--- _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: '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: '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 arxiv: 1 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 license: https://creativecommons.org/licenses/by-nc/4.0/ 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' license: https://creativecommons.org/licenses/by/4.0/ 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: '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: '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: '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: '7070' abstract: - lang: eng text: 'Torque magnetization measurements on YBa2Cu3Oy (YBCO) at doping y=6.67 (p=0.12), in dc fields (B) up to 33 T and temperatures down to 4.5 K, show that weak diamagnetism persists above the extrapolated irreversibility field Hirr(T=0)≈24 T. The differential susceptibility dM/dB, however, is more rapidly suppressed for B≳16 T than expected from the properties of the low field superconducting state, and saturates at a low value for fields B≳24 T. In addition, torque measurements on a p=0.11 YBCO crystal in pulsed field up to 65 T and temperatures down to 8 K show similar behavior, with no additional features at higher fields. We offer two candidate scenarios to explain these observations: (a) superconductivity survives but is heavily suppressed at high field by competition with charge-density-wave (CDW) order; (b) static superconductivity disappears near 24 T and is followed by a region of fluctuating superconductivity, which causes dM/dB to saturate at high field. The diamagnetic signal observed above 50 T for the p=0.11 crystal at 40 K and below may be caused by changes in the normal state susceptibility rather than bulk or fluctuating superconductivity. There will be orbital (Landau) diamagnetism from electron pockets and possibly a reduction in spin susceptibility caused by the stronger three-dimensional ordered CDW.' article_number: '180509' article_processing_charge: No article_type: original author: - first_name: Jing Fei full_name: Yu, Jing Fei last_name: Yu - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: I. full_name: Kokanović, I. last_name: Kokanović - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: N. full_name: Harrison, N. last_name: Harrison - first_name: James full_name: Day, James last_name: Day - first_name: Ruixing full_name: Liang, Ruixing last_name: Liang - first_name: W. N. full_name: Hardy, W. N. last_name: Hardy - first_name: D. A. full_name: Bonn, D. A. last_name: Bonn - first_name: A. full_name: McCollam, A. last_name: McCollam - first_name: S. R. full_name: Julian, S. R. last_name: Julian - first_name: J. R. full_name: Cooper, J. R. last_name: Cooper citation: ama: Yu JF, Ramshaw BJ, Kokanović I, et al. Magnetization of underdoped YBa2Cu3Oy above the irreversibility field. Physical Review B. 2015;92(18). doi:10.1103/physrevb.92.180509 apa: Yu, J. F., Ramshaw, B. J., Kokanović, I., Modic, K. A., Harrison, N., Day, J., … Cooper, J. R. (2015). Magnetization of underdoped YBa2Cu3Oy above the irreversibility field. Physical Review B. APS. https://doi.org/10.1103/physrevb.92.180509 chicago: Yu, Jing Fei, B. J. Ramshaw, I. Kokanović, Kimberly A Modic, N. Harrison, James Day, Ruixing Liang, et al. “Magnetization of Underdoped YBa2Cu3Oy above the Irreversibility Field.” Physical Review B. APS, 2015. https://doi.org/10.1103/physrevb.92.180509. ieee: J. F. Yu et al., “Magnetization of underdoped YBa2Cu3Oy above the irreversibility field,” Physical Review B, vol. 92, no. 18. APS, 2015. ista: Yu JF, Ramshaw BJ, Kokanović I, Modic KA, Harrison N, Day J, Liang R, Hardy WN, Bonn DA, McCollam A, Julian SR, Cooper JR. 2015. Magnetization of underdoped YBa2Cu3Oy above the irreversibility field. Physical Review B. 92(18), 180509. mla: Yu, Jing Fei, et al. “Magnetization of Underdoped YBa2Cu3Oy above the Irreversibility Field.” Physical Review B, vol. 92, no. 18, 180509, APS, 2015, doi:10.1103/physrevb.92.180509. short: J.F. Yu, B.J. Ramshaw, I. Kokanović, K.A. Modic, N. Harrison, J. Day, R. Liang, W.N. Hardy, D.A. Bonn, A. McCollam, S.R. Julian, J.R. Cooper, Physical Review B 92 (2015). date_created: 2019-11-19T13:22:06Z date_published: 2015-11-23T00:00:00Z date_updated: 2021-01-12T08:11:42Z day: '23' doi: 10.1103/physrevb.92.180509 extern: '1' intvolume: ' 92' issue: '18' language: - iso: eng month: '11' oa_version: None publication: Physical Review B publication_identifier: issn: - 1098-0121 - 1550-235X publication_status: published publisher: APS quality_controlled: '1' status: public title: Magnetization of underdoped YBa2Cu3Oy above the irreversibility field type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2015' ... --- _id: '7456' abstract: - lang: eng text: The rational design of monodisperse ferroelectric nanocrystals with controlled size and shape and their organization into hierarchical structures has been a critical step for understanding the polar ordering in nanoscale ferroelectrics, as well as the design of nanocrystal-based functional materials which harness the properties of individual nanoparticles and the collective interactions between them. We report here on the synthesis and self-assembly of aggregate-free, single-crystalline titanium-based perovskite nanoparticles with controlled morphology and surface composition by using a simple, easily scalable and highly versatile colloidal route. Single-crystalline, non-aggregated BaTiO3 colloidal nanocrystals, used as a model system, have been prepared under solvothermal conditions at temperatures as low as 180 °C. The shape of the nanocrystals was tuned from spheroidal to cubic upon changing the polarity of the solvent, whereas their size was varied from 16 to 30 nm for spheres and 5 to 78 nm for cubes by changing the concentration of the precursors and the reaction time, respectively. The hydrophobic, oleic acid-passivated nanoparticles exhibit very good solubility in non-polar solvents and can be rendered dispersible in polar solvents by a simple process involving the oxidative cleavage of the double bond upon treating the nanopowders with the Lemieux–von Rudloff reagent. Lattice dynamic analysis indicated that regardless of their size, BaTiO3 nanocrystals present local disorder within the perovskite unit cell, associated with the existence of polar ordering. We also demonstrate for the first time that, in addition to being used for fabricating large area, crack-free, highly uniform films, BaTiO3 nanocubes can serve as building blocks for the design of 2D and 3D mesoscale structures, such as superlattices and superparticles. Interestingly, the type of superlattice structure (simple cubic or face centered cubic) appears to be determined by the type of solvent in which the nanocrystals were dispersed. This approach provides an excellent platform for the synthesis of other titanium-based perovskite colloidal nanocrystals with controlled chemical composition, surface structure and morphology and for their assembly into complex architectures, therefore opening the door for the design of novel mesoscale functional materials/nanocomposites with potential applications in energy conversion, data storage and the biomedical field. article_processing_charge: No article_type: original author: - first_name: Daniela full_name: Caruntu, Daniela last_name: Caruntu - first_name: Taha full_name: Rostamzadeh, Taha last_name: Rostamzadeh - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Saman full_name: Salemizadeh Parizi, Saman last_name: Salemizadeh Parizi - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu citation: ama: Caruntu D, Rostamzadeh T, Costanzo T, Salemizadeh Parizi S, Caruntu G. Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals. Nanoscale. 2015;7(30):12955-12969. doi:10.1039/c5nr00737b apa: Caruntu, D., Rostamzadeh, T., Costanzo, T., Salemizadeh Parizi, S., & Caruntu, G. (2015). Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals. Nanoscale. RSC. https://doi.org/10.1039/c5nr00737b chicago: Caruntu, Daniela, Taha Rostamzadeh, Tommaso Costanzo, Saman Salemizadeh Parizi, and Gabriel Caruntu. “Solvothermal Synthesis and Controlled Self-Assembly of Monodisperse Titanium-Based Perovskite Colloidal Nanocrystals.” Nanoscale. RSC, 2015. https://doi.org/10.1039/c5nr00737b. ieee: D. Caruntu, T. Rostamzadeh, T. Costanzo, S. Salemizadeh Parizi, and G. Caruntu, “Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals,” Nanoscale, vol. 7, no. 30. RSC, pp. 12955–12969, 2015. ista: Caruntu D, Rostamzadeh T, Costanzo T, Salemizadeh Parizi S, Caruntu G. 2015. Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals. Nanoscale. 7(30), 12955–12969. mla: Caruntu, Daniela, et al. “Solvothermal Synthesis and Controlled Self-Assembly of Monodisperse Titanium-Based Perovskite Colloidal Nanocrystals.” Nanoscale, vol. 7, no. 30, RSC, 2015, pp. 12955–69, doi:10.1039/c5nr00737b. short: D. Caruntu, T. Rostamzadeh, T. Costanzo, S. Salemizadeh Parizi, G. Caruntu, Nanoscale 7 (2015) 12955–12969. date_created: 2020-02-05T14:16:37Z date_published: 2015-08-14T00:00:00Z date_updated: 2023-02-23T13:08:24Z day: '14' doi: 10.1039/c5nr00737b extern: '1' external_id: pmid: - '26168304' intvolume: ' 7' issue: '30' language: - iso: eng month: '08' oa_version: None page: 12955-12969 pmid: 1 publication: Nanoscale publication_identifier: issn: - 2040-3364 - 2040-3372 publication_status: published publisher: RSC quality_controlled: '1' status: public title: Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2015' ... --- _id: '7457' abstract: - lang: eng text: A new organic–inorganic ferroelectric hybrid capacitor designed by uniformly incorporating surface modified monodisperse 15 nm ferroelectric BaTiO3 nanocubes into non-polar polymer blends of poly(methyl methacrylate) (PMMA) polymer and acrylonitrile-butadiene-styrene (ABS) terpolymer is described. The investigation of spatial distribution of nanofillers via a non-distractive thermal pulse method illustrates that the surface functionalization of nanocubes plays a key role in the uniform distribution of charge polarization within the polymer matrix. The discharged energy density of the nanocomposite with 30 vol% BaTiO3 nanocubes is ∼44 × 10−3 J cm−3, which is almost six times higher than that of the neat polymer. The facile processing, along with the superior mechanical and electrical properties of the BaTiO3/PMMA–ABS nanocomposites make them suitable for implementation into capacitive electrical energy storage devices. article_processing_charge: No article_type: original author: - first_name: Saman Salemizadeh full_name: Parizi, Saman Salemizadeh last_name: Parizi - first_name: Gavin full_name: Conley, Gavin last_name: Conley - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Bob full_name: Howell, Bob last_name: Howell - first_name: Axel full_name: Mellinger, Axel last_name: Mellinger - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu citation: ama: Parizi SS, Conley G, Costanzo T, Howell B, Mellinger A, Caruntu G. Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors. RSC Advances. 2015;5(93):76356-76362. doi:10.1039/c5ra11347d apa: Parizi, S. S., Conley, G., Costanzo, T., Howell, B., Mellinger, A., & Caruntu, G. (2015). Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors. RSC Advances. RSC. https://doi.org/10.1039/c5ra11347d chicago: Parizi, Saman Salemizadeh, Gavin Conley, Tommaso Costanzo, Bob Howell, Axel Mellinger, and Gabriel Caruntu. “Fabrication of Barium Titanate/Acrylonitrile-Butadiene Styrene/Poly(Methyl Methacrylate) Nanocomposite Films for Hybrid Ferroelectric Capacitors.” RSC Advances. RSC, 2015. https://doi.org/10.1039/c5ra11347d. ieee: S. S. Parizi, G. Conley, T. Costanzo, B. Howell, A. Mellinger, and G. Caruntu, “Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors,” RSC Advances, vol. 5, no. 93. RSC, pp. 76356–76362, 2015. ista: Parizi SS, Conley G, Costanzo T, Howell B, Mellinger A, Caruntu G. 2015. Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors. RSC Advances. 5(93), 76356–76362. mla: Parizi, Saman Salemizadeh, et al. “Fabrication of Barium Titanate/Acrylonitrile-Butadiene Styrene/Poly(Methyl Methacrylate) Nanocomposite Films for Hybrid Ferroelectric Capacitors.” RSC Advances, vol. 5, no. 93, RSC, 2015, pp. 76356–62, doi:10.1039/c5ra11347d. short: S.S. Parizi, G. Conley, T. Costanzo, B. Howell, A. Mellinger, G. Caruntu, RSC Advances 5 (2015) 76356–76362. date_created: 2020-02-05T14:17:26Z date_published: 2015-09-01T00:00:00Z date_updated: 2023-02-23T13:08:26Z day: '01' doi: 10.1039/c5ra11347d extern: '1' intvolume: ' 5' issue: '93' language: - iso: eng month: '09' oa_version: Submitted Version page: 76356-76362 publication: RSC Advances publication_identifier: issn: - 2046-2069 publication_status: published publisher: RSC quality_controlled: '1' status: public title: Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2015' ... --- _id: '7739' abstract: - lang: eng text: Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long‐term studies across Europe and consequently are considered an ecological ‘model organism’. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long‐term study populations of great tits—one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population‐specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population‐specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free‐living populations. article_processing_charge: No article_type: original author: - first_name: Anna W. full_name: Santure, Anna W. last_name: Santure - first_name: Jocelyn full_name: Poissant, Jocelyn last_name: Poissant - first_name: Isabelle full_name: De Cauwer, Isabelle last_name: De Cauwer - first_name: Kees full_name: van Oers, Kees last_name: van Oers - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: John L. full_name: Quinn, John L. last_name: Quinn - first_name: Martien A. M. full_name: Groenen, Martien A. M. last_name: Groenen - first_name: Marcel E. full_name: Visser, Marcel E. last_name: Visser - first_name: Ben C. full_name: Sheldon, Ben C. last_name: Sheldon - first_name: Jon full_name: Slate, Jon last_name: Slate citation: ama: Santure AW, Poissant J, De Cauwer I, et al. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 2015;24:6148-6162. doi:10.1111/mec.13452 apa: Santure, A. W., Poissant, J., De Cauwer, I., van Oers, K., Robinson, M. R., Quinn, J. L., … Slate, J. (2015). Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.13452 chicago: Santure, Anna W., Jocelyn Poissant, Isabelle De Cauwer, Kees van Oers, Matthew Richard Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser, Ben C. Sheldon, and Jon Slate. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology. Wiley, 2015. https://doi.org/10.1111/mec.13452. ieee: A. W. Santure et al., “Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations,” Molecular Ecology, vol. 24. Wiley, pp. 6148–6162, 2015. ista: Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen MAM, Visser ME, Sheldon BC, Slate J. 2015. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 24, 6148–6162. mla: Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology, vol. 24, Wiley, 2015, pp. 6148–62, doi:10.1111/mec.13452. short: A.W. Santure, J. Poissant, I. De Cauwer, K. van Oers, M.R. Robinson, J.L. Quinn, M.A.M. Groenen, M.E. Visser, B.C. Sheldon, J. Slate, Molecular Ecology 24 (2015) 6148–6162. date_created: 2020-04-30T10:51:01Z date_published: 2015-12-10T00:00:00Z date_updated: 2021-01-12T08:15:12Z day: '10' doi: 10.1111/mec.13452 extern: '1' intvolume: ' 24' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/mec.13452 month: '12' oa: 1 oa_version: Published Version page: 6148-6162 publication: Molecular Ecology publication_identifier: issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2015' ... --- _id: '7741' abstract: - lang: eng text: Phenotypes expressed in a social context are not only a function of the individual, but can also be shaped by the phenotypes of social partners. These social effects may play a major role in the evolution of cooperative breeding if social partners differ in the quality of care they provide and if individual carers adjust their effort in relation to that of other carers. When applying social effects models to wild study systems, it is also important to explore sources of individual plasticity that could masquerade as social effects. We studied offspring provisioning rates of parents and helpers in a wild population of long-tailed tits Aegithalos caudatus using a quantitative genetic framework to identify these social effects and partition them into genetic, permanent environment and current environment components. Controlling for other effects, individuals were consistent in their provisioning effort at a given nest, but adjusted their effort based on who was in their social group, indicating the presence of social effects. However, these social effects differed between years and social contexts, indicating a current environment effect, rather than indicating a genetic or permanent environment effect. While this study reveals the importance of examining environmental and genetic sources of social effects, the framework we present is entirely general, enabling a greater understanding of potentially important social effects within any ecological population. article_number: '20150689' article_processing_charge: No article_type: original author: - first_name: Mark James full_name: Adams, Mark James last_name: Adams - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Maria-Elena full_name: Mannarelli, Maria-Elena last_name: Mannarelli - first_name: Ben J. full_name: Hatchwell, Ben J. last_name: Hatchwell citation: ama: 'Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 2015;282(1810). doi:10.1098/rspb.2015.0689' apa: 'Adams, M. J., Robinson, M. R., Mannarelli, M.-E., & Hatchwell, B. J. (2015). Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2015.0689' chicago: 'Adams, Mark James, Matthew Richard Robinson, Maria-Elena Mannarelli, and Ben J. Hatchwell. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2015.0689.' ieee: 'M. J. Adams, M. R. Robinson, M.-E. Mannarelli, and B. J. Hatchwell, “Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird,” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810. The Royal Society, 2015.' ista: 'Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. 2015. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 282(1810), 20150689.' mla: 'Adams, Mark James, et al. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810, 20150689, The Royal Society, 2015, doi:10.1098/rspb.2015.0689.' short: 'M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings of the Royal Society B: Biological Sciences 282 (2015).' date_created: 2020-04-30T10:58:07Z date_published: 2015-07-07T00:00:00Z date_updated: 2021-01-12T08:15:12Z day: '07' doi: 10.1098/rspb.2015.0689 extern: '1' external_id: pmid: - '26063846' intvolume: ' 282' issue: '1810' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rspb.2015.0689 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: 'Proceedings of the Royal Society B: Biological Sciences' publication_identifier: issn: - 0962-8452 - 1471-2954 publication_status: published publisher: The Royal Society quality_controlled: '1' status: public title: Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 282 year: '2015' ... --- _id: '7742' abstract: - lang: eng text: Across-nation differences in the mean values for complex traits are common1,2,3,4,5,6,7,8, but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95 × 10−4), and we find an among-population genetic correlation for tall and slender individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P < 0.001), but environmental differences across Europe masked genetic differentiation for BMI (P < 0.58). article_processing_charge: No article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Gibran full_name: Hemani, Gibran last_name: Hemani - first_name: Carolina full_name: Medina-Gomez, Carolina last_name: Medina-Gomez - first_name: Massimo full_name: Mezzavilla, Massimo last_name: Mezzavilla - first_name: Tonu full_name: Esko, Tonu last_name: Esko - first_name: Konstantin full_name: Shakhbazov, Konstantin last_name: Shakhbazov - first_name: Joseph E full_name: Powell, Joseph E last_name: Powell - first_name: Anna full_name: Vinkhuyzen, Anna last_name: Vinkhuyzen - first_name: Sonja I full_name: Berndt, Sonja I last_name: Berndt - first_name: Stefan full_name: Gustafsson, Stefan last_name: Gustafsson - first_name: Anne E full_name: Justice, Anne E last_name: Justice - first_name: Bratati full_name: Kahali, Bratati last_name: Kahali - first_name: Adam E full_name: Locke, Adam E last_name: Locke - first_name: Tune H full_name: Pers, Tune H last_name: Pers - first_name: Sailaja full_name: Vedantam, Sailaja last_name: Vedantam - first_name: Andrew R full_name: Wood, Andrew R last_name: Wood - first_name: Wouter full_name: van Rheenen, Wouter last_name: van Rheenen - first_name: Ole A full_name: Andreassen, Ole A last_name: Andreassen - first_name: Paolo full_name: Gasparini, Paolo last_name: Gasparini - first_name: Andres full_name: Metspalu, Andres last_name: Metspalu - first_name: Leonard H van den full_name: Berg, Leonard H van den last_name: Berg - first_name: Jan H full_name: Veldink, Jan H last_name: Veldink - first_name: Fernando full_name: Rivadeneira, Fernando last_name: Rivadeneira - first_name: Thomas M full_name: Werge, Thomas M last_name: Werge - first_name: Goncalo R full_name: Abecasis, Goncalo R last_name: Abecasis - first_name: Dorret I full_name: Boomsma, Dorret I last_name: Boomsma - first_name: Daniel I full_name: Chasman, Daniel I last_name: Chasman - first_name: Eco J C full_name: de Geus, Eco J C last_name: de Geus - first_name: Timothy M full_name: Frayling, Timothy M last_name: Frayling - first_name: Joel N full_name: Hirschhorn, Joel N last_name: Hirschhorn - first_name: Jouke Jan full_name: Hottenga, Jouke Jan last_name: Hottenga - first_name: Erik full_name: Ingelsson, Erik last_name: Ingelsson - first_name: Ruth J F full_name: Loos, Ruth J F last_name: Loos - first_name: Patrik K E full_name: Magnusson, Patrik K E last_name: Magnusson - first_name: Nicholas G full_name: Martin, Nicholas G last_name: Martin - first_name: Grant W full_name: Montgomery, Grant W last_name: Montgomery - first_name: Kari E full_name: North, Kari E last_name: North - first_name: Nancy L full_name: Pedersen, Nancy L last_name: Pedersen - first_name: Timothy D full_name: Spector, Timothy D last_name: Spector - first_name: Elizabeth K full_name: Speliotes, Elizabeth K last_name: Speliotes - first_name: Michael E full_name: Goddard, Michael E last_name: Goddard - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Peter M full_name: Visscher, Peter M last_name: Visscher citation: ama: Robinson MR, Hemani G, Medina-Gomez C, et al. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 2015;47(11):1357-1362. doi:10.1038/ng.3401 apa: Robinson, M. R., Hemani, G., Medina-Gomez, C., Mezzavilla, M., Esko, T., Shakhbazov, K., … Visscher, P. M. (2015). Population genetic differentiation of height and body mass index across Europe. Nature Genetics. Springer Nature. https://doi.org/10.1038/ng.3401 chicago: Robinson, Matthew Richard, Gibran Hemani, Carolina Medina-Gomez, Massimo Mezzavilla, Tonu Esko, Konstantin Shakhbazov, Joseph E Powell, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” Nature Genetics. Springer Nature, 2015. https://doi.org/10.1038/ng.3401. ieee: M. R. Robinson et al., “Population genetic differentiation of height and body mass index across Europe,” Nature Genetics, vol. 47, no. 11. Springer Nature, pp. 1357–1362, 2015. ista: Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K, Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S, Justice AE, Kahali B, Locke AE, Pers TH, Vedantam S, Wood AR, van Rheenen W, Andreassen OA, Gasparini P, Metspalu A, Berg LH van den, Veldink JH, Rivadeneira F, Werge TM, Abecasis GR, Boomsma DI, Chasman DI, de Geus EJC, Frayling TM, Hirschhorn JN, Hottenga JJ, Ingelsson E, Loos RJF, Magnusson PKE, Martin NG, Montgomery GW, North KE, Pedersen NL, Spector TD, Speliotes EK, Goddard ME, Yang J, Visscher PM. 2015. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 47(11), 1357–1362. mla: Robinson, Matthew Richard, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” Nature Genetics, vol. 47, no. 11, Springer Nature, 2015, pp. 1357–62, doi:10.1038/ng.3401. short: M.R. Robinson, G. Hemani, C. Medina-Gomez, M. Mezzavilla, T. Esko, K. Shakhbazov, J.E. Powell, A. Vinkhuyzen, S.I. Berndt, S. Gustafsson, A.E. Justice, B. Kahali, A.E. Locke, T.H. Pers, S. Vedantam, A.R. Wood, W. van Rheenen, O.A. Andreassen, P. Gasparini, A. Metspalu, L.H. van den Berg, J.H. Veldink, F. Rivadeneira, T.M. Werge, G.R. Abecasis, D.I. Boomsma, D.I. Chasman, E.J.C. de Geus, T.M. Frayling, J.N. Hirschhorn, J.J. Hottenga, E. Ingelsson, R.J.F. Loos, P.K.E. Magnusson, N.G. Martin, G.W. Montgomery, K.E. North, N.L. Pedersen, T.D. Spector, E.K. Speliotes, M.E. Goddard, J. Yang, P.M. Visscher, Nature Genetics 47 (2015) 1357–1362. date_created: 2020-04-30T10:58:23Z date_published: 2015-09-14T00:00:00Z date_updated: 2021-01-12T08:15:13Z day: '14' doi: 10.1038/ng.3401 extern: '1' intvolume: ' 47' issue: '11' language: - iso: eng month: '09' oa_version: None page: 1357-1362 publication: Nature Genetics publication_identifier: issn: - 1061-4036 - 1546-1718 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Population genetic differentiation of height and body mass index across Europe type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2015' ... --- _id: '776' abstract: - lang: eng text: High-performance concurrent priority queues are essential for applications such as task scheduling and discrete event simulation. Unfortunately, even the best performing implementations do not scale past a number of threads in the single digits. This is because of the sequential bottleneck in accessing the elements at the head of the queue in order to perform a DeleteMin operation. In this paper, we present the SprayList, a scalable priority queue with relaxed ordering semantics. Starting from a non-blocking SkipList, the main innovation behind our design is that the DeleteMin operations avoid a sequential bottleneck by "spraying" themselves onto the head of the SkipList list in a coordinated fashion. The spraying is implemented using a carefully designed random walk, so that DeleteMin returns an element among the first O(plog3p) in the list, with high probability, where p is the number of threads. We prove that the running time of a DeleteMin operation is O(log3p), with high probability, independent of the size of the list. Our experiments show that the relaxed semantics allow the data structure to scale for high thread counts, comparable to a classic unordered SkipList. Furthermore, we observe that, for reasonably parallel workloads, the scalability benefits of relaxation considerably outweigh the additional work due to out-of-order execution. acknowledgement: "Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle\r\nand Intel corporations." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Justin full_name: Kopinsky, Justin last_name: Kopinsky - first_name: Jerry full_name: Li, Jerry last_name: Li - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Kopinsky J, Li J, Shavit N. The SprayList: A scalable relaxed priority queue. In: Vol 2015-January. ACM; 2015:11-20. doi:10.1145/2688500.2688523' apa: 'Alistarh, D.-A., Kopinsky, J., Li, J., & Shavit, N. (2015). The SprayList: A scalable relaxed priority queue (Vol. 2015–January, pp. 11–20). Presented at the PPoPP: Principles and Practice of Parallel Pogramming, ACM. https://doi.org/10.1145/2688500.2688523' chicago: 'Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Nir Shavit. “The SprayList: A Scalable Relaxed Priority Queue,” 2015–January:11–20. ACM, 2015. https://doi.org/10.1145/2688500.2688523.' ieee: 'D.-A. Alistarh, J. Kopinsky, J. Li, and N. Shavit, “The SprayList: A scalable relaxed priority queue,” presented at the PPoPP: Principles and Practice of Parallel Pogramming, 2015, vol. 2015–January, pp. 11–20.' ista: 'Alistarh D-A, Kopinsky J, Li J, Shavit N. 2015. The SprayList: A scalable relaxed priority queue. PPoPP: Principles and Practice of Parallel Pogramming vol. 2015–January, 11–20.' mla: 'Alistarh, Dan-Adrian, et al. The SprayList: A Scalable Relaxed Priority Queue. Vol. 2015–January, ACM, 2015, pp. 11–20, doi:10.1145/2688500.2688523.' short: D.-A. Alistarh, J. Kopinsky, J. Li, N. Shavit, in:, ACM, 2015, pp. 11–20. conference: name: 'PPoPP: Principles and Practice of Parallel Pogramming' date_created: 2018-12-11T11:48:26Z date_published: 2015-01-24T00:00:00Z date_updated: 2023-02-23T13:16:43Z day: '24' doi: 10.1145/2688500.2688523 extern: '1' language: - iso: eng month: '01' oa_version: None page: 11 - 20 publication_status: published publisher: ACM publist_id: '6878' status: public title: 'The SprayList: A scalable relaxed priority queue' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015-January year: '2015' ... --- _id: '7765' abstract: - lang: eng text: 'We introduce a principle unique to disordered solids wherein the contribution of any bond to one global perturbation is uncorrelated with its contribution to another. Coupled with sufficient variability in the contributions of different bonds, this “independent bond-level response” paves the way for the design of real materials with unusual and exquisitely tuned properties. To illustrate this, we choose two global perturbations: compression and shear. By applying a bond removal procedure that is both simple and experimentally relevant to remove a very small fraction of bonds, we can drive disordered spring networks to both the incompressible and completely auxetic limits of mechanical behavior.' article_number: '225501' article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: 'Goodrich CP, Liu AJ, Nagel SR. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 2015;114(22). doi:10.1103/physrevlett.114.225501' apa: 'Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.114.225501' chicago: 'Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/physrevlett.114.225501.' ieee: 'C. P. Goodrich, A. J. Liu, and S. R. Nagel, “The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior,” Physical Review Letters, vol. 114, no. 22. American Physical Society, 2015.' ista: 'Goodrich CP, Liu AJ, Nagel SR. 2015. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 114(22), 225501.' mla: 'Goodrich, Carl Peter, et al. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters, vol. 114, no. 22, 225501, American Physical Society, 2015, doi:10.1103/physrevlett.114.225501.' short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015). date_created: 2020-04-30T11:41:08Z date_published: 2015-06-04T00:00:00Z date_updated: 2021-01-12T08:15:23Z day: '04' doi: 10.1103/physrevlett.114.225501 extern: '1' intvolume: ' 114' issue: '22' language: - iso: eng month: '06' oa_version: None publication: Physical Review Letters publication_identifier: issn: - 0031-9007 - 1079-7114 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: 'The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2015' ... --- _id: '7766' abstract: - lang: eng text: We study the vibrational properties near a free surface of disordered spring networks derived from jammed sphere packings. In bulk systems, without surfaces, it is well understood that such systems have a plateau in the density of vibrational modes extending down to a frequency scale ω*. This frequency is controlled by ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres and twice the spatial dimension, d, of the system, which vanishes at the jamming transition. In the presence of a free surface we find that there is a density of disordered vibrational modes associated with the surface that extends far below ω*. The total number of these low-frequency surface modes is controlled by ΔZ, and the profile of their decay into the bulk has two characteristic length scales, which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached. article_processing_charge: No article_type: original author: - first_name: Daniel M. full_name: Sussman, Daniel M. last_name: Sussman - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in jammed sphere packings. Soft Matter. 2015;11(14):2745-2751. doi:10.1039/c4sm02905d apa: Sussman, D. M., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). Disordered surface vibrations in jammed sphere packings. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c4sm02905d chicago: Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4sm02905d. ieee: D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface vibrations in jammed sphere packings,” Soft Matter, vol. 11, no. 14. Royal Society of Chemistry, pp. 2745–2751, 2015. ista: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations in jammed sphere packings. Soft Matter. 11(14), 2745–2751. mla: Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter, vol. 11, no. 14, Royal Society of Chemistry, 2015, pp. 2745–51, doi:10.1039/c4sm02905d. short: D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015) 2745–2751. date_created: 2020-04-30T11:41:23Z date_published: 2015-02-15T00:00:00Z date_updated: 2021-01-12T08:15:23Z day: '15' doi: 10.1039/c4sm02905d extern: '1' intvolume: ' 11' issue: '14' language: - iso: eng month: '02' oa_version: None page: 2745-2751 publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: Disordered surface vibrations in jammed sphere packings type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ...