--- _id: '8456' abstract: - lang: eng text: The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments. article_number: '8361' article_processing_charge: No article_type: original author: - first_name: Peixiang full_name: Ma, Peixiang last_name: Ma - first_name: Yi full_name: Xue, Yi last_name: Xue - first_name: Nicolas full_name: Coquelle, Nicolas last_name: Coquelle - first_name: Jens D. full_name: Haller, Jens D. last_name: Haller - first_name: Tairan full_name: Yuwen, Tairan last_name: Yuwen - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Oleg full_name: Mikhailovskii, Oleg last_name: Mikhailovskii - first_name: Dieter full_name: Willbold, Dieter last_name: Willbold - first_name: Jacques-Philippe full_name: Colletier, Jacques-Philippe last_name: Colletier - first_name: Nikolai R. full_name: Skrynnikov, Nikolai R. last_name: Skrynnikov - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361 apa: Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda, P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms9361 chicago: Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361. ieee: P. Ma et al., “Observing the overall rocking motion of a protein in a crystal,” Nature Communications, vol. 6. Springer Nature, 2015. ista: Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 6, 8361. mla: Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015, doi:10.1038/ncomms9361. short: P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii, D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 6 (2015). date_created: 2020-09-18T10:07:36Z date_published: 2015-10-05T00:00:00Z date_updated: 2021-01-12T08:19:24Z day: '05' doi: 10.1038/ncomms9361 extern: '1' intvolume: ' 6' keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '10' oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Observing the overall rocking motion of a protein in a crystal type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ... --- _id: '8457' abstract: - lang: eng text: We review recent advances in methodologies to study microseconds‐to‐milliseconds exchange processes in biological molecules using magic‐angle spinning solid‐state nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations and experimental data. These simulations reveal the potential of MAS NMR to provide detailed insight into short‐lived conformations of biological molecules. Recent studies of conformational exchange dynamics in microcrystalline ubiquitin are discussed. article_processing_charge: No article_type: original author: - first_name: Peixiang full_name: Ma, Peixiang last_name: Ma - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Ma P, Schanda P. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 2015;4(3):699-708. doi:10.1002/9780470034590.emrstm1418' apa: 'Ma, P., & Schanda, P. (2015). Conformational exchange processes in biological systems: Detection by solid-state NMR. EMagRes. Wiley. https://doi.org/10.1002/9780470034590.emrstm1418' chicago: 'Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes. Wiley, 2015. https://doi.org/10.1002/9780470034590.emrstm1418.' ieee: 'P. Ma and P. Schanda, “Conformational exchange processes in biological systems: Detection by solid-state NMR,” eMagRes, vol. 4, no. 3. Wiley, pp. 699–708, 2015.' ista: 'Ma P, Schanda P. 2015. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 4(3), 699–708.' mla: 'Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes, vol. 4, no. 3, Wiley, 2015, pp. 699–708, doi:10.1002/9780470034590.emrstm1418.' short: P. Ma, P. Schanda, EMagRes 4 (2015) 699–708. date_created: 2020-09-18T10:07:45Z date_published: 2015-09-10T00:00:00Z date_updated: 2021-01-12T08:19:24Z day: '10' doi: 10.1002/9780470034590.emrstm1418 extern: '1' intvolume: ' 4' issue: '3' language: - iso: eng month: '09' oa_version: None page: 699-708 publication: eMagRes publication_identifier: isbn: - '9780470034590' - '9780470058213' publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'Conformational exchange processes in biological systems: Detection by solid-state NMR' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2015' ... --- _id: '848' abstract: - lang: eng text: The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution. author: - first_name: Dinara full_name: Usmanova, Dinara last_name: Usmanova - first_name: Luca full_name: Ferretti, Luca last_name: Ferretti - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Peter full_name: Vlasov, Peter last_name: Vlasov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318 apa: Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov, F. (2015). A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu318 chicago: Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/molbev/msu318. ieee: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015. ista: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 32(2), 542–554. mla: Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318. short: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554. date_created: 2018-12-11T11:48:49Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T08:19:33Z day: '01' doi: 10.1093/molbev/msu318 extern: '1' intvolume: ' 32' issue: '2' language: - iso: eng month: '02' oa_version: None page: 542 - 554 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6804' quality_controlled: '1' status: public title: A model of substitution trajectories in sequence space and long-term protein evolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2015' ... --- _id: '8498' abstract: - lang: eng text: "In the present note we announce a proof of a strong form of Arnold diffusion for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$ be a 2-dimensional torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ > 0. Our main result says that for a 'generic' time-periodic perturbation of an integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad \\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur proof is a combination of geometric and variational methods. The fundamental elements of the construction are the usage of crumpled normally hyperbolic invariant cylinders from [9], flower and simple normally hyperbolic invariant manifolds from [36] as well as their kissing property at a strong double resonance. This allows us to build a 'connected' net of three-dimensional normally hyperbolic invariant manifolds. To construct diffusing orbits along this net we employ a version of the Mather variational method [41] equipped with weak KAM theory [28], proposed by Bernard in [7]." article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: K full_name: Zhang, K last_name: Zhang citation: ama: Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 2015;28(8):2699-2720. doi:10.1088/0951-7715/28/8/2699 apa: Kaloshin, V., & Zhang, K. (2015). Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. IOP Publishing. https://doi.org/10.1088/0951-7715/28/8/2699 chicago: Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity. IOP Publishing, 2015. https://doi.org/10.1088/0951-7715/28/8/2699. ieee: V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two and a half degrees of freedom,” Nonlinearity, vol. 28, no. 8. IOP Publishing, pp. 2699–2720, 2015. ista: Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720. mla: Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity, vol. 28, no. 8, IOP Publishing, 2015, pp. 2699–720, doi:10.1088/0951-7715/28/8/2699. short: V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720. date_created: 2020-09-18T10:46:43Z date_published: 2015-06-30T00:00:00Z date_updated: 2021-01-12T08:19:41Z day: '30' doi: 10.1088/0951-7715/28/8/2699 extern: '1' intvolume: ' 28' issue: '8' keyword: - Mathematical Physics - General Physics and Astronomy - Applied Mathematics - Statistical and Nonlinear Physics language: - iso: eng month: '06' oa_version: None page: 2699-2720 publication: Nonlinearity publication_identifier: issn: - 0951-7715 - 1361-6544 publication_status: published publisher: IOP Publishing quality_controlled: '1' status: public title: Arnold diffusion for smooth convex systems of two and a half degrees of freedom type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2015' ... --- _id: '8499' abstract: - lang: eng text: "We consider the cubic defocusing nonlinear Schrödinger equation in the two dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe establish the existence of solutions with polynomial time estimates. More exactly, there is c>0 such that for any K≫1 we find a solution u and a time T such that ∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0Journal of the European Mathematical Society. 2015;17(1):71-149. doi:10.4171/jems/499 apa: Guardia, M., & Kaloshin, V. (2015). Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. European Mathematical Society Publishing House. https://doi.org/10.4171/jems/499 chicago: Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical Society. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/jems/499. ieee: M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation,” Journal of the European Mathematical Society, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015. ista: Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 17(1), 71–149. mla: Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical Society, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 71–149, doi:10.4171/jems/499. short: M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17 (2015) 71–149. date_created: 2020-09-18T10:46:50Z date_published: 2015-02-05T00:00:00Z date_updated: 2021-01-12T08:19:41Z day: '05' doi: 10.4171/jems/499 extern: '1' intvolume: ' 17' issue: '1' language: - iso: eng month: '02' oa_version: None page: 71-149 publication: Journal of the European Mathematical Society publication_identifier: issn: - 1435-9855 publication_status: published publisher: European Mathematical Society Publishing House quality_controlled: '1' status: public title: Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2015' ... --- _id: '9057' abstract: - lang: eng text: Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes. article_number: e1400214 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: Anaïs full_name: Abramian, Anaïs last_name: Abramian - first_name: Jérémie full_name: Barral, Jérémie last_name: Barral - first_name: Kasey full_name: Hanson, Kasey last_name: Hanson - first_name: Alexander Y. full_name: Grosberg, Alexander Y. last_name: Grosberg - first_name: David J. full_name: Pine, David J. last_name: Pine - first_name: Paul M. full_name: Chaikin, Paul M. last_name: Chaikin citation: ama: Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science Advances. 2015;1(4). doi:10.1126/sciadv.1400214 apa: Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances. American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214 chicago: Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” Science Advances. American Association for the Advancement of Science , 2015. https://doi.org/10.1126/sciadv.1400214. ieee: J. A. Palacci et al., “Artificial rheotaxis,” Science Advances, vol. 1, no. 4. American Association for the Advancement of Science , 2015. ista: Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ, Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214. mla: Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:10.1126/sciadv.1400214. short: J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg, D.J. Pine, P.M. Chaikin, Science Advances 1 (2015). date_created: 2021-02-02T13:15:02Z date_published: 2015-05-01T00:00:00Z date_updated: 2023-02-23T13:47:52Z day: '01' ddc: - '530' doi: 10.1126/sciadv.1400214 extern: '1' external_id: arxiv: - '1505.05111' pmid: - '26601175' file: - access_level: open_access checksum: b97d62433581875c1b85210c5f6ae370 content_type: application/pdf creator: cziletti date_created: 2021-02-02T13:22:19Z date_updated: 2021-02-02T13:22:19Z file_id: '9058' file_name: 2015_ScienceAdvances_Palacci.pdf file_size: 2416780 relation: main_file success: 1 file_date_updated: 2021-02-02T13:22:19Z has_accepted_license: '1' intvolume: ' 1' issue: '4' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: 'American Association for the Advancement of Science ' quality_controlled: '1' scopus_import: '1' status: public title: Artificial rheotaxis tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 1 year: '2015' ... --- _id: '906' abstract: - lang: eng text: The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1. acknowledgement: 'Funding: The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)" and (BFU2012-31329), the European Union and the European Research Council under grant agreement 335980_EinME. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Our author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher until last days. A number of his work remains unfinished. We mourn premature care of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for the sequencing.' author: - first_name: Oksana full_name: Arkhipova, Oksana V last_name: Arkhipova - first_name: Margarita full_name: Meer, Margarita V last_name: Meer - first_name: Galina full_name: Mikoulinskaia, Galina V last_name: Mikoulinskaia - first_name: Marina full_name: Zakharova, Marina V last_name: Zakharova - first_name: Alexander full_name: Galushko, Alexander S last_name: Galushko - first_name: Vasilii full_name: Akimenko, Vasilii K last_name: Akimenko - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888 apa: Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0125888 chicago: Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888. ieee: O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015. ista: Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5). mla: Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888. short: O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015). date_created: 2018-12-11T11:49:08Z date_published: 2015-05-11T00:00:00Z date_updated: 2021-01-12T08:21:48Z day: '11' doi: 10.1371/journal.pone.0125888 extern: 1 intvolume: ' 10' issue: '5' month: '05' publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '6742' quality_controlled: 0 status: public title: Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer 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: 10 year: '2015' ... --- _id: '9141' abstract: - lang: eng text: The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere. article_processing_charge: No article_type: original author: - first_name: Adrien full_name: Lefauve, Adrien last_name: Lefauve - 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: Angélique full_name: Melet, Angélique last_name: Melet citation: ama: 'Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777. doi:10.1002/2014jc010598' apa: 'Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2014jc010598' chicago: 'Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598.' ieee: 'A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” Journal of Geophysical Research: Oceans, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.' ista: 'Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.' mla: 'Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.' short: 'A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.' date_created: 2021-02-15T14:21:49Z date_published: 2015-06-08T00:00:00Z date_updated: 2022-01-24T13:45:41Z day: '08' doi: 10.1002/2014jc010598 extern: '1' intvolume: ' 120' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/2014JC010598 month: '06' oa: 1 oa_version: Published Version page: 4760-4777 publication: 'Journal of Geophysical Research: Oceans' publication_identifier: issn: - 2169-9275 publication_status: published publisher: American Geophysical Union quality_controlled: '1' status: public title: A three-dimensional map of tidal dissipation over abyssal hills type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 120 year: '2015' ... --- _id: '928' abstract: - lang: eng text: The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events. article_number: e09206 author: - first_name: Ivonne full_name: Sehring, Ivonne last_name: Sehring - first_name: Pierre full_name: Recho, Pierre last_name: Recho - first_name: Elsa full_name: Denker, Elsa last_name: Denker - first_name: Matthew full_name: Kourakis, Matthew last_name: Kourakis - first_name: Birthe full_name: Mathiesen, Birthe last_name: Mathiesen - 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: Bo full_name: Dong, Bo last_name: Dong - first_name: Di full_name: Jiang, Di last_name: Jiang citation: ama: Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206 apa: Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206 chicago: Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/eLife.09206. ieee: I. Sehring et al., “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences Publications, 2015. ista: Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206. mla: Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications, 2015, doi:10.7554/eLife.09206. short: I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015). date_created: 2018-12-11T11:49:15Z date_published: 2015-10-21T00:00:00Z date_updated: 2021-01-12T08:21:58Z day: '21' ddc: - '539' - '570' doi: 10.7554/eLife.09206 extern: '1' file: - access_level: open_access checksum: 1e4024b3161adcae4a53a0b3dc8a946e content_type: application/pdf creator: dernst date_created: 2018-12-20T15:50:56Z date_updated: 2020-07-14T12:48:15Z file_id: '5769' file_name: 2015_eLife_Sehring.pdf file_size: 7202224 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '6512' quality_controlled: '1' status: public title: Assembly and positioning of actomyosin rings by contractility and planar cell polarity 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: '2015' ... --- _id: '9575' abstract: - lang: eng text: We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight. article_processing_charge: No article_type: original author: - first_name: Michael full_name: Krivelevich, Michael last_name: Krivelevich - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Benny full_name: Sudakov, Benny last_name: Sudakov citation: ama: Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187. doi:10.1016/j.endm.2015.06.027 apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027 chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027. ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics, vol. 49. Elsevier, pp. 181–187, 2015. ista: Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187. mla: Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier, 2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027. short: M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187. date_created: 2021-06-21T06:40:34Z date_published: 2015-11-01T00:00:00Z date_updated: 2023-02-23T14:01:28Z day: '01' doi: 10.1016/j.endm.2015.06.027 extern: '1' external_id: arxiv: - '1501.04816' intvolume: ' 49' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1501.04816 month: '11' oa: 1 oa_version: Preprint page: 181-187 publication: Electronic Notes in Discrete Mathematics publication_identifier: issn: - 1571-0653 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Cycles and matchings in randomly perturbed digraphs and hypergraphs type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 49 year: '2015' ... --- _id: '9673' abstract: - lang: eng text: Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation. article_processing_charge: No article_type: original author: - first_name: H.S. full_name: Leung, H.S. last_name: Leung - first_name: P.S.S. full_name: Leung, P.S.S. last_name: Leung - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: A.H.W. full_name: Ngan, A.H.W. last_name: Ngan citation: ama: Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009 apa: Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009 chicago: Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity. Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009. ieee: H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” International Journal of Plasticity, vol. 67. Elsevier, pp. 1–25, 2015. ista: Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 67, 1–25. mla: Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity, vol. 67, Elsevier, 2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009. short: H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25. date_created: 2021-07-15T14:09:32Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-23T14:04:28Z day: '01' doi: 10.1016/j.ijplas.2014.09.009 extern: '1' intvolume: ' 67' language: - iso: eng month: '04' oa_version: None page: 1-25 publication: International Journal of Plasticity publication_identifier: issn: - 0749-6419 publication_status: published publisher: Elsevier scopus_import: '1' status: public title: A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 67 year: '2015' ... --- _id: '9688' abstract: - lang: eng text: The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification. article_number: '180102' 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: Gareth A. full_name: Tribello, Gareth A. last_name: Tribello - first_name: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: ama: Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 2015;92(18). doi:10.1103/physrevb.92.180102 apa: Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102 chicago: Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102. ieee: B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18. American Physical Society, 2015. ista: Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 92(18), 180102. mla: Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102. short: B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015). date_created: 2021-07-19T10:07:22Z date_published: 2015-11-01T00:00:00Z date_updated: 2021-08-09T12:38:49Z day: '01' doi: 10.1103/physrevb.92.180102 extern: '1' external_id: arxiv: - '1511.08668' intvolume: ' 92' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.08668 month: '11' oa: 1 oa_version: Preprint publication: Physical Review B - Condensed Matter and Materials Physics publication_identifier: eissn: - 1550-235X issn: - 1098-0121 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Solid-liquid interfacial free energy out of equilibrium type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 92 year: '2015' ... --- _id: '9711' article_processing_charge: No author: - first_name: Guillaume full_name: Chevereau, Guillaume id: 424D78A0-F248-11E8-B48F-1D18A9856A87 last_name: Chevereau - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Tugce full_name: Batur, Tugce last_name: Batur - first_name: Aysegul full_name: Guvenek, Aysegul last_name: Guvenek - first_name: Dilay Hazal full_name: Ayhan, Dilay Hazal last_name: Ayhan - first_name: Erdal full_name: Toprak, Erdal last_name: Toprak - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw data for all figures. 2015. doi:10.1371/journal.pbio.1002299.s001 apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Excel file containing the raw data for all figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s001 chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing the Raw Data for All Figures.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s001. ieee: G. Chevereau et al., “Excel file containing the raw data for all figures.” Public Library of Science, 2015. ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Excel file containing the raw data for all figures, Public Library of Science, 10.1371/journal.pbio.1002299.s001. mla: Chevereau, Guillaume, et al. Excel File Containing the Raw Data for All Figures. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s001. short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015). date_created: 2021-07-23T11:53:50Z date_published: 2015-11-18T00:00:00Z date_updated: 2023-02-23T10:07:02Z day: '18' department: - _id: ToBo doi: 10.1371/journal.pbio.1002299.s001 month: '11' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1619' relation: used_in_publication status: public status: public title: Excel file containing the raw data for all figures type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '1855' abstract: - lang: eng text: 'Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.' acknowledgement: We thank J.R. de Miranda, L. De Smet and D. de Graaf for supplying qRT-PCR and MLPA positive controls, respectively, in the form of plasmids. This work was supported by the Insect Pollinators Initiative (IPI grants BB/1000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, The Scottish Government and The Wellcome Trust, under the Living with Environmental Change Partnership. article_processing_charge: No article_type: original author: - first_name: Dino full_name: Mcmahon, Dino last_name: Mcmahon - first_name: Matthias full_name: Fürst, Matthias id: 393B1196-F248-11E8-B48F-1D18A9856A87 last_name: Fürst orcid: 0000-0002-3712-925X - first_name: Jesicca full_name: Caspar, Jesicca last_name: Caspar - first_name: Panagiotis full_name: Theodorou, Panagiotis last_name: Theodorou - first_name: Mark full_name: Brown, Mark last_name: Brown - first_name: Robert full_name: Paxton, Robert last_name: Paxton citation: ama: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 2015;84(3):615-624. doi:10.1111/1365-2656.12345' apa: 'Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton, R. (2015). A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12345' chicago: 'Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology. Wiley, 2015. https://doi.org/10.1111/1365-2656.12345.' ieee: 'D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees,” Journal of Animal Ecology, vol. 84, no. 3. Wiley, pp. 615–624, 2015.' ista: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2015. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 84(3), 615–624.' mla: 'Mcmahon, Dino, et al. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology, vol. 84, no. 3, Wiley, 2015, pp. 615–24, doi:10.1111/1365-2656.12345.' short: D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal of Animal Ecology 84 (2015) 615–624. date_created: 2018-12-11T11:54:23Z date_published: 2015-03-03T00:00:00Z date_updated: 2023-02-23T14:06:09Z day: '03' ddc: - '570' department: - _id: SyCr doi: 10.1111/1365-2656.12345 external_id: pmid: - '25646973' file: - access_level: open_access checksum: 542a0b9b07e78050a81b35f26f0b82da content_type: application/pdf creator: system date_created: 2018-12-12T10:18:29Z date_updated: 2020-07-14T12:45:19Z file_id: '5350' file_name: IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf file_size: 1823045 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 84' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 615 - 624 pmid: 1 publication: Journal of Animal Ecology publication_status: published publisher: Wiley publist_id: '5245' pubrep_id: '460' quality_controlled: '1' related_material: record: - id: '9720' relation: research_data status: public scopus_import: '1' status: public title: 'A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees' 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: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 84 year: '2015' ... --- _id: '1830' abstract: - lang: eng text: To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems. acknowledgement: We thank Meghan L. Vyleta for the genetical fungal strain characterization and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D. Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments on the manuscript. article_processing_charge: No article_type: original author: - first_name: Fabian full_name: Theis, Fabian last_name: Theis - 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: Carsten full_name: Marr, Carsten last_name: Marr - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0108 apa: Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2014.0108 chicago: Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2015. https://doi.org/10.1098/rstb.2014.0108. ieee: F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming on disease transmission in ant societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, The, 2015. ista: Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669). mla: Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, Royal Society, The, 2015, doi:10.1098/rstb.2014.0108. short: F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015). date_created: 2018-12-11T11:54:15Z date_published: 2015-05-26T00:00:00Z date_updated: 2023-02-23T14:06:12Z day: '26' department: - _id: SyCr doi: 10.1098/rstb.2014.0108 ec_funded: 1 external_id: pmid: - '25870394' intvolume: ' 370' issue: '1669' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/ month: '05' oa: 1 oa_version: Submitted Version pmid: 1 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: 25DDF0F0-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '302004' name: 'Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach' - _id: 25E0E184-B435-11E9-9278-68D0E5697425 name: Antnet - _id: 25E24DB2-B435-11E9-9278-68D0E5697425 name: Fellowship of Wissenschaftskolleg zu Berlin publication: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences publication_identifier: eissn: - 1471-2970 issn: - 0962-8436 publication_status: published publisher: Royal Society, The publist_id: '5273' quality_controlled: '1' related_material: record: - id: '9721' relation: research_data status: public scopus_import: '1' status: public title: Opposing effects of allogrooming on disease transmission in ant societies type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 370 year: '2015' ... --- _id: '9721' abstract: - lang: eng text: To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems. article_processing_charge: No author: - first_name: Fabian full_name: Theis, Fabian last_name: Theis - 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: Carsten full_name: Marr, Carsten last_name: Marr - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming on disease transmission in ant societies. 2015. doi:10.5061/dryad.dj2bf' apa: 'Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Data from: Opposing effects of allogrooming on disease transmission in ant societies. Dryad. https://doi.org/10.5061/dryad.dj2bf' chicago: 'Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Dryad, 2015. https://doi.org/10.5061/dryad.dj2bf.' ieee: 'F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects of allogrooming on disease transmission in ant societies.” Dryad, 2015.' ista: 'Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects of allogrooming on disease transmission in ant societies, Dryad, 10.5061/dryad.dj2bf.' mla: 'Theis, Fabian, et al. Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies. Dryad, 2015, doi:10.5061/dryad.dj2bf.' short: F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015). date_created: 2021-07-26T09:38:36Z date_published: 2015-12-29T00:00:00Z date_updated: 2023-02-23T10:16:22Z day: '29' department: - _id: SyCr doi: 10.5061/dryad.dj2bf main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.dj2bf month: '12' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '1830' relation: used_in_publication status: public status: public title: 'Data from: Opposing effects of allogrooming on disease transmission in ant societies' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '9718' article_processing_charge: No author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Avraham E. full_name: Mayo, Avraham E. last_name: Mayo - first_name: Tsvi full_name: Tlusty, Tsvi last_name: Tlusty - first_name: Uri full_name: Alon, Uri last_name: Alon citation: ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:10.1371/journal.pcbi.1004055.s001 apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Supporting information text. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s001 chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s001. ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015. ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, 10.1371/journal.pcbi.1004055.s001. mla: Friedlander, Tamar, et al. Supporting Information Text. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001. short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015). date_created: 2021-07-26T08:35:23Z date_published: 2015-03-23T00:00:00Z date_updated: 2023-02-23T10:16:13Z day: '23' department: - _id: GaTk doi: 10.1371/journal.pcbi.1004055.s001 month: '03' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1827' relation: used_in_publication status: public status: public title: Supporting information text type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '1793' abstract: - lang: eng text: We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth. article_number: e0127657 author: - first_name: Olga full_name: Symonova, Olga id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87 last_name: Symonova - first_name: Christopher full_name: Topp, Christopher last_name: Topp - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 2015;10(6). doi:10.1371/journal.pone.0127657' apa: 'Symonova, O., Topp, C., & Edelsbrunner, H. (2015). DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657' chicago: 'Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.' ieee: 'O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots,” PLoS One, vol. 10, no. 6. Public Library of Science, 2015.' ista: 'Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657.' mla: 'Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One, vol. 10, no. 6, e0127657, Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.' short: O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015). date_created: 2018-12-11T11:54:02Z date_published: 2015-06-01T00:00:00Z date_updated: 2023-02-23T14:06:33Z day: '01' ddc: - '000' department: - _id: MaJö - _id: HeEd doi: 10.1371/journal.pone.0127657 file: - access_level: open_access checksum: d20f26461ca575276ad3ed9ce4bfc787 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:30Z date_updated: 2020-07-14T12:45:16Z file_id: '5150' file_name: IST-2016-454-v1+1_journal.pone.0127657.pdf file_size: 1850825 relation: main_file file_date_updated: 2020-07-14T12:45:16Z has_accepted_license: '1' intvolume: ' 10' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '5318' pubrep_id: '454' quality_controlled: '1' related_material: record: - id: '9737' relation: research_data status: public scopus_import: 1 status: public title: 'DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2015' ... --- _id: '9737' article_processing_charge: No author: - first_name: Olga full_name: Symonova, Olga id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87 last_name: Symonova - first_name: Christopher full_name: Topp, Christopher last_name: Topp - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:10.1371/journal.pone.0127657.s001 apa: Symonova, O., Topp, C., & Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657.s001 chicago: Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.s001. ieee: O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015. ista: Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, 10.1371/journal.pone.0127657.s001. mla: Symonova, Olga, et al. Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2. Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.s001. short: O. Symonova, C. Topp, H. Edelsbrunner, (2015). date_created: 2021-07-28T06:20:13Z date_published: 2015-06-01T00:00:00Z date_updated: 2023-02-23T10:14:42Z day: '01' department: - _id: MaJö - _id: HeEd doi: 10.1371/journal.pone.0127657.s001 month: '06' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1793' relation: used_in_publication status: public status: public title: Root traits computed by DynamicRoots for the maize root shown in fig 2 type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '1827' abstract: - lang: eng text: Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved. article_processing_charge: No author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Avraham full_name: Mayo, Avraham last_name: Mayo - first_name: Tsvi full_name: Tlusty, Tsvi last_name: Tlusty - first_name: Uri full_name: Alon, Uri last_name: Alon citation: ama: Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055 apa: Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of bow-tie architectures in biology. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055 chicago: Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055. ieee: T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015. ista: Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3). mla: Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055. short: T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015). date_created: 2018-12-11T11:54:14Z date_published: 2015-03-23T00:00:00Z date_updated: 2023-02-23T14:07:51Z day: '23' ddc: - '576' department: - _id: GaTk doi: 10.1371/journal.pcbi.1004055 ec_funded: 1 file: - access_level: open_access checksum: b8aa66f450ff8de393014b87ec7d2efb content_type: application/pdf creator: system date_created: 2018-12-12T10:15:39Z date_updated: 2020-07-14T12:45:17Z file_id: '5161' file_name: IST-2016-452-v1+1_journal.pcbi.1004055.pdf file_size: 1811647 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 11' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5278' pubrep_id: '452' quality_controlled: '1' related_material: record: - id: '9718' relation: research_data status: public - id: '9773' relation: research_data status: public scopus_import: 1 status: public title: Evolution of bow-tie architectures in biology 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: 11 year: '2015' ... --- _id: '1809' abstract: - lang: eng text: 'Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.' author: - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Reinmar full_name: Hager, Reinmar last_name: Hager citation: ama: Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907 apa: Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907 chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907. ieee: B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015. ista: Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5). mla: Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0126907. short: B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015). date_created: 2018-12-11T11:54:07Z date_published: 2015-05-18T00:00:00Z date_updated: 2023-02-23T14:07:48Z day: '18' ddc: - '570' - '576' department: - _id: NiBa doi: 10.1371/journal.pone.0126907 file: - access_level: open_access checksum: d3a4a58ef4bd3b3e2f32b7fd7af4a743 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:07Z date_updated: 2020-07-14T12:45:17Z file_id: '4730' file_name: IST-2016-453-v1+1_journal.pone.0126907.pdf file_size: 2748982 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 10' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '5299' pubrep_id: '453' quality_controlled: '1' related_material: record: - id: '9715' relation: research_data status: public - id: '9772' relation: research_data status: public scopus_import: 1 status: public title: Indirect genetic effects and the dynamics of social interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2015' ... --- _id: '9772' article_processing_charge: No author: - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Reinmar full_name: Hager, Reinmar last_name: Hager citation: ama: Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:10.1371/journal.pone.0126907.s003 apa: Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003 chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003. ieee: B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015. ista: Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, 10.1371/journal.pone.0126907.s003. mla: Trubenova, Barbora, et al. Description of the Agent Based Simulations. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003. short: B. Trubenova, S. Novak, R. Hager, (2015). date_created: 2021-08-05T12:55:20Z date_published: 2015-05-18T00:00:00Z date_updated: 2023-02-23T10:15:25Z day: '18' department: - _id: NiBa doi: 10.1371/journal.pone.0126907.s003 month: '05' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1809' relation: used_in_publication status: public status: public title: Description of the agent based simulations type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '9773' article_processing_charge: No author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Avraham E. full_name: Mayo, Avraham E. last_name: Mayo - first_name: Tsvi full_name: Tlusty, Tsvi last_name: Tlusty - first_name: Uri full_name: Alon, Uri last_name: Alon citation: ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:10.1371/journal.pcbi.1004055.s002 apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002 chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002. ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015. ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, 10.1371/journal.pcbi.1004055.s002. mla: Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002. short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015). date_created: 2021-08-05T12:58:07Z date_published: 2015-03-23T00:00:00Z date_updated: 2023-02-23T10:16:13Z day: '23' department: - _id: GaTk doi: 10.1371/journal.pcbi.1004055.s002 month: '03' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1827' relation: used_in_publication status: public status: public title: Evolutionary simulation code type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '981' abstract: - lang: eng text: The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials. acknowledgement: We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny, A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon for help with EDS measurements. V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004. author: - first_name: Ilija full_name: Zeljkovic, Ilija last_name: Zeljkovic - first_name: Yoshinori full_name: Okada, Yoshinori last_name: Okada - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Raman full_name: Sankar, Raman last_name: Sankar - first_name: Daniel full_name: Walkup, Daniel last_name: Walkup - first_name: Wenwen full_name: Zhou, Wenwen last_name: Zhou - first_name: Junwei full_name: Liu, Junwei last_name: Liu - first_name: Guoqing full_name: Chang, Guoqing last_name: Chang - first_name: Yungjui full_name: Wang, Yungjui last_name: Wang - first_name: Md full_name: Hasan, Md Z last_name: Hasan - first_name: Fangcheng full_name: Chou, Fangcheng last_name: Chou - first_name: Hsin full_name: Lin, Hsin last_name: Lin - first_name: Arun full_name: Bansil, Arun last_name: Bansil - first_name: Liang full_name: Fu, Liang last_name: Fu - first_name: Vidya full_name: Madhavan, Vidya last_name: Madhavan citation: ama: Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 2015;14(3):318-324. doi:10.1038/nmat4215 apa: Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. Nature Publishing Group. https://doi.org/10.1038/nmat4215 chicago: Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials. Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215. ieee: I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators,” Nature Materials, vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015. ista: Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G, Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 14(3), 318–324. mla: Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials, vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215. short: I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu, G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature Materials 14 (2015) 318–324. date_created: 2018-12-11T11:49:31Z date_published: 2015-03-01T00:00:00Z date_updated: 2021-01-12T08:22:24Z day: '01' doi: 10.1038/nmat4215 extern: 1 intvolume: ' 14' issue: '3' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1403.4906 month: '03' oa: 1 page: 318 - 324 publication: Nature Materials publication_status: published publisher: Nature Publishing Group publist_id: '6419' quality_controlled: 0 status: public title: Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators type: journal_article volume: 14 year: '2015' ... --- _id: '982' abstract: - lang: eng text: We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions. acknowledgement: We acknowledge helpful discussions with Sid Parameswaran, Andrew Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor library. 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. This research was supported by Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation, NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities of Leeds and Manchester. 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. Criterion for many-body localization-delocalization phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047 apa: Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047 chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X. American Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047. ieee: M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization phase transition,” Physical Review X, vol. 5, no. 4. American Physical Society, 2015. ista: Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization phase transition. Physical Review X. 5(4). mla: Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical Society, 2015, doi:10.1103/PhysRevX.5.041047. short: M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015). date_created: 2018-12-11T11:49:32Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T08:22:25Z day: '01' doi: 10.1103/PhysRevX.5.041047 extern: 1 intvolume: ' 5' issue: '4' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1507.01635 month: '01' oa: 1 publication: Physical Review X publication_status: published publisher: American Physical Society publist_id: '6418' quality_controlled: 0 status: public title: Criterion for many-body localization-delocalization phase transition type: journal_article volume: 5 year: '2015' ... --- _id: '99' abstract: - lang: eng text: Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms. acknowledgement: Research support by Microsoft Project Q, the Danish National Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M. acknowledges support from the Villum Foundation. author: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: S M full_name: Albrecht, S M last_name: Albrecht - first_name: Gediminas full_name: Kiršanskas, Gediminas last_name: Kiršanskas - first_name: W full_name: Chang, W last_name: Chang - first_name: Ferdinand full_name: Kuemmeth, Ferdinand last_name: Kuemmeth - first_name: Peter full_name: Krogstrup, Peter last_name: Krogstrup - first_name: Thomas full_name: Jespersen, Thomas last_name: Jespersen - first_name: Jesper full_name: Nygård, Jesper last_name: Nygård - first_name: Karsten full_name: Flensberg, Karsten last_name: Flensberg - first_name: Charles full_name: Marcus, Charles last_name: Marcus citation: ama: Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 2015;11(12):1017-1021. doi:10.1038/nphys3461 apa: Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth, F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3461 chicago: Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg, and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3461. ieee: A. P. Higginbotham et al., “Parity lifetime of bound states in a proximitized semiconductor nanowire,” Nature Physics, vol. 11, no. 12. Nature Publishing Group, pp. 1017–1021, 2015. ista: Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021. mla: Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 1017–21, doi:10.1038/nphys3461. short: A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P. Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11 (2015) 1017–1021. date_created: 2018-12-11T11:44:37Z date_published: 2015-09-14T00:00:00Z date_updated: 2021-01-12T08:22:28Z day: '14' doi: 10.1038/nphys3461 extern: '1' external_id: arxiv: - '1501.05155' intvolume: ' 11' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1501.05155 month: '09' oa: 1 oa_version: Preprint page: 1017 - 1021 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '7955' quality_controlled: '1' status: public title: Parity lifetime of bound states in a proximitized semiconductor nanowire type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '8495' abstract: - lang: eng text: 'In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'''': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \sqrt {\varepsilon }$, after a time of order $ \sqrt {\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting.' article_processing_charge: No article_type: letter_note author: - first_name: Abed full_name: Bounemoura, Abed last_name: Bounemoura - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 2015;144(4):1553-1560. doi:10.1090/proc/12796 apa: Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12796 chicago: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796. ieee: A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian systems close to integrable,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015. ista: Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 144(4), 1553–1560. mla: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796. short: A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society 144 (2015) 1553–1560. date_created: 2020-09-18T10:46:14Z date_published: 2015-12-21T00:00:00Z date_updated: 2021-01-12T08:19:40Z day: '21' doi: 10.1090/proc/12796 extern: '1' intvolume: ' 144' issue: '4' language: - iso: eng month: '12' oa_version: None page: 1553-1560 publication: Proceedings of the American Mathematical Society publication_identifier: issn: - 0002-9939 - 1088-6826 publication_status: published publisher: American Mathematical Society quality_controlled: '1' status: public title: A note on micro-instability for Hamiltonian systems close to integrable type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 144 year: '2015' ... --- _id: '866' abstract: - lang: eng text: Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF. acknowledgement: | We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist. author: - first_name: Colin full_name: Kretz, Colin A last_name: Kretz - first_name: Manhong full_name: Dai, Manhong last_name: Dai - first_name: Onuralp full_name: Soylemez, Onuralp last_name: Soylemez - first_name: Andrew full_name: Yee, Andrew last_name: Yee - first_name: Karl full_name: Desch, Karl C last_name: Desch - first_name: David full_name: Siemieniak, David R last_name: Siemieniak - first_name: Kärt full_name: Tomberg, Kärt last_name: Tomberg - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Fan full_name: Meng, Fan last_name: Meng - first_name: David full_name: Ginsburg, David B last_name: Ginsburg citation: ama: Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 2015;112(30):9328-9333. doi:10.1073/pnas.1511328112 apa: Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511328112 chicago: Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112. ieee: C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015. ista: Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333. mla: Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112. short: C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333. date_created: 2018-12-11T11:48:55Z date_published: 2015-07-28T00:00:00Z date_updated: 2021-01-12T08:20:26Z day: '28' doi: 10.1073/pnas.1511328112 extern: 1 intvolume: ' 112' issue: '30' month: '07' page: 9328 - 9333 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6783' quality_controlled: 0 status: public title: Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13 type: journal_article volume: 112 year: '2015' ... --- _id: '886' abstract: - lang: eng text: The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space. acknowledgement: 'This work has been supported by a grant from the HHMI International Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional Development Fund (ERDF), the European Union, and the European Research Council under grant agreement no 335980_EinME.' author: - first_name: Dmitry full_name: Kondrashov, Dmitry A last_name: Kondrashov - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009 apa: Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009 chicago: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015. https://doi.org/10.1016/j.tig.2014.09.009. ieee: D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33, 2015. ista: Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33. mla: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009. short: D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33. date_created: 2018-12-11T11:49:01Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T08:21:16Z day: '01' doi: 10.1016/j.tig.2014.09.009 extern: 1 intvolume: ' 31' issue: '1' month: '01' page: 24 - 33 publication: Trends in Genetics publication_status: published publisher: Elsevier publist_id: '6764' quality_controlled: 0 status: public title: Topological features of rugged fitness landscapes in sequence space type: journal_article volume: 31 year: '2015' ... --- _id: '9017' abstract: - lang: eng text: MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway. article_processing_charge: No article_type: original author: - first_name: Nicolas full_name: Richet, Nicolas last_name: Richet - first_name: Danni full_name: Liu, Danni last_name: Liu - first_name: Pierre full_name: Legrand, Pierre last_name: Legrand - first_name: Christophe full_name: Velours, Christophe last_name: Velours - first_name: Armelle full_name: Corpet, Armelle last_name: Corpet - first_name: Albane full_name: Gaubert, Albane last_name: Gaubert - first_name: May M full_name: Bakail, May M id: FB3C3F8E-522F-11EA-B186-22963DDC885E last_name: Bakail orcid: 0000-0002-9592-1587 - first_name: Gwenaelle full_name: Moal-Raisin, Gwenaelle last_name: Moal-Raisin - first_name: Raphael full_name: Guerois, Raphael last_name: Guerois - first_name: Christel full_name: Compper, Christel last_name: Compper - first_name: Arthur full_name: Besle, Arthur last_name: Besle - first_name: Berengère full_name: Guichard, Berengère last_name: Guichard - first_name: Genevieve full_name: Almouzni, Genevieve last_name: Almouzni - first_name: Françoise full_name: Ochsenbein, Françoise last_name: Ochsenbein citation: ama: Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 2015;43(3):1905-1917. doi:10.1093/nar/gkv021 apa: Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein, F. (2015). Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv021 chicago: Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv021. ieee: N. Richet et al., “Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork,” Nucleic Acids Research, vol. 43, no. 3. Oxford University Press, pp. 1905–1917, 2015. ista: Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 43(3), 1905–1917. mla: Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research, vol. 43, no. 3, Oxford University Press, 2015, pp. 1905–17, doi:10.1093/nar/gkv021. short: N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail, G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F. Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917. date_created: 2021-01-19T11:01:01Z date_published: 2015-02-18T00:00:00Z date_updated: 2023-02-23T13:46:50Z day: '18' doi: 10.1093/nar/gkv021 extern: '1' external_id: pmid: - '25618846' intvolume: ' 43' issue: '3' language: - iso: eng month: '02' oa_version: Published Version page: 1905-1917 pmid: 1 publication: Nucleic Acids Research publication_identifier: issn: - 1362-4962 - 0305-1048 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2015' ... --- _id: '924' abstract: - lang: eng text: This paper presents a numerical study of a Capillary Pumped Loop evaporator. A two-dimensional unsteady mathematical model of a flat evaporator is developed to simulate heat and mass transfer in unsaturated porous wick with phase change. The liquid-vapor phase change inside the porous wick is described by Langmuir's law. The governing equations are solved by the Finite Element Method. The results are presented then for a sintered nickel wick and methanol as a working fluid. The heat flux required to the transition from the all-liquid wick to the vapor-liquid wick is calculated. The dynamic and thermodynamic behavior of the working fluid in the capillary structure are discussed in this paper. acknowledgement: The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099). article_processing_charge: No author: - first_name: Riadh full_name: Boubaker, Riadh last_name: Boubaker - first_name: Vincent full_name: Platel, Vincent last_name: Platel - first_name: Alexis full_name: Bergès, Alexis last_name: Bergès - first_name: Mathieu full_name: Bancelin, Mathieu last_name: Bancelin - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009 apa: Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015). Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009 chicago: Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering. Elsevier, 2015. https://doi.org/10.1016/j.applthermaleng.2014.10.009. ieee: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015. ista: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 76, 1–8. mla: Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol. 76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009. short: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal Engineering 76 (2015) 1–8. date_created: 2018-12-11T11:49:13Z date_published: 2015-02-05T00:00:00Z date_updated: 2021-01-12T08:21:56Z day: '05' doi: 10.1016/j.applthermaleng.2014.10.009 extern: '1' intvolume: ' 76' language: - iso: eng month: '02' oa_version: None page: 1 - 8 publication: Applied Thermal Engineering publication_status: published publisher: Elsevier publist_id: '6514' status: public title: Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 76 year: '2015' ... --- _id: '929' abstract: - lang: eng text: 'An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. ' acknowledgement: We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro, Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto), and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions and discussion. This work was supported by the Taishan Scholar Program of Shandong and the Fundamental Research Funds for the Central Universities in China (3005000-841412019) (to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges support from the Young Researcher Prize of the Bettencourt-Schueller Foundation. article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Bo full_name: Dong, Bo last_name: Dong - first_name: Pierre full_name: Recho, Pierre last_name: Recho - first_name: Jean full_name: Joanny, Jean last_name: Joanny - first_name: Shigeo full_name: Hayashi, Shigeo last_name: Hayashi citation: ama: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 2015;112(28):8620-8625. doi:10.1073/pnas.1504762112 apa: Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015). Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112 chicago: Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112. ieee: E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS, vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015. ista: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 112(28), 8620–8625. mla: Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112. short: E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625. date_created: 2018-12-11T11:49:15Z date_published: 2015-07-14T00:00:00Z date_updated: 2021-01-12T08:21:59Z day: '14' doi: 10.1073/pnas.1504762112 extern: '1' intvolume: ' 112' issue: '28' language: - iso: eng month: '07' oa_version: None page: 8620 - 8625 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6513' status: public title: Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '933' abstract: - lang: eng text: Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data. author: - first_name: Simón full_name: García, Simón last_name: García - 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: Jens full_name: Elgeti, Jens last_name: Elgeti - first_name: Jean full_name: Joanny, Jean last_name: Joanny - first_name: Pascal full_name: Silberzan, Pascal last_name: Silberzan - first_name: Nir full_name: Gov, Nir last_name: Gov citation: ama: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319. doi:10.1073/pnas.1510973112 apa: García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112 chicago: García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan, and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112. ieee: S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov, “Physics of active jamming during collective cellular motion in a monolayer,” PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015. ista: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 112(50), 15314–15319. mla: García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:10.1073/pnas.1510973112. short: S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319. date_created: 2018-12-11T11:49:16Z date_published: 2015-12-15T00:00:00Z date_updated: 2021-01-12T08:22:01Z day: '15' doi: 10.1073/pnas.1510973112 extern: '1' external_id: pmid: - '26627719' intvolume: ' 112' issue: '50' language: - iso: eng main_file_link: - open_access: '1' url: https://www.pnas.org/content/pnas/112/50/15314.full.pdf month: '12' oa: 1 oa_version: None page: 15314 - 15319 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6511' quality_controlled: '1' status: public title: Physics of active jamming during collective cellular motion in a monolayer type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '9532' abstract: - lang: eng text: Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings. article_processing_charge: No article_type: review author: - first_name: Jessica A. full_name: Rodrigues, Jessica A. last_name: Rodrigues - 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, Zilberman D. Evolution and function of genomic imprinting in plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115 apa: Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.269902.115 chicago: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115. ieee: J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015. ista: Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531. mla: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115. short: J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531. date_created: 2021-06-08T09:56:24Z date_published: 2015-12-15T00:00:00Z date_updated: 2021-12-14T07:58:15Z day: '15' ddc: - '570' department: - _id: DaZi doi: 10.1101/gad.269902.115 extern: '1' external_id: pmid: - '26680300' file: - access_level: open_access checksum: 086a88cfca4677646da26ed960cb02e9 content_type: application/pdf creator: asandaue date_created: 2021-06-08T09:55:10Z date_updated: 2021-06-08T09:55:10Z file_id: '9533' file_name: 2015_GenesAndDevelopment_Rodrigues.pdf file_size: 1116846 relation: main_file success: 1 file_date_updated: 2021-06-08T09:55:10Z has_accepted_license: '1' intvolume: ' 29' issue: '24' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 2517–2531 pmid: 1 publication: Genes and Development publication_identifier: eissn: - 1549-5477 issn: - 0890-9369 publication_status: published publisher: Cold Spring Harbor Laboratory Press quality_controlled: '1' scopus_import: '1' status: public title: Evolution and function of genomic imprinting in plants tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 29 year: '2015' ... --- _id: '9684' abstract: - lang: eng text: The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept. article_number: '035001' article_processing_charge: No article_type: original author: - first_name: P S S full_name: Leung, P S S last_name: Leung - first_name: H S full_name: Leung, H S last_name: Leung - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: A H W full_name: Ngan, A H W last_name: Ngan citation: ama: Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 2015;23(3). doi:10.1088/0965-0393/23/3/035001 apa: Leung, P. S. S., Leung, H. S., Cheng, B., & Ngan, A. H. W. (2015). Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. IOP Publishing. https://doi.org/10.1088/0965-0393/23/3/035001 chicago: Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering. IOP Publishing, 2015. https://doi.org/10.1088/0965-0393/23/3/035001. ieee: P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence of yield strength simulated by a dislocation-density function dynamics approach,” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3. IOP Publishing, 2015. ista: Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 23(3), 035001. mla: Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:10.1088/0965-0393/23/3/035001. short: P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015). date_created: 2021-07-19T09:11:12Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-23T14:04:54Z day: '01' doi: 10.1088/0965-0393/23/3/035001 extern: '1' intvolume: ' 23' issue: '3' language: - iso: eng month: '04' oa_version: None publication: Modelling and Simulation in Materials Science and Engineering publication_identifier: eissn: - 1361-651X issn: - 0965-0393 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Size dependence of yield strength simulated by a dislocation-density function dynamics approach type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 23 year: '2015' ... --- _id: '1566' abstract: - lang: eng text: Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease. acknowledgement: 'We acknowledge the support by the EU Joint Programme in Neurodegenerative Diseases (JPND AC14/00037) project. The project is supported through the following funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland, National Science Centre; and Spain, ISCIII. ' article_number: e1004541 author: - first_name: Àngel full_name: Gómez Sicilia, Àngel last_name: Gómez Sicilia - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Marek full_name: Cieplak, Marek last_name: Cieplak - first_name: Mariano full_name: Carrión Vázquez, Mariano last_name: Carrión Vázquez citation: ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10). doi:10.1371/journal.pcbi.1004541 apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541 chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541. ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures,” PLoS Computational Biology, vol. 11, no. 10. Public Library of Science, 2015. ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 11(10), e1004541. mla: Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004541. short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational Biology 11 (2015). date_created: 2018-12-11T11:52:45Z date_published: 2015-10-23T00:00:00Z date_updated: 2023-02-23T14:05:55Z day: '23' ddc: - '570' department: - _id: CaHe doi: 10.1371/journal.pcbi.1004541 file: - access_level: open_access checksum: 8b67d729be663bfc9af04bfd94459655 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:21Z date_updated: 2020-07-14T12:45:02Z file_id: '5207' file_name: IST-2016-478-v1+1_journal.pcbi.1004541.pdf file_size: 1412511 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 11' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5605' pubrep_id: '478' quality_controlled: '1' related_material: record: - id: '9714' relation: research_data status: public scopus_import: 1 status: public title: An exploration of the universe of polyglutamine structures 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: 11 year: '2015' ... --- _id: '9712' article_processing_charge: No author: - first_name: Murat full_name: Tugrul, Murat id: 37C323C6-F248-11E8-B48F-1D18A9856A87 last_name: Tugrul orcid: 0000-0002-8523-0758 - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - 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: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001 apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness models for comparison & for interacting TFBSs. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639.s001 chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison & for Interacting TFBSs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001. ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015. ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison & for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001. mla: Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001. short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015). date_created: 2021-07-23T12:00:37Z date_published: 2015-11-06T00:00:00Z date_updated: 2023-02-23T10:09:08Z day: '06' department: - _id: NiBa - _id: CaGu - _id: GaTk doi: 10.1371/journal.pgen.1005639.s001 month: '11' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1666' relation: used_in_publication status: public status: public title: Other fitness models for comparison & for interacting TFBSs type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '9714' article_processing_charge: No author: - first_name: Àngel full_name: Gómez Sicilia, Àngel last_name: Gómez Sicilia - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Marek full_name: Cieplak, Marek last_name: Cieplak - first_name: Mariano full_name: Carrión Vázquez, Mariano last_name: Carrión Vázquez citation: ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures - submission to PLOS journals. 2015. doi:10.1371/journal.pcbi.1004541.s001 apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures - submission to PLOS journals. Public Library of Science . https://doi.org/10.1371/journal.pcbi.1004541.s001 chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals.” Public Library of Science , 2015. https://doi.org/10.1371/journal.pcbi.1004541.s001. ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures - submission to PLOS journals.” Public Library of Science , 2015. ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures - submission to PLOS journals, Public Library of Science , 10.1371/journal.pcbi.1004541.s001. mla: Gómez Sicilia, Àngel, et al. An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals. Public Library of Science , 2015, doi:10.1371/journal.pcbi.1004541.s001. short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015). date_created: 2021-07-23T12:05:28Z date_published: 2015-10-23T00:00:00Z date_updated: 2023-02-23T10:04:35Z day: '23' department: - _id: CaHe doi: 10.1371/journal.pcbi.1004541.s001 month: '10' oa_version: Published Version publisher: 'Public Library of Science ' related_material: record: - id: '1566' relation: used_in_publication status: public status: public title: An exploration of the universe of polyglutamine structures - submission to PLOS journals type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '9715' article_processing_charge: No author: - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Reinmar full_name: Hager, Reinmar last_name: Hager citation: ama: Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:10.1371/journal.pone.0126907.s001 apa: Trubenova, B., Novak, S., & Hager, R. (2015). Mathematical inference of the results. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s001 chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s001. ieee: B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015. ista: Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, 10.1371/journal.pone.0126907.s001. mla: Trubenova, Barbora, et al. Mathematical Inference of the Results. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001. short: B. Trubenova, S. Novak, R. Hager, (2015). date_created: 2021-07-23T12:11:30Z date_published: 2015-05-18T00:00:00Z date_updated: 2023-02-23T10:15:25Z day: '18' department: - _id: NiBa doi: 10.1371/journal.pone.0126907.s001 month: '05' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1809' relation: used_in_publication status: public status: public title: Mathematical inference of the results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '1993' abstract: - lang: eng text: 'The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens. ' acknowledged_ssus: - _id: EM-Fac acknowledgement: "Funding was obtained by the German Research Foundation (CR 118–2) and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank Line V. Ugelvig for help with ant collection and statistical discussion, Xavier Espadaler for detailed information on the ant collection site, Birgit Lautenschläger for the electron microscopy images and Eva Sixt for ant drawings. We further thank Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization and immune gene primer development, Paul Schmid-Hempel for discussion, and Line V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript. S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments; M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with intense contributions of A.V.G. and S.T.; all authors approved the manuscript." article_number: '20141976' article_processing_charge: No article_type: original author: - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 2015;282(1799). doi:10.1098/rspb.2014.1976 apa: Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2015). Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2014.1976 chicago: Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2014.1976. ieee: M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1799. The Royal Society, 2015. ista: Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1799), 20141976. mla: Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1799, 20141976, The Royal Society, 2015, doi:10.1098/rspb.2014.1976. short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015). date_created: 2018-12-11T11:55:06Z date_published: 2015-01-22T00:00:00Z date_updated: 2023-02-23T14:06:41Z day: '22' department: - _id: SyCr doi: 10.1098/rspb.2014.1976 ec_funded: 1 external_id: pmid: - '25473011' intvolume: ' 282' issue: '1799' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/ month: '01' oa: 1 oa_version: Submitted Version pmid: 1 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: Proceedings of the Royal Society of London Series B Biological Sciences publication_identifier: eissn: - 1471-2954 issn: - 0962-8452 publication_status: published publisher: The Royal Society publist_id: '5090' quality_controlled: '1' related_material: record: - id: '9740' relation: research_data status: public scopus_import: '1' status: public title: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 282 year: '2015' ... --- _id: '9742' abstract: - lang: eng text: 'Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects.' article_processing_charge: No author: - first_name: Claudia full_name: Westhus, Claudia last_name: Westhus - 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: Edouard full_name: Tourdot, Edouard last_name: Tourdot - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Claudie full_name: Doums, Claudie last_name: Doums - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. 2015. doi:10.5061/dryad.7kc79' apa: 'Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer, S. (2015). Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Dryad. https://doi.org/10.5061/dryad.7kc79' chicago: 'Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Dryad, 2015. https://doi.org/10.5061/dryad.7kc79.' ieee: 'C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant.” Dryad, 2015.' ista: 'Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2015. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant, Dryad, 10.5061/dryad.7kc79.' mla: 'Westhus, Claudia, et al. Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant. Dryad, 2015, doi:10.5061/dryad.7kc79.' short: C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015). date_created: 2021-07-28T08:52:53Z date_published: 2015-07-09T00:00:00Z date_updated: 2023-02-23T10:30:52Z day: '09' department: - _id: SyCr doi: 10.5061/dryad.7kc79 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.7kc79 month: '07' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2161' relation: used_in_publication status: public status: public title: 'Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '9765' article_processing_charge: No author: - first_name: Guillaume full_name: Chevereau, Guillaume id: 424D78A0-F248-11E8-B48F-1D18A9856A87 last_name: Chevereau - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Tugce full_name: Batur, Tugce last_name: Batur - first_name: Aysegul full_name: Guvenek, Aysegul last_name: Guvenek - first_name: Dilay Hazal full_name: Ayhan, Dilay Hazal last_name: Ayhan - first_name: Erdal full_name: Toprak, Erdal last_name: Toprak - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Chevereau G, Lukacisinova M, Batur T, et al. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. 2015. doi:10.1371/journal.pbio.1002299.s008 apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s008 chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s008. ieee: G. Chevereau et al., “Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs.” Public Library of Science, 2015. ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs, Public Library of Science, 10.1371/journal.pbio.1002299.s008. mla: Chevereau, Guillaume, et al. Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s008. short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015). date_created: 2021-08-03T07:05:16Z date_published: 2015-11-18T00:00:00Z date_updated: 2023-02-23T10:07:02Z day: '18' department: - _id: ToBo doi: 10.1371/journal.pbio.1002299.s008 month: '11' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1619' relation: used_in_publication status: public status: public title: Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '12630' abstract: - lang: eng text: "The hydrology of high-elevation watersheds of the Hindu Kush-Himalaya region (HKH) is poorly known. The correct representation of internal states and process dynamics in glacio-hydrological models can often not be verified due to missing in situ measurements. We use a new set of detailed ground data from the upper Langtang valley in Nepal to systematically guide a state-of-the art glacio-hydrological model through a parameter assigning process with the aim to understand the hydrology of the catchment and contribution of snow and ice processes to runoff. 14 parameters are directly calculated on the basis of local data, and 13 parameters are calibrated against 5 different datasets of in situ or remote sensing data. Spatial fields of debris thickness are reconstructed through a novel approach that employs data from an Unmanned Aerial Vehicle (UAV), energy balance modeling and statistical techniques. The model is validated against measured catchment runoff (Nash–Sutcliffe efficiency 0.87) and modeled snow cover is compared to Landsat snow cover. The advanced representation of processes allowed assessing the role played by avalanching for runoff for the first time for a Himalayan catchment (5% of annual water inputs to the hydrological system are due to snow redistribution) and to quantify the hydrological significance of sub-debris ice melt (9% of annual water inputs). Snowmelt is the most important contributor to total runoff during the hydrological year 2012/2013 (representing 40% of all sources), followed by rainfall (34%) and ice melt (26%). A sensitivity analysis is used to assess the efficiency of the monitoring network and identify the timing and location of field measurements that constrain model uncertainty. The methodology to set up a glacio-hydrological model in high-elevation regions presented in this study can be regarded as a benchmark for modelers in the HKH seeking to evaluate their calibration approach, their experimental setup and thus to reduce the predictive model uncertainty.\r\n\r\n" 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: W.W. full_name: Immerzeel, W.W. last_name: Immerzeel - first_name: E.S. full_name: Miles, E.S. last_name: Miles - first_name: L. full_name: Petersen, L. last_name: Petersen - first_name: M. full_name: Heynen, M. last_name: Heynen - first_name: J.M. full_name: Shea, J.M. last_name: Shea - first_name: D. full_name: Stumm, D. last_name: Stumm - first_name: S. full_name: Joshi, S. last_name: Joshi - first_name: A. full_name: Shrestha, A. last_name: Shrestha citation: ama: Ragettli S, Pellicciotti F, Immerzeel WW, et al. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. 2015;78(4):94-111. doi:10.1016/j.advwatres.2015.01.013 apa: Ragettli, S., Pellicciotti, F., Immerzeel, W. W., Miles, E. S., Petersen, L., Heynen, M., … Shrestha, A. (2015). Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. Elsevier. https://doi.org/10.1016/j.advwatres.2015.01.013 chicago: Ragettli, S., Francesca Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, and A. Shrestha. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources. Elsevier, 2015. https://doi.org/10.1016/j.advwatres.2015.01.013. ieee: S. Ragettli et al., “Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model,” Advances in Water Resources, vol. 78, no. 4. Elsevier, pp. 94–111, 2015. ista: Ragettli S, Pellicciotti F, Immerzeel WW, Miles ES, Petersen L, Heynen M, Shea JM, Stumm D, Joshi S, Shrestha A. 2015. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. 78(4), 94–111. mla: Ragettli, S., et al. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources, vol. 78, no. 4, Elsevier, 2015, pp. 94–111, doi:10.1016/j.advwatres.2015.01.013. short: S. Ragettli, F. Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, A. Shrestha, Advances in Water Resources 78 (2015) 94–111. date_created: 2023-02-20T08:16:21Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-24T09:28:04Z day: '01' doi: 10.1016/j.advwatres.2015.01.013 extern: '1' intvolume: ' 78' issue: '4' keyword: - Water Science and Technology language: - iso: eng month: '04' oa_version: None page: 94-111 publication: Advances in Water Resources publication_identifier: issn: - 0309-1708 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 78 year: '2015' ... --- _id: '12628' abstract: - lang: eng text: Thick debris cover on glaciers can significantly reduce ice melt. However, several studies have suggested that debris-covered glaciers in the Himalaya might have lost mass at a rate similar to debris-free glaciers. We reconstruct elevation and mass changes for the debris-covered glaciers of the upper Langtang valley, Nepalese Himalaya, using a digital elevation model (DEM) from 1974 stereo Hexagon satellite data and the 2000 SRTM (Shuttle Radar Topography Mission) DEM. Uncertainties are high in the accumulation areas, due to data gaps in the SRTM and difficulties with delineation of the glacier borders. Even with these uncertainties, we obtain thinning rates comparable to those of several other studies in the Himalaya. In particular, we obtain a total mass balance for the investigated debris-covered glaciers of the basin of –0.32 ± 0.18 m w.e. a−1. However, there are major spatial differences both between glaciers and within any single glacier, exhibiting a very distinct nonlinear mass-balance profile with elevation. Through analysis of surface velocities derived from Landsat ETM+ imagery, we show that thinning occurs in areas of low velocity and low slope. These areas are prone to a general, dynamic decay of surface features and to the development of supraglacial lakes and ice cliffs, which may be responsible for a considerable increase in overall glacier ablation. article_processing_charge: No article_type: original author: - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Christa full_name: Stephan, Christa last_name: Stephan - first_name: Evan full_name: Miles, Evan last_name: Miles - first_name: Sam full_name: Herreid, Sam last_name: Herreid - first_name: Walter W. full_name: Immerzeel, Walter W. last_name: Immerzeel - first_name: Tobias full_name: Bolch, Tobias last_name: Bolch citation: ama: Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. 2015;61(226):373-386. doi:10.3189/2015jog13j237 apa: Pellicciotti, F., Stephan, C., Miles, E., Herreid, S., Immerzeel, W. W., & Bolch, T. (2015). Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog13j237 chicago: Pellicciotti, Francesca, Christa Stephan, Evan Miles, Sam Herreid, Walter W. Immerzeel, and Tobias Bolch. “Mass-Balance Changes of the Debris-Covered Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog13j237. ieee: F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W. W. Immerzeel, and T. Bolch, “Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999,” Journal of Glaciology, vol. 61, no. 226. International Glaciological Society, pp. 373–386, 2015. ista: Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. 2015. Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. 61(226), 373–386. mla: Pellicciotti, Francesca, et al. “Mass-Balance Changes of the Debris-Covered Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology, vol. 61, no. 226, International Glaciological Society, 2015, pp. 373–86, doi:10.3189/2015jog13j237. short: F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W.W. Immerzeel, T. Bolch, Journal of Glaciology 61 (2015) 373–386. date_created: 2023-02-20T08:16:11Z date_published: 2015-03-01T00:00:00Z date_updated: 2023-02-24T09:35:21Z day: '01' doi: 10.3189/2015jog13j237 extern: '1' intvolume: ' 61' issue: '226' keyword: - Earth-Surface Processes language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3189/2015JoG13J237 month: '03' oa: 1 oa_version: Published Version page: 373-386 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: International Glaciological Society quality_controlled: '1' scopus_import: '1' status: public title: Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2015' ... --- _id: '12631' abstract: - lang: eng text: Air temperature is one of the most relevant input variables for snow and ice melt calculations. However, local meteorological conditions, complex topography, and logistical concerns in glacierized regions make the measuring and modeling of air temperature a difficult task. In this study, we investigate the spatial distribution of 2 m air temperature over mountain glaciers and propose a modification to an existing model to improve its representation. Spatially distributed meteorological data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte (Chile) Glaciers are used to examine approximate flow line temperatures during their respective ablation seasons. During warm conditions (off-glacier temperatures well above 0°C), observed air temperatures in the upper reaches of Place Glacier and Haut Glacier d'Arolla decrease down glacier along the approximate flow line. At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed over the glacier tongue. While the temperature behavior over the upper part can be explained by the cooling effect of the glacier surface, the temperature increase over the glacier tongue may be caused by several processes induced by the surrounding warm atmosphere. In order to capture the latter effect, we add an additional term to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier temperatures, the modified GB model reduces root-mean-square error up to 32% and provides a new approach for distributing air temperature over mountain glaciers as a function of off-glacier temperatures and approximate glacier flow lines. article_processing_charge: No article_type: original author: - first_name: A. full_name: Ayala, A. last_name: Ayala - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: J. M. full_name: Shea, J. M. last_name: Shea citation: ama: 'Ayala A, Pellicciotti F, Shea JM. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 2015;120(8):3139-3157. doi:10.1002/2015jd023137' apa: 'Ayala, A., Pellicciotti, F., & Shea, J. M. (2015). Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. American Geophysical Union. https://doi.org/10.1002/2015jd023137' chicago: 'Ayala, A., Francesca Pellicciotti, and J. M. Shea. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres. American Geophysical Union, 2015. https://doi.org/10.1002/2015jd023137.' ieee: 'A. Ayala, F. Pellicciotti, and J. M. Shea, “Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming,” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8. American Geophysical Union, pp. 3139–3157, 2015.' ista: 'Ayala A, Pellicciotti F, Shea JM. 2015. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 120(8), 3139–3157.' mla: 'Ayala, A., et al. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8, American Geophysical Union, 2015, pp. 3139–57, doi:10.1002/2015jd023137.' short: 'A. Ayala, F. Pellicciotti, J.M. Shea, Journal of Geophysical Research: Atmospheres 120 (2015) 3139–3157.' date_created: 2023-02-20T08:16:28Z date_published: 2015-04-18T00:00:00Z date_updated: 2023-02-24T09:16:26Z day: '18' doi: 10.1002/2015jd023137 extern: '1' intvolume: ' 120' issue: '8' keyword: - Space and Planetary Science - Earth and Planetary Sciences (miscellaneous) - Atmospheric Science - Geophysics language: - iso: eng month: '04' oa_version: Published Version page: 3139-3157 publication: 'Journal of Geophysical Research: Atmospheres' publication_identifier: eissn: - 2169-8996 issn: - 2169-897X publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: 'Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 120 year: '2015' ... --- _id: '12629' abstract: - lang: eng text: Meteorological studies in high-mountain environments form the basis of our understanding of catchment hydrology and glacier accumulation and melt processes, yet high-altitude (>4000 m above sea level, asl) observatories are rare. This research presents meteorological data recorded between December 2012 and November 2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl. Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation are compared between sites. Solar radiation strongly affects diurnal temperature and vapour pressure cycles, but local topography and valley-scale circulations alter wind speed and precipitation cycles. The observed diurnal variability in vertical temperature gradients in all seasons highlights the importance of in situ measurements for melt modelling. The monsoon signal (progressive onset and sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon Phailin in mid-October 2013 provides an interesting case study on the possible effects of such storms on glaciers in the region. article_processing_charge: No article_type: original author: - first_name: J.M. full_name: Shea, J.M. last_name: Shea - first_name: P. full_name: Wagnon, P. last_name: Wagnon - first_name: W.W. full_name: Immerzeel, W.W. last_name: Immerzeel - first_name: R. full_name: Biron, R. last_name: Biron - first_name: F. full_name: Brun, F. last_name: Brun - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 2015;31(2):174-200. doi:10.1080/07900627.2015.1020417 apa: Shea, J. M., Wagnon, P., Immerzeel, W. W., Biron, R., Brun, F., & Pellicciotti, F. (2015). A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. Taylor & Francis. https://doi.org/10.1080/07900627.2015.1020417 chicago: Shea, J.M., P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, and Francesca Pellicciotti. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development. Taylor & Francis, 2015. https://doi.org/10.1080/07900627.2015.1020417. ieee: J. M. Shea, P. Wagnon, W. W. Immerzeel, R. Biron, F. Brun, and F. Pellicciotti, “A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya,” International Journal of Water Resources Development, vol. 31, no. 2. Taylor & Francis, pp. 174–200, 2015. ista: Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. 2015. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 31(2), 174–200. mla: Shea, J. M., et al. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development, vol. 31, no. 2, Taylor & Francis, 2015, pp. 174–200, doi:10.1080/07900627.2015.1020417. short: J.M. Shea, P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, F. Pellicciotti, International Journal of Water Resources Development 31 (2015) 174–200. date_created: 2023-02-20T08:16:17Z date_published: 2015-04-18T00:00:00Z date_updated: 2023-02-24T09:30:42Z day: '18' doi: 10.1080/07900627.2015.1020417 extern: '1' intvolume: ' 31' issue: '2' keyword: - Water Science and Technology - Development language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1080/07900627.2015.1020417 month: '04' oa: 1 oa_version: Published Version page: 174-200 publication: International Journal of Water Resources Development publication_identifier: eissn: - 1360-0648 issn: - 0790-0627 publication_status: published publisher: Taylor & Francis quality_controlled: '1' scopus_import: '1' status: public title: A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2015' ... --- _id: '12626' abstract: - lang: eng text: Ice cliffs have been identified as a reason for higher ablation rates on debris-covered glaciers than are implied by the insulation effects of the debris. This study aims to improve our understanding of cliff backwasting, and the role of radiative fluxes in particular. An energy-balance model is forced with new data gathered in May and October 2013 on Lirung Glacier, Nepalese Himalaya. Observations show substantial variability in melt between cliffs, between locations on any cliff and between seasons. Using a high-resolution digital elevation model we calculate longwave fluxes incident to the cliff from surrounding terrain and include the effect of local shading on shortwave radiation. This is an advance over previous studies, that made simplified assumptions on cliff geometry and radiative fluxes. Measured melt rates varied between 3.25 and 8.6 cm d−1 in May and 0.18 and 1.34 cm d−1 in October. Model results reproduce the strong variability in space and time, suggesting considerable differences in radiative fluxes over one cliff. In October the model fails to reproduce stake readings, probably due to the lack of a refreezing component. Disregarding local topography can lead to overestimation of melt at the point scale by up to ∼9%. article_processing_charge: No article_type: original author: - first_name: Jakob F. full_name: Steiner, Jakob F. last_name: Steiner - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Pascal full_name: Buri, Pascal last_name: Buri - first_name: Evan S. full_name: Miles, Evan S. last_name: Miles - first_name: Walter W. full_name: Immerzeel, Walter W. last_name: Immerzeel - first_name: Tim D. full_name: Reid, Tim D. last_name: Reid citation: ama: Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 2015;61(229):889-907. doi:10.3189/2015jog14j194 apa: Steiner, J. F., Pellicciotti, F., Buri, P., Miles, E. S., Immerzeel, W. W., & Reid, T. D. (2015). Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j194 chicago: Steiner, Jakob F., Francesca Pellicciotti, Pascal Buri, Evan S. Miles, Walter W. Immerzeel, and Tim D. Reid. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j194. ieee: J. F. Steiner, F. Pellicciotti, P. Buri, E. S. Miles, W. W. Immerzeel, and T. D. Reid, “Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya,” Journal of Glaciology, vol. 61, no. 229. International Glaciological Society, pp. 889–907, 2015. ista: Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. 2015. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 61(229), 889–907. mla: Steiner, Jakob F., et al. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology, vol. 61, no. 229, International Glaciological Society, 2015, pp. 889–907, doi:10.3189/2015jog14j194. short: J.F. Steiner, F. Pellicciotti, P. Buri, E.S. Miles, W.W. Immerzeel, T.D. Reid, Journal of Glaciology 61 (2015) 889–907. date_created: 2023-02-20T08:16:01Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-24T09:43:14Z day: '01' doi: 10.3189/2015jog14j194 extern: '1' intvolume: ' 61' issue: '229' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3189/2015JoG14J194 month: '07' oa: 1 oa_version: Published Version page: 889-907 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: International Glaciological Society quality_controlled: '1' scopus_import: '1' status: public title: Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2015' ... --- _id: '12627' abstract: - lang: eng text: Spatial evolution of supraglacial debris cover on mountain glaciers is a largely unmonitored and poorly understood phenomenon that directly affects glacier melt. Supraglacial debris cover for 93 glaciers in the Karakoram, northern Pakistan, was mapped from Landsat imagery acquired in 1977, 1998, 2009 and 2014. Surge-type glaciers occupy 41% of the study area and were considered separately. The time series of debris-covered surface area change shows a mean value of zero or near-zero change for both surging and non-surging glaciers. An increase in debris-covered area is often associated with negative regional mass balances. We extend this logic to suggest that the stable regional mass balances in the Karakoram explain the zero or near-zero change in debris-covered area. This coupling of trends combined with our 37 year time series of data suggests the Karakoram anomaly extends further back in time than previously known. article_processing_charge: No article_type: original author: - first_name: Sam full_name: Herreid, Sam last_name: Herreid - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Alvaro full_name: Ayala, Alvaro last_name: Ayala - first_name: Anna full_name: Chesnokova, Anna last_name: Chesnokova - first_name: Christian full_name: Kienholz, Christian last_name: Kienholz - first_name: Joseph full_name: Shea, Joseph last_name: Shea - first_name: Arun full_name: Shrestha, Arun last_name: Shrestha citation: ama: Herreid S, Pellicciotti F, Ayala A, et al. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 2015;61(227):524-536. doi:10.3189/2015jog14j227 apa: Herreid, S., Pellicciotti, F., Ayala, A., Chesnokova, A., Kienholz, C., Shea, J., & Shrestha, A. (2015). Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j227 chicago: Herreid, Sam, Francesca Pellicciotti, Alvaro Ayala, Anna Chesnokova, Christian Kienholz, Joseph Shea, and Arun Shrestha. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j227. ieee: S. Herreid et al., “Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014,” Journal of Glaciology, vol. 61, no. 227. International Glaciological Society, pp. 524–536, 2015. ista: Herreid S, Pellicciotti F, Ayala A, Chesnokova A, Kienholz C, Shea J, Shrestha A. 2015. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 61(227), 524–536. mla: Herreid, Sam, et al. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology, vol. 61, no. 227, International Glaciological Society, 2015, pp. 524–36, doi:10.3189/2015jog14j227. short: S. Herreid, F. Pellicciotti, A. Ayala, A. Chesnokova, C. Kienholz, J. Shea, A. Shrestha, Journal of Glaciology 61 (2015) 524–536. date_created: 2023-02-20T08:16:06Z date_published: 2015-05-01T00:00:00Z date_updated: 2023-02-24T09:40:30Z day: '01' doi: 10.3189/2015jog14j227 extern: '1' intvolume: ' 61' issue: '227' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3189/2015JoG14J227 month: '05' oa: 1 oa_version: Published Version page: 524-536 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: International Glaciological Society quality_controlled: '1' scopus_import: '1' status: public title: Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2015' ... --- _id: '1618' abstract: - lang: eng text: CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed. article_processing_charge: No author: - first_name: Christopher full_name: Veldkamp, Christopher last_name: Veldkamp - first_name: Eva full_name: Kiermaier, Eva id: 3EB04B78-F248-11E8-B48F-1D18A9856A87 last_name: Kiermaier orcid: 0000-0001-6165-5738 - first_name: Skylar full_name: Gabel Eissens, Skylar last_name: Gabel Eissens - first_name: Miranda full_name: Gillitzer, Miranda last_name: Gillitzer - first_name: David full_name: Lippner, David last_name: Lippner - first_name: Frank full_name: Disilvio, Frank last_name: Disilvio - first_name: Casey full_name: Mueller, Casey last_name: Mueller - first_name: Paeton full_name: Wantuch, Paeton last_name: Wantuch - first_name: Gary full_name: Chaffee, Gary last_name: Chaffee - first_name: Michael full_name: Famiglietti, Michael last_name: Famiglietti - first_name: Danielle full_name: Zgoba, Danielle last_name: Zgoba - first_name: Asha full_name: Bailey, Asha last_name: Bailey - first_name: Yaya full_name: Bah, Yaya last_name: Bah - first_name: Samantha full_name: Engebretson, Samantha last_name: Engebretson - first_name: David full_name: Graupner, David last_name: Graupner - first_name: Emily full_name: Lackner, Emily last_name: Lackner - first_name: Vincent full_name: Larosa, Vincent last_name: Larosa - first_name: Tysha full_name: Medeiros, Tysha last_name: Medeiros - first_name: Michael full_name: Olson, Michael last_name: Olson - first_name: Andrew full_name: Phillips, Andrew last_name: Phillips - first_name: Harley full_name: Pyles, Harley last_name: Pyles - first_name: Amanda full_name: Richard, Amanda last_name: Richard - first_name: Scott full_name: Schoeller, Scott last_name: Schoeller - first_name: Boris full_name: Touzeau, Boris last_name: Touzeau - first_name: Larry full_name: Williams, Larry last_name: Williams - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Francis full_name: Peterson, Francis last_name: Peterson citation: ama: Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 2015;54(27):4163-4166. doi:10.1021/acs.biochem.5b00560 apa: Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D., Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. American Chemical Society. https://doi.org/10.1021/acs.biochem.5b00560 chicago: Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer, David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry. American Chemical Society, 2015. https://doi.org/10.1021/acs.biochem.5b00560. ieee: C. Veldkamp et al., “Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites,” Biochemistry, vol. 54, no. 27. American Chemical Society, pp. 4163–4166, 2015. ista: Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H, Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 54(27), 4163–4166. mla: Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry, vol. 54, no. 27, American Chemical Society, 2015, pp. 4163–66, doi:10.1021/acs.biochem.5b00560. short: C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F. Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey, Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson, A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K. Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166. date_created: 2018-12-11T11:53:03Z date_published: 2015-06-26T00:00:00Z date_updated: 2023-03-30T11:32:57Z day: '26' department: - _id: MiSi doi: 10.1021/acs.biochem.5b00560 ec_funded: 1 external_id: pmid: - '26115234' intvolume: ' 54' issue: '27' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/ month: '06' oa: 1 oa_version: Submitted Version page: 4163 - 4166 pmid: 1 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) publication: Biochemistry publication_status: published publisher: American Chemical Society publist_id: '5548' quality_controlled: '1' scopus_import: '1' status: public title: Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2015' ... --- _id: '12881' acknowledgement: This work was supported by the DFG (SPP 1527) and the EU (FP7, REA grant no 291734). article_processing_charge: No author: - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius - first_name: Eckehard full_name: Olbrich, Eckehard last_name: Olbrich citation: ama: 'Martius GS, Olbrich E. Quantifying self-organizing behavior of autonomous robots. In: Proceedings of the 13th European Conference on Artificial Life. MIT Press; 2015:78. doi:10.7551/978-0-262-33027-5-ch018' apa: 'Martius, G. S., & Olbrich, E. (2015). Quantifying self-organizing behavior of autonomous robots. In Proceedings of the 13th European Conference on Artificial Life (p. 78). York, United Kingdom: MIT Press. https://doi.org/10.7551/978-0-262-33027-5-ch018' chicago: Martius, Georg S, and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” In Proceedings of the 13th European Conference on Artificial Life, 78. MIT Press, 2015. https://doi.org/10.7551/978-0-262-33027-5-ch018. ieee: G. S. Martius and E. Olbrich, “Quantifying self-organizing behavior of autonomous robots,” in Proceedings of the 13th European Conference on Artificial Life, York, United Kingdom, 2015, p. 78. ista: 'Martius GS, Olbrich E. 2015. Quantifying self-organizing behavior of autonomous robots. Proceedings of the 13th European Conference on Artificial Life. ECAL: European Conference on Artificial Life, 78.' mla: Martius, Georg S., and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78, doi:10.7551/978-0-262-33027-5-ch018. short: G.S. Martius, E. Olbrich, in:, Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78. conference: end_date: 2015-07-24 location: York, United Kingdom name: 'ECAL: European Conference on Artificial Life' start_date: 2015-07-20 date_created: 2023-04-30T22:01:07Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-05-02T07:06:21Z day: '01' ddc: - '000' department: - _id: ChLa doi: 10.7551/978-0-262-33027-5-ch018 ec_funded: 1 file: - access_level: open_access checksum: 880eabe59c9df12f06a882aa1bc4e600 content_type: application/pdf creator: dernst date_created: 2023-05-02T07:02:59Z date_updated: 2023-05-02T07:02:59Z file_id: '12882' file_name: 2015_ECAL_Martius.pdf file_size: 1674241 relation: main_file success: 1 file_date_updated: 2023-05-02T07:02:59Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '78' project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Proceedings of the 13th European Conference on Artificial Life publication_identifier: isbn: - '9780262330275' publication_status: published publisher: MIT Press quality_controlled: '1' scopus_import: '1' status: public title: Quantifying self-organizing behavior of autonomous robots 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ...