--- _id: '6109' abstract: - lang: eng text: Neuropeptides are ubiquitous modulators of behavior and physiology. They are packaged in specialized secretory organelles called dense core vesicles (DCVs) that are released upon neural stimulation. Unlike synaptic vesicles, which can be recycled and refilled close to release sites, DCVs must be replenished by de novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in a Caenorhabditis elegans sensory neuron whose tonic activity we can control using a natural stimulus. We express fluorescently tagged neuropeptides in the neuron and define parameters that describe their subcellular distribution. We measure these parameters at high and low neural activity in 187 mutants defective in proteins implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic activity. Using unsupervised hierarchical clustering methods, we analyze these data and identify 62 groups of genes with similar mutant phenotypes. We explore the function of a subset of these groups. We recapitulate many previous findings, validating our paradigm. We uncover a large battery of proteins involved in recycling DCV membrane proteins, something hitherto poorly explored. We show that the unfolded protein response promotes DCV production, which may contribute to intertissue communication of stress. We also find evidence that different mechanisms of priming and exocytosis may operate at high and low neural activity. Our work provides a defined framework to study DCV biology at different neural activity levels. author: - first_name: Patrick full_name: Laurent, Patrick last_name: Laurent - first_name: QueeLim full_name: Ch’ng, QueeLim last_name: Ch’ng - first_name: Maëlle full_name: Jospin, Maëlle last_name: Jospin - first_name: Changchun full_name: Chen, Changchun last_name: Chen - first_name: Ramiro full_name: Lorenzo, Ramiro last_name: Lorenzo - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 2018;115(29):E6890-E6899. doi:10.1073/pnas.1714610115 apa: Laurent, P., Ch’ng, Q., Jospin, M., Chen, C., Lorenzo, R., & de Bono, M. (2018). Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1714610115 chicago: Laurent, Patrick, QueeLim Ch’ng, Maëlle Jospin, Changchun Chen, Ramiro Lorenzo, and Mario de Bono. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1714610115. ieee: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, and M. de Bono, “Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron,” Proceedings of the National Academy of Sciences, vol. 115, no. 29. National Academy of Sciences, pp. E6890–E6899, 2018. ista: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. 2018. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 115(29), E6890–E6899. mla: Laurent, Patrick, et al. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences, vol. 115, no. 29, National Academy of Sciences, 2018, pp. E6890–99, doi:10.1073/pnas.1714610115. short: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, M. de Bono, Proceedings of the National Academy of Sciences 115 (2018) E6890–E6899. date_created: 2019-03-19T12:41:33Z date_published: 2018-07-17T00:00:00Z date_updated: 2021-01-12T08:06:09Z day: '17' ddc: - '570' doi: 10.1073/pnas.1714610115 extern: '1' external_id: pmid: - '29959203' file: - access_level: open_access checksum: 5e81665377441cdd8d99ab952c534319 content_type: application/pdf creator: kschuh date_created: 2019-03-19T13:01:58Z date_updated: 2020-07-14T12:47:19Z file_id: '6110' file_name: 2018_PNAS_Laurent.pdf file_size: 1567765 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 115' issue: '29' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: E6890-E6899 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' status: public title: Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2018' ... --- _id: '6164' abstract: - lang: eng text: In this paper, we propose an algorithm to build discrete spherical shell having integer center and real-valued inner and outer radii on the face-centered cubic (FCC) grid. We address the problem by mapping it to a 2D scenario and building the shell layer by layer on hexagonal grids with additive manufacturing in mind. The layered hexagonal grids get shifted according to need as we move from one layer to another and forms the FCC grid in 3D. However, we restrict our computation strictly to 2D in order to utilize symmetry and simplicity. alternative_title: - LNCS article_processing_charge: No author: - first_name: Girish full_name: Koshti, Girish last_name: Koshti - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Gaëlle full_name: Largeteau-Skapin, Gaëlle last_name: Largeteau-Skapin - first_name: Rita full_name: Zrour, Rita last_name: Zrour - first_name: Eric full_name: Andres, Eric last_name: Andres - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: 'Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In: 19th International Workshop. Vol 11255. Cham: Springer; 2018:82-96. doi:10.1007/978-3-030-05288-1_7' apa: 'Koshti, G., Biswas, R., Largeteau-Skapin, G., Zrour, R., Andres, E., & Bhowmick, P. (2018). Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In 19th International Workshop (Vol. 11255, pp. 82–96). Cham: Springer. https://doi.org/10.1007/978-3-030-05288-1_7' chicago: 'Koshti, Girish, Ranita Biswas, Gaëlle Largeteau-Skapin, Rita Zrour, Eric Andres, and Partha Bhowmick. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” In 19th International Workshop, 11255:82–96. Cham: Springer, 2018. https://doi.org/10.1007/978-3-030-05288-1_7.' ieee: G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, and P. Bhowmick, “Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D,” in 19th International Workshop, Porto, Portugal, 2018, vol. 11255, pp. 82–96. ista: 'Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. 2018. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. 19th International Workshop. IWCIA: International Workshop on Combinatorial Image Analysis, LNCS, vol. 11255, 82–96.' mla: Koshti, Girish, et al. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” 19th International Workshop, vol. 11255, Springer, 2018, pp. 82–96, doi:10.1007/978-3-030-05288-1_7. short: G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, P. Bhowmick, in:, 19th International Workshop, Springer, Cham, 2018, pp. 82–96. conference: end_date: 2018-11-24 location: Porto, Portugal name: 'IWCIA: International Workshop on Combinatorial Image Analysis' start_date: 2018-11-22 date_created: 2019-03-21T12:16:58Z date_published: 2018-11-22T00:00:00Z date_updated: 2022-01-27T15:26:39Z day: '22' doi: 10.1007/978-3-030-05288-1_7 extern: '1' intvolume: ' 11255' language: - iso: eng month: '11' oa_version: None page: 82-96 place: Cham publication: 19th International Workshop publication_identifier: eisbn: - 978-3-030-05288-1 eissn: - 1611-3349 isbn: - 978-3-030-05287-4 issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' status: public title: Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 11255 year: '2018' ... --- _id: '6354' abstract: - lang: eng text: Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow. acknowledgement: ' FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)' article_number: e3018 author: - first_name: Shuxia full_name: Fan, Shuxia last_name: Fan - first_name: Michael full_name: Lorenz, Michael last_name: Lorenz - first_name: Steffen full_name: Massberg, Steffen last_name: Massberg - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 citation: ama: Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018 apa: Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018 chicago: Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018. ieee: S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018. ista: Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018. mla: Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018. short: S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018). date_created: 2019-04-29T09:40:33Z date_published: 2018-09-20T00:00:00Z date_updated: 2021-01-12T08:07:12Z day: '20' ddc: - '570' department: - _id: MiSi doi: 10.21769/bioprotoc.3018 ec_funded: 1 file: - access_level: open_access checksum: d4588377e789da7f360b553ae02c5119 content_type: application/pdf creator: dernst date_created: 2019-04-30T08:04:33Z date_updated: 2020-07-14T12:47:28Z file_id: '6360' file_name: 2018_BioProtocol_Fan.pdf file_size: 2928337 relation: main_file file_date_updated: 2020-07-14T12:47:28Z has_accepted_license: '1' intvolume: ' 8' issue: '18' keyword: - Platelets - Cell migration - Bacteria - Shear flow - Fibrinogen - E. coli language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells publication: Bio-Protocol publication_identifier: issn: - 2331-8325 publication_status: published publisher: Bio-Protocol quality_controlled: '1' status: public title: Platelet migration and bacterial trapping assay under flow 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: 8 year: '2018' ... --- _id: '6368' abstract: - lang: eng text: An optical network of superconducting quantum bits (qubits) is an appealing platform for quantum communication and distributed quantum computing, but developing a quantum-compatible link between the microwave and optical domains remains an outstanding challenge. Operating at T < 100 mK temperatures, as required for quantum electrical circuits, we demonstrate a mechanically mediated microwave–optical converter with 47% conversion efficiency, and use a classical feed-forward protocol to reduce added noise to 38 photons. The feed-forward protocol harnesses our discovery that noise emitted from the two converter output ports is strongly correlated because both outputs record thermal motion of the same mechanical mode. We also discuss a quantum feed-forward protocol that, given high system efficiencies, would allow quantum information to be transferred even when thermal phonons enter the mechanical element faster than the electro-optic conversion rate. 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: P. S. full_name: Burns, P. S. last_name: Burns - first_name: M. D. full_name: Urmey, M. D. last_name: Urmey - first_name: R. W. full_name: Peterson, R. W. last_name: Peterson - first_name: N. S. full_name: Kampel, N. S. last_name: Kampel - first_name: B. M. full_name: Brubaker, B. M. last_name: Brubaker - first_name: G. full_name: Smith, G. last_name: Smith - first_name: K. W. full_name: Lehnert, K. W. last_name: Lehnert - first_name: C. A. full_name: Regal, C. A. last_name: Regal citation: ama: Higginbotham AP, Burns PS, Urmey MD, et al. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 2018;14(10):1038-1042. doi:10.1038/s41567-018-0210-0 apa: Higginbotham, A. P., Burns, P. S., Urmey, M. D., Peterson, R. W., Kampel, N. S., Brubaker, B. M., … Regal, C. A. (2018). Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-018-0210-0 chicago: Higginbotham, Andrew P, P. S. Burns, M. D. Urmey, R. W. Peterson, N. S. Kampel, B. M. Brubaker, G. Smith, K. W. Lehnert, and C. A. Regal. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” Nature Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0210-0. ieee: A. P. Higginbotham et al., “Harnessing electro-optic correlations in an efficient mechanical converter,” Nature Physics, vol. 14, no. 10. Springer Nature, pp. 1038–1042, 2018. ista: Higginbotham AP, Burns PS, Urmey MD, Peterson RW, Kampel NS, Brubaker BM, Smith G, Lehnert KW, Regal CA. 2018. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 14(10), 1038–1042. mla: Higginbotham, Andrew P., et al. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” Nature Physics, vol. 14, no. 10, Springer Nature, 2018, pp. 1038–42, doi:10.1038/s41567-018-0210-0. short: A.P. Higginbotham, P.S. Burns, M.D. Urmey, R.W. Peterson, N.S. Kampel, B.M. Brubaker, G. Smith, K.W. Lehnert, C.A. Regal, Nature Physics 14 (2018) 1038–1042. date_created: 2019-05-03T09:17:20Z date_published: 2018-10-01T00:00:00Z date_updated: 2021-01-12T08:07:15Z day: '01' doi: 10.1038/s41567-018-0210-0 extern: '1' external_id: arxiv: - '1712.06535' intvolume: ' 14' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.06535 month: '10' oa: 1 oa_version: Preprint page: 1038-1042 publication: Nature Physics publication_identifier: issn: - 1745-2473 - 1745-2481 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Harnessing electro-optic correlations in an efficient mechanical converter type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2018' ... --- _id: '6369' abstract: - lang: eng text: We construct a metamaterial from radio-frequency harmonic oscillators, and find two topologically distinct phases resulting from dissipation engineered into the system. These phases are distinguished by a quantized value of bulk energy transport. The impulse response of our circuit is measured and used to reconstruct the band structure and winding number of circuit eigenfunctions around a dark mode. Our results demonstrate that dissipative topological transport can occur in a wider class of physical systems than considered before. article_number: '220301' author: - first_name: Eric I. full_name: Rosenthal, Eric I. last_name: Rosenthal - first_name: Nicole K. full_name: Ehrlich, Nicole K. last_name: Ehrlich - first_name: Mark S. full_name: Rudner, Mark S. last_name: Rudner - 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: K. W. full_name: Lehnert, K. W. last_name: Lehnert citation: ama: Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 2018;97(22). doi:10.1103/physrevb.97.220301 apa: Rosenthal, E. I., Ehrlich, N. K., Rudner, M. S., Higginbotham, A. P., & Lehnert, K. W. (2018). Topological phase transition measured in a dissipative metamaterial. Physical Review B. American Physical Society (APS). https://doi.org/10.1103/physrevb.97.220301 chicago: Rosenthal, Eric I., Nicole K. Ehrlich, Mark S. Rudner, Andrew P Higginbotham, and K. W. Lehnert. “Topological Phase Transition Measured in a Dissipative Metamaterial.” Physical Review B. American Physical Society (APS), 2018. https://doi.org/10.1103/physrevb.97.220301. ieee: E. I. Rosenthal, N. K. Ehrlich, M. S. Rudner, A. P. Higginbotham, and K. W. Lehnert, “Topological phase transition measured in a dissipative metamaterial,” Physical Review B, vol. 97, no. 22. American Physical Society (APS), 2018. ista: Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. 2018. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 97(22), 220301. mla: Rosenthal, Eric I., et al. “Topological Phase Transition Measured in a Dissipative Metamaterial.” Physical Review B, vol. 97, no. 22, 220301, American Physical Society (APS), 2018, doi:10.1103/physrevb.97.220301. short: E.I. Rosenthal, N.K. Ehrlich, M.S. Rudner, A.P. Higginbotham, K.W. Lehnert, Physical Review B 97 (2018). date_created: 2019-05-03T09:29:49Z date_published: 2018-06-04T00:00:00Z date_updated: 2021-01-12T08:07:16Z day: '04' doi: 10.1103/physrevb.97.220301 extern: '1' external_id: arxiv: - '1802.02243' intvolume: ' 97' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.02243 month: '06' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: issn: - 2469-9950 - 2469-9969 publication_status: published publisher: American Physical Society (APS) quality_controlled: '1' status: public title: Topological phase transition measured in a dissipative metamaterial type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 97 year: '2018' ... --- _id: '6459' author: - first_name: Barbara full_name: Petritsch, Barbara id: 406048EC-F248-11E8-B48F-1D18A9856A87 last_name: Petritsch orcid: 0000-0003-2724-4614 citation: ama: Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018. doi:10.5281/zenodo.1410279 apa: 'Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279' chicago: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018. https://doi.org/10.5281/zenodo.1410279. ieee: B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018. ista: Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p. mla: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018, doi:10.5281/zenodo.1410279. short: B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018. conference: end_date: 2018-09-26 location: Graz, Austria name: Open-Access-Tage start_date: 2018-09-24 date_created: 2019-05-16T07:27:14Z date_published: 2018-09-24T00:00:00Z date_updated: 2020-07-14T23:06:21Z day: '24' ddc: - '020' department: - _id: E-Lib doi: 10.5281/zenodo.1410279 file: - access_level: open_access checksum: 9063ab4d10ea93353c3a03bbf53fbcf1 content_type: application/pdf creator: dernst date_created: 2019-05-16T07:26:25Z date_updated: 2020-07-14T12:47:30Z file_id: '6460' file_name: Poster_Beitrag_125_Petritsch.pdf file_size: 1967778 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' keyword: - Open Access - Publication Analysis language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication_status: published publisher: IST Austria status: public title: Open Access at IST Austria 2009-2017 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_poster user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6525' abstract: - lang: eng text: This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal. author: - first_name: Tamás full_name: Hausel, Tamás id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Anton full_name: Mellit, Anton id: 388D3134-F248-11E8-B48F-1D18A9856A87 last_name: Mellit - first_name: Du full_name: Pei, Du last_name: Pei citation: ama: 'Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. Oxford University Press; 2018:189-218. doi:10.1093/oso/9780198802013.003.0009' apa: 'Hausel, T., Mellit, A., & Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In Geometry and Physics: Volume I (pp. 189–218). Oxford University Press. https://doi.org/10.1093/oso/9780198802013.003.0009' chicago: 'Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In Geometry and Physics: Volume I, 189–218. Oxford University Press, 2018. https://doi.org/10.1093/oso/9780198802013.003.0009.' ieee: 'T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.' ista: 'Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.' mla: 'Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218, doi:10.1093/oso/9780198802013.003.0009.' short: 'T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.' date_created: 2019-06-06T12:42:01Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T08:07:52Z day: '01' department: - _id: TaHa doi: 10.1093/oso/9780198802013.003.0009 language: - iso: eng month: '01' oa_version: None page: 189-218 publication: 'Geometry and Physics: Volume I' publication_identifier: isbn: - '9780198802013' - '9780191840500' publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: 1 status: public title: Mirror symmetry with branes by equivariant verlinde formulas type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6664' abstract: - lang: eng text: Reed-Muller (RM) and polar codes are a class of capacity-achieving channel coding schemes with the same factor graph representation. Low-complexity decoding algorithms fall short in providing a good error-correction performance for RM and polar codes. Using the symmetric group of RM and polar codes, the specific decoding algorithm can be carried out on multiple permutations of the factor graph to boost the error-correction performance. However, this approach results in high decoding complexity. In this paper, we first derive the total number of factor graph permutations on which the decoding can be performed. We further propose a successive permutation (SP) scheme which finds the permutations on the fly, thus the decoding always progresses on a single factor graph permutation. We show that SP can be used to improve the error-correction performance of RM and polar codes under successive-cancellation (SC) and SC list (SCL) decoding, while keeping the memory requirements of the decoders unaltered. Our results for RM and polar codes of length 128 and rate 0.5 show that when SP is used and at a target frame error rate of 10 -4 , up to 0.5 dB and 0.1 dB improvement can be achieved for RM and polar codes respectively. author: - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Nghia full_name: Doan, Nghia last_name: Doan - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: 'Warren ' full_name: 'Gross, Warren ' last_name: Gross citation: ama: 'Hashemi SA, Doan N, Mondelli M, Gross W. Decoding Reed-Muller and polar codes by successive factor graph permutations. In: 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing. IEEE; 2018:1-5. doi:10.1109/istc.2018.8625281' apa: 'Hashemi, S. A., Doan, N., Mondelli, M., & Gross, W. (2018). Decoding Reed-Muller and polar codes by successive factor graph permutations. In 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing (pp. 1–5). Hong Kong, China: IEEE. https://doi.org/10.1109/istc.2018.8625281' chicago: Hashemi, Seyyed Ali, Nghia Doan, Marco Mondelli, and Warren Gross. “Decoding Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” In 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, 1–5. IEEE, 2018. https://doi.org/10.1109/istc.2018.8625281. ieee: S. A. Hashemi, N. Doan, M. Mondelli, and W. Gross, “Decoding Reed-Muller and polar codes by successive factor graph permutations,” in 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, Hong Kong, China, 2018, pp. 1–5. ista: 'Hashemi SA, Doan N, Mondelli M, Gross W. 2018. Decoding Reed-Muller and polar codes by successive factor graph permutations. 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing. ISTC: Symposium on Turbo Codes & Iterative Information Processing, 1–5.' mla: Hashemi, Seyyed Ali, et al. “Decoding Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, IEEE, 2018, pp. 1–5, doi:10.1109/istc.2018.8625281. short: S.A. Hashemi, N. Doan, M. Mondelli, W. Gross, in:, 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, IEEE, 2018, pp. 1–5. conference: end_date: 2018-12-07 location: Hong Kong, China name: 'ISTC: Symposium on Turbo Codes & Iterative Information Processing' start_date: 2018-12-03 date_created: 2019-07-23T09:12:43Z date_published: 2018-12-01T00:00:00Z date_updated: 2021-01-12T08:08:29Z day: '01' doi: 10.1109/istc.2018.8625281 extern: '1' external_id: arxiv: - '1807.03912' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.03912 month: '12' oa: 1 oa_version: Preprint page: 1-5 publication: 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing publication_status: published publisher: IEEE quality_controlled: '1' status: public title: Decoding Reed-Muller and polar codes by successive factor graph permutations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6674' abstract: - lang: eng text: Polar codes represent one of the major recent breakthroughs in coding theory and, because of their attractive features, they have been selected for the incoming 5G standard. As such, a lot of attention has been devoted to the development of decoding algorithms with good error performance and efficient hardware implementation. One of the leading candidates in this regard is represented by successive-cancellation list (SCL) decoding. However, its hardware implementation requires a large amount of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly reduce the memory consumption. In this paper, we consider the paradigm of PSCL decoding from a practical standpoint, and we provide several improvements. First, by changing the target signal-to-noise ratio and consequently modifying the construction of the code, we are able to improve the performance at no additional computational, latency, or memory cost. Second, we bridge the performance gap between SCL and PSCL decoding by introducing a generalized PSCL decoder and a layered PSCL decoder. In this way, we obtain almost the same performance of the SCL decoder with a significantly lower memory requirement, as testified by hardware implementation results. Third, we present an optimal scheme to allocate cyclic redundancy checks. Finally, we provide a lower bound on the list size that guarantees optimal maximum a posteriori performance for the binary erasure channel. author: - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: S. Hamed full_name: Hassani, S. Hamed last_name: Hassani - first_name: Carlo full_name: Condo, Carlo last_name: Condo - first_name: Rudiger L. full_name: Urbanke, Rudiger L. last_name: Urbanke - first_name: Warren J. full_name: Gross, Warren J. last_name: Gross citation: ama: 'Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. 2018;66(9):3749-3759. doi:10.1109/tcomm.2018.2832207' apa: 'Hashemi, S. A., Mondelli, M., Hassani, S. H., Condo, C., Urbanke, R. L., & Gross, W. J. (2018). Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. IEEE. https://doi.org/10.1109/tcomm.2018.2832207' chicago: 'Hashemi, Seyyed Ali, Marco Mondelli, S. Hamed Hassani, Carlo Condo, Rudiger L. Urbanke, and Warren J. Gross. “Decoder Partitioning: Towards Practical List Decoding of Polar Codes.” IEEE Transactions on Communications. IEEE, 2018. https://doi.org/10.1109/tcomm.2018.2832207.' ieee: 'S. A. Hashemi, M. Mondelli, S. H. Hassani, C. Condo, R. L. Urbanke, and W. J. Gross, “Decoder partitioning: Towards practical list decoding of polar codes,” IEEE Transactions on Communications, vol. 66, no. 9. IEEE, pp. 3749–3759, 2018.' ista: 'Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. 2018. Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. 66(9), 3749–3759.' mla: 'Hashemi, Seyyed Ali, et al. “Decoder Partitioning: Towards Practical List Decoding of Polar Codes.” IEEE Transactions on Communications, vol. 66, no. 9, IEEE, 2018, pp. 3749–59, doi:10.1109/tcomm.2018.2832207.' short: S.A. Hashemi, M. Mondelli, S.H. Hassani, C. Condo, R.L. Urbanke, W.J. Gross, IEEE Transactions on Communications 66 (2018) 3749–3759. date_created: 2019-07-24T08:59:41Z date_published: 2018-09-01T00:00:00Z date_updated: 2021-01-12T08:08:31Z day: '01' doi: 10.1109/tcomm.2018.2832207 extern: '1' intvolume: ' 66' issue: '9' language: - iso: eng month: '09' oa_version: None page: 3749-3759 publication: IEEE Transactions on Communications publication_identifier: eissn: - 1558-0857 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: 'Decoder partitioning: Towards practical list decoding of polar codes' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2018' ... --- _id: '6728' abstract: - lang: eng text: Polar codes are a channel coding scheme for the next generation of wireless communications standard (5G). The belief propagation (BP) decoder allows for parallel decoding of polar codes, making it suitable for high throughput applications. However, the error-correction performance of polar codes under BP decoding is far from the requirements of 5G. It has been shown that the error-correction performance of BP can be improved if the decoding is performed on multiple permuted factor graphs of polar codes. However, a different BP decoding scheduling is required for each factor graph permutation which results in the design of a different decoder for each permutation. Moreover, the selection of the different factor graph permutations is at random, which prevents the decoder to achieve a desirable error correction performance with a small number of permutations. In this paper, we first show that the permutations on the factor graph can be mapped into suitable permutations on the codeword positions. As a result, we can make use of a single decoder for all the permutations. In addition, we introduce a method to construct a set of predetermined permutations which can provide the correct codeword if the decoding fails on the original permutation. We show that for the 5G polar code of length 1024, the error-correction performance of the proposed decoder is more than 0.25 dB better than that of the BP decoder with the same number of random permutations at the frame error rate of 10 -4 . author: - first_name: Nghia full_name: Doan, Nghia last_name: Doan - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Warren J. full_name: Gross, Warren J. last_name: Gross citation: ama: 'Doan N, Hashemi SA, Mondelli M, Gross WJ. On the decoding of polar codes on permuted factor graphs. In: 2018 IEEE Global Communications Conference . IEEE; 2018. doi:10.1109/glocom.2018.8647308' apa: 'Doan, N., Hashemi, S. A., Mondelli, M., & Gross, W. J. (2018). On the decoding of polar codes on permuted factor graphs. In 2018 IEEE Global Communications Conference . Abu Dhabi, United Arab Emirates: IEEE. https://doi.org/10.1109/glocom.2018.8647308' chicago: Doan, Nghia, Seyyed Ali Hashemi, Marco Mondelli, and Warren J. Gross. “On the Decoding of Polar Codes on Permuted Factor Graphs.” In 2018 IEEE Global Communications Conference . IEEE, 2018. https://doi.org/10.1109/glocom.2018.8647308. ieee: N. Doan, S. A. Hashemi, M. Mondelli, and W. J. Gross, “On the decoding of polar codes on permuted factor graphs,” in 2018 IEEE Global Communications Conference , Abu Dhabi, United Arab Emirates, 2018. ista: 'Doan N, Hashemi SA, Mondelli M, Gross WJ. 2018. On the decoding of polar codes on permuted factor graphs. 2018 IEEE Global Communications Conference . GLOBECOM: Global Communications Conference.' mla: Doan, Nghia, et al. “On the Decoding of Polar Codes on Permuted Factor Graphs.” 2018 IEEE Global Communications Conference , IEEE, 2018, doi:10.1109/glocom.2018.8647308. short: N. Doan, S.A. Hashemi, M. Mondelli, W.J. Gross, in:, 2018 IEEE Global Communications Conference , IEEE, 2018. conference: end_date: 2018-12-13 location: Abu Dhabi, United Arab Emirates name: 'GLOBECOM: Global Communications Conference' start_date: 2018-12-09 date_created: 2019-07-30T06:43:15Z date_published: 2018-12-01T00:00:00Z date_updated: 2021-01-12T08:08:42Z day: '01' doi: 10.1109/glocom.2018.8647308 extern: '1' external_id: arxiv: - '1806.11195' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.11195 month: '12' oa: 1 oa_version: Preprint publication: '2018 IEEE Global Communications Conference ' publication_identifier: isbn: - '9781538647271' publication_status: published publisher: IEEE quality_controlled: '1' status: public title: On the decoding of polar codes on permuted factor graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6678' abstract: - lang: eng text: We survey coding techniques that enable reliable transmission at rates that approach the capacity of an arbitrary discrete memoryless channel. In particular, we take the point of view of modern coding theory and discuss how recent advances in coding for symmetric channels help provide more efficient solutions for the asymmetric case. We consider, in more detail, three basic coding paradigms. The first one is Gallager's scheme that consists of concatenating a linear code with a non-linear mapping so that the input distribution can be appropriately shaped. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Furthermore, we derive a scaling law between the gap to capacity, the cardinality of the input and output alphabets, and the required size of the mapper. The second one is an integrated scheme in which the code is used both for source coding, in order to create codewords distributed according to the capacity-achieving input distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third paradigm is based on an idea of Böcherer and Mathar, and separates the two tasks of source coding and channel coding by a chaining construction that binds together several codewords. We present conditions for the source code and the channel code, and we describe how to combine any source code with any channel code that fulfill those conditions, in order to provide capacity-achieving schemes for asymmetric channels. In particular, we show that polar codes, spatially coupled codes, and homophonic codes are suitable as basic building blocks of the proposed coding strategy. Rather than focusing on the exact details of the schemes, the purpose of this tutorial is to present different coding techniques that can then be implemented with many variants. There is no absolute winner and, in order to understand the most suitable technique for a specific application scenario, we provide a detailed comparison that takes into account several performance metrics. article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: 'Rudiger ' full_name: 'Urbanke, Rudiger ' last_name: Urbanke citation: ama: Mondelli M, Hassani H, Urbanke R. How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. 2018;64(5):3371-3393. doi:10.1109/tit.2018.2789885 apa: Mondelli, M., Hassani, H., & Urbanke, R. (2018). How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/tit.2018.2789885 chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “How to Achieve the Capacity of Asymmetric Channels.” IEEE Transactions on Information Theory. IEEE, 2018. https://doi.org/10.1109/tit.2018.2789885. ieee: M. Mondelli, H. Hassani, and R. Urbanke, “How to achieve the capacity of asymmetric channels,” IEEE Transactions on Information Theory, vol. 64, no. 5. IEEE, pp. 3371–3393, 2018. ista: Mondelli M, Hassani H, Urbanke R. 2018. How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. 64(5), 3371–3393. mla: Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.” IEEE Transactions on Information Theory, vol. 64, no. 5, IEEE, 2018, pp. 3371–93, doi:10.1109/tit.2018.2789885. short: M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory 64 (2018) 3371–3393. date_created: 2019-07-24T12:38:49Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-02-23T12:50:46Z day: '01' doi: 10.1109/tit.2018.2789885 extern: '1' external_id: arxiv: - '1406.7373' intvolume: ' 64' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1406.7373 month: '05' oa: 1 oa_version: Preprint page: 3371-3393 publication: IEEE Transactions on Information Theory publication_identifier: issn: - 0018-9448 - 1557-9654 publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '6740' relation: earlier_version status: public status: public title: How to achieve the capacity of asymmetric channels type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 64 year: '2018' ... --- _id: '690' abstract: - lang: eng text: We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1. article_number: 543-616 author: - first_name: Jii full_name: Lee, Jii last_name: Lee - first_name: Kevin full_name: Schnelli, Kevin id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 citation: ama: Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8 apa: Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8 chicago: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields. Springer, 2018. https://doi.org/10.1007/s00440-017-0787-8. ieee: J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer, 2018. ista: Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 171(1–2), 543–616. mla: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616, Springer, 2018, doi:10.1007/s00440-017-0787-8. short: J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018). date_created: 2018-12-11T11:47:56Z date_published: 2018-06-14T00:00:00Z date_updated: 2021-01-12T08:09:33Z day: '14' department: - _id: LaEr doi: 10.1007/s00440-017-0787-8 ec_funded: 1 external_id: arxiv: - '1605.08767' intvolume: ' 171' issue: 1-2 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1605.08767 month: '06' oa: 1 oa_version: Preprint project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Probability Theory and Related Fields publication_status: published publisher: Springer publist_id: '7017' quality_controlled: '1' scopus_import: 1 status: public title: Local law and Tracy–Widom limit for sparse random matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 171 year: '2018' ... --- _id: '6675' abstract: - lang: eng text: 'We present a coding paradigm that provides a new achievable rate for the primitive relay channel by combining compress-and-forward and decode-and-forward with a chaining construction. In the primitive relay channel model, the source broadcasts a message to the relay and to the destination; and the relay facilitates this communication by sending an additional message to the destination through a separate channel. Two well-known coding approaches for this setting are decode-and-forward and compress-and-forward: in the former, the relay decodes the message and sends some of the information to the destination; in the latter, the relay does not attempt to decode, but it sends a compressed description of the received sequence to the destination via Wyner-Ziv coding. In our scheme, we transmit over pairs of blocks and we use compress-and-forward for the first block and decode-and-forward for the second. In particular, in the first block, the relay does not attempt to decode and it sends only a part of the compressed description of the received sequence; in the second block, the relay decodes the message and sends this information plus the remaining part of the compressed sequence relative to the first block. As a result, we strictly outperform both compress-and- forward and decode-and-forward. Furthermore, this paradigm can be implemented with a low-complexity polar coding scheme that has the typical attractive features of polar codes, i.e., quasi-linear encoding/decoding complexity and super-polynomial decay of the error probability. Throughout the paper we consider as a running example the special case of the erasure relay channel and we compare the rates achievable by our proposed scheme with the existing upper and lower bounds.' author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Rudiger full_name: Urbanke, Rudiger last_name: Urbanke citation: ama: 'Mondelli M, Hassani H, Urbanke R. A new coding paradigm for the primitive relay channel. In: 2018 IEEE International Symposium on Information Theory. IEEE; 2018:351-355. doi:10.1109/isit.2018.8437479' apa: 'Mondelli, M., Hassani, H., & Urbanke, R. (2018). A new coding paradigm for the primitive relay channel. In 2018 IEEE International Symposium on Information Theory (pp. 351–355). Vail, CO, United States: IEEE. https://doi.org/10.1109/isit.2018.8437479' chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” In 2018 IEEE International Symposium on Information Theory, 351–55. IEEE, 2018. https://doi.org/10.1109/isit.2018.8437479. ieee: M. Mondelli, H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” in 2018 IEEE International Symposium on Information Theory, Vail, CO, United States, 2018, pp. 351–355. ista: 'Mondelli M, Hassani H, Urbanke R. 2018. A new coding paradigm for the primitive relay channel. 2018 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory , 351–355.' mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” 2018 IEEE International Symposium on Information Theory, IEEE, 2018, pp. 351–55, doi:10.1109/isit.2018.8437479. short: M. Mondelli, H. Hassani, R. Urbanke, in:, 2018 IEEE International Symposium on Information Theory, IEEE, 2018, pp. 351–355. conference: end_date: 2018-06-22 location: Vail, CO, United States name: 'ISIT: International Symposium on Information Theory ' start_date: 2018-06-17 date_created: 2019-07-24T09:10:38Z date_published: 2018-06-16T00:00:00Z date_updated: 2023-02-23T12:56:49Z day: '16' doi: 10.1109/isit.2018.8437479 extern: '1' external_id: arxiv: - '1801.03153' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1801.03153 month: '06' oa: 1 oa_version: Preprint page: 351-355 publication: 2018 IEEE International Symposium on Information Theory publication_identifier: eissn: - 2157-8117 publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '7007' relation: later_version status: public status: public title: A new coding paradigm for the primitive relay channel type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '703' abstract: - lang: eng text: We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision. author: - first_name: Alexander full_name: Shekhovtsov, Alexander last_name: Shekhovtsov - first_name: Paul full_name: Swoboda, Paul id: 446560C6-F248-11E8-B48F-1D18A9856A87 last_name: Swoboda - first_name: Bogdan full_name: Savchynskyy, Bogdan last_name: Savchynskyy citation: ama: Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(7):1668-1682. doi:10.1109/TPAMI.2017.2730884 apa: Shekhovtsov, A., Swoboda, P., & Savchynskyy, B. (2018). Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2017.2730884 chicago: Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2017.2730884. ieee: A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative relaxed inference with graphical models,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018. ista: Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(7), 1668–1682. mla: Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:10.1109/TPAMI.2017.2730884. short: A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1668–1682. date_created: 2018-12-11T11:48:01Z date_published: 2018-07-01T00:00:00Z date_updated: 2021-01-12T08:11:32Z day: '01' department: - _id: VlKo doi: 10.1109/TPAMI.2017.2730884 external_id: arxiv: - '1508.07902' intvolume: ' 40' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1508.07902 month: '07' oa: 1 oa_version: Preprint page: 1668-1682 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_identifier: issn: - '01628828' publication_status: published publisher: IEEE publist_id: '6992' quality_controlled: '1' scopus_import: 1 status: public title: Maximum persistency via iterative relaxed inference with graphical models type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 40 year: '2018' ... --- _id: '7063' abstract: - lang: eng text: The high-pressure synthesis and incommensurately modulated structure are reported for the new compound Sr2Pt8−xAs, with x = 0.715 (5). The structure consists of Sr2Pt3As layers alternating with Pt-only corrugated grids. Ab initio calculations predict a metallic character with a dominant role of the Pt d electrons. The electrical resistivity (ρ) and Seebeck coefficient confirm the metallic character, but surprisingly, ρ showed a near-flat temperature dependence. This observation fits the description of the Mooij correlation for electrical resistivity in disordered metals, originally developed for statistically distributed point defects. The discussed material has a long-range crystallographic order, but the high concentration of Pt vacancies, incommensurately ordered, strongly influences the electronic conduction properties. This result extends the range of validity of the Mooij correlation to long-range ordered incommensurately modulated vacancies. Motivated by the layered structure, the resistivity anisotropy was measured in a focused-ion-beam micro-fabricated well oriented single crystal. A low resistivity anisotropy indicates that the layers are electrically coupled and conduction channels along different directions are intermixed. article_processing_charge: No article_type: original author: - first_name: Edoardo full_name: Martino, Edoardo last_name: Martino - first_name: Alla full_name: Arakcheeva, Alla last_name: Arakcheeva - first_name: Gabriel full_name: Autès, Gabriel last_name: Autès - first_name: Andrea full_name: Pisoni, Andrea last_name: Pisoni - first_name: Maja D. full_name: Bachmann, Maja D. last_name: Bachmann - 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: Toni full_name: Helm, Toni last_name: Helm - first_name: Oleg V. full_name: Yazyev, Oleg V. last_name: Yazyev - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll - first_name: László full_name: Forró, László last_name: Forró - first_name: Sergiy full_name: Katrych, Sergiy last_name: Katrych citation: ama: 'Martino E, Arakcheeva A, Autès G, et al. Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. 2018;5(4):470-477. doi:10.1107/s2052252518007303' apa: 'Martino, E., Arakcheeva, A., Autès, G., Pisoni, A., Bachmann, M. D., Modic, K. A., … Katrych, S. (2018). Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. International Union of Crystallography (IUCr). https://doi.org/10.1107/s2052252518007303' chicago: 'Martino, Edoardo, Alla Arakcheeva, Gabriel Autès, Andrea Pisoni, Maja D. Bachmann, Kimberly A Modic, Toni Helm, et al. “Sr2Pt8−xAs: A Layered Incommensurately Modulated Metal with Saturated Resistivity.” IUCrJ. International Union of Crystallography (IUCr), 2018. https://doi.org/10.1107/s2052252518007303.' ieee: 'E. Martino et al., “Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity,” IUCrJ, vol. 5, no. 4. International Union of Crystallography (IUCr), pp. 470–477, 2018.' ista: 'Martino E, Arakcheeva A, Autès G, Pisoni A, Bachmann MD, Modic KA, Helm T, Yazyev OV, Moll PJW, Forró L, Katrych S. 2018. Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. 5(4), 470–477.' mla: 'Martino, Edoardo, et al. “Sr2Pt8−xAs: A Layered Incommensurately Modulated Metal with Saturated Resistivity.” IUCrJ, vol. 5, no. 4, International Union of Crystallography (IUCr), 2018, pp. 470–77, doi:10.1107/s2052252518007303.' short: E. Martino, A. Arakcheeva, G. Autès, A. Pisoni, M.D. Bachmann, K.A. Modic, T. Helm, O.V. Yazyev, P.J.W. Moll, L. Forró, S. Katrych, IUCrJ 5 (2018) 470–477. date_created: 2019-11-19T13:11:15Z date_published: 2018-07-01T00:00:00Z date_updated: 2021-01-12T08:11:38Z day: '01' ddc: - '530' doi: 10.1107/s2052252518007303 extern: '1' file: - access_level: open_access checksum: 5c6180c7d19da599dd50a067eb2efd50 content_type: application/pdf creator: dernst date_created: 2019-11-20T14:00:27Z date_updated: 2020-07-14T12:47:48Z file_id: '7090' file_name: 2018_IUCrJ_Martino.pdf file_size: 1563353 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 5' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 470-477 publication: IUCrJ publication_identifier: eissn: - 2052-2525 publication_status: published publisher: International Union of Crystallography (IUCr) quality_controlled: '1' status: public title: 'Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity' 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: 5 year: '2018' ... --- _id: '7062' abstract: - lang: eng text: 'Weyl fermions are a recently discovered ingredient for correlated states of electronic matter. A key difficulty has been that real materials also contain non-Weyl quasiparticles, and disentangling the experimental signatures has proven challenging. Here we use magnetic fields up to 95 T to drive the Weyl semimetal TaAs far into its quantum limit, where only the purely chiral 0th Landau levels of the Weyl fermions are occupied. We find the electrical resistivity to be nearly independent of magnetic field up to 50 T: unusual for conventional metals but consistent with the chiral anomaly for Weyl fermions. Above 50 T we observe a two-order-of-magnitude increase in resistivity, indicating that a gap opens in the chiral Landau levels. Above 80 T we observe strong ultrasonic attenuation below 2 K, suggesting a mesoscopically textured state of matter. These results point the way to inducing new correlated states of matter in the quantum limit of Weyl semimetals.' article_number: '2217' article_processing_charge: No article_type: original author: - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - 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: Arkady full_name: Shekhter, Arkady last_name: Shekhter - first_name: Yi full_name: Zhang, Yi last_name: Zhang - first_name: Eun-Ah full_name: Kim, Eun-Ah last_name: Kim - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll - first_name: Maja D. full_name: Bachmann, Maja D. last_name: Bachmann - first_name: M. K. full_name: Chan, M. K. last_name: Chan - first_name: J. B. full_name: Betts, J. B. last_name: Betts - first_name: F. full_name: Balakirev, F. last_name: Balakirev - first_name: A. full_name: Migliori, A. last_name: Migliori - first_name: N. J. full_name: Ghimire, N. J. last_name: Ghimire - first_name: E. D. full_name: Bauer, E. D. last_name: Bauer - first_name: F. full_name: Ronning, F. last_name: Ronning - first_name: R. D. full_name: McDonald, R. D. last_name: McDonald citation: ama: Ramshaw BJ, Modic KA, Shekhter A, et al. Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-04542-9 apa: Ramshaw, B. J., Modic, K. A., Shekhter, A., Zhang, Y., Kim, E.-A., Moll, P. J. W., … McDonald, R. D. (2018). Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04542-9 chicago: Ramshaw, B. J., Kimberly A Modic, Arkady Shekhter, Yi Zhang, Eun-Ah Kim, Philip J. W. Moll, Maja D. Bachmann, et al. “Quantum Limit Transport and Destruction of the Weyl Nodes in TaAs.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04542-9. ieee: B. J. Ramshaw et al., “Quantum limit transport and destruction of the Weyl nodes in TaAs,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018. ista: Ramshaw BJ, Modic KA, Shekhter A, Zhang Y, Kim E-A, Moll PJW, Bachmann MD, Chan MK, Betts JB, Balakirev F, Migliori A, Ghimire NJ, Bauer ED, Ronning F, McDonald RD. 2018. Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. 9(1), 2217. mla: Ramshaw, B. J., et al. “Quantum Limit Transport and Destruction of the Weyl Nodes in TaAs.” Nature Communications, vol. 9, no. 1, 2217, Springer Nature, 2018, doi:10.1038/s41467-018-04542-9. short: B.J. Ramshaw, K.A. Modic, A. Shekhter, Y. Zhang, E.-A. Kim, P.J.W. Moll, M.D. Bachmann, M.K. Chan, J.B. Betts, F. Balakirev, A. Migliori, N.J. Ghimire, E.D. Bauer, F. Ronning, R.D. McDonald, Nature Communications 9 (2018). date_created: 2019-11-19T13:10:33Z date_published: 2018-06-07T00:00:00Z date_updated: 2021-01-12T08:11:38Z day: '07' ddc: - '530' doi: 10.1038/s41467-018-04542-9 extern: '1' file: - access_level: open_access checksum: 9c53f9a1f06a4d83d5fe879d2478b7d7 content_type: application/pdf creator: dernst date_created: 2019-11-20T13:55:44Z date_updated: 2020-07-14T12:47:48Z file_id: '7089' file_name: 2018_NatureComm_Ramshaw.pdf file_size: 1794797 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 9' issue: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Quantum limit transport and destruction of the Weyl nodes in TaAs 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: 9 year: '2018' ... --- _id: '7059' abstract: - lang: eng text: Unusual behavior in quantum materials commonly arises from their effective low-dimensional physics, reflecting the underlying anisotropy in the spin and charge degrees of freedom. Here we introduce the magnetotropic coefficient k = ∂2F/∂θ2, the second derivative of the free energy F with respect to the magnetic field orientation θ in the crystal. We show that the magnetotropic coefficient can be quantitatively determined from a shift in the resonant frequency of a commercially available atomic force microscopy cantilever under magnetic field. This detection method enables part per 100 million sensitivity and the ability to measure magnetic anisotropy in nanogram-scale samples, as demonstrated on the Weyl semimetal NbP. Measurement of the magnetotropic coefficient in the spin-liquid candidate RuCl3 highlights its sensitivity to anisotropic phase transitions and allows a quantitative comparison to other thermodynamic coefficients via the Ehrenfest relations. article_processing_charge: No article_type: original author: - 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: Maja D. full_name: Bachmann, Maja D. last_name: Bachmann - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: F. full_name: Arnold, F. last_name: Arnold - first_name: K. R. full_name: Shirer, K. R. last_name: Shirer - first_name: Amelia full_name: Estry, Amelia last_name: Estry - first_name: J. B. full_name: Betts, J. B. last_name: Betts - first_name: Nirmal J. full_name: Ghimire, Nirmal J. last_name: Ghimire - first_name: E. D. full_name: Bauer, E. D. last_name: Bauer - first_name: Marcus full_name: Schmidt, Marcus last_name: Schmidt - first_name: Michael full_name: Baenitz, Michael last_name: Baenitz - first_name: E. full_name: Svanidze, E. last_name: Svanidze - first_name: Ross D. full_name: McDonald, Ross D. last_name: McDonald - first_name: Arkady full_name: Shekhter, Arkady last_name: Shekhter - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll citation: ama: Modic KA, Bachmann MD, Ramshaw BJ, et al. Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. 2018;9(1):3975. doi:10.1038/s41467-018-06412-w apa: Modic, K. A., Bachmann, M. D., Ramshaw, B. J., Arnold, F., Shirer, K. R., Estry, A., … Moll, P. J. W. (2018). Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06412-w chicago: Modic, Kimberly A, Maja D. Bachmann, B. J. Ramshaw, F. Arnold, K. R. Shirer, Amelia Estry, J. B. Betts, et al. “Resonant Torsion Magnetometry in Anisotropic Quantum Materials.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06412-w. ieee: K. A. Modic et al., “Resonant torsion magnetometry in anisotropic quantum materials,” Nature Communications, vol. 9, no. 1. Springer Nature, p. 3975, 2018. ista: Modic KA, Bachmann MD, Ramshaw BJ, Arnold F, Shirer KR, Estry A, Betts JB, Ghimire NJ, Bauer ED, Schmidt M, Baenitz M, Svanidze E, McDonald RD, Shekhter A, Moll PJW. 2018. Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. 9(1), 3975. mla: Modic, Kimberly A., et al. “Resonant Torsion Magnetometry in Anisotropic Quantum Materials.” Nature Communications, vol. 9, no. 1, Springer Nature, 2018, p. 3975, doi:10.1038/s41467-018-06412-w. short: K.A. Modic, M.D. Bachmann, B.J. Ramshaw, F. Arnold, K.R. Shirer, A. Estry, J.B. Betts, N.J. Ghimire, E.D. Bauer, M. Schmidt, M. Baenitz, E. Svanidze, R.D. McDonald, A. Shekhter, P.J.W. Moll, Nature Communications 9 (2018) 3975. date_created: 2019-11-19T13:02:20Z date_published: 2018-09-28T00:00:00Z date_updated: 2021-01-12T08:11:37Z day: '28' ddc: - '530' doi: 10.1038/s41467-018-06412-w extern: '1' file: - access_level: open_access checksum: 46a313c816e66899d4dad2cf3583e5b0 content_type: application/pdf creator: dernst date_created: 2019-11-20T12:48:58Z date_updated: 2020-07-14T12:47:48Z file_id: '7088' file_name: 2018_NatureComm_Modic.pdf file_size: 1257681 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 9' issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '3975' publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Resonant torsion magnetometry in anisotropic quantum materials 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: 9 year: '2018' ... --- _id: '7058' abstract: - lang: eng text: We examine recent magnetic torque measurements in two compounds, γ−Li2IrO3 and RuCl3, which have been discussed as possible realizations of the Kitaev model. The analysis of the reported discontinuity in torque, as an external magnetic field is rotated across the c axis in both crystals, suggests that they have a translationally invariant chiral spin order of the form ⟨Si⋅(Sj×Sk)⟩≠0 in the ground state and persisting over a very wide range of magnetic field and temperature. An extraordinary |B|B2 dependence of the torque for small fields, beside the usual B2 part, is predicted by the chiral spin order. Data for small fields are available for γ−Li2IrO3 and are found to be consistent with the prediction upon further analysis. Other experiments such as inelastic scattering and thermal Hall effect and several questions raised by the discovery of chiral spin order, including its topological consequences, are discussed. article_number: '205110 ' article_processing_charge: No article_type: original author: - 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: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: A. full_name: Shekhter, A. last_name: Shekhter - first_name: C. M. full_name: Varma, C. M. last_name: Varma citation: ama: Modic KA, Ramshaw BJ, Shekhter A, Varma CM. Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. 2018;98(20). doi:10.1103/physrevb.98.205110 apa: Modic, K. A., Ramshaw, B. J., Shekhter, A., & Varma, C. M. (2018). Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. APS. https://doi.org/10.1103/physrevb.98.205110 chicago: Modic, Kimberly A, B. J. Ramshaw, A. Shekhter, and C. M. Varma. “Chiral Spin Order in Some Purported Kitaev Spin-Liquid Compounds.” Physical Review B. APS, 2018. https://doi.org/10.1103/physrevb.98.205110. ieee: K. A. Modic, B. J. Ramshaw, A. Shekhter, and C. M. Varma, “Chiral spin order in some purported Kitaev spin-liquid compounds,” Physical Review B, vol. 98, no. 20. APS, 2018. ista: Modic KA, Ramshaw BJ, Shekhter A, Varma CM. 2018. Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. 98(20), 205110. mla: Modic, Kimberly A., et al. “Chiral Spin Order in Some Purported Kitaev Spin-Liquid Compounds.” Physical Review B, vol. 98, no. 20, 205110, APS, 2018, doi:10.1103/physrevb.98.205110. short: K.A. Modic, B.J. Ramshaw, A. Shekhter, C.M. Varma, Physical Review B 98 (2018). date_created: 2019-11-19T13:01:31Z date_published: 2018-11-05T00:00:00Z date_updated: 2021-01-12T08:11:36Z day: '05' doi: 10.1103/physrevb.98.205110 extern: '1' external_id: arxiv: - '1807.06637' intvolume: ' 98' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.06637 month: '11' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: APS quality_controlled: '1' status: public title: Chiral spin order in some purported Kitaev spin-liquid compounds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 98 year: '2018' ... --- _id: '7060' abstract: - lang: eng text: The anomalous metallic state in the high-temperature superconducting cuprates is masked by superconductivity near a quantum critical point. Applying high magnetic fields to suppress superconductivity has enabled detailed studies of the normal state, yet the direct effect of strong magnetic fields on the metallic state is poorly understood. We report the high-field magnetoresistance of thin-film La2–xSrxCuO4 cuprate in the vicinity of the critical doping, 0.161 ≤ p ≤ 0.190. We find that the metallic state exposed by suppressing superconductivity is characterized by magnetoresistance that is linear in magnetic fields up to 80 tesla. The magnitude of the linear-in-field resistivity mirrors the magnitude and doping evolution of the well-known linear-in-temperature resistivity that has been associated with quantum criticality in high-temperature superconductors. article_processing_charge: No article_type: original author: - first_name: P. full_name: Giraldo-Gallo, P. last_name: Giraldo-Gallo - first_name: J. A. full_name: Galvis, J. A. last_name: Galvis - first_name: Z. full_name: Stegen, Z. last_name: Stegen - 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: F. F. full_name: Balakirev, F. F. last_name: Balakirev - first_name: J. B. full_name: Betts, J. B. last_name: Betts - first_name: X. full_name: Lian, X. last_name: Lian - first_name: C. full_name: Moir, C. last_name: Moir - first_name: S. C. full_name: Riggs, S. C. last_name: Riggs - first_name: J. full_name: Wu, J. last_name: Wu - first_name: A. T. full_name: Bollinger, A. T. last_name: Bollinger - first_name: X. full_name: He, X. last_name: He - first_name: I. full_name: Božović, I. last_name: Božović - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: R. D. full_name: McDonald, R. D. last_name: McDonald - first_name: G. S. full_name: Boebinger, G. S. last_name: Boebinger - first_name: A. full_name: Shekhter, A. last_name: Shekhter citation: ama: Giraldo-Gallo P, Galvis JA, Stegen Z, et al. Scale-invariant magnetoresistance in a cuprate superconductor. Science. 2018;361(6401):479-481. doi:10.1126/science.aan3178 apa: Giraldo-Gallo, P., Galvis, J. A., Stegen, Z., Modic, K. A., Balakirev, F. F., Betts, J. B., … Shekhter, A. (2018). Scale-invariant magnetoresistance in a cuprate superconductor. Science. AAAS. https://doi.org/10.1126/science.aan3178 chicago: Giraldo-Gallo, P., J. A. Galvis, Z. Stegen, Kimberly A Modic, F. F. Balakirev, J. B. Betts, X. Lian, et al. “Scale-Invariant Magnetoresistance in a Cuprate Superconductor.” Science. AAAS, 2018. https://doi.org/10.1126/science.aan3178. ieee: P. Giraldo-Gallo et al., “Scale-invariant magnetoresistance in a cuprate superconductor,” Science, vol. 361, no. 6401. AAAS, pp. 479–481, 2018. ista: Giraldo-Gallo P, Galvis JA, Stegen Z, Modic KA, Balakirev FF, Betts JB, Lian X, Moir C, Riggs SC, Wu J, Bollinger AT, He X, Božović I, Ramshaw BJ, McDonald RD, Boebinger GS, Shekhter A. 2018. Scale-invariant magnetoresistance in a cuprate superconductor. Science. 361(6401), 479–481. mla: Giraldo-Gallo, P., et al. “Scale-Invariant Magnetoresistance in a Cuprate Superconductor.” Science, vol. 361, no. 6401, AAAS, 2018, pp. 479–81, doi:10.1126/science.aan3178. short: P. Giraldo-Gallo, J.A. Galvis, Z. Stegen, K.A. Modic, F.F. Balakirev, J.B. Betts, X. Lian, C. Moir, S.C. Riggs, J. Wu, A.T. Bollinger, X. He, I. Božović, B.J. Ramshaw, R.D. McDonald, G.S. Boebinger, A. Shekhter, Science 361 (2018) 479–481. date_created: 2019-11-19T13:03:16Z date_published: 2018-08-03T00:00:00Z date_updated: 2021-01-12T08:11:37Z day: '03' doi: 10.1126/science.aan3178 extern: '1' intvolume: ' 361' issue: '6401' language: - iso: eng month: '08' oa_version: None page: 479-481 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: AAAS quality_controlled: '1' status: public title: Scale-invariant magnetoresistance in a cuprate superconductor type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 361 year: '2018' ... --- _id: '7116' abstract: - lang: eng text: 'Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system trade-offs—lowering communication precision could de-crease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this trade-off space, and ask:Can low-precision communication consistently improve the end-to-end performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by low-precision communication. In this paper, we conduct an empirical study to answer this question and report the insights.' article_processing_charge: No author: - first_name: Demjan full_name: Grubic, Demjan last_name: Grubic - first_name: Leo full_name: Tam, Leo last_name: Tam - 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: Ce full_name: Zhang, Ce last_name: Zhang citation: ama: 'Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In: Proceedings of the 21st International Conference on Extending Database Technology. OpenProceedings; 2018:145-156. doi:10.5441/002/EDBT.2018.14' apa: 'Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In Proceedings of the 21st International Conference on Extending Database Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14' chicago: 'Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” In Proceedings of the 21st International Conference on Extending Database Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14.' ieee: 'D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study,” in Proceedings of the 21st International Conference on Extending Database Technology, Vienna, Austria, 2018, pp. 145–156.' ista: 'Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. Proceedings of the 21st International Conference on Extending Database Technology. EDBT: Conference on Extending Database Technology, 145–156.' mla: 'Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.' short: D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–156. conference: end_date: 2018-03-29 location: Vienna, Austria name: 'EDBT: Conference on Extending Database Technology' start_date: 2018-03-26 date_created: 2019-11-26T14:19:11Z date_published: 2018-03-26T00:00:00Z date_updated: 2023-02-23T12:59:17Z day: '26' ddc: - '000' department: - _id: DaAl doi: 10.5441/002/EDBT.2018.14 file: - access_level: open_access checksum: ec979b56abc71016d6e6adfdadbb4afe content_type: application/pdf creator: dernst date_created: 2019-11-26T14:23:04Z date_updated: 2020-07-14T12:47:49Z file_id: '7118' file_name: 2018_OpenProceedings_Grubic.pdf file_size: 1603204 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 145-156 publication: Proceedings of the 21st International Conference on Extending Database Technology publication_identifier: isbn: - '9783893180783' issn: - 2367-2005 publication_status: published publisher: OpenProceedings quality_controlled: '1' scopus_import: 1 status: public title: 'Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '7126' abstract: - lang: eng text: In the Minimum Description Length (MDL) principle, learning from the data is equivalent to an optimal coding problem. We show that the codes that achieve optimal compression in MDL are critical in a very precise sense. First, when they are taken as generative models of samples, they generate samples with broad empirical distributions and with a high value of the relevance, defined as the entropy of the empirical frequencies. These results are derived for different statistical models (Dirichlet model, independent and pairwise dependent spin models, and restricted Boltzmann machines). Second, MDL codes sit precisely at a second order phase transition point where the symmetry between the sampled outcomes is spontaneously broken. The order parameter controlling the phase transition is the coding cost of the samples. The phase transition is a manifestation of the optimality of MDL codes, and it arises because codes that achieve a higher compression do not exist. These results suggest a clear interpretation of the widespread occurrence of statistical criticality as a characterization of samples which are maximally informative on the underlying generative process. article_number: '755' article_processing_charge: No article_type: original author: - first_name: Ryan J full_name: Cubero, Ryan J id: 850B2E12-9CD4-11E9-837F-E719E6697425 last_name: Cubero orcid: 0000-0003-0002-1867 - first_name: Matteo full_name: Marsili, Matteo last_name: Marsili - first_name: Yasser full_name: Roudi, Yasser last_name: Roudi citation: ama: Cubero RJ, Marsili M, Roudi Y. Minimum description length codes are critical. Entropy. 2018;20(10). doi:10.3390/e20100755 apa: Cubero, R. J., Marsili, M., & Roudi, Y. (2018). Minimum description length codes are critical. Entropy. MDPI. https://doi.org/10.3390/e20100755 chicago: Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Minimum Description Length Codes Are Critical.” Entropy. MDPI, 2018. https://doi.org/10.3390/e20100755. ieee: R. J. Cubero, M. Marsili, and Y. Roudi, “Minimum description length codes are critical,” Entropy, vol. 20, no. 10. MDPI, 2018. ista: Cubero RJ, Marsili M, Roudi Y. 2018. Minimum description length codes are critical. Entropy. 20(10), 755. mla: Cubero, Ryan J., et al. “Minimum Description Length Codes Are Critical.” Entropy, vol. 20, no. 10, 755, MDPI, 2018, doi:10.3390/e20100755. short: R.J. Cubero, M. Marsili, Y. Roudi, Entropy 20 (2018). date_created: 2019-11-26T22:18:05Z date_published: 2018-10-01T00:00:00Z date_updated: 2021-01-12T08:11:56Z day: '01' ddc: - '519' doi: 10.3390/e20100755 extern: '1' file: - access_level: open_access checksum: d642b7b661e1d5066b62e6ea9986b917 content_type: application/pdf creator: rcubero date_created: 2019-11-26T22:23:08Z date_updated: 2020-07-14T12:47:50Z file_id: '7127' file_name: entropy-20-00755-v2.pdf file_size: 1366813 relation: main_file file_date_updated: 2020-07-14T12:47:50Z has_accepted_license: '1' intvolume: ' 20' issue: '10' keyword: - Minimum Description Length - normalized maximum likelihood - statistical criticality - phase transitions - large deviations language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Entropy publication_identifier: issn: - 1099-4300 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Minimum description length codes are critical 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: 20 year: '2018' ... --- _id: '7277' abstract: - lang: eng text: 'Solid alkali metal carbonates are universal passivation layer components of intercalation battery materials and common side products in metal‐O2 batteries, and are believed to form and decompose reversibly in metal‐O2/CO2 cells. In these cathodes, Li2CO3 decomposes to CO2 when exposed to potentials above 3.8 V vs. Li/Li+. However, O2 evolution, as would be expected according to the decomposition reaction 2 Li2CO3→4 Li++4 e−+2 CO2+O2, is not detected. O atoms are thus unaccounted for, which was previously ascribed to unidentified parasitic reactions. Here, we show that highly reactive singlet oxygen (1O2) forms upon oxidizing Li2CO3 in an aprotic electrolyte and therefore does not evolve as O2. These results have substantial implications for the long‐term cyclability of batteries: they underpin the importance of avoiding 1O2 in metal‐O2 batteries, question the possibility of a reversible metal‐O2/CO2 battery based on a carbonate discharge product, and help explain the interfacial reactivity of transition‐metal cathodes with residual Li2CO3.' article_processing_charge: No article_type: original author: - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Sara E. full_name: Renfrew, Sara E. last_name: Renfrew - first_name: Bryan D. full_name: McCloskey, Bryan D. last_name: McCloskey - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. 2018;57(19):5529-5533. doi:10.1002/anie.201802277 apa: Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018). Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201802277 chicago: Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander Freunberger. “Electrochemical Oxidation of Lithium Carbonate Generates Singlet Oxygen.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201802277. ieee: N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Electrochemical oxidation of Lithium Carbonate generates singlet oxygen,” Angewandte Chemie International Edition, vol. 57, no. 19. Wiley, pp. 5529–5533, 2018. ista: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. 57(19), 5529–5533. mla: Mahne, Nika, et al. “Electrochemical Oxidation of Lithium Carbonate Generates Singlet Oxygen.” Angewandte Chemie International Edition, vol. 57, no. 19, Wiley, 2018, pp. 5529–33, doi:10.1002/anie.201802277. short: N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie International Edition 57 (2018) 5529–5533. date_created: 2020-01-15T07:20:09Z date_published: 2018-03-15T00:00:00Z date_updated: 2021-01-12T08:12:42Z day: '15' ddc: - '540' doi: 10.1002/anie.201802277 extern: '1' file: - access_level: open_access checksum: 45868d0adc2d13a506bb9a59eb4f409c content_type: application/pdf creator: dernst date_created: 2020-01-22T16:28:31Z date_updated: 2020-07-14T12:47:55Z file_id: '7357' file_name: 2018_AngewChemie_Mahne.pdf file_size: 657963 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 57' issue: '19' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 5529-5533 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Electrochemical oxidation of Lithium Carbonate generates singlet oxygen tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2018' ... --- _id: '7271' abstract: - lang: eng text: The recent demand of multifunctional materials and devices for advanced applications in energy conversion and data storage resulted into a revival of multiferroics, that is, materials characterized by the coexistence of ferromagnetism and ferroelectricity. Despite intense efforts made in the past decade, single-phase room temperature multiferroics are yet to be discovered/fabricated. Nanostructured ferroic materials could potentially exhibit multiferroism since a high fraction of their atoms/ions are superficial, thereby altering significantly the properties of the bulk phase. Alternately, a magnetic order can be induced into ferroelectric materials upon aliovalent doping with magnetic ions. Here, we report on the synthesis of aggregate-free single-phase transition-metal-doped BaTiO3 quasi-monodisperse cuboidal nanocrystals (NC) which exhibit multiferroic properties at room temperature and can be suitable for applications in data storage. The proposed synthetic route allows the inclusion of a high concentration of magnetic ions such as Mn+ (M = Cr, Mn, Fe, Co) up to a nominal concentration of 4% without the formation of any secondary phase. The size of the nanocrystals was controlled in a wide range from ∼15 up to ∼70 nm by varying the reaction time from 48 to 144 h. The presence of unpaired electrons and their magnetic ordering have been probed by electron paramagnetic resonance spectroscopy (EPR), and a vibrating sample magnetometer (VSM). Likewise, an acentric structure, associated with the existence of a dielectric polarization, was observed by lattice dynamics analysis and piezoresponse force microscopy (PFM). These results show that high-quality titanium-containing perovskite nanocrystals which display multiferroic properties at room temperature can be fabricated via soft solution-based synthetic routes, and the properties of these materials can be modulated by changing the size of the nanocrystals and the concentration of the dopant thereby opening the door to the design and study of single-phase multiferroic materials. article_processing_charge: No article_type: original author: - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: John full_name: McCracken, John last_name: McCracken - first_name: Aurelian full_name: Rotaru, Aurelian last_name: Rotaru - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu citation: ama: Costanzo T, McCracken J, Rotaru A, Caruntu G. Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. 2018;1(9):4863-4874. doi:10.1021/acsanm.8b01036 apa: Costanzo, T., McCracken, J., Rotaru, A., & Caruntu, G. (2018). Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. ACS. https://doi.org/10.1021/acsanm.8b01036 chicago: Costanzo, Tommaso, John McCracken, Aurelian Rotaru, and Gabriel Caruntu. “Quasi-Monodisperse Transition-Metal-Doped BaTiO3 (M = Cr, Mn, Fe, Co) Colloidal Nanocrystals with Multiferroic Properties.” ACS Applied Nano Materials. ACS, 2018. https://doi.org/10.1021/acsanm.8b01036. ieee: T. Costanzo, J. McCracken, A. Rotaru, and G. Caruntu, “Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties,” ACS Applied Nano Materials, vol. 1, no. 9. ACS, pp. 4863–4874, 2018. ista: Costanzo T, McCracken J, Rotaru A, Caruntu G. 2018. Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. 1(9), 4863–4874. mla: Costanzo, Tommaso, et al. “Quasi-Monodisperse Transition-Metal-Doped BaTiO3 (M = Cr, Mn, Fe, Co) Colloidal Nanocrystals with Multiferroic Properties.” ACS Applied Nano Materials, vol. 1, no. 9, ACS, 2018, pp. 4863–74, doi:10.1021/acsanm.8b01036. short: T. Costanzo, J. McCracken, A. Rotaru, G. Caruntu, ACS Applied Nano Materials 1 (2018) 4863–4874. date_created: 2020-01-13T21:58:27Z date_published: 2018-09-28T00:00:00Z date_updated: 2023-02-23T13:02:57Z day: '28' doi: 10.1021/acsanm.8b01036 extern: '1' intvolume: ' 1' issue: '9' language: - iso: eng month: '09' oa_version: None page: 4863-4874 publication: ACS Applied Nano Materials publication_identifier: issn: - 2574-0970 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2018' ... --- _id: '7287' abstract: - lang: eng text: Passivation layers on electrode materials are ubiquitous in nonaqueous battery chemistries and strongly govern performance and lifetime. They comprise breakdown products of the electrolyte including carbonate, alkyl carbonates, alkoxides, carboxylates, and polymers. Parasitic chemistry in metal–O2 batteries forms similar products and is tied to the deviation of the O2 balance from the ideal stoichiometry during formation/decomposition of alkaline peroxides or superoxides. Accurate and integral quantification of carbonaceous species and peroxides or superoxides in battery electrodes remains, however, elusive. We present a refined procedure to quantify them accurately and sensitively by pointing out and rectifying pitfalls of previous procedures. Carbonaceous compounds are differentiated into inorganic and organic ones. We combine mass and UV–vis spectrometry to quantify evolved O2 and complexed peroxide and CO2 evolved from carbonaceous compounds by acid treatment and Fenton’s reaction. The capabilities of the method are exemplified by means of Li–O2 and Na–O2 cathodes, graphite anodes, and LiNi0.8Co0.15Al0.05O2 cathodes. article_processing_charge: No article_type: letter_note author: - first_name: Bettina full_name: Schafzahl, Bettina last_name: Schafzahl - first_name: Eléonore full_name: Mourad, Eléonore last_name: Mourad - first_name: Lukas full_name: Schafzahl, Lukas last_name: Schafzahl - first_name: Yann K. full_name: Petit, Yann K. last_name: Petit - first_name: Anjana R. full_name: Raju, Anjana R. last_name: Raju - first_name: Musthafa Ottakam full_name: Thotiyl, Musthafa Ottakam last_name: Thotiyl - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Christian full_name: Slugovc, Christian last_name: Slugovc - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Schafzahl B, Mourad E, Schafzahl L, et al. Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. 2018;3(1):170-176. doi:10.1021/acsenergylett.7b01111 apa: Schafzahl, B., Mourad, E., Schafzahl, L., Petit, Y. K., Raju, A. R., Thotiyl, M. O., … Freunberger, S. A. (2018). Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. ACS. https://doi.org/10.1021/acsenergylett.7b01111 chicago: Schafzahl, Bettina, Eléonore Mourad, Lukas Schafzahl, Yann K. Petit, Anjana R. Raju, Musthafa Ottakam Thotiyl, Martin Wilkening, Christian Slugovc, and Stefan Alexander Freunberger. “Quantifying Total Superoxide, Peroxide, and Carbonaceous Compounds in Metal–O2 Batteries and the Solid Electrolyte Interphase.” ACS Energy Letters. ACS, 2018. https://doi.org/10.1021/acsenergylett.7b01111. ieee: B. Schafzahl et al., “Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase,” ACS Energy Letters, vol. 3, no. 1. ACS, pp. 170–176, 2018. ista: Schafzahl B, Mourad E, Schafzahl L, Petit YK, Raju AR, Thotiyl MO, Wilkening M, Slugovc C, Freunberger SA. 2018. Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. 3(1), 170–176. mla: Schafzahl, Bettina, et al. “Quantifying Total Superoxide, Peroxide, and Carbonaceous Compounds in Metal–O2 Batteries and the Solid Electrolyte Interphase.” ACS Energy Letters, vol. 3, no. 1, ACS, 2018, pp. 170–76, doi:10.1021/acsenergylett.7b01111. short: B. Schafzahl, E. Mourad, L. Schafzahl, Y.K. Petit, A.R. Raju, M.O. Thotiyl, M. Wilkening, C. Slugovc, S.A. Freunberger, ACS Energy Letters 3 (2018) 170–176. date_created: 2020-01-15T12:13:52Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T08:12:46Z day: '01' ddc: - '540' - '543' - '546' - '547' doi: 10.1021/acsenergylett.7b01111 extern: '1' file: - access_level: open_access checksum: 461ccf575ba077af90314fe72d20521e content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T14:19:36Z date_updated: 2020-07-14T12:47:55Z file_id: '8049' file_name: O2 TIOC_fin_incl_SI.pdf file_size: 1892355 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 3' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 170-176 publication: ACS Energy Letters publication_identifier: issn: - 2380-8195 - 2380-8195 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2018' ... --- _id: '7285' abstract: - lang: eng text: Hydrogelation, the self-assembly of molecules into soft, water-loaded networks, is one way to bridge the structural gap between single molecules and functional materials. The potential of hydrogels, such as those based on perylene bisimides, lies in their chemical, physical, optical, and electronic properties, which are governed by the supramolecular structure of the gel. However, the structural motifs and their precise role for long-range conductivity are yet to be explored. Here, we present a comprehensive structural picture of a perylene bisimide hydrogel, suggesting that its long-range conductivity is limited by charge transfer between electronic backbones. We reveal nanocrystalline ribbon-like structures as the electronic and structural backbone units between which charge transfer is mediated by polar solvent bridges. We exemplify this effect with sensing, where exposure to polar vapor enhances conductivity by 5 orders of magnitude, emphasizing the crucial role of the interplay between structural motif and surrounding medium for the rational design of devices based on nanocrystalline hydrogels. article_processing_charge: No article_type: original author: - first_name: Max full_name: Burian, Max last_name: Burian - first_name: Francesco full_name: Rigodanza, Francesco last_name: Rigodanza - first_name: Nicola full_name: Demitri, Nicola last_name: Demitri - first_name: Luka full_name: D̵ord̵ević, Luka last_name: D̵ord̵ević - first_name: Silvia full_name: Marchesan, Silvia last_name: Marchesan - first_name: Tereza full_name: Steinhartova, Tereza last_name: Steinhartova - first_name: Ilse full_name: Letofsky-Papst, Ilse last_name: Letofsky-Papst - first_name: Ivan full_name: Khalakhan, Ivan last_name: Khalakhan - first_name: Eléonore full_name: Mourad, Eléonore last_name: Mourad - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Heinz full_name: Amenitsch, Heinz last_name: Amenitsch - first_name: Maurizio full_name: Prato, Maurizio last_name: Prato - first_name: Zois full_name: Syrgiannis, Zois last_name: Syrgiannis citation: ama: Burian M, Rigodanza F, Demitri N, et al. Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. 2018;12(6):5800-5806. doi:10.1021/acsnano.8b01689 apa: Burian, M., Rigodanza, F., Demitri, N., D̵ord̵ević, L., Marchesan, S., Steinhartova, T., … Syrgiannis, Z. (2018). Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. ACS. https://doi.org/10.1021/acsnano.8b01689 chicago: Burian, Max, Francesco Rigodanza, Nicola Demitri, Luka D̵ord̵ević, Silvia Marchesan, Tereza Steinhartova, Ilse Letofsky-Papst, et al. “Inter-Backbone Charge Transfer as Prerequisite for Long-Range Conductivity in Perylene Bisimide Hydrogels.” ACS Nano. ACS, 2018. https://doi.org/10.1021/acsnano.8b01689. ieee: M. Burian et al., “Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels,” ACS Nano, vol. 12, no. 6. ACS, pp. 5800–5806, 2018. ista: Burian M, Rigodanza F, Demitri N, D̵ord̵ević L, Marchesan S, Steinhartova T, Letofsky-Papst I, Khalakhan I, Mourad E, Freunberger SA, Amenitsch H, Prato M, Syrgiannis Z. 2018. Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. 12(6), 5800–5806. mla: Burian, Max, et al. “Inter-Backbone Charge Transfer as Prerequisite for Long-Range Conductivity in Perylene Bisimide Hydrogels.” ACS Nano, vol. 12, no. 6, ACS, 2018, pp. 5800–06, doi:10.1021/acsnano.8b01689. short: M. Burian, F. Rigodanza, N. Demitri, L. D̵ord̵ević, S. Marchesan, T. Steinhartova, I. Letofsky-Papst, I. Khalakhan, E. Mourad, S.A. Freunberger, H. Amenitsch, M. Prato, Z. Syrgiannis, ACS Nano 12 (2018) 5800–5806. date_created: 2020-01-15T12:13:25Z date_published: 2018-06-05T00:00:00Z date_updated: 2021-01-12T08:12:46Z day: '05' ddc: - '540' - '541' doi: 10.1021/acsnano.8b01689 extern: '1' file: - access_level: open_access checksum: 050f7f0ba5d845c5c71779ef14ad5ef3 content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T14:56:40Z date_updated: 2020-07-14T12:47:55Z file_id: '8052' file_name: Manuscript 20092017_subm.pdf file_size: 1333353 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 12' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 5800-5806 publication: ACS Nano publication_identifier: issn: - 1936-0851 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2018' ... --- _id: '7286' abstract: - lang: eng text: The solid electrolyte interphase (SEI) in Li and Na ion batteries forms when highly reducing or oxidizing electrode materials come into contact with a liquid organic electrolyte. Its ability to form a mechanically robust, ion-conducting, and electron-insulating layer critically determines performance, cycle life, and safety. Li or Na alkyl carbonates (LiAC and NaAC, respectively) are lead SEI components in state-of-the-art carbonate based electrolytes, and our fundamental understanding of their charge transport and mechanical properties may hold the key to designing electrolytes forming an improved SEI. We synthesized a homologous series of LiACs and NaACs from methyl to octyl analogues and characterized them with respect to structure, ionic conductivity, and stiffness. The compounds assume layered structures except for the lithium methyl carbonate. Room-temperature conductivities were found to be ∼10–9 S cm–1 for lithium methyl carbonate, <10–12 S cm–1 for the other LiACs, and <10–12 S cm–1 for the NaACs with ion transport mostly attributed to grain boundaries. While LiACs show stiffnesses of ∼1 GPa, NaACs become significantly softer with increasing chain lengths. These findings will help to more precisely interpret the complex results from charge transport and mechanical characterization of real SEIs and can give a rationale for influencing the SEI’s mechanical properties via the electrolyte. article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Schafzahl, Lukas last_name: Schafzahl - first_name: Heike full_name: Ehmann, Heike last_name: Ehmann - first_name: Manfred full_name: Kriechbaum, Manfred last_name: Kriechbaum - first_name: Jürgen full_name: Sattelkow, Jürgen last_name: Sattelkow - first_name: Thomas full_name: Ganner, Thomas last_name: Ganner - first_name: Harald full_name: Plank, Harald last_name: Plank - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: 'Schafzahl L, Ehmann H, Kriechbaum M, et al. Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. 2018;30(10):3338-3345. doi:10.1021/acs.chemmater.8b00750' apa: 'Schafzahl, L., Ehmann, H., Kriechbaum, M., Sattelkow, J., Ganner, T., Plank, H., … Freunberger, S. A. (2018). Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. ACS. https://doi.org/10.1021/acs.chemmater.8b00750' chicago: 'Schafzahl, Lukas, Heike Ehmann, Manfred Kriechbaum, Jürgen Sattelkow, Thomas Ganner, Harald Plank, Martin Wilkening, and Stefan Alexander Freunberger. “Long-Chain Li and Na Alkyl Carbonates as Solid Electrolyte Interphase Components: Structure, Ion Transport, and Mechanical Properties.” Chemistry of Materials. ACS, 2018. https://doi.org/10.1021/acs.chemmater.8b00750.' ieee: 'L. Schafzahl et al., “Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties,” Chemistry of Materials, vol. 30, no. 10. ACS, pp. 3338–3345, 2018.' ista: 'Schafzahl L, Ehmann H, Kriechbaum M, Sattelkow J, Ganner T, Plank H, Wilkening M, Freunberger SA. 2018. Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. 30(10), 3338–3345.' mla: 'Schafzahl, Lukas, et al. “Long-Chain Li and Na Alkyl Carbonates as Solid Electrolyte Interphase Components: Structure, Ion Transport, and Mechanical Properties.” Chemistry of Materials, vol. 30, no. 10, ACS, 2018, pp. 3338–45, doi:10.1021/acs.chemmater.8b00750.' short: L. Schafzahl, H. Ehmann, M. Kriechbaum, J. Sattelkow, T. Ganner, H. Plank, M. Wilkening, S.A. Freunberger, Chemistry of Materials 30 (2018) 3338–3345. date_created: 2020-01-15T12:13:37Z date_published: 2018-05-03T00:00:00Z date_updated: 2021-01-12T08:12:46Z day: '03' doi: 10.1021/acs.chemmater.8b00750 extern: '1' intvolume: ' 30' issue: '10' language: - iso: eng month: '05' oa_version: None page: 3338-3345 publication: Chemistry of Materials publication_identifier: eissn: - 1520-5002 issn: - 0897-4756 publication_status: published publisher: ACS quality_controlled: '1' status: public title: 'Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2018' ... --- _id: '7407' abstract: - lang: eng text: 'Proofs of space (PoS) [Dziembowski et al., CRYPTO''15] are proof systems where a prover can convince a verifier that he "wastes" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO''15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (non-trivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. ' alternative_title: - LIPIcs article_processing_charge: No author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59' apa: 'Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.59' chicago: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), 124:59:1-59:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59. ieee: K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), San Diego, CA, United States, 2018, vol. 124, p. 59:1-59:25. ista: 'Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019). ITCS: Innovations in theoretical Computer Science Conference, LIPIcs, vol. 124, 59:1-59:25.' mla: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), vol. 124, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59. short: K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25. conference: end_date: 2019-01-12 location: San Diego, CA, United States name: 'ITCS: Innovations in theoretical Computer Science Conference' start_date: 2019-01-10 date_created: 2020-01-30T09:16:05Z date_published: 2018-12-31T00:00:00Z date_updated: 2021-01-12T08:13:26Z day: '31' ddc: - '000' department: - _id: KrPi doi: 10.4230/LIPICS.ITCS.2019.59 ec_funded: 1 file: - access_level: open_access checksum: 5cebb7f7849a3beda898f697d755dd96 content_type: application/pdf creator: dernst date_created: 2020-02-04T08:17:52Z date_updated: 2020-07-14T12:47:57Z file_id: '7443' file_name: 2018_LIPIcs_Pietrzak.pdf file_size: 822884 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 124' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2018/194 month: '12' oa: 1 oa_version: Published Version page: 59:1-59:25 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019) publication_identifier: isbn: - 978-3-95977-095-8 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Proofs of catalytic space 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 volume: 124 year: '2018' ... --- _id: '7458' abstract: - lang: eng text: The coupling between magnetic and electric subsystems in composites of ferromagnetic and ferroelectric phases is a product property that is facilitated by mechanical strain that arises due to magnetostriction and the piezoelectric effect in the constituent phases. Such multiferroic composites are of immense interests for studies on the physics of electromagnetic coupling and for use in a variety of applications. Here, we focus on magneto-electric (ME) coupling in nanocomposites. Particular emphasis is on core-shell particles and coaxial fibers, thin film heterostructures, and planar structures with a variety of mechanical connectivity. A brief review of models that predict strong ME effects in nanostructures is followed by synthesis and characterization. Core-shell particulate composites can be prepared by hydrothermal processes and chemical or deoxyribonucleic acid-assisted assembly. Electrospinning techniques have been utilized to prepare defect free core-shell nanofibers. Core-shell particles and fibers can be assembled into superstructures with the aid of magnetic and electric fields and characterized for possible use in advanced technologies. Chemical-vapor deposition techniques have been shown to be effective for the preparation of heterostructures of ferrites and ferroelectrics. Exotic planar multiferroic structures with potential for enhancing ME coupling strengths are also considered. Scanning probe microscopy techniques are ideal for probing the nature of direct- and converse-ME coupling in individual nanostructures. Magnetoelectric characterization of assemblies of nanocomposites can be done by ME voltage coefficient, magnetic field induced polarization, and magneto-dielectric effects. We conclude with a brief discussion on possible avenues for strengthening the product properties in the nanocomposites. article_number: '061101' article_processing_charge: No article_type: original author: - first_name: Dwight full_name: Viehland, Dwight last_name: Viehland - first_name: Jie Fang full_name: Li, Jie Fang last_name: Li - first_name: Yaodong full_name: Yang, Yaodong last_name: Yang - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Amin full_name: Yourdkhani, Amin last_name: Yourdkhani - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu - first_name: Peng full_name: Zhou, Peng last_name: Zhou - first_name: Tianjin full_name: Zhang, Tianjin last_name: Zhang - first_name: Tianqian full_name: Li, Tianqian last_name: Li - first_name: Arunava full_name: Gupta, Arunava last_name: Gupta - first_name: Maksym full_name: Popov, Maksym last_name: Popov - first_name: Gopalan full_name: Srinivasan, Gopalan last_name: Srinivasan citation: ama: 'Viehland D, Li JF, Yang Y, et al. Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. 2018;124(6). doi:10.1063/1.5038726' apa: 'Viehland, D., Li, J. F., Yang, Y., Costanzo, T., Yourdkhani, A., Caruntu, G., … Srinivasan, G. (2018). Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. AIP. https://doi.org/10.1063/1.5038726' chicago: 'Viehland, Dwight, Jie Fang Li, Yaodong Yang, Tommaso Costanzo, Amin Yourdkhani, Gabriel Caruntu, Peng Zhou, et al. “Tutorial: Product Properties in Multiferroic Nanocomposites.” Journal of Applied Physics. AIP, 2018. https://doi.org/10.1063/1.5038726.' ieee: 'D. Viehland et al., “Tutorial: Product properties in multiferroic nanocomposites,” Journal of Applied Physics, vol. 124, no. 6. AIP, 2018.' ista: 'Viehland D, Li JF, Yang Y, Costanzo T, Yourdkhani A, Caruntu G, Zhou P, Zhang T, Li T, Gupta A, Popov M, Srinivasan G. 2018. Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. 124(6), 061101.' mla: 'Viehland, Dwight, et al. “Tutorial: Product Properties in Multiferroic Nanocomposites.” Journal of Applied Physics, vol. 124, no. 6, 061101, AIP, 2018, doi:10.1063/1.5038726.' short: D. Viehland, J.F. Li, Y. Yang, T. Costanzo, A. Yourdkhani, G. Caruntu, P. Zhou, T. Zhang, T. Li, A. Gupta, M. Popov, G. Srinivasan, Journal of Applied Physics 124 (2018). date_created: 2020-02-05T14:18:22Z date_published: 2018-08-10T00:00:00Z date_updated: 2023-02-23T13:08:29Z day: '10' doi: 10.1063/1.5038726 extern: '1' intvolume: ' 124' issue: '6' language: - iso: eng month: '08' oa_version: None publication: Journal of Applied Physics publication_identifier: issn: - 0021-8979 - 1089-7550 publication_status: published publisher: AIP quality_controlled: '1' status: public title: 'Tutorial: Product properties in multiferroic nanocomposites' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 124 year: '2018' ... --- _id: '7717' abstract: - lang: eng text: "Background: DNA methylation levels change along with age, but few studies have examined the variation in the rate of such changes between individuals.\r\nMethods: We performed a longitudinal analysis to quantify the variation in the rate of change of DNA methylation between individuals using whole blood DNA methylation array profiles collected at 2–4 time points (N = 2894) in 954 individuals (67–90 years).\r\nResults: After stringent quality control, we identified 1507 DNA methylation CpG sites (rsCpGs) with statistically significant variation in the rate of change (random slope) of DNA methylation among individuals in a mixed linear model analysis. Genes in the vicinity of these rsCpGs were found to be enriched in Homeobox transcription factors and the Wnt signalling pathway, both of which are related to ageing processes. Furthermore, we investigated the SNP effect on the random slope. We found that 4 out of 1507 rsCpGs had one significant (P < 5 × 10−8/1507) SNP effect and 343 rsCpGs had at least one SNP effect (436 SNP-probe pairs) reaching genome-wide significance (P < 5 × 10−8). Ninety-five percent of the significant (P < 5 × 10−8) SNPs are on different chromosomes from their corresponding probes.\r\nConclusions: We identified CpG sites that have variability in the rate of change of DNA methylation between individuals, and our results suggest a genetic basis of this variation. Genes around these CpG sites have been reported to be involved in the ageing process." article_number: '75' article_processing_charge: No article_type: original author: - first_name: Qian full_name: Zhang, Qian last_name: Zhang - first_name: Riccardo E full_name: Marioni, Riccardo E last_name: Marioni - 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: Jon full_name: Higham, Jon last_name: Higham - first_name: Duncan full_name: Sproul, Duncan last_name: Sproul - first_name: Naomi R full_name: Wray, Naomi R last_name: Wray - first_name: Ian J full_name: Deary, Ian J last_name: Deary - first_name: Allan F full_name: McRae, Allan F last_name: McRae - first_name: Peter M full_name: Visscher, Peter M last_name: Visscher citation: ama: Zhang Q, Marioni RE, Robinson MR, et al. Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. 2018;10(1). doi:10.1186/s13073-018-0585-7 apa: Zhang, Q., Marioni, R. E., Robinson, M. R., Higham, J., Sproul, D., Wray, N. R., … Visscher, P. M. (2018). Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-018-0585-7 chicago: Zhang, Qian, Riccardo E Marioni, Matthew Richard Robinson, Jon Higham, Duncan Sproul, Naomi R Wray, Ian J Deary, Allan F McRae, and Peter M Visscher. “Genotype Effects Contribute to Variation in Longitudinal Methylome Patterns in Older People.” Genome Medicine. Springer Nature, 2018. https://doi.org/10.1186/s13073-018-0585-7. ieee: Q. Zhang et al., “Genotype effects contribute to variation in longitudinal methylome patterns in older people,” Genome Medicine, vol. 10, no. 1. Springer Nature, 2018. ista: Zhang Q, Marioni RE, Robinson MR, Higham J, Sproul D, Wray NR, Deary IJ, McRae AF, Visscher PM. 2018. Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. 10(1), 75. mla: Zhang, Qian, et al. “Genotype Effects Contribute to Variation in Longitudinal Methylome Patterns in Older People.” Genome Medicine, vol. 10, no. 1, 75, Springer Nature, 2018, doi:10.1186/s13073-018-0585-7. short: Q. Zhang, R.E. Marioni, M.R. Robinson, J. Higham, D. Sproul, N.R. Wray, I.J. Deary, A.F. McRae, P.M. Visscher, Genome Medicine 10 (2018). date_created: 2020-04-30T10:42:50Z date_published: 2018-10-22T00:00:00Z date_updated: 2021-01-12T08:15:04Z day: '22' doi: 10.1186/s13073-018-0585-7 extern: '1' intvolume: ' 10' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/s13073-018-0585-7 month: '10' oa: 1 oa_version: Published Version publication: Genome Medicine publication_identifier: issn: - 1756-994X publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Genotype effects contribute to variation in longitudinal methylome patterns in older people type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2018' ... --- _id: '7718' abstract: - lang: eng text: Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores. article_processing_charge: No article_type: original author: - first_name: Serena full_name: Tucci, Serena last_name: Tucci - first_name: Samuel H. full_name: Vohr, Samuel H. last_name: Vohr - first_name: Rajiv C. full_name: McCoy, Rajiv C. last_name: McCoy - first_name: Benjamin full_name: Vernot, Benjamin last_name: Vernot - 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: Chiara full_name: Barbieri, Chiara last_name: Barbieri - first_name: Brad J. full_name: Nelson, Brad J. last_name: Nelson - first_name: Wenqing full_name: Fu, Wenqing last_name: Fu - first_name: Gludhug A. full_name: Purnomo, Gludhug A. last_name: Purnomo - first_name: Herawati full_name: Sudoyo, Herawati last_name: Sudoyo - first_name: Evan E. full_name: Eichler, Evan E. last_name: Eichler - first_name: Guido full_name: Barbujani, Guido last_name: Barbujani - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Joshua M. full_name: Akey, Joshua M. last_name: Akey - first_name: Richard E. full_name: Green, Richard E. last_name: Green citation: ama: Tucci S, Vohr SH, McCoy RC, et al. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. 2018;361(6401):511-516. doi:10.1126/science.aar8486 apa: Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., … Green, R. E. (2018). Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aar8486 chicago: Tucci, Serena, Samuel H. Vohr, Rajiv C. McCoy, Benjamin Vernot, Matthew Richard Robinson, Chiara Barbieri, Brad J. Nelson, et al. “Evolutionary History and Adaptation of a Human Pygmy Population of Flores Island, Indonesia.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aar8486. ieee: S. Tucci et al., “Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia,” Science, vol. 361, no. 6401. American Association for the Advancement of Science, pp. 511–516, 2018. ista: Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE. 2018. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. 361(6401), 511–516. mla: Tucci, Serena, et al. “Evolutionary History and Adaptation of a Human Pygmy Population of Flores Island, Indonesia.” Science, vol. 361, no. 6401, American Association for the Advancement of Science, 2018, pp. 511–16, doi:10.1126/science.aar8486. short: S. Tucci, S.H. Vohr, R.C. McCoy, B. Vernot, M.R. Robinson, C. Barbieri, B.J. Nelson, W. Fu, G.A. Purnomo, H. Sudoyo, E.E. Eichler, G. Barbujani, P.M. Visscher, J.M. Akey, R.E. Green, Science 361 (2018) 511–516. date_created: 2020-04-30T10:43:24Z date_published: 2018-08-03T00:00:00Z date_updated: 2021-01-12T08:15:04Z day: '03' doi: 10.1126/science.aar8486 extern: '1' external_id: pmid: - '30072539' intvolume: ' 361' issue: '6401' language: - iso: eng month: '08' oa_version: None page: 511-516 pmid: 1 publication: Science publication_identifier: issn: - 0036-8075 - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' status: public title: Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 361 year: '2018' ... --- _id: '7712' abstract: - lang: eng text: 'Male pattern baldness (MPB) is a sex-limited, age-related, complex trait. We study MPB genetics in 205,327 European males from the UK Biobank. Here we show that MPB is strongly heritable and polygenic, with pedigree-heritability of 0.62 (SE = 0.03) estimated from close relatives, and SNP-heritability of 0.39 (SE = 0.01) from conventionally-unrelated males. We detect 624 near-independent genome-wide loci, contributing SNP-heritability of 0.25 (SE = 0.01), of which 26 X-chromosome loci explain 11.6%. Autosomal genetic variance is enriched for common variants and regions of lower linkage disequilibrium. We identify plausible genetic correlations between MPB and multiple sex-limited markers of earlier puberty, increased bone mineral density (rg = 0.15) and pancreatic β-cell function (rg = 0.12). Correlations with reproductive traits imply an effect on fitness, consistent with an estimated linear selection gradient of -0.018 per MPB standard deviation. Overall, we provide genetic insights into MPB: a phenotype of interest in its own right, with value as a model sex-limited, complex trait.' article_number: '5407' article_processing_charge: No article_type: original author: - first_name: Chloe X. full_name: Yap, Chloe X. last_name: Yap - first_name: Julia full_name: Sidorenko, Julia last_name: Sidorenko - first_name: Yang full_name: Wu, Yang last_name: Wu - first_name: Kathryn E. full_name: Kemper, Kathryn E. last_name: Kemper - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - 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: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Yap CX, Sidorenko J, Wu Y, et al. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. 2018;9. doi:10.1038/s41467-018-07862-y apa: Yap, C. X., Sidorenko, J., Wu, Y., Kemper, K. E., Yang, J., Wray, N. R., … Visscher, P. M. (2018). Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-07862-y chicago: Yap, Chloe X., Julia Sidorenko, Yang Wu, Kathryn E. Kemper, Jian Yang, Naomi R. Wray, Matthew Richard Robinson, and Peter M. Visscher. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-07862-y. ieee: C. X. Yap et al., “Dissection of genetic variation and evidence for pleiotropy in male pattern baldness,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Yap CX, Sidorenko J, Wu Y, Kemper KE, Yang J, Wray NR, Robinson MR, Visscher PM. 2018. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. 9, 5407. mla: Yap, Chloe X., et al. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” Nature Communications, vol. 9, 5407, Springer Nature, 2018, doi:10.1038/s41467-018-07862-y. short: C.X. Yap, J. Sidorenko, Y. Wu, K.E. Kemper, J. Yang, N.R. Wray, M.R. Robinson, P.M. Visscher, Nature Communications 9 (2018). date_created: 2020-04-30T10:41:19Z date_published: 2018-12-20T00:00:00Z date_updated: 2021-01-12T08:15:02Z day: '20' doi: 10.1038/s41467-018-07862-y extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-018-07862-y month: '12' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Dissection of genetic variation and evidence for pleiotropy in male pattern baldness type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7716' abstract: - lang: eng text: Genomic prediction has the potential to contribute to precision medicine. However, to date, the utility of such predictors is limited due to low accuracy for most traits. Here theory and simulation study are used to demonstrate that widespread pleiotropy among phenotypes can be utilised to improve genomic risk prediction. We show how a genetic predictor can be created as a weighted index that combines published genome-wide association study (GWAS) summary statistics across many different traits. We apply this framework to predict risk of schizophrenia and bipolar disorder in the Psychiatric Genomics consortium data, finding substantial heterogeneity in prediction accuracy increases across cohorts. For six additional phenotypes in the UK Biobank data, we find increases in prediction accuracy ranging from 0.7% for height to 47% for type 2 diabetes, when using a multi-trait predictor that combines published summary statistics from multiple traits, as compared to a predictor based only on one trait. article_number: '989' article_processing_charge: No article_type: original author: - first_name: Robert M. full_name: Maier, Robert M. last_name: Maier - first_name: Zhihong full_name: Zhu, Zhihong last_name: Zhu - first_name: Sang Hong full_name: Lee, Sang Hong last_name: Lee - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Douglas M. full_name: Ruderfer, Douglas M. last_name: Ruderfer - first_name: Eli A. full_name: Stahl, Eli A. last_name: Stahl - first_name: Stephan full_name: Ripke, Stephan last_name: Ripke - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Maier RM, Zhu Z, Lee SH, et al. Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. 2018;9. doi:10.1038/s41467-017-02769-6 apa: Maier, R. M., Zhu, Z., Lee, S. H., Trzaskowski, M., Ruderfer, D. M., Stahl, E. A., … Robinson, M. R. (2018). Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02769-6 chicago: Maier, Robert M., Zhihong Zhu, Sang Hong Lee, Maciej Trzaskowski, Douglas M. Ruderfer, Eli A. Stahl, Stephan Ripke, et al. “Improving Genetic Prediction by Leveraging Genetic Correlations among Human Diseases and Traits.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02769-6. ieee: R. M. Maier et al., “Improving genetic prediction by leveraging genetic correlations among human diseases and traits,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Maier RM, Zhu Z, Lee SH, Trzaskowski M, Ruderfer DM, Stahl EA, Ripke S, Wray NR, Yang J, Visscher PM, Robinson MR. 2018. Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. 9, 989. mla: Maier, Robert M., et al. “Improving Genetic Prediction by Leveraging Genetic Correlations among Human Diseases and Traits.” Nature Communications, vol. 9, 989, Springer Nature, 2018, doi:10.1038/s41467-017-02769-6. short: R.M. Maier, Z. Zhu, S.H. Lee, M. Trzaskowski, D.M. Ruderfer, E.A. Stahl, S. Ripke, N.R. Wray, J. Yang, P.M. Visscher, M.R. Robinson, Nature Communications 9 (2018). date_created: 2020-04-30T10:42:29Z date_published: 2018-03-07T00:00:00Z date_updated: 2021-01-12T08:15:03Z day: '07' doi: 10.1038/s41467-017-02769-6 extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-017-02769-6 month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Improving genetic prediction by leveraging genetic correlations among human diseases and traits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7715' abstract: - lang: eng text: Preference for mates with similar phenotypes; that is, assortative mating, is widely observed in humans1,2,3,4,5 and has evolutionary consequences6,7,8. Under Fisher's classical theory6, assortative mating is predicted to induce a signature in the genome at trait-associated loci that can be detected and quantified. Here, we develop and apply a method to quantify assortative mating on a specific trait by estimating the correlation (θ) between genetic predictors of the trait from single nucleotide polymorphisms on odd- versus even-numbered chromosomes. We show by theory and simulation that the effect of assortative mating can be quantified in the presence of population stratification. We applied this approach to 32 complex traits and diseases using single nucleotide polymorphism data from ~400,000 unrelated individuals of European ancestry. We found significant evidence of assortative mating for height (θ = 3.2%) and educational attainment (θ = 2.7%), both of which were consistent with theoretical predictions. Overall, our results imply that assortative mating involves multiple traits and affects the genomic architecture of loci that are associated with these traits, and that the consequence of mate choice can be detected from a random sample of genomes. article_processing_charge: No article_type: original author: - first_name: Loic full_name: Yengo, Loic last_name: Yengo - 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: Matthew C. full_name: Keller, Matthew C. last_name: Keller - first_name: Kathryn E. full_name: Kemper, Kathryn E. last_name: Kemper - first_name: Yuanhao full_name: Yang, Yuanhao last_name: Yang - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Jacob full_name: Gratten, Jacob last_name: Gratten - first_name: Patrick full_name: Turley, Patrick last_name: Turley - first_name: David full_name: Cesarini, David last_name: Cesarini - first_name: Daniel J. full_name: Benjamin, Daniel J. last_name: Benjamin - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - 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: Yengo L, Robinson MR, Keller MC, et al. Imprint of assortative mating on the human genome. Nature Human Behaviour. 2018;2(12):948-954. doi:10.1038/s41562-018-0476-3 apa: Yengo, L., Robinson, M. R., Keller, M. C., Kemper, K. E., Yang, Y., Trzaskowski, M., … Visscher, P. M. (2018). Imprint of assortative mating on the human genome. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-018-0476-3 chicago: Yengo, Loic, Matthew Richard Robinson, Matthew C. Keller, Kathryn E. Kemper, Yuanhao Yang, Maciej Trzaskowski, Jacob Gratten, et al. “Imprint of Assortative Mating on the Human Genome.” Nature Human Behaviour. Springer Nature, 2018. https://doi.org/10.1038/s41562-018-0476-3. ieee: L. Yengo et al., “Imprint of assortative mating on the human genome,” Nature Human Behaviour, vol. 2, no. 12. Springer Nature, pp. 948–954, 2018. ista: Yengo L, Robinson MR, Keller MC, Kemper KE, Yang Y, Trzaskowski M, Gratten J, Turley P, Cesarini D, Benjamin DJ, Wray NR, Goddard ME, Yang J, Visscher PM. 2018. Imprint of assortative mating on the human genome. Nature Human Behaviour. 2(12), 948–954. mla: Yengo, Loic, et al. “Imprint of Assortative Mating on the Human Genome.” Nature Human Behaviour, vol. 2, no. 12, Springer Nature, 2018, pp. 948–54, doi:10.1038/s41562-018-0476-3. short: L. Yengo, M.R. Robinson, M.C. Keller, K.E. Kemper, Y. Yang, M. Trzaskowski, J. Gratten, P. Turley, D. Cesarini, D.J. Benjamin, N.R. Wray, M.E. Goddard, J. Yang, P.M. Visscher, Nature Human Behaviour 2 (2018) 948–954. date_created: 2020-04-30T10:42:12Z date_published: 2018-11-26T00:00:00Z date_updated: 2021-01-12T08:15:03Z day: '26' doi: 10.1038/s41562-018-0476-3 extern: '1' intvolume: ' 2' issue: '12' language: - iso: eng month: '11' oa_version: None page: 948-954 publication: Nature Human Behaviour publication_identifier: issn: - 2397-3374 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Imprint of assortative mating on the human genome type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2018' ... --- _id: '7714' abstract: - lang: eng text: Health risk factors such as body mass index (BMI) and serum cholesterol are associated with many common diseases. It often remains unclear whether the risk factors are cause or consequence of disease, or whether the associations are the result of confounding. We develop and apply a method (called GSMR) that performs a multi-SNP Mendelian randomization analysis using summary-level data from genome-wide association studies to test the causal associations of BMI, waist-to-hip ratio, serum cholesterols, blood pressures, height, and years of schooling (EduYears) with common diseases (sample sizes of up to 405,072). We identify a number of causal associations including a protective effect of LDL-cholesterol against type-2 diabetes (T2D) that might explain the side effects of statins on T2D, a protective effect of EduYears against Alzheimer’s disease, and bidirectional associations with opposite effects (e.g., higher BMI increases the risk of T2D but the effect of T2D on BMI is negative). article_number: '224' article_processing_charge: No article_type: original author: - first_name: Zhihong full_name: Zhu, Zhihong last_name: Zhu - first_name: Zhili full_name: Zheng, Zhili last_name: Zheng - first_name: Futao full_name: Zhang, Futao last_name: Zhang - first_name: Yang full_name: Wu, Yang last_name: Wu - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Robert full_name: Maier, Robert last_name: Maier - 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 J. full_name: McGrath, John J. last_name: McGrath - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Jian full_name: Yang, Jian last_name: Yang citation: ama: Zhu Z, Zheng Z, Zhang F, et al. Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. 2018;9. doi:10.1038/s41467-017-02317-2 apa: Zhu, Z., Zheng, Z., Zhang, F., Wu, Y., Trzaskowski, M., Maier, R., … Yang, J. (2018). Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02317-2 chicago: Zhu, Zhihong, Zhili Zheng, Futao Zhang, Yang Wu, Maciej Trzaskowski, Robert Maier, Matthew Richard Robinson, et al. “Causal Associations between Risk Factors and Common Diseases Inferred from GWAS Summary Data.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02317-2. ieee: Z. Zhu et al., “Causal associations between risk factors and common diseases inferred from GWAS summary data,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Zhu Z, Zheng Z, Zhang F, Wu Y, Trzaskowski M, Maier R, Robinson MR, McGrath JJ, Visscher PM, Wray NR, Yang J. 2018. Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. 9, 224. mla: Zhu, Zhihong, et al. “Causal Associations between Risk Factors and Common Diseases Inferred from GWAS Summary Data.” Nature Communications, vol. 9, 224, Springer Nature, 2018, doi:10.1038/s41467-017-02317-2. short: Z. Zhu, Z. Zheng, F. Zhang, Y. Wu, M. Trzaskowski, R. Maier, M.R. Robinson, J.J. McGrath, P.M. Visscher, N.R. Wray, J. Yang, Nature Communications 9 (2018). date_created: 2020-04-30T10:41:55Z date_published: 2018-01-15T00:00:00Z date_updated: 2021-01-12T08:15:03Z day: '15' doi: 10.1038/s41467-017-02317-2 extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-017-02317-2 month: '01' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Causal associations between risk factors and common diseases inferred from GWAS summary data type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7713' abstract: - lang: eng text: There are mean differences in complex traits among global human populations. We hypothesize that part of the phenotypic differentiation is due to natural selection. To address this hypothesis, we assess the differentiation in allele frequencies of trait-associated SNPs among African, Eastern Asian, and European populations for ten complex traits using data of large sample size (up to ~405,000). We show that SNPs associated with height (P=2.46×10−5), waist-to-hip ratio (P=2.77×10−4), and schizophrenia (P=3.96×10−5) are significantly more differentiated among populations than matched “control” SNPs, suggesting that these trait-associated SNPs have undergone natural selection. We further find that SNPs associated with height (P=2.01×10−6) and schizophrenia (P=5.16×10−18) show significantly higher variance in linkage disequilibrium (LD) scores across populations than control SNPs. Our results support the hypothesis that natural selection has shaped the genetic differentiation of complex traits, such as height and schizophrenia, among worldwide populations. article_number: '1865' article_processing_charge: No article_type: original author: - first_name: Jing full_name: Guo, Jing last_name: Guo - first_name: Yang full_name: Wu, Yang last_name: Wu - first_name: Zhihong full_name: Zhu, Zhihong last_name: Zhu - first_name: Zhili full_name: Zheng, Zhili last_name: Zheng - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Jian full_name: Zeng, Jian last_name: Zeng - 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: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Jian full_name: Yang, Jian last_name: Yang citation: ama: Guo J, Wu Y, Zhu Z, et al. Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. 2018;9. doi:10.1038/s41467-018-04191-y apa: Guo, J., Wu, Y., Zhu, Z., Zheng, Z., Trzaskowski, M., Zeng, J., … Yang, J. (2018). Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04191-y chicago: Guo, Jing, Yang Wu, Zhihong Zhu, Zhili Zheng, Maciej Trzaskowski, Jian Zeng, Matthew Richard Robinson, Peter M. Visscher, and Jian Yang. “Global Genetic Differentiation of Complex Traits Shaped by Natural Selection in Humans.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04191-y. ieee: J. Guo et al., “Global genetic differentiation of complex traits shaped by natural selection in humans,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Guo J, Wu Y, Zhu Z, Zheng Z, Trzaskowski M, Zeng J, Robinson MR, Visscher PM, Yang J. 2018. Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. 9, 1865. mla: Guo, Jing, et al. “Global Genetic Differentiation of Complex Traits Shaped by Natural Selection in Humans.” Nature Communications, vol. 9, 1865, Springer Nature, 2018, doi:10.1038/s41467-018-04191-y. short: J. Guo, Y. Wu, Z. Zhu, Z. Zheng, M. Trzaskowski, J. Zeng, M.R. Robinson, P.M. Visscher, J. Yang, Nature Communications 9 (2018). date_created: 2020-04-30T10:41:36Z date_published: 2018-05-14T00:00:00Z date_updated: 2021-01-12T08:15:02Z day: '14' doi: 10.1038/s41467-018-04191-y extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-018-04191-y month: '05' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Global genetic differentiation of complex traits shaped by natural selection in humans type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7721' abstract: - lang: eng text: 'The availability of genome-wide genetic data on hundreds of thousands of people has led to an equally rapid growth in methodologies available to analyse these data. While the motivation for undertaking genome-wide association studies (GWAS) is identification of genetic markers associated with complex traits, once generated these data can be used for many other analyses. GWAS have demonstrated that complex traits exhibit a highly polygenic genetic architecture, often with shared genetic risk factors across traits. New methods to analyse data from GWAS are increasingly being used to address a diverse set of questions about the aetiology of complex traits and diseases, including psychiatric disorders. Here, we give an overview of some of these methods and present examples of how they have contributed to our understanding of psychiatric disorders. We consider: (i) estimation of the extent of genetic influence on traits, (ii) uncovering of shared genetic control between traits, (iii) predictions of genetic risk for individuals, (iv) uncovering of causal relationships between traits, (v) identifying causal single-nucleotide polymorphisms and genes or (vi) the detection of genetic heterogeneity. This classification helps organise the large number of recently developed methods, although some could be placed in more than one category. While some methods require GWAS data on individual people, others simply use GWAS summary statistics data, allowing novel well-powered analyses to be conducted at a low computational burden.' article_processing_charge: No article_type: original author: - first_name: R. M. full_name: Maier, R. M. last_name: Maier - first_name: P. M. full_name: Visscher, P. M. last_name: Visscher - 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: N. R. full_name: Wray, N. R. last_name: Wray citation: ama: 'Maier RM, Visscher PM, Robinson MR, Wray NR. Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. 2018;48(7):1055-1067. doi:10.1017/s0033291717002318' apa: 'Maier, R. M., Visscher, P. M., Robinson, M. R., & Wray, N. R. (2018). Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. Cambridge University Press. https://doi.org/10.1017/s0033291717002318' chicago: 'Maier, R. M., P. M. Visscher, Matthew Richard Robinson, and N. R. Wray. “Embracing Polygenicity: A Review of Methods and Tools for Psychiatric Genetics Research.” Psychological Medicine. Cambridge University Press, 2018. https://doi.org/10.1017/s0033291717002318.' ieee: 'R. M. Maier, P. M. Visscher, M. R. Robinson, and N. R. Wray, “Embracing polygenicity: A review of methods and tools for psychiatric genetics research,” Psychological Medicine, vol. 48, no. 7. Cambridge University Press, pp. 1055–1067, 2018.' ista: 'Maier RM, Visscher PM, Robinson MR, Wray NR. 2018. Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. 48(7), 1055–1067.' mla: 'Maier, R. M., et al. “Embracing Polygenicity: A Review of Methods and Tools for Psychiatric Genetics Research.” Psychological Medicine, vol. 48, no. 7, Cambridge University Press, 2018, pp. 1055–67, doi:10.1017/s0033291717002318.' short: R.M. Maier, P.M. Visscher, M.R. Robinson, N.R. Wray, Psychological Medicine 48 (2018) 1055–1067. date_created: 2020-04-30T10:44:35Z date_published: 2018-05-01T00:00:00Z date_updated: 2021-01-12T08:15:05Z day: '01' doi: 10.1017/s0033291717002318 extern: '1' intvolume: ' 48' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/s0033291717002318 month: '05' oa: 1 oa_version: Published Version page: 1055-1067 publication: Psychological Medicine publication_identifier: issn: - 0033-2917 - 1469-8978 publication_status: published publisher: Cambridge University Press quality_controlled: '1' status: public title: 'Embracing polygenicity: A review of methods and tools for psychiatric genetics research' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2018' ... --- _id: '7723' abstract: - lang: eng text: Genome-wide association studies (GWAS) have identified thousands of loci that are robustly associated with complex diseases. The use of linear mixed model (LMM) methodology for GWAS is becoming more prevalent due to its ability to control for population structure and cryptic relatedness and to increase power. The odds ratio (OR) is a common measure of the association of a disease with an exposure (e.g., a genetic variant) and is readably available from logistic regression. However, when the LMM is applied to all-or-none traits it provides estimates of genetic effects on the observed 0–1 scale, a different scale to that in logistic regression. This limits the comparability of results across studies, for example in a meta-analysis, and makes the interpretation of the magnitude of an effect from an LMM GWAS difficult. In this study, we derived transformations from the genetic effects estimated under the LMM to the OR that only rely on summary statistics. To test the proposed transformations, we used real genotypes from two large, publicly available data sets to simulate all-or-none phenotypes for a set of scenarios that differ in underlying model, disease prevalence, and heritability. Furthermore, we applied these transformations to GWAS summary statistics for type 2 diabetes generated from 108,042 individuals in the UK Biobank. In both simulation and real-data application, we observed very high concordance between the transformed OR from the LMM and either the simulated truth or estimates from logistic regression. The transformations derived and validated in this study improve the comparability of results from prospective and already performed LMM GWAS on complex diseases by providing a reliable transformation to a common comparative scale for the genetic effects. article_processing_charge: No article_type: original author: - first_name: Luke R. full_name: Lloyd-Jones, Luke R. last_name: Lloyd-Jones - 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: Jian full_name: Yang, Jian last_name: Yang - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 2018;208(4):1397-1408. doi:10.1534/genetics.117.300360 apa: Lloyd-Jones, L. R., Robinson, M. R., Yang, J., & Visscher, P. M. (2018). Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300360 chicago: Lloyd-Jones, Luke R., Matthew Richard Robinson, Jian Yang, and Peter M. Visscher. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300360. ieee: L. R. Lloyd-Jones, M. R. Robinson, J. Yang, and P. M. Visscher, “Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1397–1408, 2018. ista: Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. 2018. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 208(4), 1397–1408. mla: Lloyd-Jones, Luke R., et al. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1397–408, doi:10.1534/genetics.117.300360. short: L.R. Lloyd-Jones, M.R. Robinson, J. Yang, P.M. Visscher, Genetics 208 (2018) 1397–1408. date_created: 2020-04-30T10:45:19Z date_published: 2018-04-01T00:00:00Z date_updated: 2021-01-12T08:15:06Z day: '01' doi: 10.1534/genetics.117.300360 extern: '1' intvolume: ' 208' issue: '4' language: - iso: eng month: '04' oa_version: None page: 1397-1408 publication: Genetics publication_identifier: issn: - 0016-6731 - 1943-2631 publication_status: published publisher: Genetics Society of America quality_controlled: '1' status: public title: Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 208 year: '2018' ... --- _id: '7722' abstract: - lang: eng text: We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero effects), and the relationship between SNP effect size and minor allele frequency for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752) and show that on average, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance. We detect significant (P < 0.05/28) signatures of natural selection in the genetic architecture of 23 traits, including reproductive, cardiovascular, and anthropometric traits, as well as educational attainment. The significant estimates of the relationship between effect size and minor allele frequency in complex traits are consistent with a model of negative (or purifying) selection, as confirmed by forward simulation. We conclude that negative selection acts pervasively on the genetic variants associated with human complex traits. article_processing_charge: No article_type: original author: - first_name: Jian full_name: Zeng, Jian last_name: Zeng - first_name: Ronald full_name: de Vlaming, Ronald last_name: de Vlaming - first_name: Yang full_name: Wu, Yang last_name: Wu - 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: Luke R. full_name: Lloyd-Jones, Luke R. last_name: Lloyd-Jones - first_name: Loic full_name: Yengo, Loic last_name: Yengo - first_name: Chloe X. full_name: Yap, Chloe X. last_name: Yap - first_name: Angli full_name: Xue, Angli last_name: Xue - first_name: Julia full_name: Sidorenko, Julia last_name: Sidorenko - first_name: Allan F. full_name: McRae, Allan F. last_name: McRae - first_name: Joseph E. full_name: Powell, Joseph E. last_name: Powell - first_name: Grant W. full_name: Montgomery, Grant W. last_name: Montgomery - first_name: Andres full_name: Metspalu, Andres last_name: Metspalu - first_name: Tonu full_name: Esko, Tonu last_name: Esko - first_name: Greg full_name: Gibson, Greg last_name: Gibson - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Jian full_name: Yang, Jian last_name: Yang citation: ama: Zeng J, de Vlaming R, Wu Y, et al. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 2018;50(5):746-753. doi:10.1038/s41588-018-0101-4 apa: Zeng, J., de Vlaming, R., Wu, Y., Robinson, M. R., Lloyd-Jones, L. R., Yengo, L., … Yang, J. (2018). Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-018-0101-4 chicago: Zeng, Jian, Ronald de Vlaming, Yang Wu, Matthew Richard Robinson, Luke R. Lloyd-Jones, Loic Yengo, Chloe X. Yap, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics. Springer Nature, 2018. https://doi.org/10.1038/s41588-018-0101-4. ieee: J. Zeng et al., “Signatures of negative selection in the genetic architecture of human complex traits,” Nature Genetics, vol. 50, no. 5. Springer Nature, pp. 746–753, 2018. ista: Zeng J, de Vlaming R, Wu Y, Robinson MR, Lloyd-Jones LR, Yengo L, Yap CX, Xue A, Sidorenko J, McRae AF, Powell JE, Montgomery GW, Metspalu A, Esko T, Gibson G, Wray NR, Visscher PM, Yang J. 2018. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 50(5), 746–753. mla: Zeng, Jian, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics, vol. 50, no. 5, Springer Nature, 2018, pp. 746–53, doi:10.1038/s41588-018-0101-4. short: J. Zeng, R. de Vlaming, Y. Wu, M.R. Robinson, L.R. Lloyd-Jones, L. Yengo, C.X. Yap, A. Xue, J. Sidorenko, A.F. McRae, J.E. Powell, G.W. Montgomery, A. Metspalu, T. Esko, G. Gibson, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 50 (2018) 746–753. date_created: 2020-04-30T10:44:57Z date_published: 2018-04-16T00:00:00Z date_updated: 2021-01-12T08:15:06Z day: '16' doi: 10.1038/s41588-018-0101-4 extern: '1' intvolume: ' 50' issue: '5' language: - iso: eng month: '04' oa_version: None page: 746-753 publication: Nature Genetics publication_identifier: issn: - 1061-4036 - 1546-1718 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Signatures of negative selection in the genetic architecture of human complex traits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2018' ... --- _id: '7724' abstract: - lang: eng text: Modern molecular genetic datasets, primarily collected to study the biology of human health and disease, can be used to directly measure the action of natural selection and reveal important features of contemporary human evolution. Here we leverage the UK Biobank data to test for the presence of linear and nonlinear natural selection in a contemporary population of the United Kingdom. We obtain phenotypic and genetic evidence consistent with the action of linear/directional selection. Phenotypic evidence suggests that stabilizing selection, which acts to reduce variance in the population without necessarily modifying the population mean, is widespread and relatively weak in comparison with estimates from other species. article_processing_charge: No article_type: original author: - first_name: Jaleal S. full_name: Sanjak, Jaleal S. last_name: Sanjak - first_name: Julia full_name: Sidorenko, Julia last_name: Sidorenko - 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: Kevin R. full_name: Thornton, Kevin R. last_name: Thornton - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 2018;115(1):151-156. doi:10.1073/pnas.1707227114 apa: Sanjak, J. S., Sidorenko, J., Robinson, M. R., Thornton, K. R., & Visscher, P. M. (2018). Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1707227114 chicago: Sanjak, Jaleal S., Julia Sidorenko, Matthew Richard Robinson, Kevin R. Thornton, and Peter M. Visscher. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1707227114. ieee: J. S. Sanjak, J. Sidorenko, M. R. Robinson, K. R. Thornton, and P. M. Visscher, “Evidence of directional and stabilizing selection in contemporary humans,” Proceedings of the National Academy of Sciences, vol. 115, no. 1. Proceedings of the National Academy of Sciences, pp. 151–156, 2018. ista: Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. 2018. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 115(1), 151–156. mla: Sanjak, Jaleal S., et al. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences, vol. 115, no. 1, Proceedings of the National Academy of Sciences, 2018, pp. 151–56, doi:10.1073/pnas.1707227114. short: J.S. Sanjak, J. Sidorenko, M.R. Robinson, K.R. Thornton, P.M. Visscher, Proceedings of the National Academy of Sciences 115 (2018) 151–156. date_created: 2020-04-30T10:45:43Z date_published: 2018-01-02T00:00:00Z date_updated: 2021-01-12T08:15:07Z day: '02' doi: 10.1073/pnas.1707227114 extern: '1' intvolume: ' 115' issue: '1' language: - iso: eng month: '01' oa_version: None page: 151-156 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1073/pnas.1806837115 status: public title: Evidence of directional and stabilizing selection in contemporary humans type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2018' ... --- _id: '7754' abstract: - lang: eng text: Creating a selective gel that filters particles based on their interactions is a major goal of nanotechnology, with far-reaching implications from drug delivery to controlling assembly pathways. However, this is particularly difficult when the particles are larger than the gel’s characteristic mesh size because such particles cannot passively pass through the gel. Thus, filtering requires the interacting particles to transiently reorganize the gel’s internal structure. While significant advances, e.g., in DNA engineering, have enabled the design of nano-materials with programmable interactions, it is not clear what physical principles such a designer gel could exploit to achieve selective permeability. We present an equilibrium mechanism where crosslink binding dynamics are affected by interacting particles such that particle diffusion is enhanced. In addition to revealing specific design rules for manufacturing selective gels, our results have the potential to explain the origin of selective permeability in certain biological materials, including the nuclear pore complex. article_number: '4348' 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: Michael P. full_name: Brenner, Michael P. last_name: Brenner - first_name: Katharina full_name: Ribbeck, Katharina last_name: Ribbeck citation: ama: Goodrich CP, Brenner MP, Ribbeck K. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 2018;9. doi:10.1038/s41467-018-06851-5 apa: Goodrich, C. P., Brenner, M. P., & Ribbeck, K. (2018). Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06851-5 chicago: Goodrich, Carl Peter, Michael P. Brenner, and Katharina Ribbeck. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06851-5. ieee: C. P. Goodrich, M. P. Brenner, and K. Ribbeck, “Enhanced diffusion by binding to the crosslinks of a polymer gel,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Goodrich CP, Brenner MP, Ribbeck K. 2018. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 9, 4348. mla: Goodrich, Carl Peter, et al. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications, vol. 9, 4348, Springer Nature, 2018, doi:10.1038/s41467-018-06851-5. short: C.P. Goodrich, M.P. Brenner, K. Ribbeck, Nature Communications 9 (2018). date_created: 2020-04-30T11:38:01Z date_published: 2018-10-19T00:00:00Z date_updated: 2021-01-12T08:15:18Z day: '19' doi: 10.1038/s41467-018-06851-5 extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-018-06851-5 month: '10' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Enhanced diffusion by binding to the crosslinks of a polymer gel type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7783' abstract: - lang: eng text: The Drosophila Genetic Reference Panel (DGRP) serves as a valuable resource to better understand the genetic landscapes underlying quantitative traits. However, such DGRP studies have so far only focused on nuclear genetic variants. To address this, we sequenced the mitochondrial genomes of >170 DGRP lines, identifying 229 variants including 21 indels and 7 frameshifts. We used our mitochondrial variation data to identify 12 genetically distinct mitochondrial haplotypes, thus revealing important population structure at the mitochondrial level. We further examined whether this population structure was reflected on the nuclear genome by screening for the presence of potential mito-nuclear genetic incompatibilities in the form of significant genotype ratio distortions (GRDs) between mitochondrial and nuclear variants. In total, we detected a remarkable 1,845 mito-nuclear GRDs, with the highest enrichment observed in a 40 kb region around the gene Sex-lethal (Sxl). Intriguingly, downstream phenotypic analyses did not uncover major fitness effects associated with these GRDs, suggesting that a large number of mito-nuclear GRDs may reflect population structure at the mitochondrial level rather than actual genomic incompatibilities. This is further supported by the GRD landscape showing particular large genomic regions associated with a single mitochondrial haplotype. Next, we explored the functional relevance of the detected mitochondrial haplotypes through an association analysis on a set of 259 assembled, non-correlating DGRP phenotypes. We found multiple significant associations with stress- and metabolism-related phenotypes, including food intake in males. We validated the latter observation by reciprocal swapping of mitochondrial genomes from high food intake DGRP lines to low food intake ones. In conclusion, our study uncovered important mitochondrial population structure and haplotype-specific metabolic variation in the DGRP, thus demonstrating the significance of incorporating mitochondrial haplotypes in geno-phenotype relationship studies. article_processing_charge: No author: - first_name: Roel P.J. full_name: Bevers, Roel P.J. last_name: Bevers - first_name: Maria full_name: Litovchenko, Maria last_name: Litovchenko - first_name: Adamandia full_name: Kapopoulou, Adamandia last_name: Kapopoulou - first_name: Virginie S. full_name: Braman, Virginie S. last_name: Braman - 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: Johan full_name: Auwerx, Johan last_name: Auwerx - first_name: Brian full_name: Hollis, Brian last_name: Hollis - first_name: Bart full_name: Deplancke, Bart last_name: Deplancke citation: ama: Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. 2018. apa: Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2018). Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. Cold Spring Harbor Laboratory. chicago: Bevers, Roel P.J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv. Cold Spring Harbor Laboratory, 2018. ieee: R. P. J. Bevers et al., “Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel,” bioRxiv. Cold Spring Harbor Laboratory, 2018. ista: Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2018. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv, . mla: Bevers, Roel P. J., et al. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv, Cold Spring Harbor Laboratory, 2018. short: R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, BioRxiv (2018). date_created: 2020-04-30T13:09:37Z date_published: 2018-11-09T00:00:00Z date_updated: 2021-01-12T08:15:30Z day: '09' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/466771 ' month: '11' oa: 1 oa_version: Preprint page: '49' publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory status: public title: Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6001' abstract: - lang: eng text: "The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU are either prohibitively expensive or require significant programming expertise to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated.\r\nIn this article, we take a new approach to concurrent memory reclamation. Instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads.\r\nInitial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free." article_number: '18' 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: William full_name: Leiserson, William last_name: Leiserson - first_name: Alexander full_name: Matveev, Alexander last_name: Matveev - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 2018;4(4). doi:10.1145/3201897' apa: 'Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2018). ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. Association for Computing Machinery. https://doi.org/10.1145/3201897' chicago: 'Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing. Association for Computing Machinery, 2018. https://doi.org/10.1145/3201897.' ieee: 'D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” ACM Transactions on Parallel Computing, vol. 4, no. 4. Association for Computing Machinery, 2018.' ista: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2018. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 4(4), 18.' mla: 'Alistarh, Dan-Adrian, et al. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing, vol. 4, no. 4, 18, Association for Computing Machinery, 2018, doi:10.1145/3201897.' short: D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on Parallel Computing 4 (2018). date_created: 2019-02-14T13:24:11Z date_published: 2018-09-01T00:00:00Z date_updated: 2023-02-23T13:17:54Z day: '01' department: - _id: DaAl doi: 10.1145/3201897 intvolume: ' 4' issue: '4' language: - iso: eng month: '09' oa_version: None publication: ACM Transactions on Parallel Computing publication_identifier: issn: - 2329-4949 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '779' relation: earlier_version status: public scopus_import: 1 status: public title: 'ThreadScan: Automatic and scalable memory reclamation' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2018' ... --- _id: '7812' abstract: - lang: eng text: Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices. article_processing_charge: No author: - first_name: Antonio full_name: Polino, Antonio last_name: Polino - first_name: Razvan full_name: Pascanu, Razvan last_name: Pascanu - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.' apa: Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada. chicago: Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018. ieee: A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018. ista: 'Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.' mla: Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018. short: A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018. conference: end_date: 2018-05-03 location: Vancouver, Canada name: 'ICLR: International Conference on Learning Representations' start_date: 2018-04-30 date_created: 2020-05-10T22:00:51Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-02-23T13:18:41Z day: '01' ddc: - '000' department: - _id: DaAl external_id: arxiv: - '1802.05668' file: - access_level: open_access checksum: a4336c167978e81891970e4e4517a8c3 content_type: application/pdf creator: dernst date_created: 2020-05-26T13:02:00Z date_updated: 2020-07-14T12:48:03Z file_id: '7894' file_name: 2018_ICLR_Polino.pdf file_size: 308339 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: 6th International Conference on Learning Representations publication_status: published quality_controlled: '1' scopus_import: 1 status: public title: Model compression via distillation and quantization type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '7983' abstract: - lang: ger text: 'Feste Alkalicarbonate sind universelle Bestandteile von Passivierungsschichten an Materialien für Interkalationsbatterien, übliche Nebenprodukte in Metall‐O2‐Batterien, und es wird angenommen, dass sie sich reversibel in Metall‐O2 /CO2‐Zellen bilden und zersetzen. In all diesen Kathoden zersetzt sich Li2CO3 zu CO2, sobald es Spannungen >3.8 V vs. Li/Li+ ausgesetzt wird. Beachtenswert ist, dass keine O2‐Entwicklung detektiert wird, wie gemäß der Zersetzungsreaktion 2 Li2CO3 → 4 Li+ + 4 e− + 2 CO2 + O2 zu erwarten wäre. Deswegen war der Verbleib eines der O‐Atome ungeklärt und wurde nicht identifizierten parasitären Reaktionen zugerechnet. Hier zeigen wir, dass hochreaktiver Singulett‐Sauerstoff (1O2) bei der Oxidation von Li2CO3 in einem aprotischen Elektrolyten gebildet und daher nicht als O2 freigesetzt wird. Diese Ergebnisse haben weitreichende Auswirkungen auf die langfristige Zyklisierbarkeit von Batterien: sie untermauern die Wichtigkeit, 1O2 in Metall‐O2‐Batterien zu verhindern, stellen die Möglichkeit einer reversiblen Metall‐O2 /CO2‐Batterie basierend auf einem Carbonat‐Entladeprodukt in Frage und helfen, Grenzflächenreaktivität von Übergangsmetallkathoden mit Li2CO3‐Resten zu erklären.' article_processing_charge: No article_type: original author: - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Sara E. full_name: Renfrew, Sara E. last_name: Renfrew - first_name: Bryan D. full_name: McCloskey, Bryan D. last_name: McCloskey - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 2018;130(19):5627-5631. doi:10.1002/ange.201802277 apa: Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018). Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201802277 chicago: Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander Freunberger. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie. Wiley, 2018. https://doi.org/10.1002/ange.201802277. ieee: N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff,” Angewandte Chemie, vol. 130, no. 19. Wiley, pp. 5627–5631, 2018. ista: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 130(19), 5627–5631. mla: Mahne, Nika, et al. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie, vol. 130, no. 19, Wiley, 2018, pp. 5627–31, doi:10.1002/ange.201802277. short: N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie 130 (2018) 5627–5631. date_created: 2020-06-19T08:33:24Z date_published: 2018-05-04T00:00:00Z date_updated: 2021-01-12T08:16:21Z day: '04' ddc: - '540' doi: 10.1002/ange.201802277 extern: '1' file: - access_level: open_access checksum: 81506e0f7079e1e3591f3cd9f626bf67 content_type: application/pdf creator: dernst date_created: 2020-06-19T11:58:06Z date_updated: 2020-07-14T12:48:06Z file_id: '7988' file_name: 2018_AngChemieDT_Mahne.pdf file_size: 674789 relation: main_file file_date_updated: 2020-07-14T12:48:06Z has_accepted_license: '1' intvolume: ' 130' issue: '19' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 5627-5631 publication: Angewandte Chemie publication_identifier: issn: - 0044-8249 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 130 year: '2018' ... --- _id: '8015' abstract: - lang: eng text: 'The neural code of cortical processing remains uncracked; however, it must necessarily rely on faithful signal propagation between cortical areas. In this issue of Neuron, Joglekar et al. (2018) show that strong inter-areal excitation balanced by local inhibition can enable reliable signal propagation in data-constrained network models of macaque cortex. ' article_processing_charge: No article_type: original author: - first_name: Jake P. full_name: Stroud, Jake P. last_name: Stroud - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: 'Stroud JP, Vogels TP. Cortical signal propagation: Balance, amplify, transmit. Neuron. 2018;98(1):8-9. doi:10.1016/j.neuron.2018.03.028' apa: 'Stroud, J. P., & Vogels, T. P. (2018). Cortical signal propagation: Balance, amplify, transmit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.03.028' chicago: 'Stroud, Jake P., and Tim P Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.03.028.' ieee: 'J. P. Stroud and T. P. Vogels, “Cortical signal propagation: Balance, amplify, transmit,” Neuron, vol. 98, no. 1. Elsevier, pp. 8–9, 2018.' ista: 'Stroud JP, Vogels TP. 2018. Cortical signal propagation: Balance, amplify, transmit. Neuron. 98(1), 8–9.' mla: 'Stroud, Jake P., and Tim P. Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 8–9, doi:10.1016/j.neuron.2018.03.028.' short: J.P. Stroud, T.P. Vogels, Neuron 98 (2018) 8–9. date_created: 2020-06-25T12:53:39Z date_published: 2018-04-04T00:00:00Z date_updated: 2021-01-12T08:16:31Z day: '04' doi: 10.1016/j.neuron.2018.03.028 extern: '1' external_id: pmid: - '29621492' intvolume: ' 98' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2018.03.028 month: '04' oa: 1 oa_version: Published Version page: 8-9 pmid: 1 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Cortical signal propagation: Balance, amplify, transmit' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 98 year: '2018' ... --- _id: '8073' abstract: - lang: eng text: Motor cortex (M1) exhibits a rich repertoire of neuronal activities to support the generation of complex movements. Although recent neuronal-network models capture many qualitative aspects of M1 dynamics, they can generate only a few distinct movements. Additionally, it is unclear how M1 efficiently controls movements over a wide range of shapes and speeds. We demonstrate that modulation of neuronal input–output gains in recurrent neuronal-network models with a fixed architecture can dramatically reorganize neuronal activity and thus downstream muscle outputs. Consistent with the observation of diffuse neuromodulatory projections to M1, a relatively small number of modulatory control units provide sufficient flexibility to adjust high-dimensional network activity using a simple reward-based learning rule. Furthermore, it is possible to assemble novel movements from previously learned primitives, and one can separately change movement speed while preserving movement shape. Our results provide a new perspective on the role of modulatory systems in controlling recurrent cortical activity. article_processing_charge: No article_type: original author: - first_name: Jake P. full_name: Stroud, Jake P. last_name: Stroud - first_name: Mason A. full_name: Porter, Mason A. last_name: Porter - first_name: Guillaume full_name: Hennequin, Guillaume last_name: Hennequin - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Stroud JP, Porter MA, Hennequin G, Vogels TP. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 2018;21(12):1774-1783. doi:10.1038/s41593-018-0276-0 apa: Stroud, J. P., Porter, M. A., Hennequin, G., & Vogels, T. P. (2018). Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-018-0276-0 chicago: Stroud, Jake P., Mason A. Porter, Guillaume Hennequin, and Tim P Vogels. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience. Springer Nature, 2018. https://doi.org/10.1038/s41593-018-0276-0. ieee: J. P. Stroud, M. A. Porter, G. Hennequin, and T. P. Vogels, “Motor primitives in space and time via targeted gain modulation in cortical networks,” Nature Neuroscience, vol. 21, no. 12. Springer Nature, pp. 1774–1783, 2018. ista: Stroud JP, Porter MA, Hennequin G, Vogels TP. 2018. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 21(12), 1774–1783. mla: Stroud, Jake P., et al. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience, vol. 21, no. 12, Springer Nature, 2018, pp. 1774–83, doi:10.1038/s41593-018-0276-0. short: J.P. Stroud, M.A. Porter, G. Hennequin, T.P. Vogels, Nature Neuroscience 21 (2018) 1774–1783. date_created: 2020-06-30T13:18:02Z date_published: 2018-12-01T00:00:00Z date_updated: 2021-01-12T08:16:46Z day: '01' doi: 10.1038/s41593-018-0276-0 extern: '1' external_id: pmid: - '30482949' intvolume: ' 21' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276991/ month: '12' oa: 1 oa_version: Submitted Version page: 1774-1783 pmid: 1 publication: Nature Neuroscience publication_identifier: issn: - 1097-6256 - 1546-1726 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41593-018-0307-x status: public title: Motor primitives in space and time via targeted gain modulation in cortical networks type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 21 year: '2018' ... --- _id: '8231' article_processing_charge: No article_type: letter_note author: - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Josef full_name: Singer, Josef last_name: Singer - first_name: Kristina M. full_name: Ilieva, Kristina M. last_name: Ilieva - first_name: Miroslawa full_name: Matz, Miroslawa last_name: Matz - first_name: Ina full_name: Herrmann, Ina last_name: Herrmann - first_name: Edzard full_name: Spillner, Edzard last_name: Spillner - first_name: Sophia N. full_name: Karagiannis, Sophia N. last_name: Karagiannis - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim citation: ama: 'Singer J, Singer J, Ilieva KM, et al. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 2018;142(3):973-976.e11. doi:10.1016/j.jaci.2018.04.021' apa: 'Singer, J., Singer, J., Ilieva, K. M., Matz, M., Herrmann, I., Spillner, E., … Jensen-Jarolim, E. (2018). AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. Elsevier. https://doi.org/10.1016/j.jaci.2018.04.021' chicago: 'Singer, Judit, Josef Singer, Kristina M. Ilieva, Miroslawa Matz, Ina Herrmann, Edzard Spillner, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical Immunology. Elsevier, 2018. https://doi.org/10.1016/j.jaci.2018.04.021.' ieee: 'J. Singer et al., “AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor,” Journal of Allergy and Clinical Immunology, vol. 142, no. 3. Elsevier, p. 973–976.e11, 2018.' ista: 'Singer J, Singer J, Ilieva KM, Matz M, Herrmann I, Spillner E, Karagiannis SN, Jensen-Jarolim E. 2018. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 142(3), 973–976.e11.' mla: 'Singer, Judit, et al. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical Immunology, vol. 142, no. 3, Elsevier, 2018, p. 973–976.e11, doi:10.1016/j.jaci.2018.04.021.' short: J. Singer, J. Singer, K.M. Ilieva, M. Matz, I. Herrmann, E. Spillner, S.N. Karagiannis, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 142 (2018) 973–976.e11. date_created: 2020-08-10T11:51:36Z date_published: 2018-09-01T00:00:00Z date_updated: 2021-01-12T08:17:37Z day: '01' doi: 10.1016/j.jaci.2018.04.021 extern: '1' intvolume: ' 142' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.jaci.2018.04.021 month: '09' oa: 1 oa_version: Published Version page: 973-976.e11 publication: Journal of Allergy and Clinical Immunology publication_identifier: issn: - 0091-6749 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 142 year: '2018' ... --- _id: '8234' abstract: - lang: eng text: Molecular imaging probes such as PET-tracers have the potential to improve the accuracy of tumor characterization by directly visualizing the biochemical situation. Thus, molecular changes can be detected early before morphological manifestation. The A3 adenosine receptor (A3AR) is described to be highly expressed in colon cancer cell lines and human colorectal cancer (CRC), suggesting this receptor as a tumor marker. The aim of this preclinical study was the evaluation of FE@SUPPY as a PET-tracer for CRC using in vitro imaging and in vivo PET imaging. First, affinity and selectivity of FE@SUPPY and its metabolites were determined, proving the favorable binding profile of FE@SUPPY. The human adenocarcinoma cell line HT-29 was characterized regarding its hA3AR expression and was subsequently chosen as tumor graft. Promising results regarding the potential of FE@SUPPY as a PET-tracer for CRC imaging were obtained by autoradiography as ≥2.3-fold higher accumulation of FE@SUPPY was found in CRC tissue compared to adjacent healthy colon tissue from the same patient. Nevertheless, first in vivo studies using HT-29 xenografts showed insufficient tumor uptake due to (1) poor conservation of target expression in xenografts and (2) unfavorable pharmacokinetics of FE@SUPPY in mice. We therefore conclude that HT-29 xenografts are not adequate to visualize hA3ARs using FE@SUPPY. article_number: '1269830' article_processing_charge: No article_type: original author: - first_name: T. full_name: Balber, T. last_name: Balber - first_name: Judit full_name: Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Singer orcid: 0000-0002-8777-3502 - first_name: N. full_name: Berroterán-Infante, N. last_name: Berroterán-Infante - first_name: M. full_name: Dumanic, M. last_name: Dumanic - first_name: L. full_name: Fetty, L. last_name: Fetty - first_name: J. full_name: Fazekas-Singer, J. last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: C. full_name: Vraka, C. last_name: Vraka - first_name: L. full_name: Nics, L. last_name: Nics - first_name: M. full_name: Bergmann, M. last_name: Bergmann - first_name: K. full_name: Pallitsch, K. last_name: Pallitsch - first_name: H. full_name: Spreitzer, H. last_name: Spreitzer - first_name: W. full_name: Wadsak, W. last_name: Wadsak orcid: 0000-0003-4479-8053 - first_name: M. full_name: Hacker, M. last_name: Hacker - first_name: E. full_name: Jensen-Jarolim, E. last_name: Jensen-Jarolim - first_name: H. full_name: Viernstein, H. last_name: Viernstein - first_name: M. full_name: Mitterhauser, M. last_name: Mitterhauser orcid: 0000-0003-3173-5272 citation: ama: 'Balber T, Singer J, Berroterán-Infante N, et al. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018;2018. doi:10.1155/2018/1269830' apa: 'Balber, T., Singer, J., Berroterán-Infante, N., Dumanic, M., Fetty, L., Fazekas-Singer, J., … Mitterhauser, M. (2018). Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. Hindawi. https://doi.org/10.1155/2018/1269830' chicago: 'Balber, T., Judit Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging. Hindawi, 2018. https://doi.org/10.1155/2018/1269830.' ieee: 'T. Balber et al., “Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer,” Contrast Media & Molecular Imaging, vol. 2018. Hindawi, 2018.' ista: 'Balber T, Singer J, Berroterán-Infante N, Dumanic M, Fetty L, Fazekas-Singer J, Vraka C, Nics L, Bergmann M, Pallitsch K, Spreitzer H, Wadsak W, Hacker M, Jensen-Jarolim E, Viernstein H, Mitterhauser M. 2018. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018, 1269830.' mla: 'Balber, T., et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging, vol. 2018, 1269830, Hindawi, 2018, doi:10.1155/2018/1269830.' short: T. Balber, J. Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, L. Nics, M. Bergmann, K. Pallitsch, H. Spreitzer, W. Wadsak, M. Hacker, E. Jensen-Jarolim, H. Viernstein, M. Mitterhauser, Contrast Media & Molecular Imaging 2018 (2018). date_created: 2020-08-10T11:53:07Z date_published: 2018-02-13T00:00:00Z date_updated: 2021-01-12T08:17:38Z day: '13' doi: 10.1155/2018/1269830 extern: '1' intvolume: ' 2018' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1155/2018/1269830 month: '02' oa: 1 oa_version: Published Version publication: Contrast Media & Molecular Imaging publication_identifier: issn: - 1555-4309 - 1555-4317 publication_status: published publisher: Hindawi quality_controlled: '1' status: public title: 'Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2018 year: '2018' ... --- _id: '8232' abstract: - lang: eng text: 'Anti-epidermal growth factor receptor (EGFR) antibody therapy is used in EGFR expressing cancers including lung, colon, head and neck, and bladder cancers, however results have been modest. Near infrared photoimmunotherapy (NIR-PIT) is a highly selective tumor treatment that employs an antibody-photo-absorber conjugate which is activated by NIR light. NIR-PIT is in clinical trials in patients with recurrent head and neck cancers using cetuximab-IR700 as the conjugate. However, its use has otherwise been restricted to mouse models. This is an effort to explore larger animal models with NIR-PIT. We describe the use of a recombinant canine anti-EGFR monoclonal antibody (mAb), can225IgG, conjugated to the photo-absorber, IR700DX, in three EGFR expressing canine transitional cell carcinoma (TCC) cell lines as a prelude to possible canine clinical studies. Can225-IR700 conjugate showed specific binding and cell-specific killing after NIR-PIT on EGFR expressing cells in vitro. In the in vivo study, can225-IR700 conjugate demonstrated accumulation of the fluorescent conjugate with high tumor-to-background ratio. Tumor-bearing mice were separated into 4 groups: (1) no treatment; (2) 100 μg of can225-IR700 i.v. only; (3) NIR light exposure only; (4) 100 μg of can225-IR700 i.v., NIR light exposure. Tumor growth was significantly inhibited by NIR-PIT treatment compared with the other groups (p < 0.001), and significantly prolonged survival was achieved (p < 0.001 vs. other groups) in the treatment groups. In conclusion, NIR-PIT with can225-IR700 is a promising treatment for canine EGFR-expressing cancers, including invasive transitional cell carcinoma in pet dogs, that could provide a pathway to translation to humans.' article_processing_charge: No article_type: original author: - first_name: Tadanobu full_name: Nagaya, Tadanobu last_name: Nagaya - first_name: Shuhei full_name: Okuyama, Shuhei last_name: Okuyama - first_name: Fusa full_name: Ogata, Fusa last_name: Ogata - first_name: Yasuhiro full_name: Maruoka, Yasuhiro last_name: Maruoka - first_name: Deborah W. full_name: Knapp, Deborah W. last_name: Knapp - first_name: Sophia N. full_name: Karagiannis, Sophia N. last_name: Karagiannis - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Peter L. full_name: Choyke, Peter L. last_name: Choyke - first_name: Amy K. full_name: LeBlanc, Amy K. last_name: LeBlanc - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim - first_name: Hisataka full_name: Kobayashi, Hisataka last_name: Kobayashi citation: ama: Nagaya T, Okuyama S, Ogata F, et al. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 2018;9:19026-19038. doi:10.18632/oncotarget.24876 apa: Nagaya, T., Okuyama, S., Ogata, F., Maruoka, Y., Knapp, D. W., Karagiannis, S. N., … Kobayashi, H. (2018). Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.24876 chicago: Nagaya, Tadanobu, Shuhei Okuyama, Fusa Ogata, Yasuhiro Maruoka, Deborah W. Knapp, Sophia N. Karagiannis, Judit Singer, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget. Impact Journals, 2018. https://doi.org/10.18632/oncotarget.24876. ieee: T. Nagaya et al., “Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody,” Oncotarget, vol. 9. Impact Journals, pp. 19026–19038, 2018. ista: Nagaya T, Okuyama S, Ogata F, Maruoka Y, Knapp DW, Karagiannis SN, Singer J, Choyke PL, LeBlanc AK, Jensen-Jarolim E, Kobayashi H. 2018. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 9, 19026–19038. mla: Nagaya, Tadanobu, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget, vol. 9, Impact Journals, 2018, pp. 19026–38, doi:10.18632/oncotarget.24876. short: T. Nagaya, S. Okuyama, F. Ogata, Y. Maruoka, D.W. Knapp, S.N. Karagiannis, J. Singer, P.L. Choyke, A.K. LeBlanc, E. Jensen-Jarolim, H. Kobayashi, Oncotarget 9 (2018) 19026–19038. date_created: 2020-08-10T11:52:54Z date_published: 2018-04-10T00:00:00Z date_updated: 2021-01-12T08:17:37Z day: '10' doi: 10.18632/oncotarget.24876 extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.18632/oncotarget.24876 month: '04' oa: 1 oa_version: Published Version page: 19026-19038 publication: Oncotarget publication_identifier: eissn: - 1949-2553 publication_status: published publisher: Impact Journals quality_controlled: '1' status: public title: Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '8233' abstract: - lang: eng text: The M2a subtype of macrophages plays an important role in human immunoglobulin E (IgE-mediated allergies) and other Th2 type immune reactions. In contrast, very little is known about these cells in the dog. Here we describe an in vitro method to activate canine histiocytic DH82 cells and primary canine monocyte-derived macrophages (MDMs) toward the M2a macrophages using human cytokines. For a side-by-side comparison, we compared the canine cells to human MDMs, and the human monocytic cell line U937 activated towards M1 and M2a cells on the cellular and molecular level. In analogy to activated human M2a cells, canine M2a, differentiated from both DH82 and MDMs, showed an increase in CD206 surface receptor expression compared to M1. Interestingly, canine M2a, but not M1 derived from MDM, upregulated the high-affinity IgE receptor (FcεRI). Transcription levels of M2a-associated genes (IL10, CCL22, TGFβ, CD163) showed a diverse pattern between the human and dog species, whereas M1 genes (IDO1, CXCL11, IL6, TNF-α) were similarly upregulated in canine and human M1 cells (cell lines and MDMs). We suggest that our novel in vitro method will be suitable in comparative allergology studies focussing on macrophages. article_processing_charge: No article_type: original author: - first_name: Ina full_name: Herrmann, Ina last_name: Herrmann - first_name: Jelena full_name: Gotovina, Jelena last_name: Gotovina - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Michael B. full_name: Fischer, Michael B. last_name: Fischer - first_name: Karin full_name: Hufnagl, Karin last_name: Hufnagl - first_name: Rodolfo full_name: Bianchini, Rodolfo last_name: Bianchini - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim citation: ama: Herrmann I, Gotovina J, Singer J, et al. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 2018;82(5):118-127. doi:10.1016/j.dci.2018.01.005 apa: Herrmann, I., Gotovina, J., Singer, J., Fischer, M. B., Hufnagl, K., Bianchini, R., & Jensen-Jarolim, E. (2018). Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. Elsevier. https://doi.org/10.1016/j.dci.2018.01.005 chicago: Herrmann, Ina, Jelena Gotovina, Judit Singer, Michael B. Fischer, Karin Hufnagl, Rodolfo Bianchini, and Erika Jensen-Jarolim. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology. Elsevier, 2018. https://doi.org/10.1016/j.dci.2018.01.005. ieee: I. Herrmann et al., “Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy,” Developmental & Comparative Immunology, vol. 82, no. 5. Elsevier, pp. 118–127, 2018. ista: Herrmann I, Gotovina J, Singer J, Fischer MB, Hufnagl K, Bianchini R, Jensen-Jarolim E. 2018. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 82(5), 118–127. mla: Herrmann, Ina, et al. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology, vol. 82, no. 5, Elsevier, 2018, pp. 118–27, doi:10.1016/j.dci.2018.01.005. short: I. Herrmann, J. Gotovina, J. Singer, M.B. Fischer, K. Hufnagl, R. Bianchini, E. Jensen-Jarolim, Developmental & Comparative Immunology 82 (2018) 118–127. date_created: 2020-08-10T11:53:01Z date_published: 2018-05-01T00:00:00Z date_updated: 2021-01-12T08:17:38Z day: '01' doi: 10.1016/j.dci.2018.01.005 extern: '1' intvolume: ' 82' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.dci.2018.01.005 month: '05' oa: 1 oa_version: Published Version page: 118-127 publication: Developmental & Comparative Immunology publication_identifier: issn: - 0145-305X publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2018' ... --- _id: '8262' abstract: - lang: eng text: "Background: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.\r\n\r\nResults: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.\r\n\r\nConclusions: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei." article_number: '965' article_processing_charge: No article_type: original author: - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Elena V. full_name: Moroz, Elena V. last_name: Moroz - first_name: Iakov I. full_name: Davydov, Iakov I. last_name: Davydov - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 2018;19. doi:10.1186/s12864-018-5245-1 apa: Bochkareva, O., Moroz, E. V., Davydov, I. I., & Gelfand, M. S. (2018). Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. Springer Nature. https://doi.org/10.1186/s12864-018-5245-1 chicago: Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” BMC Genomics. Springer Nature, 2018. https://doi.org/10.1186/s12864-018-5245-1. ieee: O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.,” BMC Genomics, vol. 19. Springer Nature, 2018. ista: Bochkareva O, Moroz EV, Davydov II, Gelfand MS. 2018. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 19, 965. mla: Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” BMC Genomics, vol. 19, 965, Springer Nature, 2018, doi:10.1186/s12864-018-5245-1. short: O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018). date_created: 2020-08-15T11:02:08Z date_published: 2018-12-27T00:00:00Z date_updated: 2023-02-23T13:28:52Z day: '27' doi: 10.1186/s12864-018-5245-1 extern: '1' intvolume: ' 19' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/s12864-018-5245-1 month: '12' oa: 1 oa_version: Published Version publication: BMC Genomics publication_identifier: issn: - 1471-2164 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2018' ... --- _id: '8265' abstract: - lang: eng text: Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content. article_number: e4545 article_processing_charge: No article_type: original author: - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Natalia O. full_name: Dranenko, Natalia O. last_name: Dranenko - first_name: Elena S. full_name: Ocheredko, Elena S. last_name: Ocheredko - first_name: German M. full_name: Kanevsky, German M. last_name: Kanevsky - first_name: Yaroslav N. full_name: Lozinsky, Yaroslav N. last_name: Lozinsky - first_name: Vera A. full_name: Khalaycheva, Vera A. last_name: Khalaycheva - first_name: Irena I. full_name: Artamonova, Irena I. last_name: Artamonova - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 2018;6. doi:10.7717/peerj.4545 apa: Bochkareva, O., Dranenko, N. O., Ocheredko, E. S., Kanevsky, G. M., Lozinsky, Y. N., Khalaycheva, V. A., … Gelfand, M. S. (2018). Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. PeerJ. https://doi.org/10.7717/peerj.4545 chicago: Bochkareva, Olga, Natalia O. Dranenko, Elena S. Ocheredko, German M. Kanevsky, Yaroslav N. Lozinsky, Vera A. Khalaycheva, Irena I. Artamonova, and Mikhail S. Gelfand. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.4545. ieee: O. Bochkareva et al., “Genome rearrangements and phylogeny reconstruction in Yersinia pestis,” PeerJ, vol. 6. PeerJ, 2018. ista: Bochkareva O, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva VA, Artamonova II, Gelfand MS. 2018. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 6, e4545. mla: Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” PeerJ, vol. 6, e4545, PeerJ, 2018, doi:10.7717/peerj.4545. short: O. Bochkareva, N.O. Dranenko, E.S. Ocheredko, G.M. Kanevsky, Y.N. Lozinsky, V.A. Khalaycheva, I.I. Artamonova, M.S. Gelfand, PeerJ 6 (2018). date_created: 2020-08-15T11:08:23Z date_published: 2018-03-27T00:00:00Z date_updated: 2023-02-23T13:28:57Z day: '27' doi: 10.7717/peerj.4545 extern: '1' external_id: pmid: - '29607260' intvolume: ' 6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.7717/peerj.4545 month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: PeerJ publication_identifier: issn: - 2167-8359 publication_status: published publisher: PeerJ quality_controlled: '1' status: public title: Genome rearrangements and phylogeny reconstruction in Yersinia pestis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2018' ... --- _id: '8274' abstract: - lang: eng text: 'Background/Aim: Our aim was to investigate the crosstalk between tumor and immune cells (M2 macrophages) and its effects on cyclo-oxygenase-2 (COX2) regulation in canine mammary tumors (CMT). Materials and Methods: Sh1b CMT cells and human BT474 mammary or HT29 colon cancer cells were co-cultured with canine peripheral blood mononuclear cells (PBMCs) or with macrophage-like differentiated THP1 monocytes (dTHP1). Intracellular COX2 expression by PBMCs, dTHP1 and cancer cells was evaluated by flow cytometry. Results: Co-culturing of Sh1b and canine PBMCs induced COX2 overexpression in CMT cells. In turn, COX2 expression by PBMCs, mostly CD68+ macrophages, was attenuated by co-culture with Sh1b (p=0.0001). In accordance, co-culture with dTHP1 prompted intracellular production of COX2 in both Sh1b CMT cells and HT29 human colon cancer cells and reduced production of COX2 in BT474 human mammary cancer cells. The intracellular COX2 expression from dTHP1 decreased when treated with conditioned medium from cultured Sh1b and HT29 cancer cells. Conclusion: Bidirectional COX2 regulation between cancer and monocytes/macrophages might shape a tolerogenic tumor microenvironment in CMT.' article_processing_charge: No article_type: original author: - first_name: Maria Isabel full_name: Carvalho, Maria Isabel last_name: Carvalho - first_name: Rodolfo full_name: Bianchini, Rodolfo last_name: Bianchini - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Ina full_name: Herrmann, Ina last_name: Herrmann - first_name: Irene full_name: Flickinger, Irene last_name: Flickinger - first_name: Johann G. full_name: Thalhammer, Johann G. last_name: Thalhammer - first_name: Isabel full_name: Pires, Isabel last_name: Pires - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim - first_name: Felisbina L. full_name: Queiroga, Felisbina L. last_name: Queiroga citation: ama: Carvalho MI, Bianchini R, Singer J, et al. Bidirectional regulation of COX-2 expression between cancer cells and macrophages. Anticancer Research. 2018;38(5):2811-2817. doi:10.21873/anticanres.12525 apa: Carvalho, M. I., Bianchini, R., Singer, J., Herrmann, I., Flickinger, I., Thalhammer, J. G., … Queiroga, F. L. (2018). Bidirectional regulation of COX-2 expression between cancer cells and macrophages. Anticancer Research. International Institute of Anticancer Research. https://doi.org/10.21873/anticanres.12525 chicago: Carvalho, Maria Isabel, Rodolfo Bianchini, Judit Singer, Ina Herrmann, Irene Flickinger, Johann G. Thalhammer, Isabel Pires, Erika Jensen-Jarolim, and Felisbina L. Queiroga. “Bidirectional Regulation of COX-2 Expression between Cancer Cells and Macrophages.” Anticancer Research. International Institute of Anticancer Research, 2018. https://doi.org/10.21873/anticanres.12525. ieee: M. I. Carvalho et al., “Bidirectional regulation of COX-2 expression between cancer cells and macrophages,” Anticancer Research, vol. 38, no. 5. International Institute of Anticancer Research, pp. 2811–2817, 2018. ista: Carvalho MI, Bianchini R, Singer J, Herrmann I, Flickinger I, Thalhammer JG, Pires I, Jensen-Jarolim E, Queiroga FL. 2018. Bidirectional regulation of COX-2 expression between cancer cells and macrophages. Anticancer Research. 38(5), 2811–2817. mla: Carvalho, Maria Isabel, et al. “Bidirectional Regulation of COX-2 Expression between Cancer Cells and Macrophages.” Anticancer Research, vol. 38, no. 5, International Institute of Anticancer Research, 2018, pp. 2811–17, doi:10.21873/anticanres.12525. short: M.I. Carvalho, R. Bianchini, J. Singer, I. Herrmann, I. Flickinger, J.G. Thalhammer, I. Pires, E. Jensen-Jarolim, F.L. Queiroga, Anticancer Research 38 (2018) 2811–2817. date_created: 2020-08-17T07:13:55Z date_published: 2018-05-01T00:00:00Z date_updated: 2021-01-12T08:17:52Z day: '01' doi: 10.21873/anticanres.12525 extern: '1' intvolume: ' 38' issue: '5' language: - iso: eng month: '05' oa_version: None page: 2811-2817 publication: Anticancer Research publication_identifier: eissn: - 1791-7530 issn: - 0250-7005 publication_status: published publisher: International Institute of Anticancer Research quality_controlled: '1' status: public title: Bidirectional regulation of COX-2 expression between cancer cells and macrophages type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2018' ... --- _id: '8298' abstract: - lang: eng text: Sharding, or partitioning the system’s state so that different subsets of participants handle it, is a proven approach to building distributed systems whose total capacity scales horizontally with the number of participants. Many distributed ledgers have adopted this approach to increase their performance, however, they focus on the permissionless setting that assumes the existence of a strong adversary. In this paper, we deploy channels for permissioned blockchains. Our first contribution is to adapt sharding on asset-management applications for the permissioned setting, while preserving liveness and safety even on transactions spanning across-channels. Our second contribution is to leverage channels as a confidentiality boundary, enabling different organizations and consortia to preserve their privacy within their channels and still be part of a bigger collaborative ecosystem. To make our system concrete we map it on top of Hyperledger Fabric. alternative_title: - LNCS article_processing_charge: No author: - first_name: Elli full_name: Androulaki, Elli last_name: Androulaki - first_name: Christian full_name: Cachin, Christian last_name: Cachin - first_name: Angelo full_name: De Caro, Angelo last_name: De Caro - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias citation: ama: 'Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. Channels: Horizontal scaling and confidentiality on permissioned blockchains. In: Computer Security. Vol 11098. Springer Nature; 2018:111-131. doi:10.1007/978-3-319-99073-6_6' apa: 'Androulaki, E., Cachin, C., De Caro, A., & Kokoris Kogias, E. (2018). Channels: Horizontal scaling and confidentiality on permissioned blockchains. In Computer Security (Vol. 11098, pp. 111–131). Barcelona, Spain: Springer Nature. https://doi.org/10.1007/978-3-319-99073-6_6' chicago: 'Androulaki, Elli, Christian Cachin, Angelo De Caro, and Eleftherios Kokoris Kogias. “Channels: Horizontal Scaling and Confidentiality on Permissioned Blockchains.” In Computer Security, 11098:111–31. Springer Nature, 2018. https://doi.org/10.1007/978-3-319-99073-6_6.' ieee: 'E. Androulaki, C. Cachin, A. De Caro, and E. Kokoris Kogias, “Channels: Horizontal scaling and confidentiality on permissioned blockchains,” in Computer Security, Barcelona, Spain, 2018, vol. 11098, pp. 111–131.' ista: 'Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. 2018. Channels: Horizontal scaling and confidentiality on permissioned blockchains. Computer Security. ESORICS: European Symposium on Research in Computer Security, LNCS, vol. 11098, 111–131.' mla: 'Androulaki, Elli, et al. “Channels: Horizontal Scaling and Confidentiality on Permissioned Blockchains.” Computer Security, vol. 11098, Springer Nature, 2018, pp. 111–31, doi:10.1007/978-3-319-99073-6_6.' short: E. Androulaki, C. Cachin, A. De Caro, E. Kokoris Kogias, in:, Computer Security, Springer Nature, 2018, pp. 111–131. conference: end_date: 2018-09-07 location: Barcelona, Spain name: 'ESORICS: European Symposium on Research in Computer Security' start_date: 2018-09-03 date_created: 2020-08-26T11:47:34Z date_published: 2018-08-08T00:00:00Z date_updated: 2021-01-12T08:17:57Z day: '08' doi: 10.1007/978-3-319-99073-6_6 extern: '1' intvolume: ' 11098' language: - iso: eng month: '08' oa_version: None page: 111-131 publication: Computer Security publication_identifier: eisbn: - '9783319990736' isbn: - '9783319990729' issn: - 0302-9743 - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Channels: Horizontal scaling and confidentiality on permissioned blockchains' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11098 year: '2018' ... --- _id: '8297' abstract: - lang: eng text: "Designing a secure permissionless distributed ledger (blockchain) that performs on par with centralized payment\r\nprocessors, such as Visa, is a challenging task. Most existing distributed ledgers are unable to scale-out, i.e., to grow their totalprocessing capacity with the number of validators; and those that do, compromise security or decentralization. We present OmniLedger, a novel scale-out distributed ledger that preserves longterm security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient crossshard commit protocol that atomically handles transactions affecting multiple shards. OmniLedger also optimizes performance via parallel intra-shard transaction processing, ledger pruning via collectively-signed state blocks, and low-latency “trust-butverify” \r\nvalidation for low-value transactions. An evaluation ofour experimental prototype shows that OmniLedger’s throughput\r\nscales linearly in the number of active validators, supporting Visa-level workloads and beyond, while confirming typical transactions in under two seconds." article_processing_charge: No author: - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Philipp full_name: Jovanovic, Philipp last_name: Jovanovic - first_name: Linus full_name: Gasser, Linus last_name: Gasser - first_name: Nicolas full_name: Gailly, Nicolas last_name: Gailly - first_name: Ewa full_name: Syta, Ewa last_name: Syta - first_name: Bryan full_name: Ford, Bryan last_name: Ford citation: ama: 'Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. OmniLedger: A secure, scale-out, decentralized ledger via sharding. In: 2018 IEEE Symposium on Security and Privacy. IEEE; 2018:583-598. doi:10.1109/sp.2018.000-5' apa: 'Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Syta, E., & Ford, B. (2018). OmniLedger: A secure, scale-out, decentralized ledger via sharding. In 2018 IEEE Symposium on Security and Privacy (pp. 583–598). San Francisco, CA, United States: IEEE. https://doi.org/10.1109/sp.2018.000-5' chicago: 'Kokoris Kogias, Eleftherios, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, Ewa Syta, and Bryan Ford. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” In 2018 IEEE Symposium on Security and Privacy, 583–98. IEEE, 2018. https://doi.org/10.1109/sp.2018.000-5.' ieee: 'E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, and B. Ford, “OmniLedger: A secure, scale-out, decentralized ledger via sharding,” in 2018 IEEE Symposium on Security and Privacy, San Francisco, CA, United States, 2018, pp. 583–598.' ista: 'Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. 2018. OmniLedger: A secure, scale-out, decentralized ledger via sharding. 2018 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 583–598.' mla: 'Kokoris Kogias, Eleftherios, et al. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–98, doi:10.1109/sp.2018.000-5.' short: E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, B. Ford, in:, 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–598. conference: end_date: 2018-05-24 location: San Francisco, CA, United States name: 'SP: Symposium on Security and Privacy' start_date: 2018-05-20 date_created: 2020-08-26T11:46:35Z date_published: 2018-07-26T00:00:00Z date_updated: 2021-01-12T08:17:56Z day: '26' doi: 10.1109/sp.2018.000-5 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/406 month: '07' oa: 1 oa_version: Preprint page: 583-598 publication: 2018 IEEE Symposium on Security and Privacy publication_identifier: isbn: - '9781538643532' issn: - 2375-1207 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: 'OmniLedger: A secure, scale-out, decentralized ledger via sharding' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '8443' abstract: - lang: eng text: Characterizing the structure of membrane proteins (MPs) generally requires extraction from their native environment, most commonly with detergents. Yet, the physicochemical properties of detergent micelles and lipid bilayers differ markedly and could alter the structural organization of MPs, albeit without general rules. Dodecylphosphocholine (DPC) is the most widely used detergent for MP structure determination by NMR, but the physiological relevance of several prominent structures has been questioned, though indirectly, by other biophysical techniques, e.g., functional/thermostability assay (TSA) and molecular dynamics (MD) simulations. Here, we resolve unambiguously this controversy by probing the functional relevance of three different mitochondrial carriers (MCs) in DPC at the atomic level, using an exhaustive set of solution-NMR experiments, complemented by functional/TSA and MD data. Our results provide atomic-level insight into the structure, substrate interaction and dynamics of the detergent–membrane protein complexes and demonstrates cogently that, while high-resolution NMR signals can be obtained for MCs in DPC, they systematically correspond to nonfunctional states. article_processing_charge: No article_type: original author: - first_name: Vilius full_name: Kurauskas, Vilius last_name: Kurauskas - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: Peixiang full_name: Ma, Peixiang last_name: Ma - first_name: Paola full_name: Lunetti, Paola last_name: Lunetti - first_name: Katharina full_name: Weinhäupl, Katharina last_name: Weinhäupl - first_name: Lionel full_name: Imbert, Lionel last_name: Imbert - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher - first_name: Martin S. full_name: King, Martin S. last_name: King - first_name: Rémy full_name: Sounier, Rémy last_name: Sounier - first_name: Vincenza full_name: Dolce, Vincenza last_name: Dolce - first_name: Edmund R. S. full_name: Kunji, Edmund R. S. last_name: Kunji - first_name: Loredana full_name: Capobianco, Loredana last_name: Capobianco - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: François full_name: Dehez, François last_name: Dehez - first_name: Beate full_name: Bersch, Beate last_name: Bersch - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Kurauskas V, Hessel A, Ma P, et al. How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. 2018;9(5):933-938. doi:10.1021/acs.jpclett.8b00269' apa: 'Kurauskas, V., Hessel, A., Ma, P., Lunetti, P., Weinhäupl, K., Imbert, L., … Schanda, P. (2018). How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.8b00269' chicago: 'Kurauskas, Vilius, Audrey Hessel, Peixiang Ma, Paola Lunetti, Katharina Weinhäupl, Lionel Imbert, Bernhard Brutscher, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.” The Journal of Physical Chemistry Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.jpclett.8b00269.' ieee: 'V. Kurauskas et al., “How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine,” The Journal of Physical Chemistry Letters, vol. 9, no. 5. American Chemical Society, pp. 933–938, 2018.' ista: 'Kurauskas V, Hessel A, Ma P, Lunetti P, Weinhäupl K, Imbert L, Brutscher B, King MS, Sounier R, Dolce V, Kunji ERS, Capobianco L, Chipot C, Dehez F, Bersch B, Schanda P. 2018. How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. 9(5), 933–938.' mla: 'Kurauskas, Vilius, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.” The Journal of Physical Chemistry Letters, vol. 9, no. 5, American Chemical Society, 2018, pp. 933–38, doi:10.1021/acs.jpclett.8b00269.' short: V. Kurauskas, A. Hessel, P. Ma, P. Lunetti, K. Weinhäupl, L. Imbert, B. Brutscher, M.S. King, R. Sounier, V. Dolce, E.R.S. Kunji, L. Capobianco, C. Chipot, F. Dehez, B. Bersch, P. Schanda, The Journal of Physical Chemistry Letters 9 (2018) 933–938. date_created: 2020-09-18T10:05:45Z date_published: 2018-02-03T00:00:00Z date_updated: 2021-01-12T08:19:18Z day: '03' doi: 10.1021/acs.jpclett.8b00269 extern: '1' intvolume: ' 9' issue: '5' keyword: - General Materials Science language: - iso: eng month: '02' oa_version: None page: 933-938 publication: The Journal of Physical Chemistry Letters publication_identifier: issn: - 1948-7185 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: 'How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '8440' abstract: - lang: eng text: Mycobacterium tuberculosis can remain dormant in the host, an ability that explains the failure of many current tuberculosis treatments. Recently, the natural products cyclomarin, ecumicin, and lassomycin have been shown to efficiently kill Mycobacterium tuberculosis persisters. Their target is the N-terminal domain of the hexameric AAA+ ATPase ClpC1, which recognizes, unfolds, and translocates protein substrates, such as proteins containing phosphorylated arginine residues, to the ClpP1P2 protease for degradation. Surprisingly, these antibiotics do not inhibit ClpC1 ATPase activity, and how they cause cell death is still unclear. Here, using NMR and small-angle X-ray scattering, we demonstrate that arginine-phosphate binding to the ClpC1 N-terminal domain induces millisecond dynamics. We show that these dynamics are caused by conformational changes and do not result from unfolding or oligomerization of this domain. Cyclomarin binding to this domain specifically blocked these N-terminal dynamics. On the basis of these results, we propose a mechanism of action involving cyclomarin-induced restriction of ClpC1 dynamics, which modulates the chaperone enzymatic activity leading eventually to cell death. article_processing_charge: No article_type: original author: - first_name: Katharina full_name: Weinhäupl, Katharina last_name: Weinhäupl - first_name: Martha full_name: Brennich, Martha last_name: Brennich - first_name: Uli full_name: Kazmaier, Uli last_name: Kazmaier - first_name: Joel full_name: Lelievre, Joel last_name: Lelievre - first_name: Lluis full_name: Ballell, Lluis last_name: Ballell - first_name: Alfred full_name: Goldberg, Alfred last_name: Goldberg - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Hugo full_name: Fraga, Hugo last_name: Fraga citation: ama: Weinhäupl K, Brennich M, Kazmaier U, et al. The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. 2018;293(22):8379-8393. doi:10.1074/jbc.ra118.002251 apa: Weinhäupl, K., Brennich, M., Kazmaier, U., Lelievre, J., Ballell, L., Goldberg, A., … Fraga, H. (2018). The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. American Society for Biochemistry & Molecular Biology. https://doi.org/10.1074/jbc.ra118.002251 chicago: Weinhäupl, Katharina, Martha Brennich, Uli Kazmaier, Joel Lelievre, Lluis Ballell, Alfred Goldberg, Paul Schanda, and Hugo Fraga. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.” Journal of Biological Chemistry. American Society for Biochemistry & Molecular Biology, 2018. https://doi.org/10.1074/jbc.ra118.002251. ieee: K. Weinhäupl et al., “The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis,” Journal of Biological Chemistry, vol. 293, no. 22. American Society for Biochemistry & Molecular Biology, pp. 8379–8393, 2018. ista: Weinhäupl K, Brennich M, Kazmaier U, Lelievre J, Ballell L, Goldberg A, Schanda P, Fraga H. 2018. The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. 293(22), 8379–8393. mla: Weinhäupl, Katharina, et al. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.” Journal of Biological Chemistry, vol. 293, no. 22, American Society for Biochemistry & Molecular Biology, 2018, pp. 8379–93, doi:10.1074/jbc.ra118.002251. short: K. Weinhäupl, M. Brennich, U. Kazmaier, J. Lelievre, L. Ballell, A. Goldberg, P. Schanda, H. Fraga, Journal of Biological Chemistry 293 (2018) 8379–8393. date_created: 2020-09-18T10:05:18Z date_published: 2018-06-01T00:00:00Z date_updated: 2021-01-12T08:19:17Z day: '01' doi: 10.1074/jbc.ra118.002251 extern: '1' intvolume: ' 293' issue: '22' keyword: - Cell Biology - Biochemistry - Molecular Biology language: - iso: eng month: '06' oa_version: None page: 8379-8393 publication: Journal of Biological Chemistry publication_identifier: issn: - 0021-9258 - 1083-351X publication_status: published publisher: American Society for Biochemistry & Molecular Biology quality_controlled: '1' status: public title: The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 293 year: '2018' ... --- _id: '8442' abstract: - lang: eng text: Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents. article_processing_charge: No article_type: original author: - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: François full_name: Dehez, François last_name: Dehez - first_name: Jason R. full_name: Schnell, Jason R. last_name: Schnell - first_name: Nicole full_name: Zitzmann, Nicole last_name: Zitzmann - first_name: Eva full_name: Pebay-Peyroula, Eva last_name: Pebay-Peyroula - first_name: Laurent J. full_name: Catoire, Laurent J. last_name: Catoire - first_name: Bruno full_name: Miroux, Bruno last_name: Miroux - first_name: Edmund R. S. full_name: Kunji, Edmund R. S. last_name: Kunji - first_name: Gianluigi full_name: Veglia, Gianluigi last_name: Veglia - first_name: Timothy A. full_name: Cross, Timothy A. last_name: Cross - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Chipot C, Dehez F, Schnell JR, et al. Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. 2018;118(7):3559-3607. doi:10.1021/acs.chemrev.7b00570' apa: 'Chipot, C., Dehez, F., Schnell, J. R., Zitzmann, N., Pebay-Peyroula, E., Catoire, L. J., … Schanda, P. (2018). Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.7b00570' chicago: 'Chipot, Christophe, François Dehez, Jason R. Schnell, Nicole Zitzmann, Eva Pebay-Peyroula, Laurent J. Catoire, Bruno Miroux, et al. “Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.” Chemical Reviews. American Chemical Society, 2018. https://doi.org/10.1021/acs.chemrev.7b00570.' ieee: 'C. Chipot et al., “Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies,” Chemical Reviews, vol. 118, no. 7. American Chemical Society, pp. 3559–3607, 2018.' ista: 'Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. 2018. Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. 118(7), 3559–3607.' mla: 'Chipot, Christophe, et al. “Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.” Chemical Reviews, vol. 118, no. 7, American Chemical Society, 2018, pp. 3559–607, doi:10.1021/acs.chemrev.7b00570.' short: C. Chipot, F. Dehez, J.R. Schnell, N. Zitzmann, E. Pebay-Peyroula, L.J. Catoire, B. Miroux, E.R.S. Kunji, G. Veglia, T.A. Cross, P. Schanda, Chemical Reviews 118 (2018) 3559–3607. date_created: 2020-09-18T10:05:35Z date_published: 2018-02-28T00:00:00Z date_updated: 2021-01-12T08:19:18Z day: '28' doi: 10.1021/acs.chemrev.7b00570 extern: '1' intvolume: ' 118' issue: '7' keyword: - General Chemistry language: - iso: eng month: '02' oa_version: None page: 3559-3607 publication: Chemical Reviews publication_identifier: issn: - 0009-2665 - 1520-6890 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: 'Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2018' ... --- _id: '8441' abstract: - lang: eng text: Solid-state near-rotary-resonance measurements of the spin–lattice relaxation rate in the rotating frame (R1ρ) is a powerful NMR technique for studying molecular dynamics in the microsecond time scale. The small difference between the spin-lock (SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions, at the same time it brings up some methodological challenges. In this work, several issues affecting correct measurements and analysis of 15N R1ρ data are considered in detail. Among them are signal amplitude as a function of the difference between SL and MAS frequencies, “dead time” in the initial part of the relaxation decay caused by transient spin-dynamic oscillations, measurements under HORROR condition and proper treatment of the multi-exponential relaxation decays. The multiple 15N R1ρ measurements at different SL fields and temperatures have been conducted in 1D mode (i.e. without site-specific resolution) for a set of four different microcrystalline protein samples (GB1, SH3, MPD-ubiquitin and cubic-PEG-ubiquitin) to study the overall protein rocking in a crystal. While the amplitude of this motion varies very significantly, its correlation time for all four sample is practically the same, 30–50 μs. The amplitude of the rocking motion correlates with the packing density of a protein crystal. It has been suggested that the rocking motion is not diffusive but likely a jump-like dynamic process. article_processing_charge: No article_type: original author: - first_name: Alexey full_name: Krushelnitsky, Alexey last_name: Krushelnitsky - first_name: Diego full_name: Gauto, Diego last_name: Gauto - first_name: Diana C. full_name: Rodriguez Camargo, Diana C. last_name: Rodriguez Camargo - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Kay full_name: Saalwächter, Kay last_name: Saalwächter citation: ama: 'Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. 2018;71(1):53-67. doi:10.1007/s10858-018-0191-4' apa: 'Krushelnitsky, A., Gauto, D., Rodriguez Camargo, D. C., Schanda, P., & Saalwächter, K. (2018). Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-018-0191-4' chicago: 'Krushelnitsky, Alexey, Diego Gauto, Diana C. Rodriguez Camargo, Paul Schanda, and Kay Saalwächter. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.” Journal of Biomolecular NMR. Springer Nature, 2018. https://doi.org/10.1007/s10858-018-0191-4.' ieee: 'A. Krushelnitsky, D. Gauto, D. C. Rodriguez Camargo, P. Schanda, and K. Saalwächter, “Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals,” Journal of Biomolecular NMR, vol. 71, no. 1. Springer Nature, pp. 53–67, 2018.' ista: 'Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K. 2018. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. 71(1), 53–67.' mla: 'Krushelnitsky, Alexey, et al. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.” Journal of Biomolecular NMR, vol. 71, no. 1, Springer Nature, 2018, pp. 53–67, doi:10.1007/s10858-018-0191-4.' short: A. Krushelnitsky, D. Gauto, D.C. Rodriguez Camargo, P. Schanda, K. Saalwächter, Journal of Biomolecular NMR 71 (2018) 53–67. date_created: 2020-09-18T10:05:28Z date_published: 2018-05-30T00:00:00Z date_updated: 2021-01-12T08:19:17Z day: '30' doi: 10.1007/s10858-018-0191-4 extern: '1' intvolume: ' 71' issue: '1' language: - iso: eng month: '05' oa_version: Published Version page: 53-67 publication: Journal of Biomolecular NMR publication_identifier: issn: - 0925-2738 - 1573-5001 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 71 year: '2018' ... --- _id: '8439' abstract: - lang: eng text: Lipopolysaccharides (LPS) are complex glycolipids forming the outside layer of Gram-negative bacteria. Their hydrophobic and heterogeneous nature greatly hampers their structural study in an environment similar to the bacterial surface. We have studied LPS purified from E. coli and pathogenic P. aeruginosa with long O-antigen polysaccharides assembled in solution as vesicles or elongated micelles. Solid-state NMR with magic-angle spinning permitted the identification of NMR signals arising from regions with different flexibilities in the LPS, from the lipid components to the O-antigen polysaccharides. Atomic scale data on the LPS enabled the study of the interaction of gentamicin antibiotic bound to P. aeruginosa LPS, for which we could confirm that a specific oligosaccharide is involved in the antibiotic binding. The possibility to study LPS alone and bound to a ligand when it is assembled in membrane-like structures opens great prospects for the investigation of proteins and antibiotics that specifically target such an important molecule at the surface of Gram-negative bacteria. article_processing_charge: No article_type: original author: - first_name: Cedric full_name: Laguri, Cedric last_name: Laguri - first_name: Alba full_name: Silipo, Alba last_name: Silipo - first_name: Alessandra M. full_name: Martorana, Alessandra M. last_name: Martorana - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Roberta full_name: Marchetti, Roberta last_name: Marchetti - first_name: Alessandra full_name: Polissi, Alessandra last_name: Polissi - first_name: Antonio full_name: Molinaro, Antonio last_name: Molinaro - first_name: Jean-Pierre full_name: Simorre, Jean-Pierre last_name: Simorre citation: ama: Laguri C, Silipo A, Martorana AM, et al. Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. 2018;13(8):2106-2113. doi:10.1021/acschembio.8b00271 apa: Laguri, C., Silipo, A., Martorana, A. M., Schanda, P., Marchetti, R., Polissi, A., … Simorre, J.-P. (2018). Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. American Chemical Society. https://doi.org/10.1021/acschembio.8b00271 chicago: Laguri, Cedric, Alba Silipo, Alessandra M. Martorana, Paul Schanda, Roberta Marchetti, Alessandra Polissi, Antonio Molinaro, and Jean-Pierre Simorre. “Solid State NMR Studies of Intact Lipopolysaccharide Endotoxin.” ACS Chemical Biology. American Chemical Society, 2018. https://doi.org/10.1021/acschembio.8b00271. ieee: C. Laguri et al., “Solid state NMR studies of intact lipopolysaccharide endotoxin,” ACS Chemical Biology, vol. 13, no. 8. American Chemical Society, pp. 2106–2113, 2018. ista: Laguri C, Silipo A, Martorana AM, Schanda P, Marchetti R, Polissi A, Molinaro A, Simorre J-P. 2018. Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. 13(8), 2106–2113. mla: Laguri, Cedric, et al. “Solid State NMR Studies of Intact Lipopolysaccharide Endotoxin.” ACS Chemical Biology, vol. 13, no. 8, American Chemical Society, 2018, pp. 2106–13, doi:10.1021/acschembio.8b00271. short: C. Laguri, A. Silipo, A.M. Martorana, P. Schanda, R. Marchetti, A. Polissi, A. Molinaro, J.-P. Simorre, ACS Chemical Biology 13 (2018) 2106–2113. date_created: 2020-09-18T10:05:09Z date_published: 2018-07-02T00:00:00Z date_updated: 2021-01-12T08:19:16Z day: '02' doi: 10.1021/acschembio.8b00271 extern: '1' intvolume: ' 13' issue: '8' keyword: - Molecular Medicine - Biochemistry - General Medicine language: - iso: eng month: '07' oa_version: None page: 2106-2113 publication: ACS Chemical Biology publication_identifier: issn: - 1554-8929 - 1554-8937 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Solid state NMR studies of intact lipopolysaccharide endotoxin type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2018' ... --- _id: '8547' abstract: - lang: eng text: The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex. acknowledgement: We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme. article_processing_charge: No author: - first_name: Alfredo full_name: Llorca, Alfredo last_name: Llorca - first_name: Gabriele full_name: Ciceri, Gabriele last_name: Ciceri - first_name: Robert J full_name: Beattie, Robert J id: 2E26DF60-F248-11E8-B48F-1D18A9856A87 last_name: Beattie orcid: 0000-0002-8483-8753 - first_name: Fong K. full_name: Wong, Fong K. last_name: Wong - first_name: Giovanni full_name: Diana, Giovanni last_name: Diana - first_name: Eleni full_name: Serafeimidou, Eleni last_name: Serafeimidou - first_name: Marian full_name: Fernández-Otero, Marian last_name: Fernández-Otero - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Sebastian J. full_name: Arnold, Sebastian J. last_name: Arnold - first_name: Martin full_name: Meyer, Martin last_name: Meyer - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Miguel full_name: Maravall, Miguel last_name: Maravall - first_name: Oscar full_name: Marín, Oscar last_name: Marín citation: ama: Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088 apa: Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088 chicago: Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088. ieee: A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory. ista: Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, 10.1101/494088. mla: Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088. short: A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.). date_created: 2020-09-21T12:01:50Z date_published: 2018-12-13T00:00:00Z date_updated: 2021-01-12T08:20:00Z day: '13' department: - _id: SiHi doi: 10.1101/494088 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/494088 month: '12' oa: 1 oa_version: Preprint project: - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development - _id: 264E56E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02416 name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex publication: bioRxiv publication_status: submitted publisher: Cold Spring Harbor Laboratory status: public title: Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '86' abstract: - lang: eng text: Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms. acknowledgement: 'This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.' alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: 'Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9' apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9. ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161. ista: 'Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.' mla: Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9. short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161. date_created: 2018-12-11T11:44:33Z date_published: 2018-07-20T00:00:00Z date_updated: 2021-01-12T08:20:14Z day: '20' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-319-95246-8_9 ec_funded: 1 editor: - first_name: Marten full_name: Lohstroh, Marten last_name: Lohstroh - first_name: Patricia full_name: Derler, Patricia last_name: Derler - first_name: Marjan full_name: Sirjani, Marjan last_name: Sirjani file: - access_level: open_access checksum: 9995c6ce6957333baf616fc4f20be597 content_type: application/pdf creator: dernst date_created: 2019-11-19T08:22:18Z date_updated: 2020-07-14T12:48:14Z file_id: '7053' file_name: 2018_PrinciplesModeling_Chatterjee.pdf file_size: 516307 relation: main_file file_date_updated: 2020-07-14T12:48:14Z has_accepted_license: '1' intvolume: ' 10760' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 143 - 161 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: Principles of Modeling publication_status: published publisher: Springer publist_id: '7968' quality_controlled: '1' scopus_import: 1 status: public title: Computing average response time type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10760 year: '2018' ... --- _id: '9062' abstract: - lang: eng text: 'Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization1. At equilibrium, the structure is encoded through specific interactions2,3,4,5,6,7,8, at an unfavourable entropic cost for the system. An alternative approach, widely used by nature, uses energy input to bypass the entropy bottleneck and develop features otherwise impossible at equilibrium9. Dissipative building blocks that inject energy locally were made available by recent advances in colloidal science10,11 but have not been used to control self-assembly. Here we show the targeted formation of self-powered microgears from active particles and their autonomous synchronization into dynamical superstructures. We use a photoactive component that consumes fuel, haematite, to devise phototactic microswimmers that form self-spinning microgears following spatiotemporal light patterns. The gears are coupled via their chemical clouds by diffusiophoresis12 and constitute the elementary bricks of synchronized superstructures, which autonomously regulate their dynamics. The results are quantitatively rationalized on the basis of a stochastic description of diffusio-phoretic oscillators dynamically coupled by chemical gradients. Our findings harness non-equilibrium phoretic phenomena to program interactions and direct self-assembly with fidelity and specificity. It lays the groundwork for the autonomous construction of dynamical architectures and functional micro-machinery.' article_processing_charge: No article_type: original author: - first_name: Antoine full_name: Aubret, Antoine last_name: Aubret - first_name: Mena full_name: Youssef, Mena last_name: Youssef - first_name: Stefano full_name: Sacanna, Stefano last_name: Sacanna - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: Aubret A, Youssef M, Sacanna S, Palacci JA. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 2018;14(11):1114-1118. doi:10.1038/s41567-018-0227-4 apa: Aubret, A., Youssef, M., Sacanna, S., & Palacci, J. A. (2018). Targeted assembly and synchronization of self-spinning microgears. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-018-0227-4 chicago: Aubret, Antoine, Mena Youssef, Stefano Sacanna, and Jérémie A Palacci. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0227-4. ieee: A. Aubret, M. Youssef, S. Sacanna, and J. A. Palacci, “Targeted assembly and synchronization of self-spinning microgears,” Nature Physics, vol. 14, no. 11. Springer Nature, pp. 1114–1118, 2018. ista: Aubret A, Youssef M, Sacanna S, Palacci JA. 2018. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 14(11), 1114–1118. mla: Aubret, Antoine, et al. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature Physics, vol. 14, no. 11, Springer Nature, 2018, pp. 1114–18, doi:10.1038/s41567-018-0227-4. short: A. Aubret, M. Youssef, S. Sacanna, J.A. Palacci, Nature Physics 14 (2018) 1114–1118. date_created: 2021-02-02T13:52:49Z date_published: 2018-11-01T00:00:00Z date_updated: 2023-02-23T13:48:02Z day: '01' doi: 10.1038/s41567-018-0227-4 extern: '1' external_id: arxiv: - '1810.01033' intvolume: ' 14' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1810.01033 month: '11' oa: 1 oa_version: Preprint page: 1114-1118 publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Targeted assembly and synchronization of self-spinning microgears type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 14 year: '2018' ... --- _id: '9229' alternative_title: - Molecular and cellular neuroscience article_processing_charge: No article_type: letter_note author: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001 apa: Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001 chicago: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001. ieee: J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018. ista: Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11. mla: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001. short: J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11. date_created: 2021-03-07T23:01:25Z date_published: 2018-06-30T00:00:00Z date_updated: 2021-12-03T07:31:05Z day: '30' department: - _id: JoDa doi: 10.20388/omp2018.00s1.001 intvolume: ' 4' issue: S1 language: - iso: eng main_file_link: - open_access: '1' url: http://operamedphys.org/content/molecular-and-cellular-neuroscience month: '06' oa: 1 oa_version: Published Version page: '11' publication: Opera Medica et Physiologica publication_identifier: eissn: - 2500-2295 issn: - 2500-2287 publication_status: published publisher: Lobachevsky State University of Nizhny Novgorod quality_controlled: '1' scopus_import: '1' status: public title: Diffraction-unlimited optical imaging for synaptic physiology type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 4 year: '2018' ... --- _id: '6005' abstract: - lang: eng text: Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting. alternative_title: - LIPIcs article_number: '23' article_processing_charge: No author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Shibashis full_name: Guha, Shibashis last_name: Guha - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman citation: ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23' apa: 'Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23' chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23. ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.' ista: 'Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.' mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23. short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-08-31 location: Liverpool, United Kingdom name: 'MFCS: Mathematical Foundations of Computer Science' start_date: 2018-08-27 date_created: 2019-02-14T14:12:09Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-02-23T14:02:58Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.4230/LIPICS.MFCS.2018.23 file: - access_level: open_access checksum: 41ab2ae9b63f5eb49fa995250c0ba128 content_type: application/pdf creator: dernst date_created: 2019-02-14T14:22:04Z date_updated: 2020-07-14T12:47:15Z file_id: '6007' file_name: 2018_LIPIcs_Avni.pdf file_size: 542889 relation: main_file file_date_updated: 2020-07-14T12:47:15Z has_accepted_license: '1' intvolume: ' 117' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 264B3912-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02369 name: Formal Methods meets Algorithmic Game Theory publication_identifier: issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '963' relation: earlier_version status: public scopus_import: '1' status: public title: Timed network games with clocks 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 volume: 117 year: '2018' ... --- _id: '9668' abstract: - lang: eng text: Estimating the homogeneous ice nucleation rate from undercooled liquid water is crucial for understanding many important physical phenomena and technological applications, and challenging for both experiments and theory. From a theoretical point of view, difficulties arise due to the long time scales required, as well as the numerous nucleation pathways involved to form ice nuclei with different stacking disorders. We computed the homogeneous ice nucleation rate at a physically relevant undercooling for a single-site water model, taking into account the diffuse nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition rate of particles to the critical nucleus. We disentangled and investigated the relative importance of all the terms, including interfacial free energy, entropic contributions and the kinetic prefactor, that contribute to the overall nucleation rate. Breaking down the problem into pieces not only provides physical insights into ice nucleation, but also sheds light on the long-standing discrepancy between different theoretical predictions, as well as between theoretical and experimental determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings and suggest strategies to systematically improve the existing simulation methods. 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: Christoph full_name: Dellago, Christoph last_name: Dellago - first_name: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: ama: 'Cheng B, Dellago C, Ceriotti M. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 2018;20(45):28732-28740. doi:10.1039/c8cp04561e' apa: 'Cheng, B., Dellago, C., & Ceriotti, M. (2018). Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. Royal Society of Chemistry. https://doi.org/10.1039/c8cp04561e' chicago: 'Cheng, Bingqing, Christoph Dellago, and Michele Ceriotti. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical Physics. Royal Society of Chemistry, 2018. https://doi.org/10.1039/c8cp04561e.' ieee: 'B. Cheng, C. Dellago, and M. Ceriotti, “Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics,” Physical Chemistry Chemical Physics, vol. 20, no. 45. Royal Society of Chemistry, pp. 28732–28740, 2018.' ista: 'Cheng B, Dellago C, Ceriotti M. 2018. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 20(45), 28732–28740.' mla: 'Cheng, Bingqing, et al. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical Physics, vol. 20, no. 45, Royal Society of Chemistry, 2018, pp. 28732–40, doi:10.1039/c8cp04561e.' short: B. Cheng, C. Dellago, M. Ceriotti, Physical Chemistry Chemical Physics 20 (2018) 28732–28740. date_created: 2021-07-15T12:51:44Z date_published: 2018-12-07T00:00:00Z date_updated: 2021-08-09T12:36:47Z day: '07' doi: 10.1039/c8cp04561e extern: '1' external_id: arxiv: - '1807.05551' pmid: - '30412211' intvolume: ' 20' issue: '45' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.05551 month: '12' oa: 1 oa_version: Preprint page: 28732-28740 pmid: 1 publication: Physical Chemistry Chemical Physics publication_identifier: eissn: - 1463-9084 issn: - 1463-9076 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: 'Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics' type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 20 year: '2018' ... --- _id: '9687' abstract: - lang: eng text: The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures. article_number: '054102' 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: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: ama: 'Cheng B, Ceriotti M. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 2018;97(5). doi:10.1103/physrevb.97.054102' apa: 'Cheng, B., & Ceriotti, M. (2018). Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.97.054102' chicago: 'Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.054102.' ieee: 'B. Cheng and M. Ceriotti, “Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids,” Physical Review B, vol. 97, no. 5. American Physical Society, 2018.' ista: 'Cheng B, Ceriotti M. 2018. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 97(5), 054102.' mla: 'Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical Review B, vol. 97, no. 5, 054102, American Physical Society, 2018, doi:10.1103/physrevb.97.054102.' short: B. Cheng, M. Ceriotti, Physical Review B 97 (2018). date_created: 2021-07-19T09:39:48Z date_published: 2018-02-01T00:00:00Z date_updated: 2021-08-09T12:38:26Z day: '01' doi: 10.1103/physrevb.97.054102 extern: '1' external_id: arxiv: - '1710.02815' intvolume: ' 97' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1710.02815 month: '02' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids' type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 97 year: '2018' ... --- _id: '315' abstract: - lang: eng text: 'More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.' article_number: e2005372 author: - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 citation: ama: Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372 apa: Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372 chicago: Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372. ieee: J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018. ista: Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372. mla: Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372. short: J. Polechova, PLoS Biology 16 (2018). date_created: 2018-12-11T11:45:46Z date_published: 2018-06-15T00:00:00Z date_updated: 2023-02-23T14:10:16Z day: '15' ddc: - '576' department: - _id: NiBa doi: 10.1371/journal.pbio.2005372 file: - access_level: open_access checksum: 908c52751bba30c55ed36789e5e4c84d content_type: application/pdf creator: dernst date_created: 2019-01-22T08:30:03Z date_updated: 2020-07-14T12:46:01Z file_id: '5870' file_name: 2017_PLOS_Polechova.pdf file_size: 6968201 relation: main_file file_date_updated: 2020-07-14T12:46:01Z has_accepted_license: '1' intvolume: ' 16' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS Biology publication_identifier: issn: - '15449173' publication_status: published publisher: Public Library of Science publist_id: '7550' quality_controlled: '1' related_material: record: - id: '9839' relation: research_data status: public scopus_import: 1 status: public title: Is the sky the limit? On the expansion threshold of a species’ range 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: 16 year: '2018' ... --- _id: '8417' abstract: - lang: eng text: The restricted planar elliptic three body problem (RPETBP) describes the motion of a massless particle (a comet or an asteroid) under the gravitational field of two massive bodies (the primaries, say the Sun and Jupiter) revolving around their center of mass on elliptic orbits with some positive eccentricity. The aim of this paper is to show the existence of orbits whose angular momentum performs arbitrary excursions in a large region. In particular, there exist diffusive orbits, that is, with a large variation of angular momentum. The leading idea of the proof consists in analyzing parabolic motions of the comet. By a well-known result of McGehee, the union of future (resp. past) parabolic orbits is an analytic manifold P+ (resp. P−). In a properly chosen coordinate system these manifolds are stable (resp. unstable) manifolds of a manifold at infinity P∞, which we call the manifold at parabolic infinity. On P∞ it is possible to define two scattering maps, which contain the map structure of the homoclinic trajectories to it, i.e. orbits parabolic both in the future and the past. Since the inner dynamics inside P∞ is trivial, two different scattering maps are used. The combination of these two scattering maps permits the design of the desired diffusive pseudo-orbits. Using shadowing techniques and these pseudo orbits we show the existence of true trajectories of the RPETBP whose angular momentum varies in any predetermined fashion. article_processing_charge: No article_type: original author: - first_name: Amadeu full_name: Delshams, Amadeu last_name: Delshams - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Abraham full_name: de la Rosa, Abraham last_name: de la Rosa - first_name: Tere M. full_name: Seara, Tere M. last_name: Seara citation: ama: Delshams A, Kaloshin V, de la Rosa A, Seara TM. Global instability in the restricted planar elliptic three body problem. Communications in Mathematical Physics. 2018;366(3):1173-1228. doi:10.1007/s00220-018-3248-z apa: Delshams, A., Kaloshin, V., de la Rosa, A., & Seara, T. M. (2018). Global instability in the restricted planar elliptic three body problem. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-018-3248-z chicago: Delshams, Amadeu, Vadim Kaloshin, Abraham de la Rosa, and Tere M. Seara. “Global Instability in the Restricted Planar Elliptic Three Body Problem.” Communications in Mathematical Physics. Springer Nature, 2018. https://doi.org/10.1007/s00220-018-3248-z. ieee: A. Delshams, V. Kaloshin, A. de la Rosa, and T. M. Seara, “Global instability in the restricted planar elliptic three body problem,” Communications in Mathematical Physics, vol. 366, no. 3. Springer Nature, pp. 1173–1228, 2018. ista: Delshams A, Kaloshin V, de la Rosa A, Seara TM. 2018. Global instability in the restricted planar elliptic three body problem. Communications in Mathematical Physics. 366(3), 1173–1228. mla: Delshams, Amadeu, et al. “Global Instability in the Restricted Planar Elliptic Three Body Problem.” Communications in Mathematical Physics, vol. 366, no. 3, Springer Nature, 2018, pp. 1173–228, doi:10.1007/s00220-018-3248-z. short: A. Delshams, V. Kaloshin, A. de la Rosa, T.M. Seara, Communications in Mathematical Physics 366 (2018) 1173–1228. date_created: 2020-09-17T10:41:43Z date_published: 2018-09-05T00:00:00Z date_updated: 2021-01-12T08:19:08Z day: '05' doi: 10.1007/s00220-018-3248-z extern: '1' intvolume: ' 366' issue: '3' keyword: - Mathematical Physics - Statistical and Nonlinear Physics language: - iso: eng month: '09' oa_version: None page: 1173-1228 publication: Communications in Mathematical Physics publication_identifier: issn: - 0010-3616 - 1432-0916 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Global instability in the restricted planar elliptic three body problem type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 366 year: '2018' ... --- _id: '8422' abstract: - lang: eng text: 'The Birkhoff conjecture says that the boundary of a strictly convex integrable billiard table is necessarily an ellipse. In this article, we consider a stronger notion of integrability, namely integrability close to the boundary, and prove a local version of this conjecture: a small perturbation of an ellipse of small eccentricity which preserves integrability near the boundary, is itself an ellipse. This extends the result in Avila et al. (Ann Math 184:527–558, ADK16), where integrability was assumed on a larger set. In particular, it shows that (local) integrability near the boundary implies global integrability. One of the crucial ideas in the proof consists in analyzing Taylor expansion of the corresponding action-angle coordinates with respect to the eccentricity parameter, deriving and studying higher order conditions for the preservation of integrable rational caustics.' article_processing_charge: No article_type: original author: - first_name: Guan full_name: Huang, Guan last_name: Huang - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Alfonso full_name: Sorrentino, Alfonso last_name: Sorrentino citation: ama: Huang G, Kaloshin V, Sorrentino A. Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. 2018;28(2):334-392. doi:10.1007/s00039-018-0440-4 apa: Huang, G., Kaloshin, V., & Sorrentino, A. (2018). Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. Springer Nature. https://doi.org/10.1007/s00039-018-0440-4 chicago: Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “Nearly Circular Domains Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00039-018-0440-4. ieee: G. Huang, V. Kaloshin, and A. Sorrentino, “Nearly circular domains which are integrable close to the boundary are ellipses,” Geometric and Functional Analysis, vol. 28, no. 2. Springer Nature, pp. 334–392, 2018. ista: Huang G, Kaloshin V, Sorrentino A. 2018. Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. 28(2), 334–392. mla: Huang, Guan, et al. “Nearly Circular Domains Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional Analysis, vol. 28, no. 2, Springer Nature, 2018, pp. 334–92, doi:10.1007/s00039-018-0440-4. short: G. Huang, V. Kaloshin, A. Sorrentino, Geometric and Functional Analysis 28 (2018) 334–392. date_created: 2020-09-17T10:42:30Z date_published: 2018-03-18T00:00:00Z date_updated: 2021-01-12T08:19:11Z day: '18' doi: 10.1007/s00039-018-0440-4 extern: '1' external_id: arxiv: - '1705.10601' intvolume: ' 28' issue: '2' keyword: - Geometry and Topology - Analysis language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.10601 month: '03' oa: 1 oa_version: Preprint page: 334-392 publication: Geometric and Functional Analysis publication_identifier: issn: - 1016-443X - 1420-8970 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Nearly circular domains which are integrable close to the boundary are ellipses type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2018' ... --- _id: '8421' abstract: - lang: eng text: 'The classical Birkhoff conjecture claims that the boundary of a strictly convex integrable billiard table is necessarily an ellipse (or a circle as a special case). In this article we prove a complete local version of this conjecture: a small integrable perturbation of an ellipse must be an ellipse. This extends and completes the result in Avila-De Simoi-Kaloshin, where nearly circular domains were considered. One of the crucial ideas in the proof is to extend action-angle coordinates for elliptic billiards into complex domains (with respect to the angle), and to thoroughly analyze the nature of their complex singularities. As an application, we are able to prove some spectral rigidity results for elliptic domains.' 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: Alfonso full_name: Sorrentino, Alfonso last_name: Sorrentino citation: ama: Kaloshin V, Sorrentino A. On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. 2018;188(1):315-380. doi:10.4007/annals.2018.188.1.6 apa: Kaloshin, V., & Sorrentino, A. (2018). On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. Annals of Mathematics, Princeton U. https://doi.org/10.4007/annals.2018.188.1.6 chicago: Kaloshin, Vadim, and Alfonso Sorrentino. “On the Local Birkhoff Conjecture for Convex Billiards.” Annals of Mathematics. Annals of Mathematics, Princeton U, 2018. https://doi.org/10.4007/annals.2018.188.1.6. ieee: V. Kaloshin and A. Sorrentino, “On the local Birkhoff conjecture for convex billiards,” Annals of Mathematics, vol. 188, no. 1. Annals of Mathematics, Princeton U, pp. 315–380, 2018. ista: Kaloshin V, Sorrentino A. 2018. On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. 188(1), 315–380. mla: Kaloshin, Vadim, and Alfonso Sorrentino. “On the Local Birkhoff Conjecture for Convex Billiards.” Annals of Mathematics, vol. 188, no. 1, Annals of Mathematics, Princeton U, 2018, pp. 315–80, doi:10.4007/annals.2018.188.1.6. short: V. Kaloshin, A. Sorrentino, Annals of Mathematics 188 (2018) 315–380. date_created: 2020-09-17T10:42:22Z date_published: 2018-07-01T00:00:00Z date_updated: 2021-01-12T08:19:10Z day: '01' doi: 10.4007/annals.2018.188.1.6 extern: '1' external_id: arxiv: - '1612.09194' intvolume: ' 188' issue: '1' keyword: - Statistics - Probability and Uncertainty - Statistics and Probability language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1612.09194 month: '07' oa: 1 oa_version: Preprint page: 315-380 publication: Annals of Mathematics publication_identifier: issn: - 0003-486X publication_status: published publisher: Annals of Mathematics, Princeton U quality_controlled: '1' status: public title: On the local Birkhoff conjecture for convex billiards type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 188 year: '2018' ... --- _id: '8419' abstract: - lang: eng text: "In this survey, we provide a concise introduction to convex billiards and describe some recent results, obtained by the authors and collaborators, on the classification of integrable billiards, namely the so-called Birkhoff conjecture.\r\n\r\nThis article is part of the theme issue ‘Finite dimensional integrable systems: new trends and methods’." article_number: '20170419' 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: Alfonso full_name: Sorrentino, Alfonso last_name: Sorrentino citation: ama: 'Kaloshin V, Sorrentino A. On the integrability of Birkhoff billiards. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2018;376(2131). doi:10.1098/rsta.2017.0419' apa: 'Kaloshin, V., & Sorrentino, A. (2018). On the integrability of Birkhoff billiards. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rsta.2017.0419' chicago: 'Kaloshin, Vadim, and Alfonso Sorrentino. “On the Integrability of Birkhoff Billiards.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2018. https://doi.org/10.1098/rsta.2017.0419.' ieee: 'V. Kaloshin and A. Sorrentino, “On the integrability of Birkhoff billiards,” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 376, no. 2131. The Royal Society, 2018.' ista: 'Kaloshin V, Sorrentino A. 2018. On the integrability of Birkhoff billiards. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 376(2131), 20170419.' mla: 'Kaloshin, Vadim, and Alfonso Sorrentino. “On the Integrability of Birkhoff Billiards.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 376, no. 2131, 20170419, The Royal Society, 2018, doi:10.1098/rsta.2017.0419.' short: 'V. Kaloshin, A. Sorrentino, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 376 (2018).' date_created: 2020-09-17T10:42:01Z date_published: 2018-10-28T00:00:00Z date_updated: 2021-01-12T08:19:09Z day: '28' doi: 10.1098/rsta.2017.0419 extern: '1' intvolume: ' 376' issue: '2131' keyword: - General Engineering - General Physics and Astronomy - General Mathematics language: - iso: eng month: '10' oa_version: None publication: 'Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences' publication_identifier: issn: - 1364-503X - 1471-2962 publication_status: published publisher: The Royal Society quality_controlled: '1' status: public title: On the integrability of Birkhoff billiards type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 376 year: '2018' ... --- _id: '8420' abstract: - lang: eng text: We show that in the space of all convex billiard boundaries, the set of boundaries with rational caustics is dense. More precisely, the set of billiard boundaries with caustics of rotation number 1/q is polynomially sense in the smooth case, and exponentially dense in the analytic case. 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: Ke full_name: Zhang, Ke last_name: Zhang citation: ama: Kaloshin V, Zhang K. Density of convex billiards with rational caustics. Nonlinearity. 2018;31(11):5214-5234. doi:10.1088/1361-6544/aadc12 apa: Kaloshin, V., & Zhang, K. (2018). Density of convex billiards with rational caustics. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/aadc12 chicago: Kaloshin, Vadim, and Ke Zhang. “Density of Convex Billiards with Rational Caustics.” Nonlinearity. IOP Publishing, 2018. https://doi.org/10.1088/1361-6544/aadc12. ieee: V. Kaloshin and K. Zhang, “Density of convex billiards with rational caustics,” Nonlinearity, vol. 31, no. 11. IOP Publishing, pp. 5214–5234, 2018. ista: Kaloshin V, Zhang K. 2018. Density of convex billiards with rational caustics. Nonlinearity. 31(11), 5214–5234. mla: Kaloshin, Vadim, and Ke Zhang. “Density of Convex Billiards with Rational Caustics.” Nonlinearity, vol. 31, no. 11, IOP Publishing, 2018, pp. 5214–34, doi:10.1088/1361-6544/aadc12. short: V. Kaloshin, K. Zhang, Nonlinearity 31 (2018) 5214–5234. date_created: 2020-09-17T10:42:09Z date_published: 2018-10-15T00:00:00Z date_updated: 2021-01-12T08:19:10Z day: '15' doi: 10.1088/1361-6544/aadc12 extern: '1' external_id: arxiv: - '1706.07968' intvolume: ' 31' issue: '11' keyword: - Mathematical Physics - General Physics and Astronomy - Applied Mathematics - Statistical and Nonlinear Physics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.07968 month: '10' oa: 1 oa_version: Preprint page: 5214-5234 publication: Nonlinearity publication_identifier: issn: - 0951-7715 - 1361-6544 publication_status: published publisher: IOP Publishing quality_controlled: '1' status: public title: Density of convex billiards with rational caustics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2018' ... --- _id: '8437' abstract: - lang: eng text: Chaperonins are ubiquitous protein assemblies present in bacteria, eukaryota, and archaea, facilitating the folding of proteins, preventing protein aggregation, and thus participating in maintaining protein homeostasis in the cell. During their functional cycle, they bind unfolded client proteins inside their double ring structure and promote protein folding by closing the ring chamber in an adenosine 5′-triphosphate (ATP)–dependent manner. Although the static structures of fully open and closed forms of chaperonins were solved by x-ray crystallography or electron microscopy, elucidating the mechanisms of such ATP-driven molecular events requires studying the proteins at the structural level under working conditions. We introduce an approach that combines site-specific nuclear magnetic resonance observation of very large proteins, enabled by advanced isotope labeling methods, with an in situ ATP regeneration system. Using this method, we provide functional insight into the 1-MDa large hsp60 chaperonin while processing client proteins and reveal how nucleotide binding, hydrolysis, and release control switching between closed and open states. While the open conformation stabilizes the unfolded state of client proteins, the internalization of the client protein inside the chaperonin cavity speeds up its functional cycle. This approach opens new perspectives to study structures and mechanisms of various ATP-driven biological machineries in the heat of action. article_number: eaau4196 article_processing_charge: No article_type: original author: - first_name: Guillaume full_name: Mas, Guillaume last_name: Mas - first_name: Jia-Ying full_name: Guan, Jia-Ying last_name: Guan - first_name: Elodie full_name: Crublet, Elodie last_name: Crublet - first_name: Elisa Colas full_name: Debled, Elisa Colas last_name: Debled - first_name: Christine full_name: Moriscot, Christine last_name: Moriscot - first_name: Pierre full_name: Gans, Pierre last_name: Gans - first_name: Guy full_name: Schoehn, Guy last_name: Schoehn - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Jerome full_name: Boisbouvier, Jerome last_name: Boisbouvier citation: ama: Mas G, Guan J-Y, Crublet E, et al. Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. Science Advances. 2018;4(9). doi:10.1126/sciadv.aau4196 apa: Mas, G., Guan, J.-Y., Crublet, E., Debled, E. C., Moriscot, C., Gans, P., … Boisbouvier, J. (2018). Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aau4196 chicago: Mas, Guillaume, Jia-Ying Guan, Elodie Crublet, Elisa Colas Debled, Christine Moriscot, Pierre Gans, Guy Schoehn, Pavel Macek, Paul Schanda, and Jerome Boisbouvier. “Structural Investigation of a Chaperonin in Action Reveals How Nucleotide Binding Regulates the Functional Cycle.” Science Advances. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/sciadv.aau4196. ieee: G. Mas et al., “Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle,” Science Advances, vol. 4, no. 9. American Association for the Advancement of Science, 2018. ista: Mas G, Guan J-Y, Crublet E, Debled EC, Moriscot C, Gans P, Schoehn G, Macek P, Schanda P, Boisbouvier J. 2018. Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. Science Advances. 4(9), eaau4196. mla: Mas, Guillaume, et al. “Structural Investigation of a Chaperonin in Action Reveals How Nucleotide Binding Regulates the Functional Cycle.” Science Advances, vol. 4, no. 9, eaau4196, American Association for the Advancement of Science, 2018, doi:10.1126/sciadv.aau4196. short: G. Mas, J.-Y. Guan, E. Crublet, E.C. Debled, C. Moriscot, P. Gans, G. Schoehn, P. Macek, P. Schanda, J. Boisbouvier, Science Advances 4 (2018). date_created: 2020-09-18T10:04:51Z date_published: 2018-09-19T00:00:00Z date_updated: 2022-08-26T09:11:06Z day: '19' doi: 10.1126/sciadv.aau4196 extern: '1' intvolume: ' 4' issue: '9' language: - iso: eng month: '09' oa_version: None publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' status: public title: Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2018' ... --- _id: '8436' abstract: - lang: eng text: The exchange of metabolites between the mitochondrial matrix and the cytosol depends on β-barrel channels in the outer membrane and α-helical carrier proteins in the inner membrane. The essential translocase of the inner membrane (TIM) chaperones escort these proteins through the intermembrane space, but the structural and mechanistic details remain elusive. We have used an integrated structural biology approach to reveal the functional principle of TIM chaperones. Multiple clamp-like binding sites hold the mitochondrial membrane proteins in a translocation-competent elongated form, thus mimicking characteristics of co-translational membrane insertion. The bound preprotein undergoes conformational dynamics within the chaperone binding clefts, pointing to a multitude of dynamic local binding events. Mutations in these binding sites cause cell death or growth defects associated with impairment of carrier and β-barrel protein biogenesis. Our work reveals how a single mitochondrial “transfer-chaperone” system is able to guide α-helical and β-barrel membrane proteins in a “nascent chain-like” conformation through a ribosome-free compartment. article_processing_charge: No article_type: original author: - first_name: Katharina full_name: Weinhäupl, Katharina last_name: Weinhäupl - first_name: Caroline full_name: Lindau, Caroline last_name: Lindau - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: Yong full_name: Wang, Yong last_name: Wang - first_name: Conny full_name: Schütze, Conny last_name: Schütze - first_name: Tobias full_name: Jores, Tobias last_name: Jores - first_name: Laura full_name: Melchionda, Laura last_name: Melchionda - first_name: Birgit full_name: Schönfisch, Birgit last_name: Schönfisch - first_name: Hubert full_name: Kalbacher, Hubert last_name: Kalbacher - first_name: Beate full_name: Bersch, Beate last_name: Bersch - first_name: Doron full_name: Rapaport, Doron last_name: Rapaport - first_name: Martha full_name: Brennich, Martha last_name: Brennich - first_name: Kresten full_name: Lindorff-Larsen, Kresten last_name: Lindorff-Larsen - first_name: Nils full_name: Wiedemann, Nils last_name: Wiedemann - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Weinhäupl K, Lindau C, Hessel A, et al. Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell. 2018;175(5):1365-1379.e25. doi:10.1016/j.cell.2018.10.039 apa: Weinhäupl, K., Lindau, C., Hessel, A., Wang, Y., Schütze, C., Jores, T., … Schanda, P. (2018). Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell. Elsevier. https://doi.org/10.1016/j.cell.2018.10.039 chicago: Weinhäupl, Katharina, Caroline Lindau, Audrey Hessel, Yong Wang, Conny Schütze, Tobias Jores, Laura Melchionda, et al. “Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.” Cell. Elsevier, 2018. https://doi.org/10.1016/j.cell.2018.10.039. ieee: K. Weinhäupl et al., “Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space,” Cell, vol. 175, no. 5. Elsevier, p. 1365–1379.e25, 2018. ista: Weinhäupl K, Lindau C, Hessel A, Wang Y, Schütze C, Jores T, Melchionda L, Schönfisch B, Kalbacher H, Bersch B, Rapaport D, Brennich M, Lindorff-Larsen K, Wiedemann N, Schanda P. 2018. Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell. 175(5), 1365–1379.e25. mla: Weinhäupl, Katharina, et al. “Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.” Cell, vol. 175, no. 5, Elsevier, 2018, p. 1365–1379.e25, doi:10.1016/j.cell.2018.10.039. short: K. Weinhäupl, C. Lindau, A. Hessel, Y. Wang, C. Schütze, T. Jores, L. Melchionda, B. Schönfisch, H. Kalbacher, B. Bersch, D. Rapaport, M. Brennich, K. Lindorff-Larsen, N. Wiedemann, P. Schanda, Cell 175 (2018) 1365–1379.e25. date_created: 2020-09-18T10:04:39Z date_published: 2018-11-15T00:00:00Z date_updated: 2021-01-12T08:19:15Z day: '15' doi: 10.1016/j.cell.2018.10.039 extern: '1' intvolume: ' 175' issue: '5' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '11' oa_version: None page: 1365-1379.e25 publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 175 year: '2018' ... --- _id: '8426' abstract: - lang: eng text: For any strictly convex planar domain Ω ⊂ R2 with a C∞ boundary one can associate an infinite sequence of spectral invariants introduced by Marvizi–Merlose [5]. These invariants can generically be determined using the spectrum of the Dirichlet problem of the Laplace operator. A natural question asks if this collection is sufficient to determine Ω up to isometry. In this paper we give a counterexample, namely, we present two nonisometric domains Ω and Ω¯ with the same collection of Marvizi–Melrose invariants. Moreover, each domain has countably many periodic orbits {Sn}n≥1 (resp. {S¯n}n⩾1) of period going to infinity such that Sn and S¯n have the same period and perimeter for each n. article_processing_charge: No article_type: original author: - first_name: Lev full_name: Buhovsky, Lev last_name: Buhovsky - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Buhovsky L, Kaloshin V. Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. 2018;23:54-59. doi:10.1134/s1560354718010057 apa: Buhovsky, L., & Kaloshin, V. (2018). Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. Springer Nature. https://doi.org/10.1134/s1560354718010057 chicago: Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” Regular and Chaotic Dynamics. Springer Nature, 2018. https://doi.org/10.1134/s1560354718010057. ieee: L. Buhovsky and V. Kaloshin, “Nonisometric domains with the same Marvizi-Melrose invariants,” Regular and Chaotic Dynamics, vol. 23. Springer Nature, pp. 54–59, 2018. ista: Buhovsky L, Kaloshin V. 2018. Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. 23, 54–59. mla: Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” Regular and Chaotic Dynamics, vol. 23, Springer Nature, 2018, pp. 54–59, doi:10.1134/s1560354718010057. short: L. Buhovsky, V. Kaloshin, Regular and Chaotic Dynamics 23 (2018) 54–59. date_created: 2020-09-17T10:43:21Z date_published: 2018-02-05T00:00:00Z date_updated: 2021-01-12T08:19:11Z day: '05' doi: 10.1134/s1560354718010057 extern: '1' external_id: arxiv: - '1801.00952' intvolume: ' 23' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1801.00952 month: '02' oa: 1 oa_version: Preprint page: 54-59 publication: Regular and Chaotic Dynamics publication_identifier: issn: - 1560-3547 - 1468-4845 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Nonisometric domains with the same Marvizi-Melrose invariants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2018' ... --- _id: '8438' article_processing_charge: No article_type: letter_note author: - first_name: Vilius full_name: Kurauskas, Vilius last_name: Kurauskas - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: François full_name: Dehez, François last_name: Dehez - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: Beate full_name: Bersch, Beate last_name: Bersch - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. 2018;25(9):745-747. doi:10.1038/s41594-018-0127-4 apa: Kurauskas, V., Hessel, A., Dehez, F., Chipot, C., Bersch, B., & Schanda, P. (2018). Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-018-0127-4 chicago: Kurauskas, Vilius, Audrey Hessel, François Dehez, Christophe Chipot, Beate Bersch, and Paul Schanda. “Dynamics and Interactions of AAC3 in DPC Are Not Functionally Relevant.” Nature Structural & Molecular Biology. Springer Nature, 2018. https://doi.org/10.1038/s41594-018-0127-4. ieee: V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, and P. Schanda, “Dynamics and interactions of AAC3 in DPC are not functionally relevant,” Nature Structural & Molecular Biology, vol. 25, no. 9. Springer Nature, pp. 745–747, 2018. ista: Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. 2018. Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. 25(9), 745–747. mla: Kurauskas, Vilius, et al. “Dynamics and Interactions of AAC3 in DPC Are Not Functionally Relevant.” Nature Structural & Molecular Biology, vol. 25, no. 9, Springer Nature, 2018, pp. 745–47, doi:10.1038/s41594-018-0127-4. short: V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, P. Schanda, Nature Structural & Molecular Biology 25 (2018) 745–747. date_created: 2020-09-18T10:04:59Z date_published: 2018-09-03T00:00:00Z date_updated: 2021-01-12T08:19:16Z day: '03' doi: 10.1038/s41594-018-0127-4 extern: '1' intvolume: ' 25' issue: '9' keyword: - Molecular Biology - Structural Biology language: - iso: eng month: '09' oa_version: None page: 745-747 publication: Nature Structural & Molecular Biology publication_identifier: issn: - 1545-9993 - 1545-9985 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Dynamics and interactions of AAC3 in DPC are not functionally relevant type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2018' ... --- _id: '9053' abstract: - lang: eng text: The development of strategies to assemble microscopic machines from dissipative building blocks are essential on the route to novel active materials. We recently demonstrated the hierarchical self-assembly of phoretic microswimmers into self-spinning microgears and their synchronization by diffusiophoretic interactions [Aubret et al., Nat. Phys., 2018]. In this paper, we adopt a pedagogical approach and expose our strategy to control self-assembly and build machines using phoretic phenomena. We notably introduce Highly Inclined Laminated Optical sheets microscopy (HILO) to image and characterize anisotropic and dynamic diffusiophoretic interactions, which cannot be performed by conventional fluorescence microscopy. The dynamics of a (haematite) photocatalytic material immersed in (hydrogen peroxide) fuel under various illumination patterns is first described and quantitatively rationalized by a model of diffusiophoresis, the migration of a colloidal particle in a concentration gradient. It is further exploited to design phototactic microswimmers that direct towards the high intensity of light, as a result of the reorientation of the haematite in a light gradient. We finally show the assembly of self-spinning microgears from colloidal microswimmers and carefully characterize the interactions using HILO techniques. The results are compared with analytical and numerical predictions and agree quantitatively, stressing the important role played by concentration gradients induced by chemical activity to control and design interactions. Because the approach described hereby is generic, this works paves the way for the rational design of machines by controlling phoretic phenomena. article_processing_charge: No article_type: original author: - first_name: Antoine full_name: Aubret, Antoine last_name: Aubret - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: Aubret A, Palacci JA. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. 2018;14(47):9577-9588. doi:10.1039/c8sm01760c apa: Aubret, A., & Palacci, J. A. (2018). Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c8sm01760c chicago: Aubret, Antoine, and Jérémie A Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” Soft Matter. Royal Society of Chemistry , 2018. https://doi.org/10.1039/c8sm01760c. ieee: A. Aubret and J. A. Palacci, “Diffusiophoretic design of self-spinning microgears from colloidal microswimmers,” Soft Matter, vol. 14, no. 47. Royal Society of Chemistry , pp. 9577–9588, 2018. ista: Aubret A, Palacci JA. 2018. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. 14(47), 9577–9588. mla: Aubret, Antoine, and Jérémie A. Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” Soft Matter, vol. 14, no. 47, Royal Society of Chemistry , 2018, pp. 9577–88, doi:10.1039/c8sm01760c. short: A. Aubret, J.A. Palacci, Soft Matter 14 (2018) 9577–9588. date_created: 2021-02-01T13:44:41Z date_published: 2018-12-21T00:00:00Z date_updated: 2023-02-23T13:47:43Z day: '21' doi: 10.1039/c8sm01760c extern: '1' external_id: arxiv: - '1909.11121' pmid: - '30456407' intvolume: ' 14' issue: '47' keyword: - General Chemistry - Condensed Matter Physics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1909.11121 month: '12' oa: 1 oa_version: Preprint page: 9577-9588 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: 'Royal Society of Chemistry ' quality_controlled: '1' scopus_import: '1' status: public title: Diffusiophoretic design of self-spinning microgears from colloidal microswimmers type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 14 year: '2018' ... --- _id: '9066' abstract: - lang: eng text: The novel electronic state of the canted antiferromagnetic (AFM) insulator, strontium iridate (Sr2IrO4) has been well described by the spin-orbit-entangled isospin Jeff = 1/2, but the role of isospin in transport phenomena remains poorly understood. In this study, antiferromagnet-based spintronic functionality is demonstrated by combining unique characteristics of the isospin state in Sr2IrO4. Based on magnetic and transport measurements, large and highly anisotropic magnetoresistance (AMR) is obtained by manipulating the antiferromagnetic isospin domains. First-principles calculations suggest that electrons whose isospin directions are strongly coupled to in-plane net magnetic moment encounter the isospin mismatch when moving across antiferromagnetic domain boundaries, which generates a high resistance state. By rotating a magnetic field that aligns in-plane net moments and removes domain boundaries, the macroscopically-ordered isospins govern dynamic transport through the system, which leads to the extremely angle-sensitive AMR. As with this work that establishes a link between isospins and magnetotransport in strongly spin-orbit-coupled AFM Sr2IrO4, the peculiar AMR effect provides a beneficial foundation for fundamental and applied research on AFM spintronics. article_number: '1805564' article_processing_charge: No article_type: original author: - first_name: Nara full_name: Lee, Nara last_name: Lee - first_name: Eunjung full_name: Ko, Eunjung last_name: Ko - first_name: Hwan Young full_name: Choi, Hwan Young last_name: Choi - first_name: Yun Jeong full_name: Hong, Yun Jeong last_name: Hong - first_name: Muhammad full_name: Nauman, Muhammad id: 32c21954-2022-11eb-9d5f-af9f93c24e71 last_name: Nauman orcid: 0000-0002-2111-4846 - first_name: Woun full_name: Kang, Woun last_name: Kang - first_name: Hyoung Joon full_name: Choi, Hyoung Joon last_name: Choi - first_name: Young Jai full_name: Choi, Young Jai last_name: Choi - first_name: Younjung full_name: Jo, Younjung last_name: Jo citation: ama: Lee N, Ko E, Choi HY, et al. Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. Advanced Materials. 2018;30(52). doi:10.1002/adma.201805564 apa: Lee, N., Ko, E., Choi, H. Y., Hong, Y. J., Nauman, M., Kang, W., … Jo, Y. (2018). Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201805564 chicago: Lee, Nara, Eunjung Ko, Hwan Young Choi, Yun Jeong Hong, Muhammad Nauman, Woun Kang, Hyoung Joon Choi, Young Jai Choi, and Younjung Jo. “Antiferromagnet‐based Spintronic Functionality by Controlling Isospin Domains in a Layered Perovskite Iridate.” Advanced Materials. Wiley, 2018. https://doi.org/10.1002/adma.201805564. ieee: N. Lee et al., “Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate,” Advanced Materials, vol. 30, no. 52. Wiley, 2018. ista: Lee N, Ko E, Choi HY, Hong YJ, Nauman M, Kang W, Choi HJ, Choi YJ, Jo Y. 2018. Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. Advanced Materials. 30(52), 1805564. mla: Lee, Nara, et al. “Antiferromagnet‐based Spintronic Functionality by Controlling Isospin Domains in a Layered Perovskite Iridate.” Advanced Materials, vol. 30, no. 52, 1805564, Wiley, 2018, doi:10.1002/adma.201805564. short: N. Lee, E. Ko, H.Y. Choi, Y.J. Hong, M. Nauman, W. Kang, H.J. Choi, Y.J. Choi, Y. Jo, Advanced Materials 30 (2018). date_created: 2021-02-02T15:50:58Z date_published: 2018-10-29T00:00:00Z date_updated: 2021-02-03T13:58:39Z day: '29' doi: 10.1002/adma.201805564 extern: '1' external_id: arxiv: - '1811.04562' intvolume: ' 30' issue: '52' keyword: - Mechanical Engineering - General Materials Science - Mechanics of Materials language: - iso: eng month: '10' oa_version: Preprint publication: Advanced Materials publication_identifier: issn: - 0935-9648 - 1521-4095 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2018' ... --- _id: '9068' abstract: - lang: eng text: We report the temperature-dependent resistivity ρ(T) of chalcogenide NiS2-xSex (x = 0.1) using hydrostatic pressure as a control parameter in the temperature range of 4–300 K. The insulating behavior of ρ(T) survives at low temperatures in the pressure regime below 7.5 kbar, whereas a clear insulator-to-metallic transition is observed above 7.5 kbar. Two types of magnetic transitions, from the paramagnetic (PM) to the antiferromagnetic (AFM) state and from the AFM state to the weak ferromagnetic (WF) state, were evaluated and confirmed by magnetization measurement. According to the temperature–pressure phase diagram, the WF phase survives up to 7.5 kbar, and the transition temperature of the WF transition decreases as the pressure increases, whereas the metal–insulator transition temperature increases up to 9.4 kbar. We analyzed the metallic behavior and proposed Fermi-liquid behavior of NiS1.9Se0.1. article_processing_charge: No article_type: original author: - first_name: Tayyaba full_name: Hussain, Tayyaba last_name: Hussain - first_name: Myeong-jun full_name: Oh, Myeong-jun last_name: Oh - first_name: Muhammad full_name: Nauman, Muhammad id: 32c21954-2022-11eb-9d5f-af9f93c24e71 last_name: Nauman orcid: 0000-0002-2111-4846 - first_name: Younjung full_name: Jo, Younjung last_name: Jo - first_name: Garam full_name: Han, Garam last_name: Han - first_name: Changyoung full_name: Kim, Changyoung last_name: Kim - first_name: Woun full_name: Kang, Woun last_name: Kang citation: ama: 'Hussain T, Oh M, Nauman M, et al. Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. Physica B: Condensed Matter. 2018;536:235-238. doi:10.1016/j.physb.2017.11.032' apa: 'Hussain, T., Oh, M., Nauman, M., Jo, Y., Han, G., Kim, C., & Kang, W. (2018). Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. Physica B: Condensed Matter. Elsevier. https://doi.org/10.1016/j.physb.2017.11.032' chicago: 'Hussain, Tayyaba, Myeong-jun Oh, Muhammad Nauman, Younjung Jo, Garam Han, Changyoung Kim, and Woun Kang. “Pressure-Induced Metal–Insulator Transitions in Chalcogenide NiS2-Se.” Physica B: Condensed Matter. Elsevier, 2018. https://doi.org/10.1016/j.physb.2017.11.032.' ieee: 'T. Hussain et al., “Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se,” Physica B: Condensed Matter, vol. 536. Elsevier, pp. 235–238, 2018.' ista: 'Hussain T, Oh M, Nauman M, Jo Y, Han G, Kim C, Kang W. 2018. Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. Physica B: Condensed Matter. 536, 235–238.' mla: 'Hussain, Tayyaba, et al. “Pressure-Induced Metal–Insulator Transitions in Chalcogenide NiS2-Se.” Physica B: Condensed Matter, vol. 536, Elsevier, 2018, pp. 235–38, doi:10.1016/j.physb.2017.11.032.' short: 'T. Hussain, M. Oh, M. Nauman, Y. Jo, G. Han, C. Kim, W. Kang, Physica B: Condensed Matter 536 (2018) 235–238.' date_created: 2021-02-02T15:52:43Z date_published: 2018-05-01T00:00:00Z date_updated: 2021-02-04T07:18:57Z day: '01' doi: 10.1016/j.physb.2017.11.032 extern: '1' intvolume: ' 536' language: - iso: eng month: '05' oa_version: None page: 235-238 publication: 'Physica B: Condensed Matter' publication_identifier: issn: - 0921-4526 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 536 year: '2018' ... --- _id: '9136' abstract: - lang: eng text: In this study we investigate the scaling of precipitation extremes with temperature in the Mediterranean region by assessing against observations the present day and future regional climate simulations performed in the frame of the HyMeX and MED-CORDEX programs. Over the 1979–2008 period, despite differences in quantitative precipitation simulation across the various models, the change in precipitation extremes with respect to temperature is robust and consistent. The spatial variability of the temperature–precipitation extremes relationship displays a hook shape across the Mediterranean, with negative slope at high temperatures and a slope following Clausius–Clapeyron (CC)-scaling at low temperatures. The temperature at which the slope of the temperature–precipitation extreme relation sharply changes (or temperature break), ranges from about 20 °C in the western Mediterranean to <10 °C in Greece. In addition, this slope is always negative in the arid regions of the Mediterranean. The scaling of the simulated precipitation extremes is insensitive to ocean–atmosphere coupling, while it depends very weakly on the resolution at high temperatures for short precipitation accumulation times. In future climate scenario simulations covering the 2070–2100 period, the temperature break shifts to higher temperatures by a value which is on average the mean regional temperature change due to global warming. The slope of the simulated future temperature–precipitation extremes relationship is close to CC-scaling at temperatures below the temperature break, while at high temperatures, the negative slope is close, but somewhat flatter or steeper, than in the current climate depending on the model. Overall, models predict more intense precipitation extremes in the future. Adjusting the temperature–precipitation extremes relationship in the present climate using the CC law and the temperature shift in the future allows the recovery of the temperature–precipitation extremes relationship in the future climate. This implies negligible regional changes of relative humidity in the future despite the large warming and drying over the Mediterranean. This suggests that the Mediterranean Sea is the primary source of moisture which counteracts the drying and warming impacts on relative humidity in parts of the Mediterranean region. article_processing_charge: No article_type: original author: - first_name: Philippe full_name: Drobinski, Philippe last_name: Drobinski - first_name: Nicolas Da full_name: Silva, Nicolas Da last_name: Silva - first_name: Gérémy full_name: Panthou, Gérémy last_name: Panthou - first_name: Sophie full_name: Bastin, Sophie last_name: Bastin - 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: Bodo full_name: Ahrens, Bodo last_name: Ahrens - first_name: Marco full_name: Borga, Marco last_name: Borga - first_name: Dario full_name: Conte, Dario last_name: Conte - first_name: Giorgia full_name: Fosser, Giorgia last_name: Fosser - first_name: Filippo full_name: Giorgi, Filippo last_name: Giorgi - first_name: Ivan full_name: Güttler, Ivan last_name: Güttler - first_name: Vassiliki full_name: Kotroni, Vassiliki last_name: Kotroni - first_name: Laurent full_name: Li, Laurent last_name: Li - first_name: Efrat full_name: Morin, Efrat last_name: Morin - first_name: Bariş full_name: Önol, Bariş last_name: Önol - first_name: Pere full_name: Quintana-Segui, Pere last_name: Quintana-Segui - first_name: Raquel full_name: Romera, Raquel last_name: Romera - first_name: Csaba Zsolt full_name: Torma, Csaba Zsolt last_name: Torma citation: ama: 'Drobinski P, Silva ND, Panthou G, et al. Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios. Climate Dynamics. 2018;51(3):1237-1257. doi:10.1007/s00382-016-3083-x' apa: 'Drobinski, P., Silva, N. D., Panthou, G., Bastin, S., Muller, C. J., Ahrens, B., … Torma, C. Z. (2018). Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios. Climate Dynamics. Springer Nature. https://doi.org/10.1007/s00382-016-3083-x' chicago: 'Drobinski, Philippe, Nicolas Da Silva, Gérémy Panthou, Sophie Bastin, Caroline J Muller, Bodo Ahrens, Marco Borga, et al. “Scaling Precipitation Extremes with Temperature in the Mediterranean: Past Climate Assessment and Projection in Anthropogenic Scenarios.” Climate Dynamics. Springer Nature, 2018. https://doi.org/10.1007/s00382-016-3083-x.' ieee: 'P. Drobinski et al., “Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios,” Climate Dynamics, vol. 51, no. 3. Springer Nature, pp. 1237–1257, 2018.' ista: 'Drobinski P, Silva ND, Panthou G, Bastin S, Muller CJ, Ahrens B, Borga M, Conte D, Fosser G, Giorgi F, Güttler I, Kotroni V, Li L, Morin E, Önol B, Quintana-Segui P, Romera R, Torma CZ. 2018. Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios. Climate Dynamics. 51(3), 1237–1257.' mla: 'Drobinski, Philippe, et al. “Scaling Precipitation Extremes with Temperature in the Mediterranean: Past Climate Assessment and Projection in Anthropogenic Scenarios.” Climate Dynamics, vol. 51, no. 3, Springer Nature, 2018, pp. 1237–57, doi:10.1007/s00382-016-3083-x.' short: P. Drobinski, N.D. Silva, G. Panthou, S. Bastin, C.J. Muller, B. Ahrens, M. Borga, D. Conte, G. Fosser, F. Giorgi, I. Güttler, V. Kotroni, L. Li, E. Morin, B. Önol, P. Quintana-Segui, R. Romera, C.Z. Torma, Climate Dynamics 51 (2018) 1237–1257. date_created: 2021-02-15T14:18:53Z date_published: 2018-08-01T00:00:00Z date_updated: 2022-01-24T12:40:40Z day: '01' doi: 10.1007/s00382-016-3083-x extern: '1' intvolume: ' 51' issue: '3' keyword: - Atmospheric Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00382-016-3083-x month: '08' oa: 1 oa_version: Published Version page: 1237-1257 publication: Climate Dynamics publication_identifier: issn: - 0930-7575 - 1432-0894 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios' type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 51 year: '2018' ... --- _id: '9134' abstract: - lang: eng text: Several studies have shown the existence of a critical latitude where the dissipation of internal tides is strongly enhanced. Internal tides are internal waves generated by barotropic tidal currents impinging rough topography at the seafloor. Their dissipation and concomitant diapycnal mixing are believed to be important for water masses and the large‐scale ocean circulation. The purpose of this study is to clarify the physical processes at the origin of this strong latitudinal dependence of tidal energy dissipation. We find that different mechanisms are involved equatorward and poleward of the critical latitude. Triadic resonant instabilities are responsible for the dissipation of internal tides equatorward of the critical latitude. In particular, a dominant triad involving the primary internal tide and near‐inertial waves is key. At the critical latitude, the peak of energy dissipation is explained by both increased instability growth rates, and smaller scales of secondary waves thus more prone to break and dissipate their energy. Surprisingly, poleward of the critical latitude, the generation of evanescent waves appears to be crucial. Triadic instabilities have been widely studied, but the transfer of energy to evanescent waves has received comparatively little attention. Our work suggests that the nonlinear transfer of energy from the internal tide to evanescent waves (corresponding to the 2f‐pump mechanism described by Young et al., 2008, https://doi.org/10.1017/S0022112008001742) is an efficient mechanism to dissipate internal tide energy near and poleward of the critical latitude. The theoretical results are confirmed in idealized high‐resolution numerical simulations of a barotropic M2 tide impinging sinusoidal topography in a linearly stratified fluid. article_processing_charge: No article_type: original author: - first_name: O. full_name: Richet, O. last_name: Richet - first_name: J.-M. full_name: Chomaz, J.-M. last_name: Chomaz - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 citation: ama: 'Richet O, Chomaz J-M, Muller CJ. Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude. Journal of Geophysical Research: Oceans. 2018;123(9):6136-6155. doi:10.1029/2017jc013591' apa: 'Richet, O., Chomaz, J.-M., & Muller, C. J. (2018). Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1029/2017jc013591' chicago: 'Richet, O., J.-M. Chomaz, and Caroline J Muller. “Internal Tide Dissipation at Topography: Triadic Resonant Instability Equatorward and Evanescent Waves Poleward of the Critical Latitude.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2018. https://doi.org/10.1029/2017jc013591.' ieee: 'O. Richet, J.-M. Chomaz, and C. J. Muller, “Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude,” Journal of Geophysical Research: Oceans, vol. 123, no. 9. American Geophysical Union, pp. 6136–6155, 2018.' ista: 'Richet O, Chomaz J-M, Muller CJ. 2018. Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude. Journal of Geophysical Research: Oceans. 123(9), 6136–6155.' mla: 'Richet, O., et al. “Internal Tide Dissipation at Topography: Triadic Resonant Instability Equatorward and Evanescent Waves Poleward of the Critical Latitude.” Journal of Geophysical Research: Oceans, vol. 123, no. 9, American Geophysical Union, 2018, pp. 6136–55, doi:10.1029/2017jc013591.' short: 'O. Richet, J.-M. Chomaz, C.J. Muller, Journal of Geophysical Research: Oceans 123 (2018) 6136–6155.' date_created: 2021-02-15T14:17:25Z date_published: 2018-09-01T00:00:00Z date_updated: 2022-01-24T12:39:03Z day: '01' doi: 10.1029/2017jc013591 extern: '1' intvolume: ' 123' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1029/2017JC013591 month: '09' oa: 1 oa_version: Published Version page: 6136-6155 publication: 'Journal of Geophysical Research: Oceans' publication_identifier: issn: - 2169-9275 publication_status: published publisher: American Geophysical Union quality_controlled: '1' status: public title: 'Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude' type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 123 year: '2018' ... --- _id: '9135' abstract: - lang: eng text: Idealized simulations of tropical moist convection have revealed that clouds can spontaneously clump together in a process called self-aggregation. This results in a state where a moist cloudy region with intense deep convection is surrounded by extremely dry subsiding air devoid of deep convection. Because of the idealized settings of the simulations where it was discovered, the relevance of self-aggregation to the real world is still debated. Here, we show that self-aggregation feedbacks play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving simulations. Those feedbacks accelerate the cyclogenesis process by a factor of 2, and the feedbacks contributing to the cyclone formation show qualitative and quantitative agreement with the self-aggregation process. Once the cyclone is formed, wind-induced surface heat exchange (WISHE) effects dominate, although we find that self-aggregation feedbacks have a small but nonnegligible contribution to the maintenance of the mature cyclone. Our results suggest that self-aggregation, and the framework developed for its study, can help shed more light into the physical processes leading to cyclogenesis and cyclone intensification. In particular, our results point out the importance of the longwave radiative cooling outside the cyclone. article_processing_charge: No article_type: original author: - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: David M. full_name: Romps, David M. last_name: Romps citation: ama: Muller CJ, Romps DM. Acceleration of tropical cyclogenesis by self-aggregation feedbacks. Proceedings of the National Academy of Sciences. 2018;115(12):2930-2935. doi:10.1073/pnas.1719967115 apa: Muller, C. J., & Romps, D. M. (2018). Acceleration of tropical cyclogenesis by self-aggregation feedbacks. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1719967115 chicago: Muller, Caroline J, and David M. Romps. “Acceleration of Tropical Cyclogenesis by Self-Aggregation Feedbacks.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1719967115. ieee: C. J. Muller and D. M. Romps, “Acceleration of tropical cyclogenesis by self-aggregation feedbacks,” Proceedings of the National Academy of Sciences, vol. 115, no. 12. Proceedings of the National Academy of Sciences, pp. 2930–2935, 2018. ista: Muller CJ, Romps DM. 2018. Acceleration of tropical cyclogenesis by self-aggregation feedbacks. Proceedings of the National Academy of Sciences. 115(12), 2930–2935. mla: Muller, Caroline J., and David M. Romps. “Acceleration of Tropical Cyclogenesis by Self-Aggregation Feedbacks.” Proceedings of the National Academy of Sciences, vol. 115, no. 12, Proceedings of the National Academy of Sciences, 2018, pp. 2930–35, doi:10.1073/pnas.1719967115. short: C.J. Muller, D.M. Romps, Proceedings of the National Academy of Sciences 115 (2018) 2930–2935. date_created: 2021-02-15T14:18:16Z date_published: 2018-03-20T00:00:00Z date_updated: 2022-01-24T12:39:49Z day: '20' doi: 10.1073/pnas.1719967115 extern: '1' intvolume: ' 115' issue: '12' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1719967115 month: '03' oa: 1 oa_version: Published Version page: 2930-2935 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: Acceleration of tropical cyclogenesis by self-aggregation feedbacks type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 115 year: '2018' ... --- _id: '9471' abstract: - lang: eng text: The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin. article_processing_charge: No article_type: original author: - first_name: Jennifer M. full_name: Frost, Jennifer M. last_name: Frost - first_name: M. Yvonne full_name: Kim, M. Yvonne last_name: Kim - first_name: Guen Tae full_name: Park, Guen Tae last_name: Park - first_name: Ping-Hung full_name: Hsieh, Ping-Hung last_name: Hsieh - first_name: Miyuki full_name: Nakamura, Miyuki last_name: Nakamura - first_name: Samuel J. H. full_name: Lin, Samuel J. H. last_name: Lin - first_name: Hyunjin full_name: Yoo, Hyunjin last_name: Yoo - first_name: Jaemyung full_name: Choi, Jaemyung last_name: Choi - first_name: Yoko full_name: Ikeda, Yoko last_name: Ikeda - first_name: Tetsu full_name: Kinoshita, Tetsu last_name: Kinoshita - first_name: Yeonhee full_name: Choi, Yeonhee last_name: Choi - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer citation: ama: Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115 apa: Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115 chicago: Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115. ieee: J. M. Frost et al., “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” Proceedings of the National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018. ista: Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729. mla: Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:10.1073/pnas.1713333115. short: J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729. date_created: 2021-06-07T06:11:28Z date_published: 2018-05-15T00:00:00Z date_updated: 2021-12-14T07:53:40Z day: '15' ddc: - '580' department: - _id: DaZi doi: 10.1073/pnas.1713333115 extern: '1' external_id: pmid: - '29712855' file: - access_level: open_access checksum: 810260dc0e3cc3033e15c19ad0dc123e content_type: application/pdf creator: asandaue date_created: 2021-06-07T06:16:38Z date_updated: 2021-06-07T06:16:38Z file_id: '9472' file_name: 2018_PNAS_Frost.pdf file_size: 3045260 relation: main_file success: 1 file_date_updated: 2021-06-07T06:16:38Z has_accepted_license: '1' intvolume: ' 115' issue: '20' keyword: - Multidisciplinary language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: E4720-E4729 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: earlier_version url: 'https://doi.org/10.1101/187674 ' scopus_import: '1' status: public title: FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 115 year: '2018' ... --- _id: '95' abstract: - lang: eng text: Electrostatic charging of insulating fine particles can be responsible for numerous phenomena ranging from lightning in volcanic plumes to dust explosions. However, even basic aspects of how fine particles become charged are still unclear. Studying particle charging is challenging because it usually involves the complexities associated with many-particle collisions. To address these issues, we introduce a method based on acoustic levitation, which makes it possible to initiate sequences of repeated collisions of a single submillimeter particle with a flat plate, and to precisely measure the particle charge in situ after each collision. We show that collisional charge transfer between insulators is dependent on the hydrophobicity of the contacting surfaces. We use glass, which we modify by attaching nonpolar molecules to the particle, the plate, or both. We find that hydrophilic surfaces develop significant positive charges after contacting hydrophobic surfaces. Moreover, we demonstrate that charging between a hydrophilic and a hydrophobic surface is suppressed in an acidic environment and enhanced in a basic one. Application of an electric field during each collision is found to modify the charge transfer, again depending on surface hydrophobicity. We discuss these results within the context of contact charging due to ion transfer, and we show that they lend strong support to OH− ions as the charge carriers. article_number: '035602' author: - first_name: Victor full_name: Lee, Victor last_name: Lee - first_name: Nicole full_name: James, Nicole last_name: James - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Heinrich full_name: Jaeger, Heinrich last_name: Jaeger citation: ama: 'Lee V, James N, Waitukaitis SR, Jaeger H. Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer. Physical Review Materials. 2018;2(3). doi:10.1103/PhysRevMaterials.2.035602' apa: 'Lee, V., James, N., Waitukaitis, S. R., & Jaeger, H. (2018). Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.2.035602' chicago: 'Lee, Victor, Nicole James, Scott R Waitukaitis, and Heinrich Jaeger. “Collisional Charging of Individual Submillimeter Particles: Using Ultrasonic Levitation to Initiate and Track Charge Transfer.” Physical Review Materials. American Physical Society, 2018. https://doi.org/10.1103/PhysRevMaterials.2.035602.' ieee: 'V. Lee, N. James, S. R. Waitukaitis, and H. Jaeger, “Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer,” Physical Review Materials, vol. 2, no. 3. American Physical Society, 2018.' ista: 'Lee V, James N, Waitukaitis SR, Jaeger H. 2018. Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer. Physical Review Materials. 2(3), 035602.' mla: 'Lee, Victor, et al. “Collisional Charging of Individual Submillimeter Particles: Using Ultrasonic Levitation to Initiate and Track Charge Transfer.” Physical Review Materials, vol. 2, no. 3, 035602, American Physical Society, 2018, doi:10.1103/PhysRevMaterials.2.035602.' short: V. Lee, N. James, S.R. Waitukaitis, H. Jaeger, Physical Review Materials 2 (2018). date_created: 2018-12-11T11:44:36Z date_published: 2018-03-29T00:00:00Z date_updated: 2021-01-12T08:22:09Z day: '29' doi: 10.1103/PhysRevMaterials.2.035602 extern: '1' external_id: arxiv: - '1801.09278' intvolume: ' 2' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1801.09278 month: '03' oa: 1 oa_version: Preprint publication: Physical Review Materials publication_status: published publisher: American Physical Society publist_id: '7959' quality_controlled: '1' status: public title: 'Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2018' ... --- _id: '9567' abstract: - lang: eng text: Let P be a graph property which is preserved by removal of edges, and consider the random graph process that starts with the empty n-vertex graph and then adds edges one-by-one, each chosen uniformly at random subject to the constraint that P is not violated. These types of random processes have been the subject of extensive research over the last 20 years, having striking applications in extremal combinatorics, and leading to the discovery of important probabilistic tools. In this paper we consider the k-matching-free process, where P is the property of not containing a matching of size k. We are able to analyse the behaviour of this process for a wide range of values of k; in particular we prove that if k=o(n) or if n−2k=o(n−−√/logn) then this process is likely to terminate in a k-matching-free graph with the maximum possible number of edges, as characterised by Erdős and Gallai. We also show that these bounds on k are essentially best possible, and we make a first step towards understanding the behaviour of the process in the intermediate regime. 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: Po‐Shen full_name: Loh, Po‐Shen last_name: Loh - first_name: Benny full_name: Sudakov, Benny last_name: Sudakov citation: ama: Krivelevich M, Kwan MA, Loh P, Sudakov B. The random k‐matching‐free process. Random Structures and Algorithms. 2018;53(4):692-716. doi:10.1002/rsa.20814 apa: Krivelevich, M., Kwan, M. A., Loh, P., & Sudakov, B. (2018). The random k‐matching‐free process. Random Structures and Algorithms. Wiley. https://doi.org/10.1002/rsa.20814 chicago: Krivelevich, Michael, Matthew Alan Kwan, Po‐Shen Loh, and Benny Sudakov. “The Random K‐matching‐free Process.” Random Structures and Algorithms. Wiley, 2018. https://doi.org/10.1002/rsa.20814. ieee: M. Krivelevich, M. A. Kwan, P. Loh, and B. Sudakov, “The random k‐matching‐free process,” Random Structures and Algorithms, vol. 53, no. 4. Wiley, pp. 692–716, 2018. ista: Krivelevich M, Kwan MA, Loh P, Sudakov B. 2018. The random k‐matching‐free process. Random Structures and Algorithms. 53(4), 692–716. mla: Krivelevich, Michael, et al. “The Random K‐matching‐free Process.” Random Structures and Algorithms, vol. 53, no. 4, Wiley, 2018, pp. 692–716, doi:10.1002/rsa.20814. short: M. Krivelevich, M.A. Kwan, P. Loh, B. Sudakov, Random Structures and Algorithms 53 (2018) 692–716. date_created: 2021-06-18T12:37:40Z date_published: 2018-12-01T00:00:00Z date_updated: 2023-02-23T14:01:07Z day: '01' doi: 10.1002/rsa.20814 extern: '1' external_id: arxiv: - '1708.01054' intvolume: ' 53' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.01054 month: '12' oa: 1 oa_version: Preprint page: 692-716 publication: Random Structures and Algorithms publication_identifier: eissn: - 1098-2418 issn: - 1042-9832 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: The random k‐matching‐free process type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 53 year: '2018' ... --- _id: '9565' abstract: - lang: eng text: Let D(n,p) be the random directed graph on n vertices where each of the n(n-1) possible arcs is present independently with probability p. A celebrated result of Frieze shows that if p≥(logn+ω(1))/n then D(n,p) typically has a directed Hamilton cycle, and this is best possible. In this paper, we obtain a strengthening of this result, showing that under the same condition, the number of directed Hamilton cycles in D(n,p) is typically n!(p(1+o(1)))n. We also prove a hitting-time version of this statement, showing that in the random directed graph process, as soon as every vertex has in-/out-degrees at least 1, there are typically n!(logn/n(1+o(1)))n directed Hamilton cycles. article_processing_charge: No article_type: original author: - first_name: Asaf full_name: Ferber, Asaf last_name: Ferber - 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: Ferber A, Kwan MA, Sudakov B. Counting Hamilton cycles in sparse random directed graphs. Random Structures and Algorithms. 2018;53(4):592-603. doi:10.1002/rsa.20815 apa: Ferber, A., Kwan, M. A., & Sudakov, B. (2018). Counting Hamilton cycles in sparse random directed graphs. Random Structures and Algorithms. Wiley. https://doi.org/10.1002/rsa.20815 chicago: Ferber, Asaf, Matthew Alan Kwan, and Benny Sudakov. “Counting Hamilton Cycles in Sparse Random Directed Graphs.” Random Structures and Algorithms. Wiley, 2018. https://doi.org/10.1002/rsa.20815. ieee: A. Ferber, M. A. Kwan, and B. Sudakov, “Counting Hamilton cycles in sparse random directed graphs,” Random Structures and Algorithms, vol. 53, no. 4. Wiley, pp. 592–603, 2018. ista: Ferber A, Kwan MA, Sudakov B. 2018. Counting Hamilton cycles in sparse random directed graphs. Random Structures and Algorithms. 53(4), 592–603. mla: Ferber, Asaf, et al. “Counting Hamilton Cycles in Sparse Random Directed Graphs.” Random Structures and Algorithms, vol. 53, no. 4, Wiley, 2018, pp. 592–603, doi:10.1002/rsa.20815. short: A. Ferber, M.A. Kwan, B. Sudakov, Random Structures and Algorithms 53 (2018) 592–603. date_created: 2021-06-18T12:06:28Z date_published: 2018-12-01T00:00:00Z date_updated: 2023-02-23T14:01:03Z day: '01' doi: 10.1002/rsa.20815 extern: '1' external_id: arxiv: - '1708.07746' intvolume: ' 53' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.07746 month: '12' oa: 1 oa_version: Preprint page: 592-603 publication: Random Structures and Algorithms publication_identifier: eissn: - 1098-2418 issn: - 1042-9832 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Counting Hamilton cycles in sparse random directed graphs type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 53 year: '2018' ... --- _id: '9568' abstract: - lang: eng text: An intercalate in a Latin square is a 2×2 Latin subsquare. Let N be the number of intercalates in a uniformly random n×n Latin square. We prove that asymptotically almost surely N≥(1−o(1))n2/4, and that EN≤(1+o(1))n2/2 (therefore asymptotically almost surely N≤fn2 for any f→∞). This significantly improves the previous best lower and upper bounds. We also give an upper tail bound for the number of intercalates in two fixed rows of a random Latin square. In addition, we discuss a problem of Linial and Luria on low-discrepancy Latin squares. article_processing_charge: No article_type: original author: - 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: Kwan MA, Sudakov B. Intercalates and discrepancy in random Latin squares. Random Structures and Algorithms. 2018;52(2):181-196. doi:10.1002/rsa.20742 apa: Kwan, M. A., & Sudakov, B. (2018). Intercalates and discrepancy in random Latin squares. Random Structures and Algorithms. Wiley. https://doi.org/10.1002/rsa.20742 chicago: Kwan, Matthew Alan, and Benny Sudakov. “Intercalates and Discrepancy in Random Latin Squares.” Random Structures and Algorithms. Wiley, 2018. https://doi.org/10.1002/rsa.20742. ieee: M. A. Kwan and B. Sudakov, “Intercalates and discrepancy in random Latin squares,” Random Structures and Algorithms, vol. 52, no. 2. Wiley, pp. 181–196, 2018. ista: Kwan MA, Sudakov B. 2018. Intercalates and discrepancy in random Latin squares. Random Structures and Algorithms. 52(2), 181–196. mla: Kwan, Matthew Alan, and Benny Sudakov. “Intercalates and Discrepancy in Random Latin Squares.” Random Structures and Algorithms, vol. 52, no. 2, Wiley, 2018, pp. 181–96, doi:10.1002/rsa.20742. short: M.A. Kwan, B. Sudakov, Random Structures and Algorithms 52 (2018) 181–196. date_created: 2021-06-18T12:47:25Z date_published: 2018-03-01T00:00:00Z date_updated: 2023-02-23T14:01:09Z day: '01' doi: 10.1002/rsa.20742 extern: '1' external_id: arxiv: - '1607.04981' intvolume: ' 52' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.04981 month: '03' oa: 1 oa_version: Preprint page: 181-196 publication: Random Structures and Algorithms publication_identifier: eissn: - 1098-2418 issn: - 1042-9832 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Intercalates and discrepancy in random Latin squares type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 52 year: '2018' ... --- _id: '9587' abstract: - lang: eng text: We say a family of sets is intersecting if any two of its sets intersect, and we say it is trivially intersecting if there is an element which appears in every set of the family. In this paper we study the maximum size of a non-trivially intersecting family in a natural “multi-part” setting. Here the ground set is divided into parts, and one considers families of sets whose intersection with each part is of a prescribed size. Our work is motivated by classical results in the single-part setting due to Erdős, Ko and Rado, and Hilton and Milner, and by a theorem of Frankl concerning intersecting families in this multi-part setting. In the case where the part sizes are sufficiently large we determine the maximum size of a non-trivially intersecting multi-part family, disproving a conjecture of Alon and Katona. article_processing_charge: No article_type: original author: - 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 - first_name: Pedro full_name: Vieira, Pedro last_name: Vieira citation: ama: Kwan MA, Sudakov B, Vieira P. Non-trivially intersecting multi-part families. Journal of Combinatorial Theory Series A. 2018;156:44-60. doi:10.1016/j.jcta.2017.12.001 apa: Kwan, M. A., Sudakov, B., & Vieira, P. (2018). Non-trivially intersecting multi-part families. Journal of Combinatorial Theory Series A. Elsevier. https://doi.org/10.1016/j.jcta.2017.12.001 chicago: Kwan, Matthew Alan, Benny Sudakov, and Pedro Vieira. “Non-Trivially Intersecting Multi-Part Families.” Journal of Combinatorial Theory Series A. Elsevier, 2018. https://doi.org/10.1016/j.jcta.2017.12.001. ieee: M. A. Kwan, B. Sudakov, and P. Vieira, “Non-trivially intersecting multi-part families,” Journal of Combinatorial Theory Series A, vol. 156. Elsevier, pp. 44–60, 2018. ista: Kwan MA, Sudakov B, Vieira P. 2018. Non-trivially intersecting multi-part families. Journal of Combinatorial Theory Series A. 156, 44–60. mla: Kwan, Matthew Alan, et al. “Non-Trivially Intersecting Multi-Part Families.” Journal of Combinatorial Theory Series A, vol. 156, Elsevier, 2018, pp. 44–60, doi:10.1016/j.jcta.2017.12.001. short: M.A. Kwan, B. Sudakov, P. Vieira, Journal of Combinatorial Theory Series A 156 (2018) 44–60. date_created: 2021-06-22T11:42:48Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-02-23T14:01:55Z day: '01' doi: 10.1016/j.jcta.2017.12.001 extern: '1' external_id: arxiv: - '1703.09946' intvolume: ' 156' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.09946 month: '05' oa: 1 oa_version: Preprint page: 44-60 publication: Journal of Combinatorial Theory Series A publication_identifier: issn: - 0097-3165 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Non-trivially intersecting multi-part families type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 156 year: '2018' ... --- _id: '9665' abstract: - lang: eng text: We investigate the thermodynamics and kinetics of a hydrogen interstitial in magnetic α-iron, taking account of the quantum fluctuations of the proton as well as the anharmonicities of lattice vibrations and hydrogen hopping. We show that the diffusivity of hydrogen in the lattice of bcc iron deviates strongly from an Arrhenius behavior at and below room temperature. We compare a quantum transition state theory to explicit ring polymer molecular dynamics in the calculation of diffusivity. We then address the trapping of hydrogen by a vacancy as a prototype lattice defect. By a sequence of steps in a thought experiment, each involving a thermodynamic integration, we are able to separate out the binding free energy of a proton to a defect into harmonic and anharmonic, and classical and quantum contributions. We find that about 30% of a typical binding free energy of hydrogen to a lattice defect in iron is accounted for by finite temperature effects, and about half of these arise from quantum proton fluctuations. This has huge implications for the comparison between thermal desorption and permeation experiments and standard electronic structure theory. The implications are even greater for the interpretation of muon spin resonance experiments. article_number: '225901' article_processing_charge: No article_type: review author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Anthony T. full_name: Paxton, Anthony T. last_name: Paxton - first_name: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: ama: 'Cheng B, Paxton AT, Ceriotti M. Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations. Physical Review Letters. 2018;120(22). doi:10.1103/physrevlett.120.225901' apa: 'Cheng, B., Paxton, A. T., & Ceriotti, M. (2018). Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.120.225901' chicago: 'Cheng, Bingqing, Anthony T. Paxton, and Michele Ceriotti. “Hydrogen Diffusion and Trapping in α-Iron: The Role of Quantum and Anharmonic Fluctuations.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.120.225901.' ieee: 'B. Cheng, A. T. Paxton, and M. Ceriotti, “Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations,” Physical Review Letters, vol. 120, no. 22. American Physical Society, 2018.' ista: 'Cheng B, Paxton AT, Ceriotti M. 2018. Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations. Physical Review Letters. 120(22), 225901.' mla: 'Cheng, Bingqing, et al. “Hydrogen Diffusion and Trapping in α-Iron: The Role of Quantum and Anharmonic Fluctuations.” Physical Review Letters, vol. 120, no. 22, 225901, American Physical Society, 2018, doi:10.1103/physrevlett.120.225901.' short: B. Cheng, A.T. Paxton, M. Ceriotti, Physical Review Letters 120 (2018). date_created: 2021-07-15T12:22:41Z date_published: 2018-06-01T00:00:00Z date_updated: 2021-08-09T12:36:22Z day: '01' doi: 10.1103/physrevlett.120.225901 extern: '1' external_id: arxiv: - '1803.00600' pmid: - '29906144' intvolume: ' 120' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.00600 month: '06' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations' type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 120 year: '2018' ... --- _id: '9659' abstract: - lang: eng text: The curvature dependence of interfacial free energy, which is crucial in quantitatively predicting nucleation kinetics and the stability of bubbles and droplets, is quantified by the Tolman length δ. For solid-liquid interfaces, however, δ has never been computed directly due to various theoretical and practical challenges. Here we perform a direct evaluation of the Tolman length from atomistic simulations of a solid-liquid planar interface in out-of-equilibrium conditions, by first computing the surface tension from the amplitude of thermal capillary fluctuations of a localized version of the Gibbs dividing surface and by then calculating how much the surface energy changes when it is defined relative to the equimolar dividing surface. We computed δ for a model potential, and found a good agreement with the values indirectly inferred from nucleation simulations. The agreement not only validates our approach but also suggests that the nucleation free energy of the system can be perfectly described using classical nucleation theory if the Tolman length is taken into account. article_number: '231102' 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: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: ama: 'Cheng B, Ceriotti M. Communication: Computing the Tolman length for solid-liquid interfaces. The Journal of Chemical Physics. 2018;148(23). doi:10.1063/1.5038396' apa: 'Cheng, B., & Ceriotti, M. (2018). Communication: Computing the Tolman length for solid-liquid interfaces. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5038396' chicago: 'Cheng, Bingqing, and Michele Ceriotti. “Communication: Computing the Tolman Length for Solid-Liquid Interfaces.” The Journal of Chemical Physics. AIP Publishing, 2018. https://doi.org/10.1063/1.5038396.' ieee: 'B. Cheng and M. Ceriotti, “Communication: Computing the Tolman length for solid-liquid interfaces,” The Journal of Chemical Physics, vol. 148, no. 23. AIP Publishing, 2018.' ista: 'Cheng B, Ceriotti M. 2018. Communication: Computing the Tolman length for solid-liquid interfaces. The Journal of Chemical Physics. 148(23), 231102.' mla: 'Cheng, Bingqing, and Michele Ceriotti. “Communication: Computing the Tolman Length for Solid-Liquid Interfaces.” The Journal of Chemical Physics, vol. 148, no. 23, 231102, AIP Publishing, 2018, doi:10.1063/1.5038396.' short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 148 (2018). date_created: 2021-07-15T07:51:42Z date_published: 2018-06-21T00:00:00Z date_updated: 2023-02-23T14:03:57Z day: '21' doi: 10.1063/1.5038396 extern: '1' external_id: arxiv: - '1803.09140' pmid: - '29935495' intvolume: ' 148' issue: '23' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1063/1.5038396 month: '06' oa: 1 oa_version: Submitted Version pmid: 1 publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'Communication: Computing the Tolman length for solid-liquid interfaces' type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 148 year: '2018' ... --- _id: '12603' abstract: - lang: eng text: We present a field-data rich modelling analysis to reconstruct the climatic forcing, glacier response, and runoff generation from a high-elevation catchment in central Chile over the period 2000–2015 to provide insights into the differing contributions of debris-covered and debris-free glaciers under current and future changing climatic conditions. Model simulations with the physically based glacio-hydrological model TOPKAPI-ETH reveal a period of neutral or slightly positive mass balance between 2000 and 2010, followed by a transition to increasingly large annual mass losses, associated with a recent mega drought. Mass losses commence earlier, and are more severe, for a heavily debris-covered glacier, most likely due to its strong dependence on snow avalanche accumulation, which has declined in recent years. Catchment runoff shows a marked decreasing trend over the study period, but with high interannual variability directly linked to winter snow accumulation, and high contribution from ice melt in dry periods and drought conditions. The study demonstrates the importance of incorporating local-scale processes such as snow avalanche accumulation and spatially variable debris thickness, in understanding the responses of different glacier types to climate change. We highlight the increased dependency of runoff from high Andean catchments on the diminishing resource of glacier ice during dry years. article_processing_charge: No article_type: original author: - first_name: Flavia full_name: Burger, Flavia last_name: Burger - first_name: Alvaro full_name: Ayala, Alvaro last_name: Ayala - first_name: David full_name: Farias, David last_name: Farias - first_name: Thomas E. full_name: Shaw, Thomas E. last_name: Shaw - first_name: Shelley full_name: MacDonell, Shelley last_name: MacDonell - first_name: Ben full_name: Brock, Ben last_name: Brock - first_name: James full_name: McPhee, James last_name: McPhee - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: 'Burger F, Ayala A, Farias D, et al. Interannual variability in glacier contribution to runoff from a high‐elevation Andean catchment: Understanding the role of debris cover in glacier hydrology. Hydrological Processes. 2018;33(2):214-229. doi:10.1002/hyp.13354' apa: 'Burger, F., Ayala, A., Farias, D., Shaw, T. E., MacDonell, S., Brock, B., … Pellicciotti, F. (2018). Interannual variability in glacier contribution to runoff from a high‐elevation Andean catchment: Understanding the role of debris cover in glacier hydrology. Hydrological Processes. Wiley. https://doi.org/10.1002/hyp.13354' chicago: 'Burger, Flavia, Alvaro Ayala, David Farias, Thomas E. Shaw, Shelley MacDonell, Ben Brock, James McPhee, and Francesca Pellicciotti. “Interannual Variability in Glacier Contribution to Runoff from a High‐elevation Andean Catchment: Understanding the Role of Debris Cover in Glacier Hydrology.” Hydrological Processes. Wiley, 2018. https://doi.org/10.1002/hyp.13354.' ieee: 'F. Burger et al., “Interannual variability in glacier contribution to runoff from a high‐elevation Andean catchment: Understanding the role of debris cover in glacier hydrology,” Hydrological Processes, vol. 33, no. 2. Wiley, pp. 214–229, 2018.' ista: 'Burger F, Ayala A, Farias D, Shaw TE, MacDonell S, Brock B, McPhee J, Pellicciotti F. 2018. Interannual variability in glacier contribution to runoff from a high‐elevation Andean catchment: Understanding the role of debris cover in glacier hydrology. Hydrological Processes. 33(2), 214–229.' mla: 'Burger, Flavia, et al. “Interannual Variability in Glacier Contribution to Runoff from a High‐elevation Andean Catchment: Understanding the Role of Debris Cover in Glacier Hydrology.” Hydrological Processes, vol. 33, no. 2, Wiley, 2018, pp. 214–29, doi:10.1002/hyp.13354.' short: F. Burger, A. Ayala, D. Farias, T.E. Shaw, S. MacDonell, B. Brock, J. McPhee, F. Pellicciotti, Hydrological Processes 33 (2018) 214–229. date_created: 2023-02-20T08:13:14Z date_published: 2018-11-26T00:00:00Z date_updated: 2023-02-28T11:49:36Z day: '26' doi: 10.1002/hyp.13354 extern: '1' intvolume: ' 33' issue: '2' keyword: - Water Science and Technology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/hyp.13354 month: '11' oa: 1 oa_version: Published Version page: 214-229 publication: Hydrological Processes publication_identifier: eissn: - 1099-1085 issn: - 0885-6087 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Interannual variability in glacier contribution to runoff from a high‐elevation Andean catchment: Understanding the role of debris cover in glacier hydrology' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2018' ... --- _id: '12605' abstract: - lang: eng text: Snow depth patterns over glaciers are controlled by precipitation, snow redistribution due to wind and avalanches, and the exchange of energy with the atmosphere that determines snow ablation. While many studies have advanced the understanding of ablation processes, less is known about winter snow patterns and their variability over glaciers. We analyze snow depth on Haut Glacier d'Arolla, Switzerland, in the two winter seasons 2006–2007 and 2010–2011 to (1) understand whether snow depth over an alpine glacier at the end of the accumulation season exhibits a behavior similar to the one observed on single slopes and vegetated areas; and (2) investigate the snow pattern consistency over the two accumulation seasons. We perform this analysis on a data set of high-resolution lidar-derived snow depth using variograms and fractal parameters. Our first main result is that snow depth patterns on the glacier exhibit a multiscale behavior, with a scale break around 20 m after which the fractal dimension increases, indicating more autocorrelated structure before the scale break than after. Second, this behavior is consistent over the two years, with fractal parameters and their spatial variability almost constant in the two seasons. We also show that snow depth patterns exhibit a distinct behavior in the glacier tongue and the upper catchment, with longer correlation distances on the tongue in the direction of the main winds, suggesting spatial distinctions that are likely induced by different processes and that should be taken into account when extrapolating snow depth from limited samples. article_processing_charge: No article_type: original author: - first_name: I. full_name: Clemenzi, I. last_name: Clemenzi - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: P. full_name: Burlando, P. last_name: Burlando citation: ama: Clemenzi I, Pellicciotti F, Burlando P. Snow depth structure, fractal behavior, and interannual consistency over Haut Glacier d’Arolla, Switzerland. Water Resources Research. 2018;54(10):7929-7945. doi:10.1029/2017wr021606 apa: Clemenzi, I., Pellicciotti, F., & Burlando, P. (2018). Snow depth structure, fractal behavior, and interannual consistency over Haut Glacier d’Arolla, Switzerland. Water Resources Research. American Geophysical Union. https://doi.org/10.1029/2017wr021606 chicago: Clemenzi, I., Francesca Pellicciotti, and P. Burlando. “Snow Depth Structure, Fractal Behavior, and Interannual Consistency over Haut Glacier d’Arolla, Switzerland.” Water Resources Research. American Geophysical Union, 2018. https://doi.org/10.1029/2017wr021606. ieee: I. Clemenzi, F. Pellicciotti, and P. Burlando, “Snow depth structure, fractal behavior, and interannual consistency over Haut Glacier d’Arolla, Switzerland,” Water Resources Research, vol. 54, no. 10. American Geophysical Union, pp. 7929–7945, 2018. ista: Clemenzi I, Pellicciotti F, Burlando P. 2018. Snow depth structure, fractal behavior, and interannual consistency over Haut Glacier d’Arolla, Switzerland. Water Resources Research. 54(10), 7929–7945. mla: Clemenzi, I., et al. “Snow Depth Structure, Fractal Behavior, and Interannual Consistency over Haut Glacier d’Arolla, Switzerland.” Water Resources Research, vol. 54, no. 10, American Geophysical Union, 2018, pp. 7929–45, doi:10.1029/2017wr021606. short: I. Clemenzi, F. Pellicciotti, P. Burlando, Water Resources Research 54 (2018) 7929–7945. date_created: 2023-02-20T08:13:31Z date_published: 2018-06-07T00:00:00Z date_updated: 2023-02-28T11:42:40Z day: '07' doi: 10.1029/2017wr021606 extern: '1' intvolume: ' 54' issue: '10' keyword: - Water Science and Technology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1029/2017WR021606 month: '06' oa: 1 oa_version: Published Version page: 7929-7945 publication: Water Resources Research publication_identifier: eissn: - 1944-7973 issn: - 0043-1397 publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: Snow depth structure, fractal behavior, and interannual consistency over Haut Glacier d'Arolla, Switzerland type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2018' ... --- _id: '12604' abstract: - lang: eng text: Glaciers in the high mountains of Asia provide an important water resource for millions of people. Many of these glaciers are partially covered by rocky debris, which protects the ice from solar radiation and warm air. However, studies have found that the surface of these debris-covered glaciers is actually lowering as fast as glaciers without debris. Water ponded on the surface of the glaciers may be partially responsible, as water can absorb atmospheric energy very efficiently. However, the overall effect of these ponds has not been thoroughly assessed yet. We study a valley in Nepal for which we have extensive weather measurements, and we use a numerical model to calculate the energy absorbed by ponds on the surface of the glaciers over 6 months. As we have not observed each individual pond thoroughly, we run the model 5,000 times with different setups. We find that ponds are extremely important for glacier melt and absorb energy 14 times as quickly as the debris-covered ice. Although the ponds account for 1% of the glacier area covered by rocks, and only 0.3% of the total glacier area, they absorb enough energy to account for one eighth of the whole valley's ice loss. article_processing_charge: No article_type: letter_note author: - first_name: Evan S. full_name: Miles, Evan S. last_name: Miles - first_name: Ian full_name: Willis, Ian last_name: Willis - first_name: Pascal full_name: Buri, Pascal last_name: Buri - first_name: Jakob F. full_name: Steiner, Jakob F. last_name: Steiner - first_name: Neil S. full_name: Arnold, Neil S. last_name: Arnold - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: Miles ES, Willis I, Buri P, Steiner JF, Arnold NS, Pellicciotti F. Surface pond energy absorption across four Himalayan Glaciers accounts for 1/8 of total catchment ice loss. Geophysical Research Letters. 2018;45(19):10464-10473. doi:10.1029/2018gl079678 apa: Miles, E. S., Willis, I., Buri, P., Steiner, J. F., Arnold, N. S., & Pellicciotti, F. (2018). Surface pond energy absorption across four Himalayan Glaciers accounts for 1/8 of total catchment ice loss. Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2018gl079678 chicago: Miles, Evan S., Ian Willis, Pascal Buri, Jakob F. Steiner, Neil S. Arnold, and Francesca Pellicciotti. “Surface Pond Energy Absorption across Four Himalayan Glaciers Accounts for 1/8 of Total Catchment Ice Loss.” Geophysical Research Letters. American Geophysical Union, 2018. https://doi.org/10.1029/2018gl079678. ieee: E. S. Miles, I. Willis, P. Buri, J. F. Steiner, N. S. Arnold, and F. Pellicciotti, “Surface pond energy absorption across four Himalayan Glaciers accounts for 1/8 of total catchment ice loss,” Geophysical Research Letters, vol. 45, no. 19. American Geophysical Union, pp. 10464–10473, 2018. ista: Miles ES, Willis I, Buri P, Steiner JF, Arnold NS, Pellicciotti F. 2018. Surface pond energy absorption across four Himalayan Glaciers accounts for 1/8 of total catchment ice loss. Geophysical Research Letters. 45(19), 10464–10473. mla: Miles, Evan S., et al. “Surface Pond Energy Absorption across Four Himalayan Glaciers Accounts for 1/8 of Total Catchment Ice Loss.” Geophysical Research Letters, vol. 45, no. 19, American Geophysical Union, 2018, pp. 10464–73, doi:10.1029/2018gl079678. short: E.S. Miles, I. Willis, P. Buri, J.F. Steiner, N.S. Arnold, F. Pellicciotti, Geophysical Research Letters 45 (2018) 10464–10473. date_created: 2023-02-20T08:13:18Z date_published: 2018-10-18T00:00:00Z date_updated: 2023-02-28T11:46:48Z day: '18' doi: 10.1029/2018gl079678 extern: '1' intvolume: ' 45' issue: '19' keyword: - General Earth and Planetary Sciences - Geophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1029/2018GL079678 month: '10' oa: 1 oa_version: Published Version page: 10464-10473 publication: Geophysical Research Letters publication_identifier: eissn: - 1944-8007 issn: - 0094-8276 publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: Surface pond energy absorption across four Himalayan Glaciers accounts for 1/8 of total catchment ice loss type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2018' ... --- _id: '12607' abstract: - lang: eng text: Supraglacial ice cliffs exist on debris-covered glaciers worldwide, but despite their importance as melt hot spots, their life cycle is little understood. Early field observations had advanced a hypothesis of survival of north-facing and disappearance of south-facing cliffs, which is central for predicting the contribution of cliffs to total glacier mass losses. Their role as windows of energy transfer suggests they may explain the anomalously high mass losses of debris-covered glaciers in High Mountain Asia (HMA) despite the insulating debris, currently at the center of a debated controversy. We use a 3D model of cliff evolution coupled to very high-resolution topographic data to demonstrate that ice cliffs facing south (in the Northern Hemisphere) disappear within a few months due to enhanced solar radiation receipts and that aspect is the key control on cliffs evolution. We reproduce continuous flattening of south-facing cliffs, a result of their vertical gradient of incoming solar radiation and sky view factor. Our results establish that only north-facing cliffs are recurrent features and thus stable contributors to the melting of debris-covered glaciers. Satellite observations and mass balance modeling confirms that few south-facing cliffs of small size exist on the glaciers of Langtang, and their contribution to the glacier volume losses is very small (∼1%). This has major implications for the mass balance of HMA debris-covered glaciers as it provides the basis for new parameterizations of cliff evolution and distribution to constrain volume losses in a region where glaciers are highly relevant as water sources for millions of people. article_processing_charge: No article_type: original author: - first_name: Pascal full_name: Buri, Pascal last_name: Buri - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: Buri P, Pellicciotti F. Aspect controls the survival of ice cliffs on debris-covered glaciers. PNAS. 2018;115(17):4369-4374. doi:10.1073/pnas.1713892115 apa: Buri, P., & Pellicciotti, F. (2018). Aspect controls the survival of ice cliffs on debris-covered glaciers. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1713892115 chicago: Buri, Pascal, and Francesca Pellicciotti. “Aspect Controls the Survival of Ice Cliffs on Debris-Covered Glaciers.” PNAS. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713892115. ieee: P. Buri and F. Pellicciotti, “Aspect controls the survival of ice cliffs on debris-covered glaciers,” PNAS, vol. 115, no. 17. Proceedings of the National Academy of Sciences, pp. 4369–4374, 2018. ista: Buri P, Pellicciotti F. 2018. Aspect controls the survival of ice cliffs on debris-covered glaciers. PNAS. 115(17), 4369–4374. mla: Buri, Pascal, and Francesca Pellicciotti. “Aspect Controls the Survival of Ice Cliffs on Debris-Covered Glaciers.” PNAS, vol. 115, no. 17, Proceedings of the National Academy of Sciences, 2018, pp. 4369–74, doi:10.1073/pnas.1713892115. short: P. Buri, F. Pellicciotti, PNAS 115 (2018) 4369–4374. date_created: 2023-02-20T08:13:41Z date_published: 2018-04-09T00:00:00Z date_updated: 2023-02-28T11:35:18Z day: '09' doi: 10.1073/pnas.1713892115 extern: '1' intvolume: ' 115' issue: '17' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1713892115 month: '04' oa: 1 oa_version: Published Version page: 4369-4374 publication: PNAS publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Aspect controls the survival of ice cliffs on debris-covered glaciers type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2018' ... --- _id: '12606' abstract: - lang: eng text: Ice cliffs within a supraglacial debris cover have been identified as a source for high ablation relative to the surrounding debris-covered area. Due to their small relative size and steep orientation, ice cliffs are difficult to detect using nadir-looking space borne sensors. The method presented here uses surface slopes calculated from digital elevation model (DEM) data to map ice cliff geometry and produce an ice cliff probability map. Surface slope thresholds, which can be sensitive to geographic location and/or data quality, are selected automatically. The method also attempts to include area at the (often narrowing) ends of ice cliffs which could otherwise be neglected due to signal saturation in surface slope data. The method was calibrated in the eastern Alaska Range, Alaska, USA, against a control ice cliff dataset derived from high-resolution visible and thermal data. Using the same input parameter set that performed best in Alaska, the method was tested against ice cliffs manually mapped in the Khumbu Himal, Nepal. Our results suggest the method can accommodate different glaciological settings and different DEM data sources without a data intensive (high-resolution, multi-data source) recalibration. 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 citation: ama: Herreid S, Pellicciotti F. Automated detection of ice cliffs within supraglacial debris cover. The Cryosphere. 2018;12(5):1811-1829. doi:10.5194/tc-12-1811-2018 apa: Herreid, S., & Pellicciotti, F. (2018). Automated detection of ice cliffs within supraglacial debris cover. The Cryosphere. Copernicus Publications. https://doi.org/10.5194/tc-12-1811-2018 chicago: Herreid, Sam, and Francesca Pellicciotti. “Automated Detection of Ice Cliffs within Supraglacial Debris Cover.” The Cryosphere. Copernicus Publications, 2018. https://doi.org/10.5194/tc-12-1811-2018. ieee: S. Herreid and F. Pellicciotti, “Automated detection of ice cliffs within supraglacial debris cover,” The Cryosphere, vol. 12, no. 5. Copernicus Publications, pp. 1811–1829, 2018. ista: Herreid S, Pellicciotti F. 2018. Automated detection of ice cliffs within supraglacial debris cover. The Cryosphere. 12(5), 1811–1829. mla: Herreid, Sam, and Francesca Pellicciotti. “Automated Detection of Ice Cliffs within Supraglacial Debris Cover.” The Cryosphere, vol. 12, no. 5, Copernicus Publications, 2018, pp. 1811–29, doi:10.5194/tc-12-1811-2018. short: S. Herreid, F. Pellicciotti, The Cryosphere 12 (2018) 1811–1829. date_created: 2023-02-20T08:13:36Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-02-28T11:39:26Z day: '31' doi: 10.5194/tc-12-1811-2018 extern: '1' intvolume: ' 12' issue: '5' keyword: - Earth-Surface Processes - Water Science and Technology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.5194/tc-12-1811-2018 month: '05' oa: 1 oa_version: Published Version page: 1811-1829 publication: The Cryosphere publication_identifier: issn: - 1994-0424 publication_status: published publisher: Copernicus Publications quality_controlled: '1' scopus_import: '1' status: public title: Automated detection of ice cliffs within supraglacial debris cover type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2018' ... --- _id: '13255' abstract: - lang: eng text: Focused ion beams perfectly suit for patterning two-dimensional (2D) materials, but the optimization of irradiation parameters requires full microscopic understanding of defect production mechanisms. In contrast to freestanding 2D systems, the details of damage creation in supported 2D materials are not fully understood, whereas the majority of experiments have been carried out for 2D targets deposited on substrates. Here, we suggest a universal and computationally efficient scheme to model the irradiation of supported 2D materials, which combines analytical potential molecular dynamics with Monte Carlo simulations and makes it possible to independently assess the contributions to the damage from backscattered ions and atoms sputtered from the substrate. Using the scheme, we study the defect production in graphene and MoS2 sheets, which are the two most important and wide-spread 2D materials, deposited on a SiO2 substrate. For helium and neon ions with a wide range of initial ion energies including those used in a commercial helium ion microscope (HIM), we demonstrate that depending on the ion energy and mass, the defect production in 2D systems can be dominated by backscattered ions and sputtered substrate atoms rather than by the direct ion impacts and that the amount of damage in 2D materials heavily depends on whether a substrate is present or not. We also study the factors which limit the spatial resolution of the patterning process. Our results, which agree well with the available experimental data, provide not only insights into defect production but also quantitative information, which can be used for the minimization of damage during imaging in HIM or optimization of the patterning process. article_processing_charge: No article_type: original author: - first_name: Silvan full_name: Kretschmer, Silvan last_name: Kretschmer - first_name: Mikhail full_name: Maslov, Mikhail id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87 last_name: Maslov orcid: 0000-0003-4074-2570 - first_name: Sadegh full_name: Ghaderzadeh, Sadegh last_name: Ghaderzadeh - first_name: Mahdi full_name: Ghorbani-Asl, Mahdi last_name: Ghorbani-Asl - first_name: Gregor full_name: Hlawacek, Gregor last_name: Hlawacek - first_name: Arkady V. full_name: Krasheninnikov, Arkady V. last_name: Krasheninnikov citation: ama: 'Kretschmer S, Maslov M, Ghaderzadeh S, Ghorbani-Asl M, Hlawacek G, Krasheninnikov AV. Supported two-dimensional materials under ion irradiation: The substrate governs defect production. ACS Applied Materials & Interfaces. 2018;10(36):30827-30836. doi:10.1021/acsami.8b08471' apa: 'Kretschmer, S., Maslov, M., Ghaderzadeh, S., Ghorbani-Asl, M., Hlawacek, G., & Krasheninnikov, A. V. (2018). Supported two-dimensional materials under ion irradiation: The substrate governs defect production. ACS Applied Materials & Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.8b08471' chicago: 'Kretschmer, Silvan, Mikhail Maslov, Sadegh Ghaderzadeh, Mahdi Ghorbani-Asl, Gregor Hlawacek, and Arkady V. Krasheninnikov. “Supported Two-Dimensional Materials under Ion Irradiation: The Substrate Governs Defect Production.” ACS Applied Materials & Interfaces. American Chemical Society, 2018. https://doi.org/10.1021/acsami.8b08471.' ieee: 'S. Kretschmer, M. Maslov, S. Ghaderzadeh, M. Ghorbani-Asl, G. Hlawacek, and A. V. Krasheninnikov, “Supported two-dimensional materials under ion irradiation: The substrate governs defect production,” ACS Applied Materials & Interfaces, vol. 10, no. 36. American Chemical Society, pp. 30827–30836, 2018.' ista: 'Kretschmer S, Maslov M, Ghaderzadeh S, Ghorbani-Asl M, Hlawacek G, Krasheninnikov AV. 2018. Supported two-dimensional materials under ion irradiation: The substrate governs defect production. ACS Applied Materials & Interfaces. 10(36), 30827–30836.' mla: 'Kretschmer, Silvan, et al. “Supported Two-Dimensional Materials under Ion Irradiation: The Substrate Governs Defect Production.” ACS Applied Materials & Interfaces, vol. 10, no. 36, American Chemical Society, 2018, pp. 30827–36, doi:10.1021/acsami.8b08471.' short: S. Kretschmer, M. Maslov, S. Ghaderzadeh, M. Ghorbani-Asl, G. Hlawacek, A.V. Krasheninnikov, ACS Applied Materials & Interfaces 10 (2018) 30827–30836. date_created: 2023-07-21T11:43:00Z date_published: 2018-08-17T00:00:00Z date_updated: 2023-08-01T07:18:30Z day: '17' doi: 10.1021/acsami.8b08471 extern: '1' external_id: pmid: - '30117320' intvolume: ' 10' issue: '36' keyword: - General Materials Science language: - iso: eng month: '08' oa_version: None page: 30827-30836 pmid: 1 publication: ACS Applied Materials & Interfaces publication_identifier: issn: - 1944-8244 - 1944-8252 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: 'Supported two-dimensional materials under ion irradiation: The substrate governs defect production' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2018' ... --- _id: '13376' abstract: - lang: eng text: Efficient molecular switching in confined spaces is critical for the successful development of artificial molecular machines. However, molecular switching events often entail large structural changes and therefore require conformational freedom, which is typically limited under confinement conditions. Here, we investigated the behavior of azobenzene—the key building block of light-controlled molecular machines—in a confined environment that is flexible and can adapt its shape to that of the bound guest. To this end, we encapsulated several structurally diverse azobenzenes within the cavity of a flexible, water-soluble coordination cage, and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy and a combination of NMR methods, we showed that each of the encapsulated azobenzenes exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest inclusion complex could be efficiently photoisomerized in a reversible fashion. In contrast, successful switching in inclusion complexes incorporating two azobenzene guests was dependent on the availability of free cages in the system, and it involved reversible trafficking of azobenzene between the cages. In the absence of extra cages, photoswitching was either suppressed or it involved expulsion of azobenzene from the cage and consequently its precipitation from the solution. This finding was utilized to develop an information storage medium in which messages could be written and erased in a reversible fashion using light. article_processing_charge: No article_type: original author: - first_name: Dipak full_name: Samanta, Dipak last_name: Samanta - first_name: Julius full_name: Gemen, Julius last_name: Gemen - first_name: Zonglin full_name: Chu, Zonglin last_name: Chu - first_name: Yael full_name: Diskin-Posner, Yael last_name: Diskin-Posner - first_name: Linda J. W. full_name: Shimon, Linda J. W. last_name: Shimon - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. Reversible photoswitching of encapsulated azobenzenes in water. Proceedings of the National Academy of Sciences. 2018;115(38):9379-9384. doi:10.1073/pnas.1712787115 apa: Samanta, D., Gemen, J., Chu, Z., Diskin-Posner, Y., Shimon, L. J. W., & Klajn, R. (2018). Reversible photoswitching of encapsulated azobenzenes in water. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1712787115 chicago: Samanta, Dipak, Julius Gemen, Zonglin Chu, Yael Diskin-Posner, Linda J. W. Shimon, and Rafal Klajn. “Reversible Photoswitching of Encapsulated Azobenzenes in Water.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1712787115. ieee: D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L. J. W. Shimon, and R. Klajn, “Reversible photoswitching of encapsulated azobenzenes in water,” Proceedings of the National Academy of Sciences, vol. 115, no. 38. Proceedings of the National Academy of Sciences, pp. 9379–9384, 2018. ista: Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. 2018. Reversible photoswitching of encapsulated azobenzenes in water. Proceedings of the National Academy of Sciences. 115(38), 9379–9384. mla: Samanta, Dipak, et al. “Reversible Photoswitching of Encapsulated Azobenzenes in Water.” Proceedings of the National Academy of Sciences, vol. 115, no. 38, Proceedings of the National Academy of Sciences, 2018, pp. 9379–84, doi:10.1073/pnas.1712787115. short: D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L.J.W. Shimon, R. Klajn, Proceedings of the National Academy of Sciences 115 (2018) 9379–9384. date_created: 2023-08-01T09:40:00Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-08-07T10:58:11Z day: '01' doi: 10.1073/pnas.1712787115 extern: '1' external_id: pmid: - '29717041' intvolume: ' 115' issue: '38' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1712787115 month: '05' oa: 1 oa_version: Published Version page: 9379-9384 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Reversible photoswitching of encapsulated azobenzenes in water type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2018' ... --- _id: '13374' abstract: - lang: eng text: Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches—entities that can be toggled between two or more forms upon exposure to an external stimulus—often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating—and solubilizing in water—several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments. article_number: '641' article_processing_charge: No article_type: original author: - first_name: Dipak full_name: Samanta, Dipak last_name: Samanta - first_name: Daria full_name: Galaktionova, Daria last_name: Galaktionova - first_name: Julius full_name: Gemen, Julius last_name: Gemen - first_name: Linda J. W. full_name: Shimon, Linda J. W. last_name: Shimon - first_name: Yael full_name: Diskin-Posner, Yael last_name: Diskin-Posner - first_name: Liat full_name: Avram, Liat last_name: Avram - first_name: Petr full_name: Král, Petr last_name: Král - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Samanta D, Galaktionova D, Gemen J, et al. Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nature Communications. 2018;9. doi:10.1038/s41467-017-02715-6 apa: Samanta, D., Galaktionova, D., Gemen, J., Shimon, L. J. W., Diskin-Posner, Y., Avram, L., … Klajn, R. (2018). Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02715-6 chicago: Samanta, Dipak, Daria Galaktionova, Julius Gemen, Linda J. W. Shimon, Yael Diskin-Posner, Liat Avram, Petr Král, and Rafal Klajn. “Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02715-6. ieee: D. Samanta et al., “Reversible chromism of spiropyran in the cavity of a flexible coordination cage,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Samanta D, Galaktionova D, Gemen J, Shimon LJW, Diskin-Posner Y, Avram L, Král P, Klajn R. 2018. Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nature Communications. 9, 641. mla: Samanta, Dipak, et al. “Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage.” Nature Communications, vol. 9, 641, Springer Nature, 2018, doi:10.1038/s41467-017-02715-6. short: D. Samanta, D. Galaktionova, J. Gemen, L.J.W. Shimon, Y. Diskin-Posner, L. Avram, P. Král, R. Klajn, Nature Communications 9 (2018). date_created: 2023-08-01T09:39:32Z date_published: 2018-02-13T00:00:00Z date_updated: 2023-08-07T10:54:05Z day: '13' doi: 10.1038/s41467-017-02715-6 extern: '1' external_id: pmid: - '29440687' intvolume: ' 9' keyword: - General Physics and Astronomy - General Biochemistry - Genetics and Molecular Biology - General Chemistry - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-017-02715-6 month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-018-03701-2 scopus_import: '1' status: public title: Reversible chromism of spiropyran in the cavity of a flexible coordination cage type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '13377' abstract: - lang: eng text: Confining organic molecules to the surfaces of inorganic nanoparticles can induce intermolecular interactions between them, which can affect the composition of the mixed self-assembled monolayers obtained by co-adsorption from solution of two different molecules. Two thiolated ligands (a dialkylviologen and a zwitterionic sulfobetaine) that can interact with each other electrostatically were coadsorbed onto gold nanoparticles. The nanoparticles favor a narrow range of ratios of these two molecules that is largely independent of the molar ratio in solution. Changing the solution molar ratio of the two ligands by a factor of 5 000 affects the on-nanoparticle ratio of these ligands by only threefold. This behavior is reminiscent of the formation of insoluble inorganic salts (such as AgCl), which similarly compensate positive and negative charges upon crystallizing. Our results pave the way towards developing well-defined hybrid organic–inorganic nanostructures. article_processing_charge: No article_type: original author: - first_name: Zonglin full_name: Chu, Zonglin last_name: Chu - first_name: Yanxiao full_name: Han, Yanxiao last_name: Han - first_name: Petr full_name: Král, Petr last_name: Král - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: 'Chu Z, Han Y, Král P, Klajn R. “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. Angewandte Chemie International Edition. 2018;57(24):7023-7027. doi:10.1002/anie.201800673' apa: 'Chu, Z., Han, Y., Král, P., & Klajn, R. (2018). “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201800673' chicago: 'Chu, Zonglin, Yanxiao Han, Petr Král, and Rafal Klajn. “‘Precipitation on Nanoparticles’: Attractive Intermolecular Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201800673.' ieee: 'Z. Chu, Y. Han, P. Král, and R. Klajn, “‘Precipitation on nanoparticles’: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles,” Angewandte Chemie International Edition, vol. 57, no. 24. Wiley, pp. 7023–7027, 2018.' ista: 'Chu Z, Han Y, Král P, Klajn R. 2018. “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. Angewandte Chemie International Edition. 57(24), 7023–7027.' mla: 'Chu, Zonglin, et al. “‘Precipitation on Nanoparticles’: Attractive Intermolecular Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles.” Angewandte Chemie International Edition, vol. 57, no. 24, Wiley, 2018, pp. 7023–27, doi:10.1002/anie.201800673.' short: Z. Chu, Y. Han, P. Král, R. Klajn, Angewandte Chemie International Edition 57 (2018) 7023–7027. date_created: 2023-08-01T09:40:16Z date_published: 2018-06-11T00:00:00Z date_updated: 2023-08-07T11:14:28Z day: '11' doi: 10.1002/anie.201800673 extern: '1' external_id: pmid: - '29673022' intvolume: ' 57' issue: '24' keyword: - General Chemistry - Catalysis language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/anie.201800673 month: '06' oa: 1 oa_version: Published Version page: 7023-7027 pmid: 1 publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: '“Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2018' ...