--- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21095' abstract: - lang: eng text: 'Inspired by DNA mimic proteins, we have introduced aromatic foldamers bearing phosphonate groups as synthetic mimics of the charge surface of B-DNA and competitive inhibitors of some therapeutically relevant DNA-binding enzymes: the human DNA Topoisomerase 1 (Top1) and the human HIV-1 integrase (HIV-1 IN). We now report on variants of these anionic foldamers bearing carboxylates instead of phosphonates. Several new monomers have been synthesized with protecting groups suitable for solid phase synthesis (SPS). Six hexadecaamides have been prepared using SPS. Proof of their resemblance to B-DNA was brought by the first crystal structure of one of these DNA-mimic foldamers in its polyanionic form. While some of the foldamers were found to be as active as, or even more active than, the original phosphonate oligomers, others had no activity at all or could even stimulate enzyme activity in vitro. Some foldamers were found to have differential inhibitory effects on the two enzymes. These results demonstrate a strong dependence of inhibitory activity on foldamer structure and charge distribution. They open broad avenues for the development of new classes of derivatives that could inhibit the interaction of specific proteins with their DNA target thereby influencing the cellular pathways in which they are involved.' article_processing_charge: No article_type: original author: - first_name: Valentina full_name: Corvaglia, Valentina last_name: Corvaglia - first_name: Daniel full_name: Carbajo, Daniel last_name: Carbajo - first_name: Panchami full_name: Prabhakaran, Panchami last_name: Prabhakaran - first_name: Krzysztof full_name: Ziach, Krzysztof last_name: Ziach - first_name: Pradeep K full_name: Mandal, Pradeep K id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3 last_name: Mandal orcid: 0000-0001-5996-956X - first_name: Victor Dos full_name: Santos, Victor Dos last_name: Santos - first_name: Carole full_name: Legeay, Carole last_name: Legeay - first_name: Rachel full_name: Vogel, Rachel last_name: Vogel - first_name: Vincent full_name: Parissi, Vincent last_name: Parissi - first_name: Philippe full_name: Pourquier, Philippe last_name: Pourquier - first_name: Ivan full_name: Huc, Ivan last_name: Huc citation: ama: 'Corvaglia V, Carbajo D, Prabhakaran P, et al. Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: Artificial analogues of DNA mimic proteins. Nucleic Acids Research. 2019;47(11):5511-5521. doi:10.1093/nar/gkz352' apa: 'Corvaglia, V., Carbajo, D., Prabhakaran, P., Ziach, K., Mandal, P. K., Santos, V. D., … Huc, I. (2019). Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: Artificial analogues of DNA mimic proteins. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkz352' chicago: 'Corvaglia, Valentina, Daniel Carbajo, Panchami Prabhakaran, Krzysztof Ziach, Pradeep K Mandal, Victor Dos Santos, Carole Legeay, et al. “Carboxylate-Functionalized Foldamer Inhibitors of HIV-1 Integrase and Topoisomerase 1: Artificial Analogues of DNA Mimic Proteins.” Nucleic Acids Research. Oxford University Press, 2019. https://doi.org/10.1093/nar/gkz352.' ieee: 'V. Corvaglia et al., “Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: Artificial analogues of DNA mimic proteins,” Nucleic Acids Research, vol. 47, no. 11. Oxford University Press, pp. 5511–5521, 2019.' ista: 'Corvaglia V, Carbajo D, Prabhakaran P, Ziach K, Mandal PK, Santos VD, Legeay C, Vogel R, Parissi V, Pourquier P, Huc I. 2019. Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: Artificial analogues of DNA mimic proteins. Nucleic Acids Research. 47(11), 5511–5521.' mla: 'Corvaglia, Valentina, et al. “Carboxylate-Functionalized Foldamer Inhibitors of HIV-1 Integrase and Topoisomerase 1: Artificial Analogues of DNA Mimic Proteins.” Nucleic Acids Research, vol. 47, no. 11, Oxford University Press, 2019, pp. 5511–21, doi:10.1093/nar/gkz352.' short: V. Corvaglia, D. Carbajo, P. Prabhakaran, K. Ziach, P.K. Mandal, V.D. Santos, C. Legeay, R. Vogel, V. Parissi, P. Pourquier, I. Huc, Nucleic Acids Research 47 (2019) 5511–5521. date_created: 2026-01-29T21:17:15Z date_published: 2019-06-20T00:00:00Z date_updated: 2026-02-23T09:56:28Z day: '20' doi: 10.1093/nar/gkz352 extern: '1' has_accepted_license: '1' intvolume: ' 47' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/nar/gkz352 month: '06' oa: 1 oa_version: Published Version page: 5511-5521 publication: Nucleic Acids Research publication_identifier: eissn: - 1362-4962 issn: - 0305-1048 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: 'Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: Artificial analogues of DNA mimic proteins' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2019' ... --- _id: '170' abstract: - lang: eng text: Upper and lower bounds, of the expected order of magnitude, are obtained for the number of rational points of bounded height on any quartic del Pezzo surface over ℚ that contains a conic defined over ℚ . arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Efthymios full_name: Sofos, Efthymios last_name: Sofos citation: ama: Browning TD, Sofos E. Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. 2019;373(3-4):977-1016. doi:10.1007/s00208-018-1716-6 apa: Browning, T. D., & Sofos, E. (2019). Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-018-1716-6 chicago: Browning, Timothy D, and Efthymios Sofos. “Counting Rational Points on Quartic Del Pezzo Surfaces with a Rational Conic.” Mathematische Annalen. Springer Nature, 2019. https://doi.org/10.1007/s00208-018-1716-6. ieee: T. D. Browning and E. Sofos, “Counting rational points on quartic del Pezzo surfaces with a rational conic,” Mathematische Annalen, vol. 373, no. 3–4. Springer Nature, pp. 977–1016, 2019. ista: Browning TD, Sofos E. 2019. Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. 373(3–4), 977–1016. mla: Browning, Timothy D., and Efthymios Sofos. “Counting Rational Points on Quartic Del Pezzo Surfaces with a Rational Conic.” Mathematische Annalen, vol. 373, no. 3–4, Springer Nature, 2019, pp. 977–1016, doi:10.1007/s00208-018-1716-6. short: T.D. Browning, E. Sofos, Mathematische Annalen 373 (2019) 977–1016. date_created: 2018-12-11T11:44:59Z date_published: 2019-04-01T00:00:00Z date_updated: 2021-01-12T06:52:37Z day: '01' ddc: - '510' doi: 10.1007/s00208-018-1716-6 extern: '1' external_id: arxiv: - '1609.09057' file: - access_level: open_access checksum: 4061dc2fe99bee25d9adf2d2018cf608 content_type: application/pdf creator: dernst date_created: 2019-05-23T07:53:27Z date_updated: 2020-07-14T12:45:12Z file_id: '6479' file_name: 2019_MathAnnalen_Browning.pdf file_size: 712847 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 373' issue: 3-4 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 977-1016 publication: Mathematische Annalen publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Counting rational points on quartic del Pezzo surfaces with a rational conic 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: 373 year: '2019' ... --- _id: '175' abstract: - lang: eng text: An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points. article_processing_charge: No arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Daniel full_name: Loughran, Daniel last_name: Loughran citation: ama: Browning TD, Loughran D. Sieving rational points on varieties. Transactions of the American Mathematical Society. 2019;371(8):5757-5785. doi:10.1090/tran/7514 apa: Browning, T. D., & Loughran, D. (2019). Sieving rational points on varieties. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7514 chicago: Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7514. ieee: T. D. Browning and D. Loughran, “Sieving rational points on varieties,” Transactions of the American Mathematical Society, vol. 371, no. 8. American Mathematical Society, pp. 5757–5785, 2019. ista: Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785. mla: Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society, vol. 371, no. 8, American Mathematical Society, 2019, pp. 5757–85, doi:10.1090/tran/7514. short: T.D. Browning, D. Loughran, Transactions of the American Mathematical Society 371 (2019) 5757–5785. date_created: 2018-12-11T11:45:01Z date_published: 2019-04-15T00:00:00Z date_updated: 2025-07-10T11:51:20Z day: '15' department: - _id: TiBr doi: 10.1090/tran/7514 external_id: arxiv: - '1705.01999' isi: - '000464034200019' intvolume: ' 371' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.01999 month: '04' oa: 1 oa_version: Preprint page: 5757-5785 publication: Transactions of the American Mathematical Society publication_identifier: eissn: - 1088-6850 issn: - 0002-9947 publication_status: published publisher: American Mathematical Society publist_id: '7746' quality_controlled: '1' scopus_import: '1' status: public title: Sieving rational points on varieties type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 371 year: '2019' ... --- _id: '17506' abstract: - lang: eng text: Sandboxing is a common technique that allows low-level, untrusted components to safely interact with trusted code. However, previous work has only investigated the low-level memory isolation guarantees of sandboxing, leaving open the question of the end-to-end guarantees that sandboxing affords programmers. In this paper, we fill this gap by showing that sandboxing enables reasoning about the known concept of robust safety, i.e., safety of the trusted code even in the presence of arbitrary untrusted code. To do this, we first present an idealized operational semantics for a language that combines trusted code with untrusted code. Sandboxing is built into our semantics. Then, we prove that safety properties of the trusted code (as enforced through a rich type system) are upheld in the presence of arbitrary untrusted code, so long as all interactions with untrusted code occur at the “any” type (a type inhabited by all values). Finally, to alleviate the burden of having to interact with untrusted code at only the “any” type, we formalize and prove safe several wrappers, which automatically convert values between the “any” type and much richer types. All our results are mechanized in the Coq proof assistant. article_processing_charge: No article_type: original author: - first_name: Michael Joachim full_name: Sammler, Michael Joachim id: 510d3901-2a03-11ee-914d-d9ae9011f0a7 last_name: Sammler - first_name: Deepak full_name: Garg, Deepak last_name: Garg - first_name: Derek full_name: Dreyer, Derek last_name: Dreyer - first_name: Tadeusz full_name: Litak, Tadeusz last_name: Litak citation: ama: Sammler MJ, Garg D, Dreyer D, Litak T. The high-level benefits of low-level sandboxing. Proceedings of the ACM on Programming Languages. 2019;4(POPL):1-32. doi:10.1145/3371100 apa: Sammler, M. J., Garg, D., Dreyer, D., & Litak, T. (2019). The high-level benefits of low-level sandboxing. Proceedings of the ACM on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3371100 chicago: Sammler, Michael Joachim, Deepak Garg, Derek Dreyer, and Tadeusz Litak. “The High-Level Benefits of Low-Level Sandboxing.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2019. https://doi.org/10.1145/3371100. ieee: M. J. Sammler, D. Garg, D. Dreyer, and T. Litak, “The high-level benefits of low-level sandboxing,” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL. Association for Computing Machinery, pp. 1–32, 2019. ista: Sammler MJ, Garg D, Dreyer D, Litak T. 2019. The high-level benefits of low-level sandboxing. Proceedings of the ACM on Programming Languages. 4(POPL), 1–32. mla: Sammler, Michael Joachim, et al. “The High-Level Benefits of Low-Level Sandboxing.” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL, Association for Computing Machinery, 2019, pp. 1–32, doi:10.1145/3371100. short: M.J. Sammler, D. Garg, D. Dreyer, T. Litak, Proceedings of the ACM on Programming Languages 4 (2019) 1–32. date_created: 2024-09-05T08:36:52Z date_published: 2019-12-20T00:00:00Z date_updated: 2024-09-10T09:58:57Z day: '20' doi: 10.1145/3371100 extern: '1' intvolume: ' 4' issue: POPL language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/3371100 month: '12' oa: 1 oa_version: Published Version page: 1-32 publication: Proceedings of the ACM on Programming Languages publication_identifier: issn: - 2475-1421 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: The high-level benefits of low-level sandboxing type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 4 year: '2019' ... --- _id: '17510' abstract: - lang: eng text: Weak lensing surveys are reaching sensitivities at which uncertainties in the galaxy redshift distributions n(z) from photo-z errors degrade cosmological constraints. We use ray-tracing simulations and a simple treatment of photo-z errors to assess cosmological parameter biases from uncertainties in n(z) in an LSST-like survey. We use lensing peak counts and the power spectrum to infer cosmological parameters, and find that the latter is somewhat more resilient to photo-z errors. We place conservative lower limits on the survey size at which different types of photo-z errors significantly degrade (${\sim }50{{\ \rm per\ cent}}$) ΛCDM (cold dark matter, wCDM) parameter constraints. A residual constant photo-z bias of |δz| &lt; 0.003(1 + z), the current LSST requirement, does not significantly degrade surveys smaller than ≈1300 (≈490) deg2 using peaks and ≈6500 (≈4900) deg2 using the power spectrum. Surveys smaller than ≈920 (≈450) deg2 and ≈4600 (≈4000) deg2 avoid 25 per cent degradation. Adopting a recent prediction for LSST’s full photo-z probability distribution function (PDF), we find that simply approximating n(z) with the photo-z galaxy distribution computed from this PDF significantly degrades surveys as small as ≈60 (≈65) deg2 using peaks or the power spectrum. If the centroid bias in each tomographic bin is removed from the photo-z galaxy distribution, using peaks or the power spectrum still significantly degrades surveys larger than ≈200 (≈255) or ≈248 (≈315) deg2; 25 per cent degradations occur at survey sizes of ≈140 (≈180) deg2 or ≈165 (≈210) deg2. These results imply that the expected broad photo-z PDF significantly biases parameters, which must be further mitigated using more sophisticated photo-z treatments. article_processing_charge: No article_type: original author: - first_name: Matthew W full_name: Abruzzo, Matthew W last_name: Abruzzo - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman citation: ama: Abruzzo MW, Haiman Z. The impact of photometric redshift errors on lensing statistics in ray-tracing simulations. Monthly Notices of the Royal Astronomical Society. 2019;486(2):2730-2753. doi:10.1093/mnras/stz1016 apa: Abruzzo, M. W., & Haiman, Z. (2019). The impact of photometric redshift errors on lensing statistics in ray-tracing simulations. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz1016 chicago: Abruzzo, Matthew W, and Zoltán Haiman. “The Impact of Photometric Redshift Errors on Lensing Statistics in Ray-Tracing Simulations.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz1016. ieee: M. W. Abruzzo and Z. Haiman, “The impact of photometric redshift errors on lensing statistics in ray-tracing simulations,” Monthly Notices of the Royal Astronomical Society, vol. 486, no. 2. Oxford University Press, pp. 2730–2753, 2019. ista: Abruzzo MW, Haiman Z. 2019. The impact of photometric redshift errors on lensing statistics in ray-tracing simulations. Monthly Notices of the Royal Astronomical Society. 486(2), 2730–2753. mla: Abruzzo, Matthew W., and Zoltán Haiman. “The Impact of Photometric Redshift Errors on Lensing Statistics in Ray-Tracing Simulations.” Monthly Notices of the Royal Astronomical Society, vol. 486, no. 2, Oxford University Press, 2019, pp. 2730–53, doi:10.1093/mnras/stz1016. short: M.W. Abruzzo, Z. Haiman, Monthly Notices of the Royal Astronomical Society 486 (2019) 2730–2753. date_created: 2024-09-05T08:49:24Z date_published: 2019-04-18T00:00:00Z date_updated: 2024-09-10T12:49:04Z day: '18' doi: 10.1093/mnras/stz1016 extern: '1' intvolume: ' 486' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/stz1016 month: '04' oa: 1 oa_version: Published Version page: 2730-2753 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The impact of photometric redshift errors on lensing statistics in ray-tracing simulations type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 486 year: '2019' ... --- _id: '17511' article_number: '019' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Gabriela A. full_name: Marques, Gabriela A. last_name: Marques - first_name: Jia full_name: Liu, Jia last_name: Liu - first_name: José Manuel Zorrilla full_name: Matilla, José Manuel Zorrilla last_name: Matilla - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: Armando full_name: Bernui, Armando last_name: Bernui - first_name: Camila P. full_name: Novaes, Camila P. last_name: Novaes citation: ama: Marques GA, Liu J, Matilla JMZ, Haiman Z, Bernui A, Novaes CP. Constraining neutrino mass with weak lensing Minkowski Functionals. Journal of Cosmology and Astroparticle Physics. 2019;2019(06). doi:10.1088/1475-7516/2019/06/019 apa: Marques, G. A., Liu, J., Matilla, J. M. Z., Haiman, Z., Bernui, A., & Novaes, C. P. (2019). Constraining neutrino mass with weak lensing Minkowski Functionals. Journal of Cosmology and Astroparticle Physics. IOP Publishing. https://doi.org/10.1088/1475-7516/2019/06/019 chicago: Marques, Gabriela A., Jia Liu, José Manuel Zorrilla Matilla, Zoltán Haiman, Armando Bernui, and Camila P. Novaes. “Constraining Neutrino Mass with Weak Lensing Minkowski Functionals.” Journal of Cosmology and Astroparticle Physics. IOP Publishing, 2019. https://doi.org/10.1088/1475-7516/2019/06/019. ieee: G. A. Marques, J. Liu, J. M. Z. Matilla, Z. Haiman, A. Bernui, and C. P. Novaes, “Constraining neutrino mass with weak lensing Minkowski Functionals,” Journal of Cosmology and Astroparticle Physics, vol. 2019, no. 06. IOP Publishing, 2019. ista: Marques GA, Liu J, Matilla JMZ, Haiman Z, Bernui A, Novaes CP. 2019. Constraining neutrino mass with weak lensing Minkowski Functionals. Journal of Cosmology and Astroparticle Physics. 2019(06), 019. mla: Marques, Gabriela A., et al. “Constraining Neutrino Mass with Weak Lensing Minkowski Functionals.” Journal of Cosmology and Astroparticle Physics, vol. 2019, no. 06, 019, IOP Publishing, 2019, doi:10.1088/1475-7516/2019/06/019. short: G.A. Marques, J. Liu, J.M.Z. Matilla, Z. Haiman, A. Bernui, C.P. Novaes, Journal of Cosmology and Astroparticle Physics 2019 (2019). date_created: 2024-09-05T08:50:20Z date_published: 2019-06-07T00:00:00Z date_updated: 2024-09-10T13:10:34Z day: '07' doi: 10.1088/1475-7516/2019/06/019 extern: '1' external_id: arxiv: - '1812.08206' intvolume: ' 2019' issue: '06' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1812.08206' month: '06' oa: 1 oa_version: Preprint publication: Journal of Cosmology and Astroparticle Physics publication_identifier: issn: - 1475-7516 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Constraining neutrino mass with weak lensing Minkowski Functionals type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 2019 year: '2019' ... --- _id: '17512' abstract: - lang: eng text: 'The localization of stellar-mass binary black hole mergers using gravitational waves is critical in understanding the properties of the binaries’ host galaxies, observing possible electromagnetic emission from the mergers, or using them as a cosmological distance ladder. The precision of this localization can be substantially increased with prior astrophysical information about the binary system. In particular, constraining the inclination of the binary can reduce the distance uncertainty of the source. Here, we present the first realistic set of localizations for binary black hole mergers, including different prior constraints on the binaries’ inclinations. We find that prior information on the inclination can reduce the localization volume by a factor of 3. We discuss two astrophysical scenarios of interest: (i) follow-up searches for beamed electromagnetic/neutrino counterparts and (ii) mergers in the accretion discs of active galactic nuclei.' article_processing_charge: No article_type: original author: - first_name: K Rainer full_name: Corley, K Rainer last_name: Corley - first_name: Imre full_name: Bartos, Imre last_name: Bartos - first_name: Leo P full_name: Singer, Leo P last_name: Singer - first_name: Andrew R full_name: Williamson, Andrew R last_name: Williamson - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: Bence full_name: Kocsis, Bence last_name: Kocsis - first_name: Samaya full_name: Nissanke, Samaya last_name: Nissanke - first_name: Zsuzsa full_name: Márka, Zsuzsa last_name: Márka - first_name: Szabolcs full_name: Márka, Szabolcs last_name: Márka citation: ama: Corley KR, Bartos I, Singer LP, et al. Localization of binary black hole mergers with known inclination. Monthly Notices of the Royal Astronomical Society. 2019;488(3):4459-4463. doi:10.1093/mnras/stz2072 apa: Corley, K. R., Bartos, I., Singer, L. P., Williamson, A. R., Haiman, Z., Kocsis, B., … Márka, S. (2019). Localization of binary black hole mergers with known inclination. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz2072 chicago: Corley, K Rainer, Imre Bartos, Leo P Singer, Andrew R Williamson, Zoltán Haiman, Bence Kocsis, Samaya Nissanke, Zsuzsa Márka, and Szabolcs Márka. “Localization of Binary Black Hole Mergers with Known Inclination.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz2072. ieee: K. R. Corley et al., “Localization of binary black hole mergers with known inclination,” Monthly Notices of the Royal Astronomical Society, vol. 488, no. 3. Oxford University Press, pp. 4459–4463, 2019. ista: Corley KR, Bartos I, Singer LP, Williamson AR, Haiman Z, Kocsis B, Nissanke S, Márka Z, Márka S. 2019. Localization of binary black hole mergers with known inclination. Monthly Notices of the Royal Astronomical Society. 488(3), 4459–4463. mla: Corley, K. Rainer, et al. “Localization of Binary Black Hole Mergers with Known Inclination.” Monthly Notices of the Royal Astronomical Society, vol. 488, no. 3, Oxford University Press, 2019, pp. 4459–63, doi:10.1093/mnras/stz2072. short: K.R. Corley, I. Bartos, L.P. Singer, A.R. Williamson, Z. Haiman, B. Kocsis, S. Nissanke, Z. Márka, S. Márka, Monthly Notices of the Royal Astronomical Society 488 (2019) 4459–4463. date_created: 2024-09-05T08:51:22Z date_published: 2019-07-30T00:00:00Z date_updated: 2024-09-10T13:26:28Z day: '30' doi: 10.1093/mnras/stz2072 extern: '1' intvolume: ' 488' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/stz2072 month: '07' oa: 1 oa_version: Published Version page: 4459-4463 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Localization of binary black hole mergers with known inclination type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 488 year: '2019' ... --- _id: '17530' abstract: - lang: eng text: Based on the cosmic shear data from the Canada-France-Hawaii Telescope Lensing Survey (CFHTLenS), Kilbinger et al. (2013) obtained a constraint on the amplitude of matter fluctuations of σ8(Ωm/0.27)0.6=0.79±0.03 from the two-point correlation function (2PCF). This is ≈3σ lower than the value 0.89±0.01 derived from Planck data on cosmic microwave background (CMB) anisotropies. On the other hand, based on the same CFHTLenS data, but using the power spectrum, and performing a different analysis, Liu et al. (2015) obtained the higher value of σ8(Ωm/0.27)0.64=0.87+0.05−0.06. We here investigate the origin of this difference, by performing a fair side-by-side comparison of the 2PCF and power spectrum analyses on CFHTLenS data. We find that these two statistics indeed deliver different results, even when applied to the same data in an otherwise identical procedure. We identify excess power in the data on small scales (ℓ>5,000) driving the larger values inferred from the power spectrum. We speculate on the possible origin of this excess small-scale power. More generally, our results highlight the utility of analysing the 2PCF and the power spectrum in tandem, to discover (and to help control) systematic errors. article_processing_charge: No article_type: original author: - first_name: Tianhuan full_name: Lu, Tianhuan last_name: Lu - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman citation: ama: Lu T, Haiman Z. The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data. Monthly Notices of the Royal Astronomical Society. 2019;490(4):5033-5042. doi:10.1093/mnras/stz2931 apa: Lu, T., & Haiman, Z. (2019). The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz2931 chicago: Lu, Tianhuan, and Zoltán Haiman. “The Matter Fluctuation Amplitude Inferred from the Weak Lensing Power Spectrum and Correlation Function in CFHTLenS Data.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz2931. ieee: T. Lu and Z. Haiman, “The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data,” Monthly Notices of the Royal Astronomical Society, vol. 490, no. 4. Oxford University Press, pp. 5033–5042, 2019. ista: Lu T, Haiman Z. 2019. The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data. Monthly Notices of the Royal Astronomical Society. 490(4), 5033–5042. mla: Lu, Tianhuan, and Zoltán Haiman. “The Matter Fluctuation Amplitude Inferred from the Weak Lensing Power Spectrum and Correlation Function in CFHTLenS Data.” Monthly Notices of the Royal Astronomical Society, vol. 490, no. 4, Oxford University Press, 2019, pp. 5033–42, doi:10.1093/mnras/stz2931. short: T. Lu, Z. Haiman, Monthly Notices of the Royal Astronomical Society 490 (2019) 5033–5042. date_created: 2024-09-05T09:37:20Z date_published: 2019-10-18T00:00:00Z date_updated: 2024-09-11T08:01:58Z day: '18' doi: 10.1093/mnras/stz2931 extern: '1' intvolume: ' 490' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/stz2931 month: '10' oa: 1 oa_version: Published Version page: 5033-5042 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1093/mnras/stad1748 scopus_import: '1' status: public title: The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 490 year: '2019' ... --- _id: '17533' abstract: - lang: eng text: "The origins of the stellar-mass black hole mergers discovered by LIGO/Virgo are still unknown. Here we show that if migration traps develop in the accretion disks of active galactic nuclei (AGNs) and promote the mergers of their captive black holes, the majority of black holes within disks will undergo hierarchical mergers—with one of the black holes being the remnant of a previous merger. 40% of AGN-assisted mergers detected by LIGO/Virgo will include a black hole with mass ≳50⁢\U0001D440⊙, the mass limit from stellar core collapse. Hierarchical mergers at traps in AGNs will exhibit black hole spins (anti)aligned with the binary’s orbital axis, a distinct property from other hierarchical channels. Our results suggest, although not definitively (with odds ratio of ∼1), that LIGO’s heaviest merger so far, GW170729, could have originated from this channel." article_number: '181101' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Y. full_name: Yang, Y. last_name: Yang - first_name: I. full_name: Bartos, I. last_name: Bartos - first_name: V. full_name: Gayathri, V. last_name: Gayathri - first_name: K. E. S. full_name: Ford, K. E. S. last_name: Ford - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: S. full_name: Klimenko, S. last_name: Klimenko - first_name: B. full_name: Kocsis, B. last_name: Kocsis - first_name: S. full_name: Márka, S. last_name: Márka - first_name: Z. full_name: Márka, Z. last_name: Márka - first_name: B. full_name: McKernan, B. last_name: McKernan - first_name: R. full_name: O’Shaughnessy, R. last_name: O’Shaughnessy citation: ama: Yang Y, Bartos I, Gayathri V, et al. Hierarchical black hole mergers in active galactic nuclei. Physical Review Letters. 2019;123(18). doi:10.1103/physrevlett.123.181101 apa: Yang, Y., Bartos, I., Gayathri, V., Ford, K. E. S., Haiman, Z., Klimenko, S., … O’Shaughnessy, R. (2019). Hierarchical black hole mergers in active galactic nuclei. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.123.181101 chicago: Yang, Y., I. Bartos, V. Gayathri, K. E. S. Ford, Zoltán Haiman, S. Klimenko, B. Kocsis, et al. “Hierarchical Black Hole Mergers in Active Galactic Nuclei.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.123.181101. ieee: Y. Yang et al., “Hierarchical black hole mergers in active galactic nuclei,” Physical Review Letters, vol. 123, no. 18. American Physical Society, 2019. ista: Yang Y, Bartos I, Gayathri V, Ford KES, Haiman Z, Klimenko S, Kocsis B, Márka S, Márka Z, McKernan B, O’Shaughnessy R. 2019. Hierarchical black hole mergers in active galactic nuclei. Physical Review Letters. 123(18), 181101. mla: Yang, Y., et al. “Hierarchical Black Hole Mergers in Active Galactic Nuclei.” Physical Review Letters, vol. 123, no. 18, 181101, American Physical Society, 2019, doi:10.1103/physrevlett.123.181101. short: Y. Yang, I. Bartos, V. Gayathri, K.E.S. Ford, Z. Haiman, S. Klimenko, B. Kocsis, S. Márka, Z. Márka, B. McKernan, R. O’Shaughnessy, Physical Review Letters 123 (2019). date_created: 2024-09-05T09:39:53Z date_published: 2019-11-01T00:00:00Z date_updated: 2024-09-11T14:39:29Z day: '1' doi: 10.1103/physrevlett.123.181101 extern: '1' external_id: arxiv: - '1906.09281' intvolume: ' 123' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1906.09281' month: '11' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_identifier: issn: - 0031-9007 - 1079-7114 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Hierarchical black hole mergers in active galactic nuclei type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 123 year: '2019' ... --- _id: '17541' abstract: - lang: eng text: 'In recent years, the discovery of massive quasars at z~7 has provided a striking challenge to our understanding of the origin and growth of supermassive black holes in the early Universe. Mounting observational and theoretical evidence indicates the viability of massive seeds, formed by the collapse of supermassive stars, as a progenitor model for such early, massive accreting black holes. Although considerable progress has been made in our theoretical understanding, many questions remain regarding how (and how often) such objects may form, how they live and die, and how next generation observatories may yield new insight into the origin of these primordial titans. This review focusses on our present understanding of this remarkable formation scenario, based on discussions held at the Monash Prato Centre from November 20--24, 2017, during the workshop "Titans of the Early Universe: The Origin of the First Supermassive Black Holes."' article_number: e027 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Tyrone E. full_name: Woods, Tyrone E. last_name: Woods - first_name: Bhaskar full_name: Agarwal, Bhaskar last_name: Agarwal - first_name: Volker full_name: Bromm, Volker last_name: Bromm - first_name: Andrew full_name: Bunker, Andrew last_name: Bunker - first_name: Ke-Jung full_name: Chen, Ke-Jung last_name: Chen - first_name: Sunmyon full_name: Chon, Sunmyon last_name: Chon - first_name: Andrea full_name: Ferrara, Andrea last_name: Ferrara - first_name: Simon C. O. full_name: Glover, Simon C. O. last_name: Glover - first_name: Lionel full_name: Haemmerlé, Lionel last_name: Haemmerlé - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: Tilman full_name: Hartwig, Tilman last_name: Hartwig - first_name: Alexander full_name: Heger, Alexander last_name: Heger - first_name: Shingo full_name: Hirano, Shingo last_name: Hirano - first_name: Takashi full_name: Hosokawa, Takashi last_name: Hosokawa - first_name: Kohei full_name: Inayoshi, Kohei last_name: Inayoshi - first_name: Ralf S. full_name: Klessen, Ralf S. last_name: Klessen - first_name: Chiaki full_name: Kobayashi, Chiaki last_name: Kobayashi - first_name: Filippos full_name: Koliopanos, Filippos last_name: Koliopanos - first_name: Muhammad A. full_name: Latif, Muhammad A. last_name: Latif - first_name: Yuexing full_name: Li, Yuexing last_name: Li - first_name: Lucio full_name: Mayer, Lucio last_name: Mayer - first_name: Mar full_name: Mezcua, Mar last_name: Mezcua - first_name: Priyamvada full_name: Natarajan, Priyamvada last_name: Natarajan - first_name: Fabio full_name: Pacucci, Fabio last_name: Pacucci - first_name: Martin J. full_name: Rees, Martin J. last_name: Rees - first_name: John A. full_name: Regan, John A. last_name: Regan - first_name: Yuya full_name: Sakurai, Yuya last_name: Sakurai - first_name: Stefania full_name: Salvadori, Stefania last_name: Salvadori - first_name: Raffaella full_name: Schneider, Raffaella last_name: Schneider - first_name: Marco full_name: Surace, Marco last_name: Surace - first_name: Takamitsu L. full_name: Tanaka, Takamitsu L. last_name: Tanaka - first_name: Daniel J. full_name: Whalen, Daniel J. last_name: Whalen - first_name: Naoki full_name: Yoshida, Naoki last_name: Yoshida citation: ama: 'Woods TE, Agarwal B, Bromm V, et al. Titans of the early universe: The prato statement on the origin of the first supermassive black holes. Publications of the Astronomical Society of Australia. 2019;36. doi:10.1017/pasa.2019.14' apa: 'Woods, T. E., Agarwal, B., Bromm, V., Bunker, A., Chen, K.-J., Chon, S., … Yoshida, N. (2019). Titans of the early universe: The prato statement on the origin of the first supermassive black holes. Publications of the Astronomical Society of Australia. Cambridge University Press. https://doi.org/10.1017/pasa.2019.14' chicago: 'Woods, Tyrone E., Bhaskar Agarwal, Volker Bromm, Andrew Bunker, Ke-Jung Chen, Sunmyon Chon, Andrea Ferrara, et al. “Titans of the Early Universe: The Prato Statement on the Origin of the First Supermassive Black Holes.” Publications of the Astronomical Society of Australia. Cambridge University Press, 2019. https://doi.org/10.1017/pasa.2019.14.' ieee: 'T. E. Woods et al., “Titans of the early universe: The prato statement on the origin of the first supermassive black holes,” Publications of the Astronomical Society of Australia, vol. 36. Cambridge University Press, 2019.' ista: 'Woods TE, Agarwal B, Bromm V, Bunker A, Chen K-J, Chon S, Ferrara A, Glover SCO, Haemmerlé L, Haiman Z, Hartwig T, Heger A, Hirano S, Hosokawa T, Inayoshi K, Klessen RS, Kobayashi C, Koliopanos F, Latif MA, Li Y, Mayer L, Mezcua M, Natarajan P, Pacucci F, Rees MJ, Regan JA, Sakurai Y, Salvadori S, Schneider R, Surace M, Tanaka TL, Whalen DJ, Yoshida N. 2019. Titans of the early universe: The prato statement on the origin of the first supermassive black holes. Publications of the Astronomical Society of Australia. 36, e027.' mla: 'Woods, Tyrone E., et al. “Titans of the Early Universe: The Prato Statement on the Origin of the First Supermassive Black Holes.” Publications of the Astronomical Society of Australia, vol. 36, e027, Cambridge University Press, 2019, doi:10.1017/pasa.2019.14.' short: T.E. Woods, B. Agarwal, V. Bromm, A. Bunker, K.-J. Chen, S. Chon, A. Ferrara, S.C.O. Glover, L. Haemmerlé, Z. Haiman, T. Hartwig, A. Heger, S. Hirano, T. Hosokawa, K. Inayoshi, R.S. Klessen, C. Kobayashi, F. Koliopanos, M.A. Latif, Y. Li, L. Mayer, M. Mezcua, P. Natarajan, F. Pacucci, M.J. Rees, J.A. Regan, Y. Sakurai, S. Salvadori, R. Schneider, M. Surace, T.L. Tanaka, D.J. Whalen, N. Yoshida, Publications of the Astronomical Society of Australia 36 (2019). date_created: 2024-09-05T09:57:20Z date_published: 2019-08-06T00:00:00Z date_updated: 2024-09-12T13:20:41Z day: '06' doi: 10.1017/pasa.2019.14 extern: '1' external_id: arxiv: - '1810.12310' intvolume: ' 36' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1810.12310' month: '08' oa: 1 oa_version: Preprint publication: Publications of the Astronomical Society of Australia publication_identifier: issn: - 1323-3580 - 1448-6083 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Titans of the early universe: The prato statement on the origin of the first supermassive black holes' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 36 year: '2019' ... --- _id: '17543' abstract: - lang: eng text: 'Massive black-hole (MBH) binaries, which are expected to form following the merger of their parent galaxies, produce gravitational waves which will be detectable by Pulsar Timing Arrays at nanohertz frequencies (year periods). While no confirmed, compact MBH binary systems have been seen in electromagnetic observations, a large number of candidates have recently been identified in optical surveys of AGN variability. Using a combination of cosmological, hydrodynamic simulations; comprehensive, semi-analytic binary merger models; and analytic AGN spectra and variability prescriptions; we calculate the expected electromagnetic detection rates of MBH binaries as periodically variable AGN. In particular, we consider two independent variability models: (i) Doppler boosting due to large orbital velocities, and (ii) hydrodynamic variability in which the fueling of MBH accretion disks is periodically modulated by the companion. Our models predict that numerous MBH binaries should be present and distinguishable in the existing data. In particular, our fiducial models produce an expectation value of 0.2 (Doppler) and 5 (hydrodynamic) binaries to be identifiable in CRTS, while 20 and 100 are expected after five years of LSST observations. The brightness variations in most systems are too small to be distinguishable, but almost 1% of AGN at redshifts z≲0.6 could be in massive binaries. We analyze the predicted binary parameters of observable systems and their selection biases, and include an extensive discussion of our model parameters and uncertainties.' article_processing_charge: No article_type: original author: - first_name: Luke Zoltan full_name: Kelley, Luke Zoltan last_name: Kelley - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: Alberto full_name: Sesana, Alberto last_name: Sesana - first_name: Lars full_name: Hernquist, Lars last_name: Hernquist citation: ama: Kelley LZ, Haiman Z, Sesana A, Hernquist L. Massive BH binaries as periodically variable AGN. Monthly Notices of the Royal Astronomical Society. 2019;485(2):1579-1594. doi:10.1093/mnras/stz150 apa: Kelley, L. Z., Haiman, Z., Sesana, A., & Hernquist, L. (2019). Massive BH binaries as periodically variable AGN. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz150 chicago: Kelley, Luke Zoltan, Zoltán Haiman, Alberto Sesana, and Lars Hernquist. “Massive BH Binaries as Periodically Variable AGN.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz150. ieee: L. Z. Kelley, Z. Haiman, A. Sesana, and L. Hernquist, “Massive BH binaries as periodically variable AGN,” Monthly Notices of the Royal Astronomical Society, vol. 485, no. 2. Oxford University Press, pp. 1579–1594, 2019. ista: Kelley LZ, Haiman Z, Sesana A, Hernquist L. 2019. Massive BH binaries as periodically variable AGN. Monthly Notices of the Royal Astronomical Society. 485(2), 1579–1594. mla: Kelley, Luke Zoltan, et al. “Massive BH Binaries as Periodically Variable AGN.” Monthly Notices of the Royal Astronomical Society, vol. 485, no. 2, Oxford University Press, 2019, pp. 1579–94, doi:10.1093/mnras/stz150. short: L.Z. Kelley, Z. Haiman, A. Sesana, L. Hernquist, Monthly Notices of the Royal Astronomical Society 485 (2019) 1579–1594. date_created: 2024-09-05T09:59:54Z date_published: 2019-01-30T00:00:00Z date_updated: 2024-09-18T08:52:07Z day: '30' doi: 10.1093/mnras/stz150 extern: '1' intvolume: ' 485' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/stz150 month: '01' oa: 1 oa_version: Published Version page: 1579-1594 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Massive BH binaries as periodically variable AGN type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 485 year: '2019' ... --- _id: '17556' abstract: - lang: eng text: The abundance of molecular hydrogen (H2), the primary coolant in primordial gas, is critical for the thermodynamic evolution and star-formation histories in early protogalaxies. Determining the photodissociation rate of H2 by an incident Lyman-Werner (LW) flux is thus crucial, but prohibitively expensive to calculate on the fly in simulations. The rate is sensitive to the H2 rovibrational distribution, which in turn depends on the gas density, temperature, and incident LW radiation field. We use the publicly available cloudy package to model primordial gas clouds and compare exact photodissociation rate calculations to commonly-used fitting formulae. We find the fit from Wolcott-Green et al. (2011) is most accurate for moderate densities n~10^3 cm^{-3} and temperatures, T~10^3K, and we provide a new fit, which captures the increase in the rate at higher densities and temperatures, owing to the increased excited rovibrational populations in this regime. Our new fit has typical errors of a few percent percent up to n =<10^7 cm^{-3}, T =< 8000K, and H2 column density NH2 =<10^{17} cm^{-2}, and can be easily utilized in simulations. We also show that pumping of the excited rovibrational states of H2 by a strong LW flux further modifies the level populations when the gas density is low, and noticeably decreases self-shielding for J_21 > 10^3 and n < 10^2 cm^{-3}. This may lower the "critical flux" at which primordial gas remains H2-poor in some protogalaxies, enabling massive black hole seed formation. article_processing_charge: No article_type: original author: - first_name: J full_name: Wolcott-Green, J last_name: Wolcott-Green - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman citation: ama: 'Wolcott-Green J, Haiman Z. H2 self-shielding with non-LTE rovibrational populations: Implications for cooling in protogalaxies. Monthly Notices of the Royal Astronomical Society. 2019;484(2):2467-2473. doi:10.1093/mnras/sty3280' apa: 'Wolcott-Green, J., & Haiman, Z. (2019). H2 self-shielding with non-LTE rovibrational populations: Implications for cooling in protogalaxies. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty3280' chicago: 'Wolcott-Green, J, and Zoltán Haiman. “H2 Self-Shielding with Non-LTE Rovibrational Populations: Implications for Cooling in Protogalaxies.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/sty3280.' ieee: 'J. Wolcott-Green and Z. Haiman, “H2 self-shielding with non-LTE rovibrational populations: Implications for cooling in protogalaxies,” Monthly Notices of the Royal Astronomical Society, vol. 484, no. 2. Oxford University Press, pp. 2467–2473, 2019.' ista: 'Wolcott-Green J, Haiman Z. 2019. H2 self-shielding with non-LTE rovibrational populations: Implications for cooling in protogalaxies. Monthly Notices of the Royal Astronomical Society. 484(2), 2467–2473.' mla: 'Wolcott-Green, J., and Zoltán Haiman. “H2 Self-Shielding with Non-LTE Rovibrational Populations: Implications for Cooling in Protogalaxies.” Monthly Notices of the Royal Astronomical Society, vol. 484, no. 2, Oxford University Press, 2019, pp. 2467–73, doi:10.1093/mnras/sty3280.' short: J. Wolcott-Green, Z. Haiman, Monthly Notices of the Royal Astronomical Society 484 (2019) 2467–2473. date_created: 2024-09-05T10:24:40Z date_published: 2019-01-16T00:00:00Z date_updated: 2024-09-18T12:00:29Z day: '16' doi: 10.1093/mnras/sty3280 extern: '1' intvolume: ' 484' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/sty3280 month: '01' oa: 1 oa_version: Published Version page: 2467-2473 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'H2 self-shielding with non-LTE rovibrational populations: Implications for cooling in protogalaxies' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 484 year: '2019' ... --- _id: '17565' abstract: - lang: eng text: 'The coalescence of a compact object with a 104−107M⊙ supermassive black hole (SMBH) produces mHz gravitational waves (GWs) detectable by the future Laser Interferometer Space Antenna (LISA). If such an inspiral occurs in the accretion disc of an active galactic nucleus (AGN), the gas torques imprint a small deviation in the GW waveform. Here we present two-dimensional hydrodynamical simulations with the moving-mesh code DISCO of a BH inspiraling at the GW rate in a binary system with a mass ratio q=M2/M1=10−3, embedded in an accretion disc. We assume a locally isothermal equation of state for the gas (with Mach number M=20) and implement a standard α-prescription for its viscosity (with α=0.03). We find disc torques on the binary that are weaker than in previous semi-analytic toy models, and are in the opposite direction: the gas disc slows down, rather than speeds up the inspiral. We compute the resulting deviations in the GW waveform, which scale linearly with the mass of the disc. The SNR of these deviations accumulates mostly at high frequencies, and becomes detectable in a 5-year LISA observation if the total phase shift exceeds a few radians. We find that this occurs if the disc surface density exceeds Σ0≳102−3gcm−2, as may be the case in thin discs with near-Eddington accretion rates. Since the characteristic imprint on the GW signal is strongly dependent on disc parameters, a LISA detection of an intermediate mass ratio inspiral would probe the physics of AGN discs and migration.' article_processing_charge: No article_type: original author: - first_name: A M full_name: Derdzinski, A M last_name: Derdzinski - first_name: D full_name: D’Orazio, D last_name: D’Orazio - first_name: P full_name: Duffell, P last_name: Duffell - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: A full_name: MacFadyen, A last_name: MacFadyen citation: ama: 'Derdzinski AM, D’Orazio D, Duffell P, Haiman Z, MacFadyen A. Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc. Monthly Notices of the Royal Astronomical Society. 2019;486(2):2754-2765. doi:10.1093/mnras/stz1026' apa: 'Derdzinski, A. M., D’Orazio, D., Duffell, P., Haiman, Z., & MacFadyen, A. (2019). Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz1026' chicago: 'Derdzinski, A M, D D’Orazio, P Duffell, Zoltán Haiman, and A MacFadyen. “Probing Gas Disc Physics with LISA: Simulations of an Intermediate Mass Ratio Inspiral in an Accretion Disc.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz1026.' ieee: 'A. M. Derdzinski, D. D’Orazio, P. Duffell, Z. Haiman, and A. MacFadyen, “Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc,” Monthly Notices of the Royal Astronomical Society, vol. 486, no. 2. Oxford University Press, pp. 2754–2765, 2019.' ista: 'Derdzinski AM, D’Orazio D, Duffell P, Haiman Z, MacFadyen A. 2019. Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc. Monthly Notices of the Royal Astronomical Society. 486(2), 2754–2765.' mla: 'Derdzinski, A. M., et al. “Probing Gas Disc Physics with LISA: Simulations of an Intermediate Mass Ratio Inspiral in an Accretion Disc.” Monthly Notices of the Royal Astronomical Society, vol. 486, no. 2, Oxford University Press, 2019, pp. 2754–65, doi:10.1093/mnras/stz1026.' short: A.M. Derdzinski, D. D’Orazio, P. Duffell, Z. Haiman, A. MacFadyen, Monthly Notices of the Royal Astronomical Society 486 (2019) 2754–2765. date_created: 2024-09-05T12:05:43Z date_published: 2019-09-05T00:00:00Z date_updated: 2024-09-18T11:01:36Z day: '05' doi: 10.1093/mnras/stz1026 extern: '1' intvolume: ' 486' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/stz1026 month: '09' oa: 1 oa_version: Published Version page: 2754-2765 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1093/mnras/stz2435 scopus_import: '1' status: public title: 'Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 486 year: '2019' ... --- _id: '17567' abstract: - lang: eng text: The growing number of stellar-mass binary black hole mergers discovered by Advanced LIGO and Advanced Virgo are starting to constrain the binaries' origin and environment. However, we still lack sufficiently accurate modeling of binary formation channels to obtain strong constraints, or to identify sub-populations. One promising formation mechanism that could result in different black hole properties is binaries merging within the accretion disks of Active Galactic Nuclei (AGN). Here we show that the black holes' orbital alignment with the AGN disks preferentially selects heavier black holes. We carry out Monte Carlo simulations of orbital alignment with AGN disks, and find that AGNs harden the initial black hole mass function. Assuming an initial power law mass distribution M−βbh, we find that the power law index changes by Δβ∼1.3, resulting in a more top-heavy population of merging black holes. This change is independent of the mass of, and accretion rate onto, the supermassive black hole in the center of the AGN. Our simulations predict an AGN-assisted merger rate of ∼4Gpc−3yr−1. With its hardened mass spectra, the AGN channel could be responsible for 10−50% of gravitational-wave detections. article_number: '122' article_processing_charge: No article_type: original author: - first_name: Y. full_name: Yang, Y. last_name: Yang - first_name: I. full_name: Bartos, I. last_name: Bartos - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: B. full_name: Kocsis, B. last_name: Kocsis - first_name: Z. full_name: Márka, Z. last_name: Márka - first_name: N. C. full_name: Stone, N. C. last_name: Stone - first_name: S. full_name: Márka, S. last_name: Márka citation: ama: Yang Y, Bartos I, Haiman Z, et al. AGN disks harden the mass distribution of stellar-mass binary black hole mergers. The Astrophysical Journal. 2019;876(2). doi:10.3847/1538-4357/ab16e3 apa: Yang, Y., Bartos, I., Haiman, Z., Kocsis, B., Márka, Z., Stone, N. C., & Márka, S. (2019). AGN disks harden the mass distribution of stellar-mass binary black hole mergers. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ab16e3 chicago: Yang, Y., I. Bartos, Zoltán Haiman, B. Kocsis, Z. Márka, N. C. Stone, and S. Márka. “AGN Disks Harden the Mass Distribution of Stellar-Mass Binary Black Hole Mergers.” The Astrophysical Journal. American Astronomical Society, 2019. https://doi.org/10.3847/1538-4357/ab16e3. ieee: Y. Yang et al., “AGN disks harden the mass distribution of stellar-mass binary black hole mergers,” The Astrophysical Journal, vol. 876, no. 2. American Astronomical Society, 2019. ista: Yang Y, Bartos I, Haiman Z, Kocsis B, Márka Z, Stone NC, Márka S. 2019. AGN disks harden the mass distribution of stellar-mass binary black hole mergers. The Astrophysical Journal. 876(2), 122. mla: Yang, Y., et al. “AGN Disks Harden the Mass Distribution of Stellar-Mass Binary Black Hole Mergers.” The Astrophysical Journal, vol. 876, no. 2, 122, American Astronomical Society, 2019, doi:10.3847/1538-4357/ab16e3. short: Y. Yang, I. Bartos, Z. Haiman, B. Kocsis, Z. Márka, N.C. Stone, S. Márka, The Astrophysical Journal 876 (2019). date_created: 2024-09-05T12:11:39Z date_published: 2019-05-10T00:00:00Z date_updated: 2024-09-18T13:26:34Z day: '10' doi: 10.3847/1538-4357/ab16e3 extern: '1' intvolume: ' 876' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3847/1538-4357/ab16e3 month: '05' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: issn: - 0004-637X - 1538-4357 publication_status: published publisher: American Astronomical Society quality_controlled: '1' scopus_import: '1' status: public title: AGN disks harden the mass distribution of stellar-mass binary black hole mergers type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 876 year: '2019' ... --- _id: '17603' abstract: - lang: eng text: Weak gravitational lensing is one of the most promising cosmological probes of the late universe. Several large ongoing (DES, KiDS, HSC) and planned (LSST, Euclid, WFIRST) astronomical surveys attempt to collect even deeper and larger scale data on weak lensing. Due to gravitational collapse, the distribution of dark matter is non-Gaussian on small scales. However, observations are typically evaluated through the two-point correlation function of galaxy shear, which does not capture non-Gaussian features of the lensing maps. Previous studies attempted to extract non-Gaussian information from weak lensing observations through several higher order statistics such as the three-point correlation function, peak counts, or Minkowski functionals. Deep convolutional neural networks (CNN) emerged in the field of computer vision with tremendous success, and they offer a new and very promising framework to extract information from 2D or 3D astronomical data sets, confirmed by recent studies on weak lensing. We show that a CNN is able to yield significantly stricter constraints of (σ8, Ωm) cosmological parameters than the power spectrum using convergence maps generated by full N-body simulations and ray-tracing, at angular scales and shape noise levels relevant for future observations. In a scenario mimicking LSST or Euclid, the CNN yields 2.4–2.8 times smaller credible contours than the power spectrum, and 3.5–4.2 times smaller at noise levels corresponding to a deep space survey such as WFIRST. We also show that at shape noise levels achievable in future space surveys the CNN yields 1.4–2.1 times smaller contours than peak counts, a higher order statistic capable of extracting non-Gaussian information from weak lensing maps. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Dezső full_name: Ribli, Dezső last_name: Ribli - first_name: Bálint Ármin full_name: Pataki, Bálint Ármin last_name: Pataki - first_name: José Manuel full_name: Zorrilla Matilla, José Manuel last_name: Zorrilla Matilla - first_name: Daniel full_name: Hsu, Daniel last_name: Hsu - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: István full_name: Csabai, István last_name: Csabai citation: ama: Ribli D, Pataki BÁ, Zorrilla Matilla JM, Hsu D, Haiman Z, Csabai I. Weak lensing cosmology with convolutional neural networks on noisy data. Monthly Notices of the Royal Astronomical Society. 2019;490(2):1843-1860. doi:10.1093/mnras/stz2610 apa: Ribli, D., Pataki, B. Á., Zorrilla Matilla, J. M., Hsu, D., Haiman, Z., & Csabai, I. (2019). Weak lensing cosmology with convolutional neural networks on noisy data. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz2610 chicago: Ribli, Dezső, Bálint Ármin Pataki, José Manuel Zorrilla Matilla, Daniel Hsu, Zoltán Haiman, and István Csabai. “Weak Lensing Cosmology with Convolutional Neural Networks on Noisy Data.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz2610. ieee: D. Ribli, B. Á. Pataki, J. M. Zorrilla Matilla, D. Hsu, Z. Haiman, and I. Csabai, “Weak lensing cosmology with convolutional neural networks on noisy data,” Monthly Notices of the Royal Astronomical Society, vol. 490, no. 2. Oxford University Press, pp. 1843–1860, 2019. ista: Ribli D, Pataki BÁ, Zorrilla Matilla JM, Hsu D, Haiman Z, Csabai I. 2019. Weak lensing cosmology with convolutional neural networks on noisy data. Monthly Notices of the Royal Astronomical Society. 490(2), 1843–1860. mla: Ribli, Dezső, et al. “Weak Lensing Cosmology with Convolutional Neural Networks on Noisy Data.” Monthly Notices of the Royal Astronomical Society, vol. 490, no. 2, Oxford University Press, 2019, pp. 1843–60, doi:10.1093/mnras/stz2610. short: D. Ribli, B.Á. Pataki, J.M. Zorrilla Matilla, D. Hsu, Z. Haiman, I. Csabai, Monthly Notices of the Royal Astronomical Society 490 (2019) 1843–1860. date_created: 2024-09-05T13:11:16Z date_published: 2019-09-17T00:00:00Z date_updated: 2024-09-23T13:50:39Z day: '17' doi: 10.1093/mnras/stz2610 extern: '1' external_id: arxiv: - '1902.03663' intvolume: ' 490' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1902.03663' month: '09' oa: 1 oa_version: Preprint page: 1843-1860 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Weak lensing cosmology with convolutional neural networks on noisy data type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 490 year: '2019' ... --- _id: '7710' abstract: - lang: eng text: 'The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.' article_number: '5436' article_processing_charge: No article_type: original author: - first_name: Olivier full_name: Delaneau, Olivier last_name: Delaneau - first_name: Jean-François full_name: Zagury, Jean-François last_name: Zagury - 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: Jonathan L. full_name: Marchini, Jonathan L. last_name: Marchini - first_name: Emmanouil T. full_name: Dermitzakis, Emmanouil T. last_name: Dermitzakis citation: ama: Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. Accurate, scalable and integrative haplotype estimation. Nature Communications. 2019;10. doi:10.1038/s41467-019-13225-y apa: Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L., & Dermitzakis, E. T. (2019). Accurate, scalable and integrative haplotype estimation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13225-y chicago: Delaneau, Olivier, Jean-François Zagury, Matthew Richard Robinson, Jonathan L. Marchini, and Emmanouil T. Dermitzakis. “Accurate, Scalable and Integrative Haplotype Estimation.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13225-y. ieee: O. Delaneau, J.-F. Zagury, M. R. Robinson, J. L. Marchini, and E. T. Dermitzakis, “Accurate, scalable and integrative haplotype estimation,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. 2019. Accurate, scalable and integrative haplotype estimation. Nature Communications. 10, 5436. mla: Delaneau, Olivier, et al. “Accurate, Scalable and Integrative Haplotype Estimation.” Nature Communications, vol. 10, 5436, Springer Nature, 2019, doi:10.1038/s41467-019-13225-y. short: O. Delaneau, J.-F. Zagury, M.R. Robinson, J.L. Marchini, E.T. Dermitzakis, Nature Communications 10 (2019). date_created: 2020-04-30T10:40:32Z date_published: 2019-11-28T00:00:00Z date_updated: 2021-01-12T08:15:01Z day: '28' doi: 10.1038/s41467-019-13225-y extern: '1' intvolume: ' 10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-019-13225-y month: '11' 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: Accurate, scalable and integrative haplotype estimation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2019' ... --- _id: '7711' abstract: - lang: eng text: The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies. article_processing_charge: No article_type: original 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. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 2019;1(12):1226-1242. doi:10.1038/s42255-019-0147-3 apa: Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2019). Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-019-0147-3 chicago: Bevers, Roel P. J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism. Springer Nature, 2019. https://doi.org/10.1038/s42255-019-0147-3. ieee: R. P. J. Bevers et al., “Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel,” Nature Metabolism, vol. 1, no. 12. Springer Nature, pp. 1226–1242, 2019. ista: Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2019. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 1(12), 1226–1242. mla: Bevers, Roel P. J., et al. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism, vol. 1, no. 12, Springer Nature, 2019, pp. 1226–42, doi:10.1038/s42255-019-0147-3. short: R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, Nature Metabolism 1 (2019) 1226–1242. date_created: 2020-04-30T10:40:56Z date_published: 2019-12-09T00:00:00Z date_updated: 2021-01-12T08:15:01Z day: '09' doi: 10.1038/s42255-019-0147-3 extern: '1' intvolume: ' 1' issue: '12' language: - iso: eng month: '12' oa_version: None page: 1226-1242 publication: Nature Metabolism publication_identifier: issn: - 2522-5812 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s42255-020-0202-0 status: public title: Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2019' ... --- _id: '7782' abstract: - lang: eng text: As genome-wide association studies (GWAS) increased in size, numerous gene-environment interactions (GxE) have been discovered, many of which however explore only one environment at a time and may suffer from statistical artefacts leading to biased interaction estimates. Here we propose a maximum likelihood method to estimate the contribution of GxE to complex traits taking into account all interacting environmental variables at the same time, without the need to measure any. This is possible because GxE induces fluctuations in the conditional trait variance, the extent of which depends on the strength of GxE. The approach can be applied to continuous outcomes and for single SNPs or genetic risk scores (GRS). Extensive simulations demonstrated that our method yields unbiased interaction estimates and excellent confidence interval coverage. We also offer a strategy to distinguish specific GxE from general heteroscedasticity (scale effects). Applying our method to 32 complex traits in the UK Biobank reveals that for body mass index (BMI) the GRSxE explains an additional 1.9% variance on top of the 5.2% GRS contribution. However, this interaction is not specific to the GRS and holds for any variable similarly correlated with BMI. On the contrary, the GRSxE interaction effect for leg impedance Embedded Image is significantly (P < 10−56) larger than it would be expected for a similarly correlated variable Embedded Image. We showed that our method could robustly detect the global contribution of GxE to complex traits, which turned out to be substantial for certain obesity measures. article_processing_charge: No author: - first_name: Jonathan full_name: Sulc, Jonathan last_name: Sulc - first_name: Ninon full_name: Mounier, Ninon last_name: Mounier - first_name: Felix full_name: Günther, Felix last_name: Günther - first_name: Thomas full_name: Winkler, Thomas last_name: Winkler - first_name: Andrew R. full_name: Wood, Andrew R. last_name: Wood - first_name: Timothy M. full_name: Frayling, Timothy M. last_name: Frayling - first_name: Iris M. full_name: Heid, Iris M. last_name: Heid - 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: Zoltán full_name: Kutalik, Zoltán last_name: Kutalik citation: ama: 'Sulc J, Mounier N, Günther F, et al. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. 2019.' apa: 'Sulc, J., Mounier, N., Günther, F., Winkler, T., Wood, A. R., Frayling, T. M., … Kutalik, Z. (2019). Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. Cold Spring Harbor Laboratory.' chicago: 'Sulc, Jonathan, Ninon Mounier, Felix Günther, Thomas Winkler, Andrew R. Wood, Timothy M. Frayling, Iris M. Heid, Matthew Richard Robinson, and Zoltán Kutalik. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv. Cold Spring Harbor Laboratory, 2019.' ieee: 'J. Sulc et al., “Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank,” bioRxiv. Cold Spring Harbor Laboratory, 2019.' ista: 'Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson MR, Kutalik Z. 2019. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv, .' mla: 'Sulc, Jonathan, et al. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv, Cold Spring Harbor Laboratory, 2019.' short: J. Sulc, N. Mounier, F. Günther, T. Winkler, A.R. Wood, T.M. Frayling, I.M. Heid, M.R. Robinson, Z. Kutalik, BioRxiv (2019). date_created: 2020-04-30T13:04:26Z date_published: 2019-06-14T00:00:00Z date_updated: 2021-01-12T08:15:30Z day: '14' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/632380 ' month: '06' oa: 1 oa_version: Preprint page: '20' publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory status: public title: 'Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8' abstract: - lang: eng text: Despite their different origins, Drosophila glia and hemocytes are related cell populations that provide an immune function. Drosophila hemocytes patrol the body cavity and act as macrophages outside the nervous system whereas glia originate from the neuroepithelium and provide the scavenger population of the nervous system. Drosophila glia are hence the functional orthologs of vertebrate microglia, even though the latter are cells of immune origin that subsequently move into the brain during development. Interestingly, the Drosophila immune cells within (glia) and outside the nervous system (hemocytes) require the same transcription factor Glide/Gcm for their development. This raises the issue of how do glia specifically differentiate in the nervous system and hemocytes in the procephalic mesoderm. The Repo homeodomain transcription factor and pan-glial direct target of Glide/Gcm is known to ensure glial terminal differentiation. Here we show that Repo also takes center stage in the process that discriminates between glia and hemocytes. First, Repo expression is repressed in the hemocyte anlagen by mesoderm-specific factors. Second, Repo ectopic activation in the procephalic mesoderm is sufficient to repress the expression of hemocyte-specific genes. Third, the lack of Repo triggers the expression of hemocyte markers in glia. Thus, a complex network of tissue-specific cues biases the potential of Glide/Gcm. These data allow us to revise the concept of fate determinants and help us understand the bases of cell specification. Both sexes were analyzed.SIGNIFICANCE STATEMENTDistinct cell types often require the same pioneer transcription factor, raising the issue of how does one factor trigger different fates. In Drosophila, glia and hemocytes provide a scavenger activity within and outside the nervous system, respectively. While they both require the Glide/Gcm transcription factor, glia originate from the ectoderm, hemocytes from the mesoderm. Here we show that tissue-specific factors inhibit the gliogenic potential of Glide/Gcm in the mesoderm by repressing the expression of the homeodomain protein Repo, a major glial-specific target of Glide/Gcm. Repo expression in turn inhibits the expression of hemocyte-specific genes in the nervous system. These cell-specific networks secure the establishment of the glial fate only in the nervous system and allow cell diversification. acknowledgement: This work was supported by INSERM, CNRS, UDS, Ligue Régionale contre le Cancer, Hôpital de Strasbourg, Association pour la Recherche sur le Cancer (ARC) and Agence Nationale de la Recherche (ANR) grants. P.B.C. was funded by the ANR and by the ARSEP (Fondation pour l'Aide à la Recherche sur la Sclérose en Plaques), and G.T. by governmental and ARC fellowships. This work was also supported by grants from the Ataxia UK (2491) and the NC3R (NC/L000199/1) awarded to M.F. The Institut de Génétique et de Biologie Moléculaire et Cellulaire was also supported by a French state fund through the ANR labex. D.E.S. was funded by Marie Curie Grant CIG 334077/IRTIM. We thank B. Altenhein, K. Brückner, M. Crozatier, L. Waltzer, M. Logan, E. Kurant, R. Reuter, E. Kurucz, J.L Dimarcq, J. Hoffmann, C. Goodman, the DHSB, and the BDSC for reagents and flies. We also thank all of the laboratory members for comments on the manuscript; C. Diebold, C. Delaporte, M. Pezze, the fly, and imaging and antibody facilities for technical assistance; and D. Dembele for help with statistics. In addition, we thank Alison Brewer for help with Luciferase assays. article_processing_charge: No article_type: original author: - first_name: Guillaume full_name: Trébuchet, Guillaume last_name: Trébuchet - first_name: Pierre B full_name: Cattenoz, Pierre B last_name: Cattenoz - first_name: János full_name: Zsámboki, János last_name: Zsámboki - first_name: David full_name: Mazaud, David last_name: Mazaud - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Manolis full_name: Fanto, Manolis last_name: Fanto - first_name: Angela full_name: Giangrande, Angela last_name: Giangrande citation: ama: Trébuchet G, Cattenoz PB, Zsámboki J, et al. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 2019;39(2):238-255. doi:10.1523/JNEUROSCI.1059-18.2018 apa: Trébuchet, G., Cattenoz, P. B., Zsámboki, J., Mazaud, D., Siekhaus, D. E., Fanto, M., & Giangrande, A. (2019). The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1059-18.2018 chicago: Trébuchet, Guillaume, Pierre B Cattenoz, János Zsámboki, David Mazaud, Daria E Siekhaus, Manolis Fanto, and Angela Giangrande. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience. Society for Neuroscience, 2019. https://doi.org/10.1523/JNEUROSCI.1059-18.2018. ieee: G. Trébuchet et al., “The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate,” Journal of Neuroscience, vol. 39, no. 2. Society for Neuroscience, pp. 238–255, 2019. ista: Trébuchet G, Cattenoz PB, Zsámboki J, Mazaud D, Siekhaus DE, Fanto M, Giangrande A. 2019. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 39(2), 238–255. mla: Trébuchet, Guillaume, et al. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience, vol. 39, no. 2, Society for Neuroscience, 2019, pp. 238–55, doi:10.1523/JNEUROSCI.1059-18.2018. short: G. Trébuchet, P.B. Cattenoz, J. Zsámboki, D. Mazaud, D.E. Siekhaus, M. Fanto, A. Giangrande, Journal of Neuroscience 39 (2019) 238–255. date_created: 2018-12-11T11:44:07Z date_published: 2019-01-09T00:00:00Z date_updated: 2025-04-15T06:52:10Z day: '09' ddc: - '570' department: - _id: DaSi doi: 10.1523/JNEUROSCI.1059-18.2018 ec_funded: 1 external_id: isi: - '000455189900006' pmid: - '30504274' file: - access_level: open_access checksum: 8f6925eb4cd1e8747d8ea25929c68de6 content_type: application/pdf creator: dernst date_created: 2020-10-02T09:33:28Z date_updated: 2020-10-02T09:33:28Z file_id: '8596' file_name: 2019_JournNeuroscience_Trebuchet.pdf file_size: 9455414 relation: main_file success: 1 file_date_updated: 2020-10-02T09:33:28Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 238-255 pmid: 1 project: - _id: 2536F660-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '334077' name: Investigating the role of transporters in invasive migration through junctions publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '8048' quality_controlled: '1' scopus_import: '1' status: public title: The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 39 year: '2019' ... --- _id: '80' abstract: - lang: eng text: 'We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Andreas full_name: Deuchert, Andreas id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87 last_name: Deuchert orcid: 0000-0003-3146-6746 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason citation: ama: Deuchert A, Seiringer R, Yngvason J. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 2019;368(2):723-776. doi:10.1007/s00220-018-3239-0 apa: Deuchert, A., Seiringer, R., & Yngvason, J. (2019). Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-018-3239-0 chicago: Deuchert, Andreas, Robert Seiringer, and Jakob Yngvason. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics. Springer, 2019. https://doi.org/10.1007/s00220-018-3239-0. ieee: A. Deuchert, R. Seiringer, and J. Yngvason, “Bose–Einstein condensation in a dilute, trapped gas at positive temperature,” Communications in Mathematical Physics, vol. 368, no. 2. Springer, pp. 723–776, 2019. ista: Deuchert A, Seiringer R, Yngvason J. 2019. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 368(2), 723–776. mla: Deuchert, Andreas, et al. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics, vol. 368, no. 2, Springer, 2019, pp. 723–76, doi:10.1007/s00220-018-3239-0. short: A. Deuchert, R. Seiringer, J. Yngvason, Communications in Mathematical Physics 368 (2019) 723–776. date_created: 2018-12-11T11:44:31Z date_published: 2019-06-01T00:00:00Z date_updated: 2025-04-14T07:27:00Z day: '01' ddc: - '530' department: - _id: RoSe doi: 10.1007/s00220-018-3239-0 ec_funded: 1 external_id: isi: - '000467796800007' file: - access_level: open_access checksum: c7e9880b43ac726712c1365e9f2f73a6 content_type: application/pdf creator: dernst date_created: 2018-12-17T10:34:06Z date_updated: 2020-07-14T12:48:07Z file_id: '5688' file_name: 2018_CommunMathPhys_Deuchert.pdf file_size: 893902 relation: main_file file_date_updated: 2020-07-14T12:48:07Z has_accepted_license: '1' intvolume: ' 368' isi: 1 issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 723-776 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '7974' quality_controlled: '1' scopus_import: '1' status: public title: Bose–Einstein condensation in a dilute, trapped gas at positive temperature 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 368 year: '2019' ...