--- _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' ... --- _id: '9167' abstract: - lang: eng text: We introduce a self-propelled colloidal hematite docker that can be steered to a small particle cargo many times its size, dock, transport the cargo to a remote location, and then release it. The self-propulsion and docking are reversible and activated by visible light. The docker can be steered either by a weak uniform magnetic field or by nanoscale tracks in a textured substrate. The light-activated motion and docking originate from osmotic/phoretic particle transport in a concentration gradient of fuel, hydrogen peroxide, induced by the photocatalytic activity of the hematite. The docking mechanism is versatile and can be applied to various materials and shapes. The hematite dockers are simple single-component particles and are synthesized in bulk quantities. This system opens up new possibilities for designing complex micrometer-size factories as well as new biomimetic systems. 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: Stefano full_name: Sacanna, Stefano last_name: Sacanna - first_name: Adrian full_name: Vatchinsky, Adrian last_name: Vatchinsky - first_name: Paul M. full_name: Chaikin, Paul M. last_name: Chaikin - first_name: David J. full_name: Pine, David J. last_name: Pine citation: ama: Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. 2013;135(43):15978-15981. doi:10.1021/ja406090s apa: Palacci, J. A., Sacanna, S., Vatchinsky, A., Chaikin, P. M., & Pine, D. J. (2013). Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja406090s chicago: Palacci, Jérémie A, Stefano Sacanna, Adrian Vatchinsky, Paul M. Chaikin, and David J. Pine. “Photoactivated Colloidal Dockers for Cargo Transportation.” Journal of the American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja406090s. ieee: J. A. Palacci, S. Sacanna, A. Vatchinsky, P. M. Chaikin, and D. J. Pine, “Photoactivated colloidal dockers for cargo transportation,” Journal of the American Chemical Society, vol. 135, no. 43. American Chemical Society, pp. 15978–15981, 2013. ista: Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. 2013. Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. 135(43), 15978–15981. mla: Palacci, Jérémie A., et al. “Photoactivated Colloidal Dockers for Cargo Transportation.” Journal of the American Chemical Society, vol. 135, no. 43, American Chemical Society, 2013, pp. 15978–81, doi:10.1021/ja406090s. short: J.A. Palacci, S. Sacanna, A. Vatchinsky, P.M. Chaikin, D.J. Pine, Journal of the American Chemical Society 135 (2013) 15978–15981. date_created: 2021-02-18T14:31:26Z date_published: 2013-10-30T00:00:00Z date_updated: 2021-02-22T10:10:41Z day: '30' doi: 10.1021/ja406090s extern: '1' external_id: arxiv: - '1310.5724' pmid: - '24131488' intvolume: ' 135' issue: '43' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1310.5724 month: '10' oa: 1 oa_version: Preprint page: 15978-15981 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - '15205126' issn: - '00027863' publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Photoactivated colloidal dockers for cargo transportation type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 135 year: '2013' ... --- _id: '921' abstract: - lang: eng text: Recent experiments have shown that spreading epithelial sheets exhibit a long-range coordination of motility forces that leads to a buildup of tension in the tissue, which may enhance cell division and the speed of wound healing. Furthermore, the edges of these epithelial sheets commonly show finger-like protrusions whereas the bulk often displays spontaneous swirls of motile cells. To explain these experimental observations, we propose a simple flocking-type mechanism, in which cells tend to align their motility forceswith their velocity. Implementing this idea in amechanical tissue simulation, the proposed model gives rise to efficient spreading and can explain the experimentally observed long-range alignment of motility forces in highly disordered patterns, as well as the buildup of tensile stress throughout the tissue. Our model also qualitatively reproduces the dependence of swirl size and swirl velocity on cell density reported in experiments and exhibits an undulation instability at the edge of the spreading tissue commonly observed in vivo. Finally, we study the dependence of colony spreading speed on important physical and biological parameters and derive simple scaling relations that show that coordination of motility forces leads to an improvement of the wound healing process for realistic tissue parameters. acknowledgement: "This work was supported by National Science Foundation (NSF) Grant DMS-1068869 and by the NSF Center for Theoretical Biological Physics (Grant NSF PHY-0822283).\r\nWe acknowledge useful discussions with Eshel Ben-Jacob and Assaf Zaritsky. " article_processing_charge: No author: - first_name: Markus full_name: Basan, Markus last_name: Basan - first_name: Jens full_name: Elgeti, Jens last_name: Elgeti - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Wouter full_name: Rappel, Wouter last_name: Rappel - first_name: Herbert full_name: Levine, Herbert last_name: Levine citation: ama: Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. 2013;110(7):2452-2459. doi:10.1073/pnas.1219937110 apa: Basan, M., Elgeti, J., Hannezo, E. B., Rappel, W., & Levine, H. (2013). Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1219937110 chicago: Basan, Markus, Jens Elgeti, Edouard B Hannezo, Wouter Rappel, and Herbert Levine. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism for Efficient Wound Healing.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1219937110. ieee: M. Basan, J. Elgeti, E. B. Hannezo, W. Rappel, and H. Levine, “Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2452–2459, 2013. ista: Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. 2013. Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. 110(7), 2452–2459. mla: Basan, Markus, et al. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism for Efficient Wound Healing.” PNAS, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2452–59, doi:10.1073/pnas.1219937110. short: M. Basan, J. Elgeti, E.B. Hannezo, W. Rappel, H. Levine, PNAS 110 (2013) 2452–2459. date_created: 2018-12-11T11:49:12Z date_published: 2013-02-12T00:00:00Z date_updated: 2021-01-12T08:21:55Z day: '12' doi: 10.1073/pnas.1219937110 extern: '1' intvolume: ' 110' issue: '7' language: - iso: eng month: '02' oa_version: None page: 2452 - 2459 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6518' status: public title: Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '9459' abstract: - lang: eng text: Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway. article_processing_charge: No article_type: original author: - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach - first_name: M. Yvonne full_name: Kim, M. Yvonne last_name: Kim - first_name: Ping-Hung full_name: Hsieh, Ping-Hung last_name: Hsieh - first_name: Devin full_name: Coleman-Derr, Devin last_name: Coleman-Derr - first_name: Leor full_name: Eshed-Williams, Leor last_name: Eshed-Williams - first_name: Ka full_name: Thao, Ka last_name: Thao - first_name: Stacey L. full_name: Harmer, Stacey L. last_name: Harmer - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013;153(1):193-205. doi:10.1016/j.cell.2013.02.033 apa: Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.02.033 chicago: Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.02.033. ieee: A. Zemach et al., “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” Cell, vol. 153, no. 1. Elsevier, pp. 193–205, 2013. ista: Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205. mla: Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” Cell, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:10.1016/j.cell.2013.02.033. short: A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205. date_created: 2021-06-04T12:23:28Z date_published: 2013-03-28T00:00:00Z date_updated: 2021-12-14T08:25:35Z day: '28' department: - _id: DaZi doi: 10.1016/j.cell.2013.02.033 extern: '1' external_id: pmid: - '23540698' intvolume: ' 153' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2013.02.033 month: '03' oa: 1 oa_version: Published Version page: 193-205 pmid: 1 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 153 year: '2013' ... --- _id: '9481' abstract: - lang: eng text: Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants. article_processing_charge: No article_type: original author: - first_name: Jessica A. full_name: Rodrigues, Jessica A. last_name: Rodrigues - first_name: Randy full_name: Ruan, Randy last_name: Ruan - first_name: Toshiro full_name: Nishimura, Toshiro last_name: Nishimura - first_name: Manoj K. full_name: Sharma, Manoj K. last_name: Sharma - first_name: Rita full_name: Sharma, Rita last_name: Sharma - first_name: Pamela C full_name: Ronald, Pamela C last_name: Ronald - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939. doi:10.1073/pnas.1306164110 apa: Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1306164110 chicago: Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110. ieee: J. A. Rodrigues et al., “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” Proceedings of the National Academy of Sciences, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013. ista: Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 110(19), 7934–7939. mla: Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy of Sciences, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7934–39, doi:10.1073/pnas.1306164110. short: J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939. date_created: 2021-06-07T07:31:02Z date_published: 2013-05-07T00:00:00Z date_updated: 2021-12-14T08:26:44Z day: '07' department: - _id: DaZi doi: 10.1073/pnas.1306164110 extern: '1' external_id: pmid: - '23613580' intvolume: ' 110' issue: '19' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1306164110 month: '05' oa: 1 oa_version: Published Version page: 7934-7939 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 110 year: '2013' ... --- _id: '9663' abstract: - lang: eng text: 'Molecular dynamics simulations of small Cu nanoparticles using three different interatomic potentials at rising temperature indicate that small nanoparticles can undergo solid-solid structural transitions through a direct geometrical conversion route. The direct geometrical conversion can happen for cuboctahedral nanoparticles, which turn into an icosahedra shape: one diagonal of the square faces contracts, and the faces are folded along the diagonal to give rise to two equilateral triangles. The transition is a kinetic process that cannot be fully explained through an energetic point of view. It has low activation energy and fast reaction time in the simulations. The transition mechanism is via the transmission of shear waves initiated from the particle surface and does not involve dislocation activity.' article_number: '164314' 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. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. 2013;138(16). doi:10.1063/1.4802025 apa: Cheng, B., & Ngan, A. H. W. (2013). Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4802025 chicago: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” The Journal of Chemical Physics. AIP Publishing, 2013. https://doi.org/10.1063/1.4802025. ieee: B. Cheng and A. H. W. Ngan, “Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion,” The Journal of Chemical Physics, vol. 138, no. 16. AIP Publishing, 2013. ista: Cheng B, Ngan AHW. 2013. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. 138(16), 164314. mla: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” The Journal of Chemical Physics, vol. 138, no. 16, 164314, AIP Publishing, 2013, doi:10.1063/1.4802025. short: B. Cheng, A.H.W. Ngan, The Journal of Chemical Physics 138 (2013). date_created: 2021-07-15T09:27:58Z date_published: 2013-04-28T00:00:00Z date_updated: 2021-08-09T12:35:34Z day: '28' doi: 10.1063/1.4802025 extern: '1' external_id: pmid: - '23635145' intvolume: ' 138' issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://pubmed.ncbi.nlm.nih.gov/23635145/ month: '04' oa: 1 oa_version: Submitted Version pmid: 1 publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 138 year: '2013' ... --- _id: '9682' abstract: - lang: eng text: In this work, we simulate the response of two Cu nanoparticles colliding at different approaching rates at room temperature by MD. For small nanospheres, the formation of single twins is favored at high approach rates, whereas larger nanospheres mainly deform by dislocation slip. For small nanocubes with large {100} flat surfaces, however, a dislocation-free direct geometrical conversion process that leads to five-fold twinning dominates except at highly retarded approaching rates. For larger nanocubes, single twin formation is the governing plasticity mechanism. The probability for plastic deformation by dislocation slip or twinning is attributed to the abundance of surface steps, which act as sites for dislocation nucleation. 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. Crystal plasticity of Cu nanocrystals during collision. Materials Science and Engineering: A. 2013;585:326-334. doi:10.1016/j.msea.2013.07.065' apa: 'Cheng, B., & Ngan, A. H. W. (2013). Crystal plasticity of Cu nanocrystals during collision. Materials Science and Engineering: A. Elsevier. https://doi.org/10.1016/j.msea.2013.07.065' chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “Crystal Plasticity of Cu Nanocrystals during Collision.” Materials Science and Engineering: A. Elsevier, 2013. https://doi.org/10.1016/j.msea.2013.07.065.' ieee: 'B. Cheng and A. H. W. Ngan, “Crystal plasticity of Cu nanocrystals during collision,” Materials Science and Engineering: A, vol. 585. Elsevier, pp. 326–334, 2013.' ista: 'Cheng B, Ngan AHW. 2013. Crystal plasticity of Cu nanocrystals during collision. Materials Science and Engineering: A. 585, 326–334.' mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “Crystal Plasticity of Cu Nanocrystals during Collision.” Materials Science and Engineering: A, vol. 585, Elsevier, 2013, pp. 326–34, doi:10.1016/j.msea.2013.07.065.' short: 'B. Cheng, A.H.W. Ngan, Materials Science and Engineering: A 585 (2013) 326–334.' date_created: 2021-07-19T09:04:36Z date_published: 2013-11-15T00:00:00Z date_updated: 2023-02-23T14:04:51Z day: '15' doi: 10.1016/j.msea.2013.07.065 extern: '1' intvolume: ' 585' language: - iso: eng month: '11' oa_version: None page: 326-334 publication: 'Materials Science and Engineering: A' publication_identifier: issn: - 0921-5093 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Crystal plasticity of Cu nanocrystals during collision type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 585 year: '2013' ... --- _id: '970' abstract: - lang: eng text: 'Recently a new high-mobility Dirac material, trilayer graphene, was realized experimentally. The band structure of ABA-stacked trilayer graphene consists of a monolayer-like and a bilayer-like pair of bands. Here we study electronic properties of ABA-stacked trilayer graphene biased by a perpendicular electric field. We find that the combination of the bias and trigonal warping gives rise to a set of new Dirac points: In each valley, seven species of Dirac fermions with small masses of order of a few meV emerge. The positions and masses of the emergent Dirac fermions are tunable by bias, and one group of Dirac fermions becomes massless at a certain bias value. Therefore, in contrast to bilayer graphene, the conductivity at the neutrality point is expected to show nonmonotonic behavior, becoming of the order of a few e2/h when some Dirac masses vanish. Further, we analyze the evolution of the Landau level spectrum as a function of bias. The emergence of new Dirac points in the band structure translates into new threefold-degenerate groups of Landau levels. This leads to an anomalous quantum Hall effect, in which some quantum Hall steps have a height of 3e2/h. At an intermediate bias, the degeneracies of all Landau levels get lifted, and in this regime all quantum Hall plateaus are spaced by e2/h. Finally, we show that the pattern of Landau level crossings is very sensitive to certain band structure parameters, and can therefore provide a useful tool for determining their precise values.' acknowledgement: We thank Pablo Jarillo-Herrero, Leonardo Campos, and Thiti Taychatanapat for attracting our attention to the problem of biased trilayer graphene, and for many helpful 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: Dmitry full_name: Abanin, Dmitry A last_name: Abanin citation: ama: Serbyn M, Abanin D. New Dirac points and multiple Landau level crossings in biased trilayer graphene. Physical Review B - Condensed Matter and Materials Physics. 2013;87(11). doi:10.1103/PhysRevB.87.115422 apa: Serbyn, M., & Abanin, D. (2013). New Dirac points and multiple Landau level crossings in biased trilayer graphene. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.115422 chicago: Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau Level Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.115422. ieee: M. Serbyn and D. Abanin, “New Dirac points and multiple Landau level crossings in biased trilayer graphene,” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 11. American Physical Society, 2013. ista: Serbyn M, Abanin D. 2013. New Dirac points and multiple Landau level crossings in biased trilayer graphene. Physical Review B - Condensed Matter and Materials Physics. 87(11). mla: Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau Level Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 11, American Physical Society, 2013, doi:10.1103/PhysRevB.87.115422. short: M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 87 (2013). date_created: 2018-12-11T11:49:28Z date_published: 2013-03-18T00:00:00Z date_updated: 2021-01-12T08:22:20Z day: '18' doi: 10.1103/PhysRevB.87.115422 extern: 1 intvolume: ' 87' issue: '11' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1212.6251 month: '03' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6428' quality_controlled: 0 status: public title: New Dirac points and multiple Landau level crossings in biased trilayer graphene type: journal_article volume: 87 year: '2013' ... --- _id: '973' abstract: - lang: eng text: We construct a complete set of local integrals of motion that characterize the many-body localized (MBL) phase. Our approach relies on the assumption that local perturbations act locally on the eigenstates in the MBL phase, which is supported by numerical simulations of the random-field XXZ spin chain. We describe the structure of the eigenstates in the MBL phase and discuss the implications of local conservation laws for its nonequilibrium quantum dynamics. We argue that the many-body localization can be used to protect coherence in the system by suppressing relaxation between eigenstates with different local integrals of motion. acknowledgement: We thank J. Moore for useful discussions. 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. M. S. was supported by the National Science Foundation under Grant No. DMR-1104498. 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. Local conservation laws and the structure of the many body localized states. Physical Review Letters. 2013;111(12). doi:10.1103/PhysRevLett.111.127201 apa: Serbyn, M., Papić, Z., & Abanin, D. (2013). Local conservation laws and the structure of the many body localized states. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.111.127201 chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Local Conservation Laws and the Structure of the Many Body Localized States.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.111.127201. ieee: M. Serbyn, Z. Papić, and D. Abanin, “Local conservation laws and the structure of the many body localized states,” Physical Review Letters, vol. 111, no. 12. American Physical Society, 2013. ista: Serbyn M, Papić Z, Abanin D. 2013. Local conservation laws and the structure of the many body localized states. Physical Review Letters. 111(12). mla: Serbyn, Maksym, et al. “Local Conservation Laws and the Structure of the Many Body Localized States.” Physical Review Letters, vol. 111, no. 12, American Physical Society, 2013, doi:10.1103/PhysRevLett.111.127201. short: M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 111 (2013). date_created: 2018-12-11T11:49:29Z date_published: 2013-09-17T00:00:00Z date_updated: 2021-01-12T08:22:21Z day: '17' doi: 10.1103/PhysRevLett.111.127201 extern: 1 intvolume: ' 111' issue: '12' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1305.5554 month: '09' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6424' quality_controlled: 0 status: public title: Local conservation laws and the structure of the many body localized states type: journal_article volume: 111 year: '2013' ... --- _id: '974' abstract: - lang: eng text: We propose a possible realization of the overscreened Kondo impurity problem by a magnetic s=1/2 impurity embedded in a two-dimensional S=1 U(1) spin liquid with a Fermi surface. This problem contains an interesting interplay between non-Fermi-liquid behavior induced by a U(1) gauge field coupled to fermions and a non-Fermi-liquid fixed point in the overscreened Kondo problem. Using a large-N expansion together with an expansion in the dynamical exponent of the gauge field, we find that the coupling to the gauge field leads to weak but observable changes in the physical properties of the system at the overscreened Kondo fixed point. We discuss the extrapolation of this result to a physical case and argue that the realization of overscreened Kondo physics could lead to observations of effects due to gauge fields. author: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Todadri full_name: Senthil, Todadri last_name: Senthil - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: ama: Serbyn M, Senthil T, Lee P. Overscreened Kondo fixed point in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics. 2013;88(2). doi:10.1103/PhysRevB.88.024419 apa: Serbyn, M., Senthil, T., & Lee, P. (2013). Overscreened Kondo fixed point in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.88.024419 chicago: Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Overscreened Kondo Fixed Point in S=1 Spin Liquid.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.024419. ieee: M. Serbyn, T. Senthil, and P. Lee, “Overscreened Kondo fixed point in S=1 spin liquid,” Physical Review B - Condensed Matter and Materials Physics, vol. 88, no. 2. American Physical Society, 2013. ista: Serbyn M, Senthil T, Lee P. 2013. Overscreened Kondo fixed point in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics. 88(2). mla: Serbyn, Maksym, et al. “Overscreened Kondo Fixed Point in S=1 Spin Liquid.” Physical Review B - Condensed Matter and Materials Physics, vol. 88, no. 2, American Physical Society, 2013, doi:10.1103/PhysRevB.88.024419. short: M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 88 (2013). date_created: 2018-12-11T11:49:29Z date_published: 2013-07-19T00:00:00Z date_updated: 2021-01-12T08:22:21Z day: '19' doi: 10.1103/PhysRevB.88.024419 extern: '1' external_id: arxiv: - '1212.5179' intvolume: ' 88' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1212.5179 month: '07' oa: 1 oa_version: Preprint publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6425' quality_controlled: '1' status: public title: Overscreened Kondo fixed point in S=1 spin liquid type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 88 year: '2013' ... --- _id: '2284' abstract: - lang: eng text: 'Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal-originally described for honeybees as "hygienic behaviour"-is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.' acknowledgement: "The study was funded by the European Research Council (Marie Curie ERG 036569) and Marie Curie IEF 302204 to LVU\r\nCC BY 2.0\r\n" article_number: '225' author: - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Michel full_name: Chapuisat, Michel last_name: Chapuisat - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. 2013;13(1). doi:10.1186/1471-2148-13-225 apa: Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., & Cremer, S. (2013). Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-225 chicago: Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-225. ieee: S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013. ista: Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2013. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. 13(1), 225. mla: Tragust, Simon, et al. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” BMC Evolutionary Biology, vol. 13, no. 1, 225, BioMed Central, 2013, doi:10.1186/1471-2148-13-225. short: S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, BMC Evolutionary Biology 13 (2013). date_created: 2018-12-11T11:56:46Z date_published: 2013-10-14T00:00:00Z date_updated: 2023-02-23T14:07:06Z day: '14' ddc: - '570' department: - _id: SyCr doi: 10.1186/1471-2148-13-225 ec_funded: 1 file: - access_level: open_access checksum: c16ef36f2a10786a7885e19c4528d707 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:41Z date_updated: 2020-07-14T12:45:37Z file_id: '5026' file_name: IST-2016-402-v1+1_1471-2148-13-225.pdf file_size: 281736 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' - _id: 25DAF0B2-B435-11E9-9278-68D0E5697425 grant_number: CR-118/3-1 name: Host-Parasite Coevolution publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '4647' pubrep_id: '402' quality_controlled: '1' related_material: record: - id: '9753' relation: research_data status: public scopus_import: 1 status: public title: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2013' ... --- _id: '2277' abstract: - lang: eng text: Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible. article_number: e1003344 author: - first_name: Kristina full_name: Simmons, Kristina last_name: Simmons - first_name: Jason full_name: Prentice, Jason last_name: Prentice - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Jan full_name: Homann, Jan last_name: Homann - first_name: Heather full_name: Yee, Heather last_name: Yee - first_name: Stephanie full_name: Palmer, Stephanie last_name: Palmer - first_name: Philip full_name: Nelson, Philip last_name: Nelson - first_name: Vijay full_name: Balasubramanian, Vijay last_name: Balasubramanian citation: ama: Simmons K, Prentice J, Tkačik G, et al. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003344 apa: Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2013). Transformation of stimulus correlations by the retina. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003344 chicago: Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1003344. ieee: K. Simmons et al., “Transformation of stimulus correlations by the retina,” PLoS Computational Biology, vol. 9, no. 12. Public Library of Science, 2013. ista: Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2013. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 9(12), e1003344. mla: Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology, vol. 9, no. 12, e1003344, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003344. short: K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, PLoS Computational Biology 9 (2013). date_created: 2018-12-11T11:56:43Z date_published: 2013-12-05T00:00:00Z date_updated: 2023-02-23T14:07:04Z day: '05' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pcbi.1003344 file: - access_level: open_access checksum: 46722afc4f7eabb0831165d9c1b171ad content_type: application/pdf creator: system date_created: 2018-12-12T10:14:36Z date_updated: 2020-07-14T12:45:36Z file_id: '5089' file_name: IST-2016-410-v1+1_journal.pcbi.1003344.pdf file_size: 3115568 relation: main_file file_date_updated: 2020-07-14T12:45:36Z has_accepted_license: '1' intvolume: ' 9' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '4667' pubrep_id: '410' quality_controlled: '1' related_material: record: - id: '9752' relation: research_data status: public scopus_import: 1 status: public title: Transformation of stimulus correlations by the retina 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: '9754' abstract: - lang: eng text: Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources. article_processing_charge: No author: - first_name: Jack full_name: Hearn, Jack last_name: Hearn - first_name: Graham full_name: Stone, Graham last_name: Stone - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Lynsey full_name: Bunnefeld, Lynsey last_name: Bunnefeld citation: ama: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. 2013. doi:10.5061/dryad.r3r60' apa: 'Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013). Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60' chicago: 'Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.' ieee: 'J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013.' ista: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies, Dryad, 10.5061/dryad.r3r60.' mla: 'Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.' short: J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013). date_created: 2021-07-30T08:31:22Z date_published: 2013-10-01T00:00:00Z date_updated: 2023-02-23T10:31:17Z day: '01' department: - _id: NiBa doi: 10.5061/dryad.r3r60 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.r3r60 month: '10' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2170' relation: used_in_publication status: public status: public title: 'Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2013' ... --- _id: '976' abstract: - lang: eng text: 'Motivated by a search for experimental probes to access the physics of fractionalized excitations called spinons in spin liquids, we study the interaction of spinons with lattice vibrations. We consider the case of algebraic spin liquid, when spinons have fermionic statistics and a Dirac-like dispersion. We establish the general procedure for deriving spinon-phonon interactions, which is based on symmetry considerations. The procedure is illustrated for four different algebraic spin liquids: π-flux and staggered-flux phases on a square lattice, π-flux phase on a kagome lattice, and zero-flux phase on a honeycomb lattice. Although the low-energy description is similar for all these phases, different underlying symmetry groups lead to a distinct form of spinon-phonon interaction Hamiltonian. The explicit form of the spinon-phonon interaction is used to estimate the attenuation of ultrasound in an algebraic spin liquid. The prospects of the sound attenuation as a probe of spinons are discussed.' acknowledgement: M. S. is grateful to X.-G. Wen, L. Levitov, M. Metlitski, K. Michaeli, K.-T. Chen, and A. Potter for many useful discussions. We acknowledge support by Grant No. NSF DMR 1104498. We acknowledge the hospitality of KITP, where final stages of this project were completed. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: ama: Serbyn M, Lee P. Spinon-phonon interaction in algebraic spin liquids. Physical Review B - Condensed Matter and Materials Physics. 2013;87(17). doi:10.1103/PhysRevB.87.174424 apa: Serbyn, M., & Lee, P. (2013). Spinon-phonon interaction in algebraic spin liquids. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.174424 chicago: Serbyn, Maksym, and Patrick Lee. “Spinon-Phonon Interaction in Algebraic Spin Liquids.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.174424. ieee: M. Serbyn and P. Lee, “Spinon-phonon interaction in algebraic spin liquids,” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 17. American Physical Society, 2013. ista: Serbyn M, Lee P. 2013. Spinon-phonon interaction in algebraic spin liquids. Physical Review B - Condensed Matter and Materials Physics. 87(17). mla: Serbyn, Maksym, and Patrick Lee. “Spinon-Phonon Interaction in Algebraic Spin Liquids.” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 17, American Physical Society, 2013, doi:10.1103/PhysRevB.87.174424. short: M. Serbyn, P. Lee, Physical Review B - Condensed Matter and Materials Physics 87 (2013). date_created: 2018-12-11T11:49:30Z date_published: 2013-05-22T00:00:00Z date_updated: 2021-01-12T08:22:22Z day: '22' doi: 10.1103/PhysRevB.87.174424 extern: 1 intvolume: ' 87' issue: '17' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1303.0772 month: '05' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6427' quality_controlled: 0 status: public title: Spinon-phonon interaction in algebraic spin liquids type: journal_article volume: 87 year: '2013' ... --- _id: '12638' abstract: - lang: eng text: Central Asian water resources largely depend on melt water generated in the Pamir and Tien Shan mountain ranges. To estimate future water availability in this region, it is necessary to use climate projections to estimate the future glacier extent and volume. In this study, we evaluate the impact of uncertainty in climate change projections on the future glacier extent in the Amu and Syr Darya river basins. To this end we use the latest climate change projections generated for the upcoming IPCC report (CMIP5) and, for comparison, projections used in the fourth IPCC assessment (CMIP3). With these projections we force a regionalized glacier mass balance model, and estimate changes in the basins' glacier extent as a function of the glacier size distribution in the basins and projected temperature and precipitation. This glacier mass balance model is specifically developed for implementation in large scale hydrological models, where the spatial resolution does not allow for simulating individual glaciers and data scarcity is an issue. Although the CMIP5 ensemble results in greater regional warming than the CMIP3 ensemble and the range in projections for temperature as well as precipitation is wider for the CMIP5 than for the CMIP3, the spread in projections of future glacier extent in Central Asia is similar for both ensembles. This is because differences in temperature rise are small during periods of maximum melt (July–September) while differences in precipitation change are small during the period of maximum accumulation (October–February). However, the model uncertainty due to parameter uncertainty is high, and has roughly the same importance as uncertainty in the climate projections. Uncertainty about the size of the decline in glacier extent remains large, making estimates of future Central Asian glacier evolution and downstream water availability uncertain. article_processing_charge: No article_type: original author: - first_name: A. F. full_name: Lutz, A. F. last_name: Lutz - first_name: W. W. full_name: Immerzeel, W. W. last_name: Immerzeel - first_name: A. full_name: Gobiet, A. last_name: Gobiet - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: M. F. P. full_name: Bierkens, M. F. P. last_name: Bierkens citation: ama: Lutz AF, Immerzeel WW, Gobiet A, Pellicciotti F, Bierkens MFP. Comparison of climate change signals in CMIP3 and CMIP5 multi-model ensembles and implications for Central Asian glaciers. Hydrology and Earth System Sciences. 2013;17(9):3661-3677. doi:10.5194/hess-17-3661-2013 apa: Lutz, A. F., Immerzeel, W. W., Gobiet, A., Pellicciotti, F., & Bierkens, M. F. P. (2013). Comparison of climate change signals in CMIP3 and CMIP5 multi-model ensembles and implications for Central Asian glaciers. Hydrology and Earth System Sciences. Copernicus GmbH. https://doi.org/10.5194/hess-17-3661-2013 chicago: Lutz, A. F., W. W. Immerzeel, A. Gobiet, Francesca Pellicciotti, and M. F. P. Bierkens. “Comparison of Climate Change Signals in CMIP3 and CMIP5 Multi-Model Ensembles and Implications for Central Asian Glaciers.” Hydrology and Earth System Sciences. Copernicus GmbH, 2013. https://doi.org/10.5194/hess-17-3661-2013. ieee: A. F. Lutz, W. W. Immerzeel, A. Gobiet, F. Pellicciotti, and M. F. P. Bierkens, “Comparison of climate change signals in CMIP3 and CMIP5 multi-model ensembles and implications for Central Asian glaciers,” Hydrology and Earth System Sciences, vol. 17, no. 9. Copernicus GmbH, pp. 3661–3677, 2013. ista: Lutz AF, Immerzeel WW, Gobiet A, Pellicciotti F, Bierkens MFP. 2013. Comparison of climate change signals in CMIP3 and CMIP5 multi-model ensembles and implications for Central Asian glaciers. Hydrology and Earth System Sciences. 17(9), 3661–3677. mla: Lutz, A. F., et al. “Comparison of Climate Change Signals in CMIP3 and CMIP5 Multi-Model Ensembles and Implications for Central Asian Glaciers.” Hydrology and Earth System Sciences, vol. 17, no. 9, Copernicus GmbH, 2013, pp. 3661–77, doi:10.5194/hess-17-3661-2013. short: A.F. Lutz, W.W. Immerzeel, A. Gobiet, F. Pellicciotti, M.F.P. Bierkens, Hydrology and Earth System Sciences 17 (2013) 3661–3677. date_created: 2023-02-20T08:17:05Z date_published: 2013-09-01T00:00:00Z date_updated: 2023-02-24T08:19:48Z day: '01' doi: 10.5194/hess-17-3661-2013 extern: '1' intvolume: ' 17' issue: '9' keyword: - General Earth and Planetary Sciences - General Engineering - General Environmental Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.5194/hess-17-3661-2013 month: '09' oa: 1 oa_version: Published Version page: 3661-3677 publication: Hydrology and Earth System Sciences publication_identifier: issn: - 1607-7938 publication_status: published publisher: Copernicus GmbH quality_controlled: '1' scopus_import: '1' status: public title: Comparison of climate change signals in CMIP3 and CMIP5 multi-model ensembles and implications for Central Asian glaciers type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2013' ... --- _id: '12639' abstract: - lang: eng text: 'In the headwater catchments of the main Asian rivers, glaciohydrological models are a useful tool to anticipate impacts of climatic changes. However, the reliability of their projections strongly depends on the quality and quantity of data that are available for parameter estimation, model calibration and validation, as well as on the accuracy of climate change projections. In this study the physically oriented, glaciohydrological model TOPKAPI-ETH is used to simulate future changes in snow, glacier, and runoff from the Hunza River Basin in northern Pakistan. Three key sources of model uncertainty in future runoff projections are compared: model parameters, climate projections, and natural climate variability. A novel approach, applicable also to ungauged catchments, is used to determine which model parameters and model components significantly affect the overall model uncertainty. We show that the model is capable of reproducing streamflow and glacier mass balances, but that all analyzed sources of uncertainty significantly affect the reliability of future projections, and that their effect is variable in time and in space. The effect of parametric uncertainty often exceeds the impact of climate uncertainty and natural climate variability, especially in heavily glacierized subcatchments. The results of the uncertainty analysis allow detailed recommendations on network design and the timing and location of field measurements, which could efficiently help to reduce model uncertainty in the future.' article_processing_charge: No article_type: original author: - first_name: S. full_name: Ragettli, S. last_name: Ragettli - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: R. full_name: Bordoy, R. last_name: Bordoy - first_name: W. W. full_name: Immerzeel, W. W. last_name: Immerzeel citation: ama: Ragettli S, Pellicciotti F, Bordoy R, Immerzeel WW. Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change. Water Resources Research. 2013;49(9):6048-6066. doi:10.1002/wrcr.20450 apa: Ragettli, S., Pellicciotti, F., Bordoy, R., & Immerzeel, W. W. (2013). Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change. Water Resources Research. American Geophysical Union. https://doi.org/10.1002/wrcr.20450 chicago: Ragettli, S., Francesca Pellicciotti, R. Bordoy, and W. W. Immerzeel. “Sources of Uncertainty in Modeling the Glaciohydrological Response of a Karakoram Watershed to Climate Change.” Water Resources Research. American Geophysical Union, 2013. https://doi.org/10.1002/wrcr.20450. ieee: S. Ragettli, F. Pellicciotti, R. Bordoy, and W. W. Immerzeel, “Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change,” Water Resources Research, vol. 49, no. 9. American Geophysical Union, pp. 6048–6066, 2013. ista: Ragettli S, Pellicciotti F, Bordoy R, Immerzeel WW. 2013. Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change. Water Resources Research. 49(9), 6048–6066. mla: Ragettli, S., et al. “Sources of Uncertainty in Modeling the Glaciohydrological Response of a Karakoram Watershed to Climate Change.” Water Resources Research, vol. 49, no. 9, American Geophysical Union, 2013, pp. 6048–66, doi:10.1002/wrcr.20450. short: S. Ragettli, F. Pellicciotti, R. Bordoy, W.W. Immerzeel, Water Resources Research 49 (2013) 6048–6066. date_created: 2023-02-20T08:17:12Z date_published: 2013-03-01T00:00:00Z date_updated: 2023-02-24T08:16:19Z day: '01' doi: 10.1002/wrcr.20450 extern: '1' intvolume: ' 49' issue: '9' keyword: - Water Science and Technology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/wrcr.20450 month: '03' oa: 1 oa_version: Published Version page: 6048-6066 publication: Water Resources Research publication_identifier: issn: - 0043-1397 publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 49 year: '2013' ... --- _id: '12633' abstract: - lang: eng text: We use two hydrological models of varying complexity to study the Juncal River Basin in the Central Andes of Chile with the aim to understand the degree of conceptualization and the spatial structure that are needed to model present and future streamflows. We use a conceptual semi-distributed model based on elevation bands [Water Evaluation and Planning (WEAP)], frequently used for water management, and a physically oriented, fully distributed model [Topographic Kinematic Wave Approximation and Integration ETH Zurich (TOPKAPI-ETH)] developed for research purposes mainly. We evaluate the ability of the two models to reproduce the key hydrological processes in the basin with emphasis on snow accumulation and melt, streamflow and the relationships between internal processes. Both models are capable of reproducing observed runoff and the evolution of Moderate-resolution Imaging Spectroradiometer snow cover adequately. In spite of WEAP's simple and conceptual approach for modelling snowmelt and its lack of glacier representation and snow gravitational redistribution as well as a proper routing algorithm, this model can reproduce historical data with a similar goodness of fit as the more complex TOPKAPI-ETH. We show that the performance of both models can be improved by using measured precipitation gradients of higher temporal resolution. In contrast to the good performance of the conceptual model for the present climate, however, we demonstrate that the simplifications in WEAP lead to error compensation, which results in different predictions in simulated melt and runoff for a potentially warmer future climate. TOPKAPI-ETH, using a more physical representation of processes, depends less on calibration and thus is less subject to a compensation of errors through different model components. Our results show that data obtained locally in ad hoc short-term field campaigns are needed to complement data extrapolated from long-term records for simulating changes in the water cycle of high-elevation catchments but that these data can only be efficiently used by a model applying a spatially distributed physical representation of hydrological processes. article_processing_charge: No article_type: original author: - first_name: S. full_name: Ragettli, S. last_name: Ragettli - first_name: G. full_name: Cortés, G. last_name: Cortés - first_name: J. full_name: McPhee, J. last_name: McPhee - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: Ragettli S, Cortés G, McPhee J, Pellicciotti F. An evaluation of approaches for modelling hydrological processes in high-elevation, glacierized Andean watersheds. Hydrological Processes. 2013;28(23):5674-5695. doi:10.1002/hyp.10055 apa: Ragettli, S., Cortés, G., McPhee, J., & Pellicciotti, F. (2013). An evaluation of approaches for modelling hydrological processes in high-elevation, glacierized Andean watersheds. Hydrological Processes. Wiley. https://doi.org/10.1002/hyp.10055 chicago: Ragettli, S., G. Cortés, J. McPhee, and Francesca Pellicciotti. “An Evaluation of Approaches for Modelling Hydrological Processes in High-Elevation, Glacierized Andean Watersheds.” Hydrological Processes. Wiley, 2013. https://doi.org/10.1002/hyp.10055. ieee: S. Ragettli, G. Cortés, J. McPhee, and F. Pellicciotti, “An evaluation of approaches for modelling hydrological processes in high-elevation, glacierized Andean watersheds,” Hydrological Processes, vol. 28, no. 23. Wiley, pp. 5674–5695, 2013. ista: Ragettli S, Cortés G, McPhee J, Pellicciotti F. 2013. An evaluation of approaches for modelling hydrological processes in high-elevation, glacierized Andean watersheds. Hydrological Processes. 28(23), 5674–5695. mla: Ragettli, S., et al. “An Evaluation of Approaches for Modelling Hydrological Processes in High-Elevation, Glacierized Andean Watersheds.” Hydrological Processes, vol. 28, no. 23, Wiley, 2013, pp. 5674–95, doi:10.1002/hyp.10055. short: S. Ragettli, G. Cortés, J. McPhee, F. Pellicciotti, Hydrological Processes 28 (2013) 5674–5695. date_created: 2023-02-20T08:16:39Z date_published: 2013-09-06T00:00:00Z date_updated: 2023-02-24T08:48:40Z day: '06' doi: 10.1002/hyp.10055 extern: '1' intvolume: ' 28' issue: '23' keyword: - Water Science and Technology language: - iso: eng month: '09' oa_version: None page: 5674-5695 publication: Hydrological Processes publication_identifier: issn: - 0885-6087 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: An evaluation of approaches for modelling hydrological processes in high-elevation, glacierized Andean watersheds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2013' ... --- _id: '9520' abstract: - lang: eng text: Plants undergo alternation of generation in which reproductive cells develop in the plant body ("sporophytic generation") and then differentiate into a multicellular gamete-forming "gametophytic generation." Different populations of helper cells assist in this transgenerational journey, with somatic tissues supporting early development and single nurse cells supporting gametogenesis. New data reveal a two-way relationship between early reproductive cells and their helpers involving complex epigenetic and signaling networks determining cell number and fate. Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes. article_processing_charge: No article_type: review author: - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Hugh full_name: Dickinson, Hugh last_name: Dickinson citation: ama: 'Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 2013;24(3):215-225. doi:10.1016/j.devcel.2013.01.014' apa: 'Feng, X., Zilberman, D., & Dickinson, H. (2013). A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2013.01.014' chicago: 'Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell. Elsevier, 2013. https://doi.org/10.1016/j.devcel.2013.01.014.' ieee: 'X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” Developmental Cell, vol. 24, no. 3. Elsevier, pp. 215–225, 2013.' ista: 'Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.' mla: 'Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell, vol. 24, no. 3, Elsevier, 2013, pp. 215–25, doi:10.1016/j.devcel.2013.01.014.' short: X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225. date_created: 2021-06-08T06:14:50Z date_published: 2013-02-11T00:00:00Z date_updated: 2023-05-08T11:00:59Z day: '11' department: - _id: DaZi - _id: XiFe doi: 10.1016/j.devcel.2013.01.014 extern: '1' external_id: pmid: - '23410937' intvolume: ' 24' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2013.01.014 month: '02' oa: 1 oa_version: Published Version page: 215-225 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'A conversation across generations: Soma-germ cell crosstalk in plants' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2013' ... --- _id: '13405' abstract: - lang: eng text: We report a method for preparing electrode–molecule–electrode junctions that incorporate nonsymmetrical azobenzene dithiols. Our approach is based on sequential deprotection of thiol moieties originally carrying two different protecting groups. The azobenzene derivatives retained their switching properties within monolayers and permitted the photocontrol of electrical conductance. article_processing_charge: No article_type: original author: - first_name: Tal full_name: Ely, Tal last_name: Ely - first_name: Sanjib full_name: Das, Sanjib last_name: Das - first_name: Wenjie full_name: Li, Wenjie last_name: Li - first_name: Pintu full_name: Kundu, Pintu last_name: Kundu - first_name: Einat full_name: Tirosh, Einat last_name: Tirosh - first_name: David full_name: Cahen, David last_name: Cahen - first_name: Ayelet full_name: Vilan, Ayelet last_name: Vilan - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Ely T, Das S, Li W, et al. Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. Synlett. 2013;24(18):2370-2374. doi:10.1055/s-0033-1340087 apa: Ely, T., Das, S., Li, W., Kundu, P., Tirosh, E., Cahen, D., … Klajn, R. (2013). Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. Synlett. Georg Thieme Verlag. https://doi.org/10.1055/s-0033-1340087 chicago: Ely, Tal, Sanjib Das, Wenjie Li, Pintu Kundu, Einat Tirosh, David Cahen, Ayelet Vilan, and Rafal Klajn. “Photocontrol of Electrical Conductance with a Nonsymmetrical Azobenzene Dithiol.” Synlett. Georg Thieme Verlag, 2013. https://doi.org/10.1055/s-0033-1340087. ieee: T. Ely et al., “Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol,” Synlett, vol. 24, no. 18. Georg Thieme Verlag, pp. 2370–2374, 2013. ista: Ely T, Das S, Li W, Kundu P, Tirosh E, Cahen D, Vilan A, Klajn R. 2013. Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. Synlett. 24(18), 2370–2374. mla: Ely, Tal, et al. “Photocontrol of Electrical Conductance with a Nonsymmetrical Azobenzene Dithiol.” Synlett, vol. 24, no. 18, Georg Thieme Verlag, 2013, pp. 2370–74, doi:10.1055/s-0033-1340087. short: T. Ely, S. Das, W. Li, P. Kundu, E. Tirosh, D. Cahen, A. Vilan, R. Klajn, Synlett 24 (2013) 2370–2374. date_created: 2023-08-01T09:47:17Z date_published: 2013-10-22T00:00:00Z date_updated: 2023-08-08T07:47:35Z day: '22' doi: 10.1055/s-0033-1340087 extern: '1' intvolume: ' 24' issue: '18' keyword: - Organic Chemistry language: - iso: eng month: '10' oa_version: None page: 2370-2374 publication: Synlett publication_identifier: eissn: - 1437-2096 issn: - 0936-5214 publication_status: published publisher: Georg Thieme Verlag quality_controlled: '1' scopus_import: '1' status: public title: Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2013' ... --- _id: '13406' abstract: - lang: eng text: Dual-responsive nanoparticles are designed by functionalizing magnetic cores with light-responsive ligands. These materials respond to both light and magnetic fields and can be assembled into various higher-order structures, depending on the relative contributions of these two stimuli. article_processing_charge: No article_type: original author: - first_name: Sanjib full_name: Das, Sanjib last_name: Das - first_name: Priyadarshi full_name: Ranjan, Priyadarshi last_name: Ranjan - first_name: Pradipta Sankar full_name: Maiti, Pradipta Sankar last_name: Maiti - first_name: Gurvinder full_name: Singh, Gurvinder last_name: Singh - first_name: Gregory full_name: Leitus, Gregory last_name: Leitus - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Das S, Ranjan P, Maiti PS, Singh G, Leitus G, Klajn R. Dual-responsive nanoparticles and their self-assembly. Advanced Materials. 2013;25(3):422-426. doi:10.1002/adma.201201734 apa: Das, S., Ranjan, P., Maiti, P. S., Singh, G., Leitus, G., & Klajn, R. (2013). Dual-responsive nanoparticles and their self-assembly. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201201734 chicago: Das, Sanjib, Priyadarshi Ranjan, Pradipta Sankar Maiti, Gurvinder Singh, Gregory Leitus, and Rafal Klajn. “Dual-Responsive Nanoparticles and Their Self-Assembly.” Advanced Materials. Wiley, 2013. https://doi.org/10.1002/adma.201201734. ieee: S. Das, P. Ranjan, P. S. Maiti, G. Singh, G. Leitus, and R. Klajn, “Dual-responsive nanoparticles and their self-assembly,” Advanced Materials, vol. 25, no. 3. Wiley, pp. 422–426, 2013. ista: Das S, Ranjan P, Maiti PS, Singh G, Leitus G, Klajn R. 2013. Dual-responsive nanoparticles and their self-assembly. Advanced Materials. 25(3), 422–426. mla: Das, Sanjib, et al. “Dual-Responsive Nanoparticles and Their Self-Assembly.” Advanced Materials, vol. 25, no. 3, Wiley, 2013, pp. 422–26, doi:10.1002/adma.201201734. short: S. Das, P. Ranjan, P.S. Maiti, G. Singh, G. Leitus, R. Klajn, Advanced Materials 25 (2013) 422–426. date_created: 2023-08-01T09:47:30Z date_published: 2013-01-18T00:00:00Z date_updated: 2023-08-08T07:49:36Z day: '18' doi: 10.1002/adma.201201734 extern: '1' external_id: pmid: - '22933327' intvolume: ' 25' issue: '3' keyword: - Mechanical Engineering - Mechanics of Materials - General Materials Science language: - iso: eng month: '01' oa_version: None page: 422-426 pmid: 1 publication: Advanced Materials publication_identifier: issn: - 0935-9648 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Dual-responsive nanoparticles and their self-assembly type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '2914' abstract: - lang: eng text: The scale invariance of natural images suggests an analogy to the statistical mechanics of physical systems at a critical point. Here we examine the distribution of pixels in small image patches and show how to construct the corresponding thermodynamics. We find evidence for criticality in a diverging specific heat, which corresponds to large fluctuations in how "surprising" we find individual images, and in the quantitative form of the entropy vs energy. We identify special image configurations as local energy minima and show that average patches within each basin are interpretable as lines and edges in all orientations. acknowledgement: "This work was supported in part by NSF Grants No. IIS-0613435, No. IBN-0344678, and No. PHY-0957573, by NIH Grant No. T32 MH065214, by the Human Frontier Science Program, and by the Swartz Foundation.\r\nCC BY 3.0\r\n" article_number: '018701' article_processing_charge: No article_type: original author: - first_name: Greg full_name: Stephens, Greg last_name: Stephens - first_name: Thierry full_name: Mora, Thierry last_name: Mora - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: William full_name: Bialek, William last_name: Bialek citation: ama: Stephens G, Mora T, Tkačik G, Bialek W. Statistical thermodynamics of natural images. Physical Review Letters. 2013;110(1). doi:10.1103/PhysRevLett.110.018701 apa: Stephens, G., Mora, T., Tkačik, G., & Bialek, W. (2013). Statistical thermodynamics of natural images. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.018701 chicago: Stephens, Greg, Thierry Mora, Gašper Tkačik, and William Bialek. “Statistical Thermodynamics of Natural Images.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.018701. ieee: G. Stephens, T. Mora, G. Tkačik, and W. Bialek, “Statistical thermodynamics of natural images,” Physical Review Letters, vol. 110, no. 1. American Physical Society, 2013. ista: Stephens G, Mora T, Tkačik G, Bialek W. 2013. Statistical thermodynamics of natural images. Physical Review Letters. 110(1), 018701. mla: Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.” Physical Review Letters, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.018701. short: G. Stephens, T. Mora, G. Tkačik, W. Bialek, Physical Review Letters 110 (2013). date_created: 2018-12-11T12:00:19Z date_published: 2013-01-02T00:00:00Z date_updated: 2023-09-04T11:47:51Z day: '02' ddc: - '530' department: - _id: GaTk doi: 10.1103/PhysRevLett.110.018701 external_id: arxiv: - '0806.2694' file: - access_level: open_access checksum: 72bfbc2094c4680e8a8a6bed668cd06d content_type: application/pdf creator: system date_created: 2018-12-12T10:18:44Z date_updated: 2020-07-14T12:45:53Z file_id: '5366' file_name: IST-2016-401-v1+1_1281.full.pdf file_size: 416965 relation: main_file file_date_updated: 2020-07-14T12:45:53Z has_accepted_license: '1' intvolume: ' 110' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '3829' pubrep_id: '401' quality_controlled: '1' status: public title: Statistical thermodynamics of natural images 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: 110 year: '2013' ... --- _id: '10900' abstract: - lang: eng text: Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays. acknowledgement: We would like to thank Alexander Eichner and Ingrid de Vries for discussion and critical reading of the manuscript, and Mary Frank for assistance with the recording of videos and images in Fig. 1. M.S. is supported through funding from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt Foundation for funding. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Michele full_name: Weber, Michele id: 3A3FC708-F248-11E8-B48F-1D18A9856A87 last_name: Weber - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: 'Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. Chemokines. Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:10.1007/978-1-62703-426-5_14' apa: 'Weber, M., & Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona & E. Ubogu (Eds.), Chemokines (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press. https://doi.org/10.1007/978-1-62703-426-5_14' chicago: 'Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In Chemokines, edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ: Humana Press, 2013. https://doi.org/10.1007/978-1-62703-426-5_14.' ieee: 'M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in Chemokines, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.' ista: 'Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology, vol. 1013, 215–226.' mla: Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” Chemokines, edited by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26, doi:10.1007/978-1-62703-426-5_14. short: M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226. date_created: 2022-03-21T07:47:41Z date_published: 2013-04-03T00:00:00Z date_updated: 2023-09-05T13:15:33Z day: '03' department: - _id: MiSi doi: 10.1007/978-1-62703-426-5_14 editor: - first_name: Astrid full_name: Cardona, Astrid last_name: Cardona - first_name: Eroboghene full_name: Ubogu, Eroboghene last_name: Ubogu external_id: pmid: - '23625502' intvolume: ' 1013' language: - iso: eng month: '04' oa_version: None page: 215-226 place: Totowa, NJ pmid: 1 publication: Chemokines publication_identifier: eisbn: - '9781627034265' eissn: - 1940-6029 isbn: - '9781627034258' issn: - 1064-3745 publication_status: published publisher: Humana Press quality_controlled: '1' scopus_import: '1' series_title: MIMB status: public title: Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 1013 year: '2013' ... --- _id: '5747' article_processing_charge: No author: - first_name: Cezara full_name: Dragoi, Cezara id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87 last_name: Dragoi - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Dragoi C, Gupta A, Henzinger TA. Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In: Computer Aided Verification. Vol 8044. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg; 2013:174-190. doi:10.1007/978-3-642-39799-8_11' apa: 'Dragoi, C., Gupta, A., & Henzinger, T. A. (2013). Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In Computer Aided Verification (Vol. 8044, pp. 174–190). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-39799-8_11' chicago: 'Dragoi, Cezara, Ashutosh Gupta, and Thomas A Henzinger. “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates.” In Computer Aided Verification, 8044:174–90. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. https://doi.org/10.1007/978-3-642-39799-8_11.' ieee: 'C. Dragoi, A. Gupta, and T. A. Henzinger, “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates,” in Computer Aided Verification, vol. 8044, Berlin, Heidelberg: Springer Berlin Heidelberg, 2013, pp. 174–190.' ista: 'Dragoi C, Gupta A, Henzinger TA. 2013.Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In: Computer Aided Verification. vol. 8044, 174–190.' mla: Dragoi, Cezara, et al. “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates.” Computer Aided Verification, vol. 8044, Springer Berlin Heidelberg, 2013, pp. 174–90, doi:10.1007/978-3-642-39799-8_11. short: C. Dragoi, A. Gupta, T.A. Henzinger, in:, Computer Aided Verification, Springer Berlin Heidelberg, Berlin, Heidelberg, 2013, pp. 174–190. conference: end_date: 2013-07-19 location: Saint Petersburg, Russia name: CAV 2013 start_date: 2013-07-13 date_created: 2018-12-18T13:10:21Z date_published: 2013-01-01T00:00:00Z date_updated: 2023-09-05T14:16:07Z ddc: - '005' department: - _id: ToHe doi: 10.1007/978-3-642-39799-8_11 ec_funded: 1 file: - access_level: open_access checksum: a901cc6b71db08b61c0d4c0cbacc6287 content_type: application/pdf creator: dernst date_created: 2018-12-18T13:13:33Z date_updated: 2020-07-14T12:47:10Z file_id: '5748' file_name: 2013_CAV_Dragoi.pdf file_size: 236480 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 8044' language: - iso: eng oa: 1 oa_version: None page: 174-190 place: Berlin, Heidelberg project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Computer Aided Verification publication_identifier: eissn: - 1611-3349 isbn: - '9783642397981' - '9783642397998' issn: - 0302-9743 publication_status: published publisher: Springer Berlin Heidelberg pubrep_id: '195' quality_controlled: '1' scopus_import: '1' series_title: CAV status: public title: Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8044 year: '2013' ... --- _id: '10902' abstract: - lang: eng text: We consider how to edit strings from a source language so that the edited strings belong to a target language, where the languages are given as deterministic finite automata. Non-streaming (or offline) transducers perform edits given the whole source string. We show that the class of deterministic one-pass transducers with registers along with increment and min operation suffices for computing optimal edit distance, whereas the same class of transducers without the min operation is not sufficient. Streaming (or online) transducers perform edits as the letters of the source string are received. We present a polynomial time algorithm for the partial-repair problem that given a bound α asks for the construction of a deterministic streaming transducer (if one exists) that ensures that the ‘maximum fraction’ η of the strings of the source language are edited, within cost α, to the target language. acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award. Thanks to Gabriele Puppis for suggesting the problem of identifying a deterministic transducer to compute the optimal cost, and to Martin Chmelik for his comments on the introduction.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Siddhesh full_name: Chaubal, Siddhesh last_name: Chaubal - first_name: Sasha full_name: Rubin, Sasha id: 2EC51194-F248-11E8-B48F-1D18A9856A87 last_name: Rubin citation: ama: 'Chatterjee K, Chaubal S, Rubin S. How to travel between languages. In: 7th International Conference on Language and Automata Theory and Applications. Vol 7810. LNCS. Berlin, Heidelberg: Springer Nature; 2013:214-225. doi:10.1007/978-3-642-37064-9_20' apa: 'Chatterjee, K., Chaubal, S., & Rubin, S. (2013). How to travel between languages. In 7th International Conference on Language and Automata Theory and Applications (Vol. 7810, pp. 214–225). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-642-37064-9_20' chicago: 'Chatterjee, Krishnendu, Siddhesh Chaubal, and Sasha Rubin. “How to Travel between Languages.” In 7th International Conference on Language and Automata Theory and Applications, 7810:214–25. LNCS. Berlin, Heidelberg: Springer Nature, 2013. https://doi.org/10.1007/978-3-642-37064-9_20.' ieee: K. Chatterjee, S. Chaubal, and S. Rubin, “How to travel between languages,” in 7th International Conference on Language and Automata Theory and Applications, Bilbao, Spain, 2013, vol. 7810, pp. 214–225. ista: 'Chatterjee K, Chaubal S, Rubin S. 2013. How to travel between languages. 7th International Conference on Language and Automata Theory and Applications. LATA: Conference on Language and Automata Theory and ApplicationsLNCS, LNCS, vol. 7810, 214–225.' mla: Chatterjee, Krishnendu, et al. “How to Travel between Languages.” 7th International Conference on Language and Automata Theory and Applications, vol. 7810, Springer Nature, 2013, pp. 214–25, doi:10.1007/978-3-642-37064-9_20. short: K. Chatterjee, S. Chaubal, S. Rubin, in:, 7th International Conference on Language and Automata Theory and Applications, Springer Nature, Berlin, Heidelberg, 2013, pp. 214–225. conference: end_date: 2013-04-05 location: Bilbao, Spain name: 'LATA: Conference on Language and Automata Theory and Applications' start_date: 2013-04-02 date_created: 2022-03-21T07:56:21Z date_published: 2013-04-15T00:00:00Z date_updated: 2023-09-05T15:10:38Z day: '15' department: - _id: KrCh doi: 10.1007/978-3-642-37064-9_20 ec_funded: 1 intvolume: ' 7810' language: - iso: eng month: '04' oa_version: None page: 214-225 place: Berlin, Heidelberg 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: 7th International Conference on Language and Automata Theory and Applications publication_identifier: eisbn: - '9783642370649' eissn: - 1611-3349 isbn: - '9783642370632' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: How to travel between languages type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7810 year: '2013' ... --- _id: '10897' abstract: - lang: eng text: Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing. acknowledgement: This research is partially supported by the European Science Foundation (ESF) under the Research Network Programme, the European Union under the Toposys Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053. article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Edelsbrunner H. Persistent homology in image processing. In: Graph-Based Representations in Pattern Recognition. Vol 7877. LNCS. Berlin, Heidelberg: Springer Nature; 2013:182-183. doi:10.1007/978-3-642-38221-5_19' apa: 'Edelsbrunner, H. (2013). Persistent homology in image processing. In Graph-Based Representations in Pattern Recognition (Vol. 7877, pp. 182–183). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-642-38221-5_19' chicago: 'Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In Graph-Based Representations in Pattern Recognition, 7877:182–83. LNCS. Berlin, Heidelberg: Springer Nature, 2013. https://doi.org/10.1007/978-3-642-38221-5_19.' ieee: H. Edelsbrunner, “Persistent homology in image processing,” in Graph-Based Representations in Pattern Recognition, Vienna, Austria, 2013, vol. 7877, pp. 182–183. ista: 'Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNCS vol. 7877, 182–183.' mla: Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” Graph-Based Representations in Pattern Recognition, vol. 7877, Springer Nature, 2013, pp. 182–83, doi:10.1007/978-3-642-38221-5_19. short: H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition, Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183. conference: end_date: 2013-05-17 location: Vienna, Austria name: 'GbRPR: Graph-based Representations in Pattern Recognition' start_date: 2013-05-15 date_created: 2022-03-21T07:30:33Z date_published: 2013-06-01T00:00:00Z date_updated: 2023-09-05T15:10:20Z day: '01' department: - _id: HeEd doi: 10.1007/978-3-642-38221-5_19 ec_funded: 1 intvolume: ' 7877' language: - iso: eng month: '06' oa_version: None page: 182-183 place: Berlin, Heidelberg project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Graph-Based Representations in Pattern Recognition publication_identifier: eisbn: - '9783642382215' eissn: - 1611-3349 isbn: - '9783642382208' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: Persistent homology in image processing type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7877 year: '2013' ...