet R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King J, De Smet I, Pridmore T, Owen M, Bennett M. 2013. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 9. mla: Péret, Benjamin, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” Molecular Systems Biology, vol. 9, Nature Publishing Group, 2013, doi:10.1038/msb.2013.43. short: B. Péret, A. Middleton, A. French, A. Larrieu, A. Bishopp, M. Njo, D. Wells, S. Porco, N. Mellor, L. Band, I. Casimiro, J. Kleine Vehn, S. Vanneste, I. Sairanen, R. Mallet, G. Sandberg, K. Ljung, T. Beeckman, E. Benková, J. Friml, E. Kramer, J. King, I. De Smet, T. Pridmore, M. Owen, M. Bennett, Molecular Systems Biology 9 (2013). date_created: 2018-12-11T11:48:44Z date_published: 2013-10-22T00:00:00Z date_updated: 2021-01-12T08:18:03Z day: '22' doi: 10.1038/msb.2013.43 extern: 1 intvolume: ' 9' month: '10' publication: Molecular Systems Biology publication_status: published publisher: Nature Publishing Group publist_id: '6817' quality_controlled: 0 status: public title: Sequential induction of auxin efflux and influx carriers regulates lateral root emergence 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 volume: 9 year: '2013' ... --- _id: '8461' abstract: - lang: eng text: Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps–μs motions in proteins by solid-state NMR. article_processing_charge: No article_type: original author: - first_name: Jens D. full_name: Haller, Jens D. last_name: Haller - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 2013;57(3):263-280. doi:10.1007/s10858-013-9787-x' apa: 'Haller, J. D., & Schanda, P. (2013). Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-013-9787-x' chicago: 'Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular NMR. Springer Nature, 2013. https://doi.org/10.1007/s10858-013-9787-x.' ieee: 'J. D. Haller and P. Schanda, “Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin,” Journal of Biomolecular NMR, vol. 57, no. 3. Springer Nature, pp. 263–280, 2013.' ista: 'Haller JD, Schanda P. 2013. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 57(3), 263–280.' mla: 'Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular NMR, vol. 57, no. 3, Springer Nature, 2013, pp. 263–80, doi:10.1007/s10858-013-9787-x.' short: J.D. Haller, P. Schanda, Journal of Biomolecular NMR 57 (2013) 263–280. date_created: 2020-09-18T10:09:05Z date_published: 2013-10-09T00:00:00Z date_updated: 2021-01-12T08:19:26Z day: '09' doi: 10.1007/s10858-013-9787-x extern: '1' intvolume: ' 57' issue: '3' keyword: - Spectroscopy - Biochemistry language: - iso: eng month: '10' oa_version: None page: 263-280 publication: Journal of Biomolecular NMR publication_identifier: issn: - 0925-2738 - 1573-5001 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2013' ... --- _id: '8462' abstract: - lang: eng text: The transition of proteins from their soluble functional state to amyloid fibrils and aggregates is associated with the onset of several human diseases. Protein aggregation often requires some structural reshaping and the subsequent formation of intermolecular contacts. Therefore, the study of the conformation of excited protein states and their ability to form oligomers is of primary importance for understanding the molecular basis of amyloid fibril formation. Here, we investigated the oligomerization processes that occur along the folding of the amyloidogenic human protein β2-microglobulin. The combination of real-time two-dimensional NMR data with real-time small-angle X-ray scattering measurements allowed us to derive thermodynamic and kinetic information on protein oligomerization of different conformational states populated along the folding pathways. In particular, we could demonstrate that a long-lived folding intermediate (I-state) has a higher propensity to oligomerize compared to the native state. Our data agree well with a simple five-state kinetic model that involves only monomeric and dimeric species. The dimers have an elongated shape with the dimerization interface located at the apical side of β2-microglobulin close to Pro32, the residue that has a trans conformation in the I-state and a cis conformation in the native (N) state. Our experimental data suggest that partial unfolding in the apical half of the protein close to Pro32 leads to an excited state conformation with enhanced propensity for oligomerization. This excited state becomes more populated in the transient I-state due to the destabilization of the native conformation by the trans-Pro32 configuration. article_processing_charge: No article_type: original author: - first_name: E. full_name: Rennella, E. last_name: Rennella - first_name: T. full_name: Cutuil, T. 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: I. full_name: Ayala, I. last_name: Ayala - first_name: F. full_name: Gabel, F. last_name: Gabel - first_name: V. full_name: Forge, V. last_name: Forge - first_name: A. full_name: Corazza, A. last_name: Corazza - first_name: G. full_name: Esposito, G. last_name: Esposito - first_name: B. full_name: Brutscher, B. last_name: Brutscher citation: ama: 'Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 2013;425(15):2722-2736. doi:10.1016/j.jmb.2013.04.028' apa: 'Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., … Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2013.04.028' chicago: 'Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” Journal of Molecular Biology. Elsevier, 2013. https://doi.org/10.1016/j.jmb.2013.04.028.' ieee: 'E. Rennella et al., “Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure,” Journal of Molecular Biology, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.' ista: 'Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15), 2722–2736.' mla: 'Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” Journal of Molecular Biology, vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:10.1016/j.jmb.2013.04.028.' short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736. date_created: 2020-09-18T10:09:12Z date_published: 2013-08-09T00:00:00Z date_updated: 2022-08-25T14:56:24Z day: '09' doi: 10.1016/j.jmb.2013.04.028 extern: '1' intvolume: ' 425' issue: '15' keyword: - Molecular Biology language: - iso: eng month: '08' oa_version: None page: 2722-2736 publication: Journal of Molecular Biology publication_identifier: issn: - 0022-2836 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 425 year: '2013' ... --- _id: '899' abstract: - lang: eng text: Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype relationship, is crucial to many areas of biology. Two aspects of fitness landscapes are the focus of contemporary studies of molecular evolution. First, the local shape of the fitness landscape defined by the contribution of individual alleles to fitness that is independent of all genetic interactions. Second, the global, multidimensional fitness landscape shape determined by how interactions between alleles at different loci change each other’s fitness impact, or epistasis. In explaining the high amino-acid usage (u), we focused on the global shape of the fitness landscape, ignoring the perturbations at individual sites. 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. Breen et al. reply. Nature. 2013;497(7451):E2-E3. doi:10.1038/nature12220 apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2013). Breen et al. reply. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12220 chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Breen et Al. Reply.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature12220. ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et al. reply,” Nature, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3, 2013. ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al. reply. Nature. 497(7451), E2–E3. mla: Breen, Michael, et al. “Breen et Al. Reply.” Nature, vol. 497, no. 7451, Nature Publishing Group, 2013, pp. E2–3, doi:10.1038/nature12220. short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013) E2–E3. date_created: 2018-12-11T11:49:05Z date_published: 2013-05-30T00:00:00Z date_updated: 2021-01-12T08:21:40Z day: '30' doi: 10.1038/nature12220 extern: 1 intvolume: ' 497' issue: '7451' month: '05' page: E2 - E3 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6747' quality_controlled: 0 status: public title: Breen et al. reply type: journal_article volume: 497 year: '2013' ... --- _id: '9674' abstract: - lang: eng text: The coalescence of nano-crystals during sintering is often found to result in interesting crystalline structures such as multi-fold twins, and yet the plasticity mechanism accompanying their formation is unclear. In this work, the sintering behavior of two unsupported copper nanoparticles initially at room temperature is investigated by molecular dynamics simulations under the constant-energy ensemble. The results reveal that once the two nanoparticles are brought into contact, they often go through drastic structural changes with the inter-particle grain boundary quickly eliminated, and single- and multi-fold twinning occurs frequently in the coalesced product. Whereas the formation of single twins is found to be via the more usual mechanism of emission of Shockley partials on {1 1 1} planes, the formation of fivefold twins, however, takes place via a novel dislocation-free mechanism involving a series of shear and rigid-body rotation processes caused by elastic waves with amplitudes not corresponding to any allowable Burgers vector in the fcc lattice. Such a lattice-wave, dislocation-free twinning mechanism has never been reported before. article_processing_charge: No article_type: original author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Alfonso H.W. full_name: Ngan, Alfonso H.W. last_name: Ngan citation: ama: 'Cheng B, Ngan AHW. The crystal structures of sintered copper nanoparticles: A molecular dynamics study. International Journal of Plasticity. 2013;47:65-79. doi:10.1016/j.ijplas.2013.01.006' apa: 'Cheng, B., & Ngan, A. H. W. (2013). The crystal structures of sintered copper nanoparticles: A molecular dynamics study. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2013.01.006' chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “The Crystal Structures of Sintered Copper Nanoparticles: A Molecular Dynamics Study.” International Journal of Plasticity. Elsevier, 2013. https://doi.org/10.1016/j.ijplas.2013.01.006.' ieee: 'B. Cheng and A. H. W. Ngan, “The crystal structures of sintered copper nanoparticles: A molecular dynamics study,” International Journal of Plasticity, vol. 47. Elsevier, pp. 65–79, 2013.' ista: 'Cheng B, Ngan AHW. 2013. The crystal structures of sintered copper nanoparticles: A molecular dynamics study. International Journal of Plasticity. 47, 65–79.' mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “The Crystal Structures of Sintered Copper Nanoparticles: A Molecular Dynamics Study.” International Journal of Plasticity, vol. 47, Elsevier, 2013, pp. 65–79, doi:10.1016/j.ijplas.2013.01.006.' short: B. Cheng, A.H.W. Ngan, International Journal of Plasticity 47 (2013) 65–79. date_created: 2021-07-15T14:27:44Z date_published: 2013-08-01T00:00:00Z date_updated: 2023-02-23T14:04:30Z day: '01' doi: 10.1016/j.ijplas.2013.01.006 extern: '1' intvolume: ' 47' language: - iso: eng month: '08' oa_version: None page: 65-79 publication: International Journal of Plasticity publication_identifier: issn: - 0749-6419 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'The crystal structures of sintered copper nanoparticles: A molecular dynamics study' type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 47 year: '2013' ... --- _id: '9676' abstract: - lang: eng text: Despite its relevance to a range of technological applications including nanocrystalline material fabrication, the sintering mechanisms of nanoparticles have not been well understood. It has been recognized that extrapolation from understanding of macro-particle sintering is unreliable for the nano-particle size regime. In this work, the sintering behaviour of copper nanoparticles under periodic boundary conditions at different temperatures and pressures was investigated by Molecular Dynamics simulations. It was found that smaller particle sizes, higher temperature and higher external pressure facilitate densification. Through a comparison with a two-sphere model, the governing mechanisms for many nanoparticles sintered at low temperature (T⩽900K) were identified to be a variety of plasticity processes including dislocation, twinning and even amorphization at the contact neck regions, due to the presence of high stresses. article_processing_charge: No article_type: original author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Alfonso H.W. full_name: Ngan, Alfonso H.W. last_name: Ngan citation: ama: 'Cheng B, Ngan AHW. The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. Computational Materials Science. 2013;74:1-11. doi:10.1016/j.commatsci.2013.03.014' apa: 'Cheng, B., & Ngan, A. H. W. (2013). The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. Computational Materials Science. Elsevier. https://doi.org/10.1016/j.commatsci.2013.03.014' chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “The Sintering and Densification Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” Computational Materials Science. Elsevier, 2013. https://doi.org/10.1016/j.commatsci.2013.03.014.' ieee: 'B. Cheng and A. H. W. Ngan, “The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study,” Computational Materials Science, vol. 74. Elsevier, pp. 1–11, 2013.' ista: 'Cheng B, Ngan AHW. 2013. The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. Computational Materials Science. 74, 1–11.' mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “The Sintering and Densification Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” Computational Materials Science, vol. 74, Elsevier, 2013, pp. 1–11, doi:10.1016/j.commatsci.2013.03.014.' short: B. Cheng, A.H.W. Ngan, Computational Materials Science 74 (2013) 1–11. date_created: 2021-07-16T06:46:38Z date_published: 2013-06-01T00:00:00Z date_updated: 2023-02-23T14:04:35Z day: '01' doi: 10.1016/j.commatsci.2013.03.014 extern: '1' intvolume: ' 74' language: - iso: eng month: '06' oa_version: None page: 1-11 publication: Computational Materials Science publication_identifier: issn: - 0927-0256 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study' type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 74 year: '2013' ... --- _id: '971' abstract: - lang: eng text: We study the stability of the normal state in a mesoscopic NSN junction biased by a constant voltage V with respect to the formation of the superconducting order. Using the linearized time-dependent Ginzburg-Landau equation, we obtain the temperature dependence of the instability line, V inst(T), where nucleation of superconductivity takes place. For sufficiently low biases, a stationary symmetric superconducting state emerges below the instability line. For higher biases, the normal phase is destroyed by the formation of a nonstationary bimodal state with two superconducting nuclei localized near the opposite terminals. The low-temperature and large-voltage behavior of the instability line is highly sensitive to the details of the inelastic relaxation mechanism in the wire. Therefore, experimental studies of Vinst(T) in NSN junctions may be used as an effective tool to access the parameters of the inelastic relaxation in the normal state. acknowledgement: We are grateful to M. V. Feigel'man, A. Kamenev, T. M. Klapwijk, J. P. Pekola, V. V. Ryazanov, J. C. W. Song, and D. Y. Vodolazov for discussions. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Mikhail full_name: Skvortsov, Mikhail A last_name: Skvortsov citation: ama: Serbyn M, Skvortsov M. Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. Physical Review B - Condensed Matter and Materials Physics. 2013;87(2). doi:10.1103/PhysRevB.87.020501 apa: Serbyn, M., & Skvortsov, M. (2013). Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.020501 chicago: Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a Voltage-Biased Normal-Superconducting-Normal Microbridge.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.020501. ieee: M. Serbyn and M. Skvortsov, “Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge,” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 2. American Physical Society, 2013. ista: Serbyn M, Skvortsov M. 2013. Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. Physical Review B - Condensed Matter and Materials Physics. 87(2). mla: Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a Voltage-Biased Normal-Superconducting-Normal Microbridge.” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 2, American Physical Society, 2013, doi:10.1103/PhysRevB.87.020501. short: M. Serbyn, M. Skvortsov, Physical Review B - Condensed Matter and Materials Physics 87 (2013). date_created: 2018-12-11T11:49:28Z date_published: 2013-01-02T00:00:00Z date_updated: 2021-01-12T08:22:20Z day: '02' doi: 10.1103/PhysRevB.87.020501 extern: 1 intvolume: ' 87' issue: '2' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1208.6004 month: '01' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6429' quality_controlled: 0 status: public title: Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge type: journal_article volume: 87 year: '2013' ... --- _id: '972' abstract: - lang: eng text: In topological crystalline insulators (TCIs), topology and crystal symmetry intertwine to create surface states with distinct characteristics. The breaking of crystal symmetry in TCIs is predicted to impart mass to the massless Dirac fermions. Here, we report high-resolution scanning tunneling microscopy studies of a TCI, Pb1-xSnxSe that reveal the coexistence of zero-mass Dirac fermions protected by crystal symmetry with massive Dirac fermions consistent with crystal symmetry breaking. In addition, we show two distinct regimes of the Fermi surface topology separated by a Van-Hove singularity at the Lifshitz transition point. Our work paves the way for engineering the Dirac band gap and realizing interaction-driven topological quantum phenomena in TCIs. author: - first_name: Yoshinori full_name: Okada, Yoshinori last_name: Okada - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Hsin full_name: Lin, Hsin last_name: Lin - first_name: Daniel full_name: Walkup, Daniel last_name: Walkup - first_name: Wenwen full_name: Zhou, Wenwen last_name: Zhou - first_name: Chetan full_name: Dhital, Chetan last_name: Dhital - first_name: Madhab full_name: Neupane, Madhab last_name: Neupane - first_name: Suyang full_name: Xu, Suyang last_name: Xu - first_name: Yungjui full_name: Wang, Yungjui last_name: Wang - first_name: Raman full_name: Sankar, Raman last_name: Sankar - first_name: Fangcheng full_name: Chou, Fangcheng last_name: Chou - first_name: Arun full_name: Bansil, Arun last_name: Bansil - first_name: Md full_name: Hasan, Md last_name: Hasan - first_name: Stephen full_name: Wilson, Stephen last_name: Wilson - first_name: Liang full_name: Fu, Liang last_name: Fu - first_name: Vidya full_name: Madhavan, Vidya last_name: Madhavan citation: ama: Okada Y, Serbyn M, Lin H, et al. Observation of dirac node formation and mass acquisition in a topological crystalline insulator. Science. 2013;341(6153):1496-1499. doi:10.1126/science.1239451 apa: Okada, Y., Serbyn, M., Lin, H., Walkup, D., Zhou, W., Dhital, C., … Madhavan, V. (2013). Observation of dirac node formation and mass acquisition in a topological crystalline insulator. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1239451 chicago: Okada, Yoshinori, Maksym Serbyn, Hsin Lin, Daniel Walkup, Wenwen Zhou, Chetan Dhital, Madhab Neupane, et al. “Observation of Dirac Node Formation and Mass Acquisition in a Topological Crystalline Insulator.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1239451. ieee: Y. Okada et al., “Observation of dirac node formation and mass acquisition in a topological crystalline insulator,” Science, vol. 341, no. 6153. American Association for the Advancement of Science, pp. 1496–1499, 2013. ista: Okada Y, Serbyn M, Lin H, Walkup D, Zhou W, Dhital C, Neupane M, Xu S, Wang Y, Sankar R, Chou F, Bansil A, Hasan M, Wilson S, Fu L, Madhavan V. 2013. Observation of dirac node formation and mass acquisition in a topological crystalline insulator. Science. 341(6153), 1496–1499. mla: Okada, Yoshinori, et al. “Observation of Dirac Node Formation and Mass Acquisition in a Topological Crystalline Insulator.” Science, vol. 341, no. 6153, American Association for the Advancement of Science, 2013, pp. 1496–99, doi:10.1126/science.1239451. short: Y. Okada, M. Serbyn, H. Lin, D. Walkup, W. Zhou, C. Dhital, M. Neupane, S. Xu, Y. Wang, R. Sankar, F. Chou, A. Bansil, M. Hasan, S. Wilson, L. Fu, V. Madhavan, Science 341 (2013) 1496–1499. date_created: 2018-12-11T11:49:29Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T08:22:20Z day: '01' doi: 10.1126/science.1239451 extern: '1' external_id: arxiv: - '1305.2823' intvolume: ' 341' issue: '6153' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1305.2823 month: '01' oa: 1 oa_version: Preprint page: 1496 - 1499 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '6430' quality_controlled: '1' status: public title: Observation of dirac node formation and mass acquisition in a topological crystalline insulator type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 341 year: '2013' ... --- _id: '975' abstract: - lang: eng text: Recent numerical work by Bardarson, Pollmann, and Moore revealed a slow, logarithmic in time, growth of the entanglement entropy for initial product states in a putative many-body localized phase. We show that this surprising phenomenon results from the dephasing due to exponentially small interaction-induced corrections to the eigenenergies of different states. For weak interactions, we find that the entanglement entropy grows as ξln (Vt/), where V is the interaction strength, and ξ is the single-particle localization length. The saturated value of the entanglement entropy at long times is determined by the participation ratios of the initial state over the eigenstates of the subsystem. Our work shows that the logarithmic entanglement growth is a universal phenomenon characteristic of the many-body localized phase in any number of spatial dimensions, and reveals a broad hierarchy of dephasing time scales present in such a phase. acknowledgement: We would like to thank E. Altman and J. Moore for useful comments on the manuscript. This research was supported in part by Perimeter Institute for Theoretical Physics. Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. Z. P. was supported by DOE Grant No. DE-SC0002140. The simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić - first_name: Dmitry full_name: Abanin, Dmitry A last_name: Abanin citation: ama: Serbyn M, Papić Z, Abanin D. Universal slow growth of entanglement in interacting strongly disordered systems. Physical Review Letters. 2013;110(26). doi:10.1103/PhysRevLett.110.260601 apa: Serbyn, M., Papić, Z., & Abanin, D. (2013). Universal slow growth of entanglement in interacting strongly disordered systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.260601 chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Universal Slow Growth of Entanglement in Interacting Strongly Disordered Systems.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.260601. ieee: M. Serbyn, Z. Papić, and D. Abanin, “Universal slow growth of entanglement in interacting strongly disordered systems,” Physical Review Letters, vol. 110, no. 26. American Physical Society, 2013. ista: Serbyn M, Papić Z, Abanin D. 2013. Universal slow growth of entanglement in interacting strongly disordered systems. Physical Review Letters. 110(26). mla: Serbyn, Maksym, et al. “Universal Slow Growth of Entanglement in Interacting Strongly Disordered Systems.” Physical Review Letters, vol. 110, no. 26, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.260601. short: M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:49:29Z date_published: 2013-06-28T00:00:00Z date_updated: 2021-01-12T08:22:22Z day: '28' doi: 10.1103/PhysRevLett.110.260601 extern: 1 intvolume: ' 110' issue: '26' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1304.4605 month: '06' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6426' quality_controlled: 0 status: public title: Universal slow growth of entanglement in interacting strongly disordered systems type: journal_article volume: 110 year: '2013' ... --- _id: '9749' abstract: - lang: eng text: Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise. article_processing_charge: No author: - first_name: Benjamin full_name: Zagorsky, Benjamin last_name: Zagorsky - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . 2013. doi:10.1371/journal.pone.0080814.s001 apa: Zagorsky, B., Reiter, J., Chatterjee, K., & Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . Public Library of Science. https://doi.org/10.1371/journal.pone.0080814.s001 chicago: Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0080814.s001. ieee: B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma .” Public Library of Science, 2013. ista: Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma , Public Library of Science, 10.1371/journal.pone.0080814.s001. mla: Zagorsky, Benjamin, et al. Forgiver Triumphs in Alternating Prisoner’s Dilemma . Public Library of Science, 2013, doi:10.1371/journal.pone.0080814.s001. short: B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013). date_created: 2021-07-28T15:45:07Z date_published: 2013-12-12T00:00:00Z date_updated: 2023-02-23T10:34:39Z day: '12' department: - _id: KrCh doi: 10.1371/journal.pone.0080814.s001 month: '12' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '2247' relation: used_in_publication status: public status: public title: 'Forgiver triumphs in alternating prisoner''s dilemma ' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2013' ... --- _id: '2944' 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.' acknowledged_ssus: - _id: ScienComp acknowledgement: This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13). 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. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165' apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165' chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/mec.12165.' ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.' ista: 'Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.' mla: 'Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.' short: S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002. date_created: 2018-12-11T12:00:28Z date_published: 2013-02-01T00:00:00Z date_updated: 2023-02-23T14:07:19Z day: '01' department: - _id: NiBa doi: 10.1111/mec.12165 intvolume: ' 22' issue: '4' language: - iso: eng month: '02' oa_version: None page: 987 - 1002 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3788' quality_controlled: '1' related_material: record: - id: '9758' relation: research_data status: public scopus_import: 1 status: public title: 'Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2013' ... --- _id: '894' abstract: - lang: eng text: 'Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. Conclusions: Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.' acknowledgement: Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329. Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute) 003803 and EMBO 003691 EUI-EURYIP-2011-4320. author: - first_name: Romain full_name: Derelle, Romain last_name: Derelle - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Vladimir full_name: Arkhipov, Vladimir last_name: Arkhipov - first_name: Hélène full_name: Corbel, Hélène last_name: Corbel - first_name: Adrien full_name: Frantz, Adrien last_name: Frantz - first_name: Julien full_name: Gasparini, Julien last_name: Gasparini - first_name: Lisa full_name: Jacquin, Lisa last_name: Jacquin - first_name: Gwenaël full_name: Jacob, Gwenaël last_name: Jacob - first_name: Sophie full_name: Thibault, Sophie last_name: Thibault - first_name: Emmanuelle full_name: Baudry, Emmanuelle last_name: Baudry citation: ama: Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 2013;6(1). doi:10.1186/1756-0500-6-310 apa: Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini, J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. BioMed Central. https://doi.org/10.1186/1756-0500-6-310 chicago: Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes. BioMed Central, 2013. https://doi.org/10.1186/1756-0500-6-310. ieee: R. Derelle et al., “Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R,” BMC Research Notes, vol. 6, no. 1. BioMed Central, 2013. ista: Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1). mla: Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes, vol. 6, no. 1, BioMed Central, 2013, doi:10.1186/1756-0500-6-310. short: R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini, L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013). date_created: 2018-12-11T11:49:04Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T08:21:25Z day: '01' doi: 10.1186/1756-0500-6-310 extern: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '01' oa_version: None publication: BMC Research Notes publication_status: published publisher: BioMed Central publist_id: '6752' status: public title: Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2013' ... --- _id: '9055' abstract: - lang: eng text: Spontaneous formation of colonies of bacteria or flocks of birds are examples of self-organization in active living matter. Here, we demonstrate a form of self-organization from nonequilibrium driving forces in a suspension of synthetic photoactivated colloidal particles. They lead to two-dimensional "living crystals," which form, break, explode, and re-form elsewhere. The dynamic assembly results from a competition between self-propulsion of particles and an attractive interaction induced respectively by osmotic and phoretic effects and activated by light. We measured a transition from normal to giant-number fluctuations. Our experiments are quantitatively described by simple numerical simulations. We show that the existence of the living crystals is intrinsically related to the out-of-equilibrium collisions of the self-propelled particles. 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: S. full_name: Sacanna, S. last_name: Sacanna - first_name: A. P. full_name: Steinberg, A. P. last_name: Steinberg - first_name: D. J. full_name: Pine, D. J. last_name: Pine - first_name: P. M. full_name: Chaikin, P. M. last_name: Chaikin citation: ama: Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. Living crystals of light-activated colloidal surfers. Science. 2013;339(6122):936-940. doi:10.1126/science.1230020 apa: Palacci, J. A., Sacanna, S., Steinberg, A. P., Pine, D. J., & Chaikin, P. M. (2013). Living crystals of light-activated colloidal surfers. Science. American Association for the Advancement of Science . https://doi.org/10.1126/science.1230020 chicago: Palacci, Jérémie A, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin. “Living Crystals of Light-Activated Colloidal Surfers.” Science. American Association for the Advancement of Science , 2013. https://doi.org/10.1126/science.1230020. ieee: J. A. Palacci, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin, “Living crystals of light-activated colloidal surfers,” Science, vol. 339, no. 6122. American Association for the Advancement of Science , pp. 936–940, 2013. ista: Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. 2013. Living crystals of light-activated colloidal surfers. Science. 339(6122), 936–940. mla: Palacci, Jérémie A., et al. “Living Crystals of Light-Activated Colloidal Surfers.” Science, vol. 339, no. 6122, American Association for the Advancement of Science , 2013, pp. 936–40, doi:10.1126/science.1230020. short: J.A. Palacci, S. Sacanna, A.P. Steinberg, D.J. Pine, P.M. Chaikin, Science 339 (2013) 936–940. date_created: 2021-02-01T14:37:29Z date_published: 2013-02-22T00:00:00Z date_updated: 2022-08-25T14:57:43Z day: '22' doi: 10.1126/science.1230020 extern: '1' external_id: pmid: - '23371555' intvolume: ' 339' issue: '6122' keyword: - Multidisciplinary language: - iso: eng month: '02' oa_version: None page: 936-940 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: Living crystals of light-activated colloidal surfers type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 339 year: '2013' ... --- _id: '905' abstract: - lang: eng text: A survey of avifauna was carried out in the Mys Shmidta area, north Chukotka, Russia from 8 June to 12 July 2011. A total of 90 species was recorded in the area, which together with literature data made a final list of 104 species. For several species this area is beyond the northern, north-eastern or north-western limits of their known distribution. We collected new data for 19 globally or locally threatened species. Tundra Swan Cygnus columbianus, Emperor Goose Anser canagica, American Golden Plover Pluvialis dominica, Western Sandpiper Calidris mauri, Semipalmated Sandpiper C. pusilla, Northern House Martin Delichon urbica and Barn Swallow Hirundo rustica were all confirmed to be breeding. Breeding of Brent Goose Branta bernicla nigricans, Spectacled Eider Somateria fischeri and Steller's Eider Polysticta stelleri was judged to be 'very likely'. There was no evidence for breeding of Ross's Gull Rhodostethia rosea despite several records. Two Eurasian Dotterels Eudromias morinellus were recorded displaying for the first time in the area, but the status of the species is unclear. The area is important for Snowy Owl Nyctea scandiaca, and as moulting grounds for Emperor Goose. Canada Goose Branta canadensis, Baikal Teal Anas formosa, Bar-tailed Godwit Limosa lapponica, Slaty-backed Gull Larus schistisagus, Thayer's Gull L. thayeri, Black-headed Gull L. ridibundus, White-tailed Eagle Haliaeetus albicilla, Steller's Sea Eagle H. pelagicus, Osprey Pandion haliaetus, Arctic Warbler Phylloscopus borealis and House Sparrow Passer domesticus are more likely to be rare vagrants or migrants. An observation of a Pine Siskin Carduelis pinus is the first record for Eurasia. acknowledgement: We thank Natalya Kveten and Oksana Makarova, heads of administrations of Mys Shmidta and Ryrkaypiy for hospitality and for help with organising our excursions. Warm thanks too to Pavel Tomkovich for useful comments on local birds and ornithological literature. We are very grateful to The David and Lucile Packard Foundation for the support to Birds Russia’s Spoon-billed Sandpiper conservation programme in 2011 and to Evgeny Syroechkovsky Jr, the leader of the Spoon-billed Sandpiper conservation team in Russia. author: - first_name: Vladimir full_name: Arkhipov, Vladimir Y last_name: Arkhipov - first_name: T full_name: Noah T last_name: Noah - first_name: Steffen full_name: Koschkar, Steffen last_name: Koschkar - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Arkhipov V, Noah T, Koschkar S, Kondrashov F. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. 2013;(29):25-30. apa: Arkhipov, V., Noah, T., Koschkar, S., & Kondrashov, F. (2013). Birds of Mys Shmidta, north Chukotka, Russia. Forktail. Oriental Bird Club. chicago: Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail. Oriental Bird Club, 2013. ieee: V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta, north Chukotka, Russia,” Forktail, no. 29. Oriental Bird Club, pp. 25–30, 2013. ista: Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. (29), 25–30. mla: Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail, no. 29, Oriental Bird Club, 2013, pp. 25–30. short: V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30. date_created: 2018-12-11T11:49:07Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T08:21:48Z day: '01' extern: 1 issue: '29' main_file_link: - open_access: '1' url: http://orientalbirdclub.org/forktail29/ month: '09' oa: 1 page: 25 - 30 publication: Forktail publication_status: published publisher: Oriental Bird Club publist_id: '6741' quality_controlled: 0 status: public title: Birds of Mys Shmidta, north Chukotka, Russia type: journal_article year: '2013' ... --- _id: '9153' abstract: - lang: eng text: Internal tide driven mixing plays a key role in sustaining the deep ocean stratification and meridional overturning circulation. Internal tides can be generated by topographic horizontal scales ranging from hundreds of meters to tens of kilometers. State of the art topographic products barely resolve scales smaller than ∼10 km in the deep ocean. On these scales abyssal hills dominate ocean floor roughness. The impact of abyssal hill roughness on internal‐tide generation is evaluated in this study. The conversion of M2 barotropic to baroclinic tidal energy is calculated based on linear wave theory both in real and spectral space using the Shuttle Radar Topography Mission SRTM30_PLUS bathymetric product at 1/120° resolution with and without the addition of synthetic abyssal hill roughness. Internal tide generation by abyssal hills integrates to 0.1 TW globally or 0.03 TW when the energy flux is empirically corrected for supercritical slope (i.e., ∼10% of the energy flux due to larger topographic scales resolved in standard products in both cases). The abyssal hill driven energy conversion is dominated by mid‐ocean ridges, where abyssal hill roughness is large. Focusing on two regions located over the Mid‐Atlantic Ridge and the East Pacific Rise, it is shown that regionally linear theory predicts an increase of the energy flux due to abyssal hills of up to 100% or 60% when an empirical correction for supercritical slopes is attempted. Therefore, abyssal hills, unresolved in state of the art topographic products, can have a strong impact on internal tide generation, especially over mid‐ocean ridges. article_processing_charge: No article_type: original author: - first_name: Angélique full_name: Melet, Angélique last_name: Melet - first_name: Maxim full_name: Nikurashin, Maxim last_name: Nikurashin - 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: S. full_name: Falahat, S. last_name: Falahat - first_name: Jonas full_name: Nycander, Jonas last_name: Nycander - first_name: Patrick G. full_name: Timko, Patrick G. last_name: Timko - first_name: Brian K. full_name: Arbic, Brian K. last_name: Arbic - first_name: John A. full_name: Goff, John A. last_name: Goff citation: ama: 'Melet A, Nikurashin M, Muller CJ, et al. Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. 2013;118(11):6303-6318. doi:10.1002/2013jc009212' apa: 'Melet, A., Nikurashin, M., Muller, C. J., Falahat, S., Nycander, J., Timko, P. G., … Goff, J. A. (2013). Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2013jc009212' chicago: 'Melet, Angélique, Maxim Nikurashin, Caroline J Muller, S. Falahat, Jonas Nycander, Patrick G. Timko, Brian K. Arbic, and John A. Goff. “Internal Tide Generation by Abyssal Hills Using Analytical Theory.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2013. https://doi.org/10.1002/2013jc009212.' ieee: 'A. Melet et al., “Internal tide generation by abyssal hills using analytical theory,” Journal of Geophysical Research: Oceans, vol. 118, no. 11. American Geophysical Union, pp. 6303–6318, 2013.' ista: 'Melet A, Nikurashin M, Muller CJ, Falahat S, Nycander J, Timko PG, Arbic BK, Goff JA. 2013. Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. 118(11), 6303–6318.' mla: 'Melet, Angélique, et al. “Internal Tide Generation by Abyssal Hills Using Analytical Theory.” Journal of Geophysical Research: Oceans, vol. 118, no. 11, American Geophysical Union, 2013, pp. 6303–18, doi:10.1002/2013jc009212.' short: 'A. Melet, M. Nikurashin, C.J. Muller, S. Falahat, J. Nycander, P.G. Timko, B.K. Arbic, J.A. Goff, Journal of Geophysical Research: Oceans 118 (2013) 6303–6318.' date_created: 2021-02-15T15:11:39Z date_published: 2013-11-07T00:00:00Z date_updated: 2022-01-24T13:46:15Z day: '07' doi: 10.1002/2013jc009212 extern: '1' intvolume: ' 118' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/2013JC009212 month: '11' oa: 1 oa_version: Published Version page: 6303-6318 publication: 'Journal of Geophysical Research: Oceans' publication_identifier: issn: - 2169-9275 publication_status: published publisher: American Geophysical Union quality_controlled: '1' status: public title: Internal tide generation by abyssal hills using analytical theory type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 118 year: '2013' ... --- _id: '9154' abstract: - lang: eng text: "In this study the response of tropical precipitation extremes to warming in organized convection is examined using a cloud-resolving model. Vertical shear is imposed to organize the convection into squall lines. Earlier studies show that in disorganized convection, the fractional increase of precipitation extremes is similar to that of surface water vapor, which is substantially smaller than the increase in column water vapor. It has been suggested that organized convection could lead to stronger amplifications.\r\nRegardless of the strength of the shear, amplifications of precipitation extremes in the cloud-resolving simulations are comparable to those of surface water vapor and are substantially less than increases in column water vapor. The results without shear and with critical shear, for which the squall lines are perpendicular to the shear, are surprisingly similar with a fractional rate of increase of precipitation extremes slightly smaller than that of surface water vapor. Interestingly, the dependence on shear is nonmonotonic, and stronger supercritical shear yields larger rates, close to or slightly larger than surface humidity.\r\nA scaling is used to evaluate the thermodynamic and dynamic contributions to precipitation extreme changes. To first order, they are dominated by the thermodynamic component, which has the same magnitude for all shears, close to the change in surface water vapor. The dynamic contribution plays a secondary role and tends to weaken extremes without shear and with critical shear, while it strengthens extremes with supercritical shear. These different dynamic contributions for different shears are due to different responses of convective mass fluxes in individual updrafts to warming." 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 citation: ama: Muller CJ. Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. 2013;26(14):5028-5043. doi:10.1175/jcli-d-12-00655.1 apa: Muller, C. J. (2013). Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. American Meteorological Society. https://doi.org/10.1175/jcli-d-12-00655.1 chicago: Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical Precipitation Extremes to Warming.” Journal of Climate. American Meteorological Society, 2013. https://doi.org/10.1175/jcli-d-12-00655.1. ieee: C. J. Muller, “Impact of convective organization on the response of tropical precipitation extremes to warming,” Journal of Climate, vol. 26, no. 14. American Meteorological Society, pp. 5028–5043, 2013. ista: Muller CJ. 2013. Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. 26(14), 5028–5043. mla: Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical Precipitation Extremes to Warming.” Journal of Climate, vol. 26, no. 14, American Meteorological Society, 2013, pp. 5028–43, doi:10.1175/jcli-d-12-00655.1. short: C.J. Muller, Journal of Climate 26 (2013) 5028–5043. date_created: 2021-02-15T15:26:39Z date_published: 2013-07-15T00:00:00Z date_updated: 2022-01-24T13:46:41Z day: '15' doi: 10.1175/jcli-d-12-00655.1 extern: '1' intvolume: ' 26' issue: '14' keyword: - Atmospheric Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1175/JCLI-D-12-00655.1 month: '07' oa: 1 oa_version: Published Version page: 5028-5043 publication: Journal of Climate publication_identifier: issn: - 0894-8755 - 1520-0442 publication_status: published publisher: American Meteorological Society quality_controlled: '1' status: public title: Impact of convective organization on the response of tropical precipitation extremes to warming type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 26 year: '2013' ...