[{"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"page":"4457-4467","date_updated":"2024-09-25T07:32:20Z","author":[{"full_name":"Visbal, Eli","last_name":"Visbal","first_name":"Eli"},{"last_name":"Haiman","full_name":"Haiman, Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán"},{"last_name":"Bryan","full_name":"Bryan, Greg L.","first_name":"Greg L."}],"title":"Limits on population III star formation in minihaloes implied by Planck","oa_version":"Preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Monthly Notices of the Royal Astronomical Society","arxiv":1,"year":"2015","publication_identifier":{"issn":["0035-8711","1365-2966"]},"article_type":"original","date_published":"2015-09-16T00:00:00Z","intvolume":" 453","oa":1,"day":"16","doi":"10.1093/mnras/stv1941","scopus_import":"1","issue":"4","month":"09","_id":"17663","external_id":{"arxiv":["1505.06359"]},"date_created":"2024-09-06T07:40:38Z","publication_status":"published","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1505.06359","open_access":"1"}],"publisher":"Oxford University Press","volume":453,"quality_controlled":"1","citation":{"short":"E. Visbal, Z. Haiman, G.L. Bryan, Monthly Notices of the Royal Astronomical Society 453 (2015) 4457–4467.","ama":"Visbal E, Haiman Z, Bryan GL. Limits on population III star formation in minihaloes implied by Planck. Monthly Notices of the Royal Astronomical Society. 2015;453(4):4457-4467. doi:10.1093/mnras/stv1941","ieee":"E. Visbal, Z. Haiman, and G. L. Bryan, “Limits on population III star formation in minihaloes implied by Planck,” Monthly Notices of the Royal Astronomical Society, vol. 453, no. 4. Oxford University Press, pp. 4457–4467, 2015.","apa":"Visbal, E., Haiman, Z., & Bryan, G. L. (2015). Limits on population III star formation in minihaloes implied by Planck. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stv1941","mla":"Visbal, Eli, et al. “Limits on Population III Star Formation in Minihaloes Implied by Planck.” Monthly Notices of the Royal Astronomical Society, vol. 453, no. 4, Oxford University Press, 2015, pp. 4457–67, doi:10.1093/mnras/stv1941.","chicago":"Visbal, Eli, Zoltán Haiman, and Greg L. Bryan. “Limits on Population III Star Formation in Minihaloes Implied by Planck.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2015. https://doi.org/10.1093/mnras/stv1941.","ista":"Visbal E, Haiman Z, Bryan GL. 2015. Limits on population III star formation in minihaloes implied by Planck. Monthly Notices of the Royal Astronomical Society. 453(4), 4457–4467."},"extern":"1","type":"journal_article","abstract":[{"lang":"eng","text":"Recently, Planck measured a value of the cosmic microwave background (CMB) optical depth due to electron scattering of τ=0.066±0.016. Here we show that this low value leaves essentially no room for an early partial reionisation of the intergalactic medium (IGM) by high-redshift Population III (Pop III) stars, expected to have formed in low-mass minihaloes. We perform semi-analytic calculations of reionisation which include the contribution from Pop II stars in atomic cooling haloes, calibrated with high-redshift galaxy observations, and Pop III stars in minihaloes with feedback due to Lyman-Werner (LW) radiation and metal enrichment. We find that without LW feedback or prompt metal enrichment (and assuming a minihalo escape fraction of 0.5) the Pop III star formation efficiency cannot exceed ∼a few×10−4, without violating the constraints set by Planck data. This excludes massive Pop III star formation in typical 106M⊙ minihaloes. Including LW feedback and metal enrichment alleviates this tension, allowing large Pop III stars to form early on before they are quenched by feedback. We find that the total density of Pop III stars formed across cosmic time is ≲104−5 M⊙ Mpc−3 and does not depend strongly on the feedback prescription adopted. Additionally, we perform a simple estimate of the possible impact on reionisation of X-rays produced by accretion onto black hole remnants of Pop III stars. We find that unless the accretion duty cycle is very low (≲0.01), this could lead to an optical depth inconsistent with Planck."}]},{"publication":"Monthly Notices of the Royal Astronomical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-11-02T00:00:00Z","intvolume":" 455","oa":1,"doi":"10.1093/mnras/stv2371","day":"02","publication_identifier":{"issn":["0035-8711","1365-2966"]},"article_type":"original","year":"2015","date_updated":"2024-09-25T09:18:47Z","page":"484-492","title":"A statistical method to search for recoiling supermassive black holes in active galactic nuclei","author":[{"first_name":"P.","last_name":"Raffai","full_name":"Raffai, P."},{"first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","last_name":"Haiman"},{"first_name":"Z.","full_name":"Frei, Z.","last_name":"Frei"}],"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"oa_version":"Published Version","volume":455,"main_file_link":[{"url":"https://doi.org/10.1093/mnras/stv2371","open_access":"1"}],"publisher":"Oxford University Press","quality_controlled":"1","citation":{"chicago":"Raffai, P., Zoltán Haiman, and Z. Frei. “A Statistical Method to Search for Recoiling Supermassive Black Holes in Active Galactic Nuclei.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2015. https://doi.org/10.1093/mnras/stv2371.","ista":"Raffai P, Haiman Z, Frei Z. 2015. A statistical method to search for recoiling supermassive black holes in active galactic nuclei. Monthly Notices of the Royal Astronomical Society. 455(1), 484–492.","mla":"Raffai, P., et al. “A Statistical Method to Search for Recoiling Supermassive Black Holes in Active Galactic Nuclei.” Monthly Notices of the Royal Astronomical Society, vol. 455, no. 1, Oxford University Press, 2015, pp. 484–92, doi:10.1093/mnras/stv2371.","apa":"Raffai, P., Haiman, Z., & Frei, Z. (2015). A statistical method to search for recoiling supermassive black holes in active galactic nuclei. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stv2371","ieee":"P. Raffai, Z. Haiman, and Z. Frei, “A statistical method to search for recoiling supermassive black holes in active galactic nuclei,” Monthly Notices of the Royal Astronomical Society, vol. 455, no. 1. Oxford University Press, pp. 484–492, 2015.","ama":"Raffai P, Haiman Z, Frei Z. A statistical method to search for recoiling supermassive black holes in active galactic nuclei. Monthly Notices of the Royal Astronomical Society. 2015;455(1):484-492. doi:10.1093/mnras/stv2371","short":"P. Raffai, Z. Haiman, Z. Frei, Monthly Notices of the Royal Astronomical Society 455 (2015) 484–492."},"abstract":[{"text":"We propose an observational test for gravitationally recoiling supermassive black holes (BHs) in active galactic nuclei, based on a correlation between the velocities of BHs relative to their host galaxies, |\\Delta v|, and their obscuring dust column densities, \\Sigma_{dust} (both measured along the line of sight). We use toy models for the distribution of recoil velocities, BH trajectories, and the geometry of obscuring dust tori in galactic centres, to simulate 2.5x10^5 random observations of recoiling quasars. BHs with recoil velocities comparable to the escape velocity from the galactic centre remain bound to the nucleus, and do not fully settle back to the centre of the torus due to dynamical friction in a typical quasar lifetime. We find that |\\Delta v| and \\Sigma_ {dust} for these BHs are positively correlated. For obscured (\\Sigma_{dust}>0) and for partially obscured (0<\\Sigma_{dust}<~2.3 g/m^2) quasars with |\\Delta v|>=45 km/s, the sample correlation coefficient between log10(|\\Delta v|) and \\Sigma_{dust} is r_{45} = 0.28+/-0.02 and r_{45} = 0.13+/-0.02, respectively. Allowing for random +/-100 km/s errors in |\\Delta v| unrelated to the recoil dilutes the correlation for the partially obscured quasars to r_{45} = 0.026+/-0.004 measured between |\\Delta v| and \\Sigma_{dust}. A random sample of >~3,500 obscured quasars with |\\Delta v|>=45 km/s would allow rejection of the no-correlation hypothesis with 3 sigma significance 95% of the time. Finally, we find that the fraction of obscured quasars, F_{obs}(|\\Delta v|), decreases with |\\Delta v| from F_{obs}(<10 km/s)>~0.8 to F_{obs}(>10^3 km/s)<~0.4. This predicted trend can be compared to the observed fraction of type II quasars, and can further test combinations of recoil, trajectory, and dust torus models.","lang":"eng"}],"type":"journal_article","extern":"1","_id":"17685","issue":"1","scopus_import":"1","month":"11","date_created":"2024-09-06T08:20:30Z","publication_status":"published"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Monthly Notices of the Royal Astronomical Society","article_type":"original","year":"2015","publication_identifier":{"issn":["0035-8711","1365-2966"]},"intvolume":" 450","date_published":"2015-05-06T00:00:00Z","doi":"10.1093/mnras/stv785","day":"06","oa":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2024-09-25T10:05:24Z","page":"2506-2513","author":[{"last_name":"Visbal","full_name":"Visbal, Eli","first_name":"Eli"},{"id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","last_name":"Haiman","full_name":"Haiman, Zoltán","first_name":"Zoltán"},{"full_name":"Bryan, Greg L.","last_name":"Bryan","first_name":"Greg L."}],"title":"Looking for Population III stars with He ii line intensity mapping","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/mnras/stv785"}],"publisher":"Oxford University Press","volume":450,"quality_controlled":"1","abstract":[{"text":"Constraining the properties of Population III (Pop III) stars will be very challenging because they reside in small galaxies at high redshift which will be difficult to directly detect. In this paper, we suggest that intensity mapping may be a promising method to study Pop III stars. Intensity mapping is a technique proposed to measure large-scale fluctuations of galaxy line emission in three dimensions without resolving individual sources. This technique is well suited for observing many faint galaxies because it can measure their cumulative emission even if they cannot be directly detected. We focus on intensity mapping of He ii recombination lines. These lines are much stronger in Pop III stars than Pop II stars because the harder spectra of Pop III stars are expected to produce many He ii ionizing photons. Measuring the He ii 1640 Å intensity mapping signal, along with the signals from other lines such as Lyα, Hα, and metal lines, could give constraints on the initial mass function (IMF) and star formation rate density of Pop III stars as a function of redshift. To demonstrate the feasibility of these observations, we estimate the strength of the Pop III He ii 1640 Å intensity mapping signal from z = 10–20. We show that at z ≈ 10, the signal could be measured accurately by two different hypothetical future instruments, one which cross-correlates He ii 1640 Å with CO(1–0) line emission from galaxies and the other with 21 cm emission from the intergalactic medium.","lang":"eng"}],"extern":"1","type":"journal_article","citation":{"ama":"Visbal E, Haiman Z, Bryan GL. Looking for Population III stars with He ii line intensity mapping. Monthly Notices of the Royal Astronomical Society. 2015;450(3):2506-2513. doi:10.1093/mnras/stv785","ieee":"E. Visbal, Z. Haiman, and G. L. Bryan, “Looking for Population III stars with He ii line intensity mapping,” Monthly Notices of the Royal Astronomical Society, vol. 450, no. 3. Oxford University Press, pp. 2506–2513, 2015.","apa":"Visbal, E., Haiman, Z., & Bryan, G. L. (2015). Looking for Population III stars with He ii line intensity mapping. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stv785","ista":"Visbal E, Haiman Z, Bryan GL. 2015. Looking for Population III stars with He ii line intensity mapping. Monthly Notices of the Royal Astronomical Society. 450(3), 2506–2513.","chicago":"Visbal, Eli, Zoltán Haiman, and Greg L. Bryan. “Looking for Population III Stars with He Ii Line Intensity Mapping.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2015. https://doi.org/10.1093/mnras/stv785.","mla":"Visbal, Eli, et al. “Looking for Population III Stars with He Ii Line Intensity Mapping.” Monthly Notices of the Royal Astronomical Society, vol. 450, no. 3, Oxford University Press, 2015, pp. 2506–13, doi:10.1093/mnras/stv785.","short":"E. Visbal, Z. Haiman, G.L. Bryan, Monthly Notices of the Royal Astronomical Society 450 (2015) 2506–2513."},"scopus_import":"1","issue":"3","month":"05","_id":"17694","date_created":"2024-09-06T08:40:33Z","publication_status":"published"},{"volume":91,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1503.06214"}],"publisher":"American Physical Society","quality_controlled":"1","citation":{"short":"A. Petri, J. Liu, Z. Haiman, M. May, L. Hui, J.M. Kratochvil, Physical Review D 91 (2015).","ieee":"A. Petri, J. Liu, Z. Haiman, M. May, L. Hui, and J. M. Kratochvil, “Emulating the CFHTLenS weak lensing data: Cosmological constraints from moments and Minkowski functionals,” Physical Review D, vol. 91, no. 10. American Physical Society, 2015.","apa":"Petri, A., Liu, J., Haiman, Z., May, M., Hui, L., & Kratochvil, J. M. (2015). Emulating the CFHTLenS weak lensing data: Cosmological constraints from moments and Minkowski functionals. Physical Review D. American Physical Society. https://doi.org/10.1103/physrevd.91.103511","ama":"Petri A, Liu J, Haiman Z, May M, Hui L, Kratochvil JM. Emulating the CFHTLenS weak lensing data: Cosmological constraints from moments and Minkowski functionals. Physical Review D. 2015;91(10). doi:10.1103/physrevd.91.103511","mla":"Petri, Andrea, et al. “Emulating the CFHTLenS Weak Lensing Data: Cosmological Constraints from Moments and Minkowski Functionals.” Physical Review D, vol. 91, no. 10, 103511, American Physical Society, 2015, doi:10.1103/physrevd.91.103511.","ista":"Petri A, Liu J, Haiman Z, May M, Hui L, Kratochvil JM. 2015. Emulating the CFHTLenS weak lensing data: Cosmological constraints from moments and Minkowski functionals. Physical Review D. 91(10), 103511.","chicago":"Petri, Andrea, Jia Liu, Zoltán Haiman, Morgan May, Lam Hui, and Jan M. Kratochvil. “Emulating the CFHTLenS Weak Lensing Data: Cosmological Constraints from Moments and Minkowski Functionals.” Physical Review D. American Physical Society, 2015. https://doi.org/10.1103/physrevd.91.103511."},"abstract":[{"text":"Weak gravitational lensing is a powerful cosmological probe, with non--Gaussian features potentially containing the majority of the information. We examine constraints on the parameter triplet (Ωm,w,σ8) from non-Gaussian features of the weak lensing convergence field, including a set of moments (up to 4th order) and Minkowski functionals, using publicly available data from the 154deg2 CFHTLenS survey. We utilize a suite of ray--tracing N-body simulations spanning 91 points in (Ωm,w,σ8) parameter space, replicating the galaxy sky positions, redshifts and shape noise in the CFHTLenS catalogs. We then build an emulator that interpolates the simulated descriptors as a function of (Ωm,w,σ8), and use it to compute the likelihood function and parameter constraints. We employ a principal component analysis to reduce dimensionality and to help stabilize the constraints with respect to the number of bins used to construct each statistic. Using the full set of statistics, we find Σ8≡σ8(Ωm/0.27)^0.55=0.75±0.04 (68% C.L.), in agreement with previous values. We find that constraints on the (Ωm,σ8) doublet from the Minkowski functionals suffer a strong bias. However, high-order moments break the (Ωm,σ8) degeneracy and provide a tight constraint on these parameters with no apparent bias. The main contribution comes from quartic moments of derivatives.","lang":"eng"}],"extern":"1","type":"journal_article","_id":"17702","scopus_import":"1","issue":"10","month":"05","date_created":"2024-09-06T08:48:07Z","publication_status":"published","external_id":{"arxiv":["1503.06214"]},"publication":"Physical Review D","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-05-15T00:00:00Z","intvolume":" 91","oa":1,"doi":"10.1103/physrevd.91.103511","day":"15","publication_identifier":{"issn":["1550-7998","1550-2368"]},"article_type":"original","year":"2015","article_number":"103511","date_updated":"2024-09-25T11:29:05Z","title":"Emulating the CFHTLenS weak lensing data: Cosmological constraints from moments and Minkowski functionals","author":[{"last_name":"Petri","full_name":"Petri, Andrea","first_name":"Andrea"},{"last_name":"Liu","full_name":"Liu, Jia","first_name":"Jia"},{"full_name":"Haiman, Zoltán","last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán"},{"first_name":"Morgan","full_name":"May, Morgan","last_name":"May"},{"first_name":"Lam","last_name":"Hui","full_name":"Hui, Lam"},{"first_name":"Jan M.","last_name":"Kratochvil","full_name":"Kratochvil, Jan M."}],"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint"},{"title":"Cosmology constraints from the weak lensing peak counts and the power spectrum in CFHTLenS data","author":[{"full_name":"Liu, Jia","last_name":"Liu","first_name":"Jia"},{"first_name":"Andrea","last_name":"Petri","full_name":"Petri, Andrea"},{"full_name":"Haiman, Zoltán","last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán"},{"first_name":"Lam","last_name":"Hui","full_name":"Hui, Lam"},{"last_name":"Kratochvil","full_name":"Kratochvil, Jan M.","first_name":"Jan M."},{"first_name":"Morgan","full_name":"May, Morgan","last_name":"May"}],"date_updated":"2024-09-25T12:03:54Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Preprint","publication":"Physical Review D","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"day":"04","doi":"10.1103/physrevd.91.063507","date_published":"2015-03-04T00:00:00Z","intvolume":" 91","article_number":"063507","publication_identifier":{"issn":["1550-7998","1550-2368"]},"year":"2015","article_type":"original","_id":"17710","month":"03","scopus_import":"1","issue":"6","publication_status":"published","date_created":"2024-09-06T08:54:57Z","external_id":{"arxiv":["1412.0757"]},"volume":91,"publisher":"American Physical Society","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1412.0757","open_access":"1"}],"citation":{"short":"J. Liu, A. Petri, Z. Haiman, L. Hui, J.M. Kratochvil, M. May, Physical Review D 91 (2015).","ista":"Liu J, Petri A, Haiman Z, Hui L, Kratochvil JM, May M. 2015. Cosmology constraints from the weak lensing peak counts and the power spectrum in CFHTLenS data. Physical Review D. 91(6), 063507.","chicago":"Liu, Jia, Andrea Petri, Zoltán Haiman, Lam Hui, Jan M. Kratochvil, and Morgan May. “Cosmology Constraints from the Weak Lensing Peak Counts and the Power Spectrum in CFHTLenS Data.” Physical Review D. American Physical Society, 2015. https://doi.org/10.1103/physrevd.91.063507.","mla":"Liu, Jia, et al. “Cosmology Constraints from the Weak Lensing Peak Counts and the Power Spectrum in CFHTLenS Data.” Physical Review D, vol. 91, no. 6, 063507, American Physical Society, 2015, doi:10.1103/physrevd.91.063507.","ieee":"J. Liu, A. Petri, Z. Haiman, L. Hui, J. M. Kratochvil, and M. May, “Cosmology constraints from the weak lensing peak counts and the power spectrum in CFHTLenS data,” Physical Review D, vol. 91, no. 6. American Physical Society, 2015.","ama":"Liu J, Petri A, Haiman Z, Hui L, Kratochvil JM, May M. Cosmology constraints from the weak lensing peak counts and the power spectrum in CFHTLenS data. Physical Review D. 2015;91(6). doi:10.1103/physrevd.91.063507","apa":"Liu, J., Petri, A., Haiman, Z., Hui, L., Kratochvil, J. M., & May, M. (2015). Cosmology constraints from the weak lensing peak counts and the power spectrum in CFHTLenS data. Physical Review D. American Physical Society. https://doi.org/10.1103/physrevd.91.063507"},"extern":"1","abstract":[{"lang":"eng","text":"Lensing peaks have been proposed as a useful statistic, containing cosmological information from non-Gaussianities that is inaccessible from traditional two-point statistics such as the power spectrum or two-point correlation functions. Here we examine constraints on cosmological parameters from weak lensing peak counts, using the publicly available data from the 154 deg^2 CFHTLenS survey. We utilize a new suite of ray-tracing N-body simulations on a grid of 91 cosmological models, covering broad ranges of the three parameters Ωm, σ8, and w, and replicating the Galaxy sky positions, redshifts, and shape noise in the CFHTLenS observations. We then build an emulator that interpolates the power spectrum and the peak counts to an accuracy of ≤5%, and compute the likelihood in the three-dimensional parameter space (Ωm, σ8, w) from both observables. We find that constraints from peak counts are comparable to those from the power spectrum, and somewhat tighter when different smoothing scales are combined. Neither observable can constrain w without external data. When the power spectrum and peak counts are combined, the area of the error \"banana'' in the (Ωm, σ8) plane reduces by a factor of ≈2, compared to using the power spectrum alone. For a flat Λ cold dark matter model, combining both statistics, we obtain the constraint σ8(Ωm/0.27)^0.63=0.85+0.03−0.03."}],"type":"journal_article","quality_controlled":"1"},{"publication":"Molecular Ecology","volume":24,"main_file_link":[{"url":"https://doi.org/10.1111/mec.13452","open_access":"1"}],"publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-12-10T00:00:00Z","intvolume":" 24","quality_controlled":"1","oa":1,"citation":{"short":"A.W. Santure, J. Poissant, I. De Cauwer, K. van Oers, M.R. Robinson, J.L. Quinn, M.A.M. Groenen, M.E. Visser, B.C. Sheldon, J. Slate, Molecular Ecology 24 (2015) 6148–6162.","ista":"Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen MAM, Visser ME, Sheldon BC, Slate J. 2015. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 24, 6148–6162.","chicago":"Santure, Anna W., Jocelyn Poissant, Isabelle De Cauwer, Kees van Oers, Matthew Richard Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser, Ben C. Sheldon, and Jon Slate. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology. Wiley, 2015. https://doi.org/10.1111/mec.13452.","mla":"Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology, vol. 24, Wiley, 2015, pp. 6148–62, doi:10.1111/mec.13452.","apa":"Santure, A. W., Poissant, J., De Cauwer, I., van Oers, K., Robinson, M. R., Quinn, J. L., … Slate, J. (2015). Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.13452","ieee":"A. W. Santure et al., “Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations,” Molecular Ecology, vol. 24. Wiley, pp. 6148–6162, 2015.","ama":"Santure AW, Poissant J, De Cauwer I, et al. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 2015;24:6148-6162. doi:10.1111/mec.13452"},"extern":"1","day":"10","abstract":[{"text":"Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long‐term studies across Europe and consequently are considered an ecological ‘model organism’. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long‐term study populations of great tits—one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population‐specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population‐specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free‐living populations.","lang":"eng"}],"type":"journal_article","doi":"10.1111/mec.13452","year":"2015","publication_identifier":{"issn":["0962-1083"]},"article_type":"original","_id":"7739","page":"6148-6162","date_updated":"2021-01-12T08:15:12Z","title":"Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations","author":[{"first_name":"Anna W.","full_name":"Santure, Anna W.","last_name":"Santure"},{"first_name":"Jocelyn","full_name":"Poissant, Jocelyn","last_name":"Poissant"},{"first_name":"Isabelle","last_name":"De Cauwer","full_name":"De Cauwer, Isabelle"},{"first_name":"Kees","full_name":"van Oers, Kees","last_name":"van Oers"},{"first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"},{"first_name":"John L.","last_name":"Quinn","full_name":"Quinn, John L."},{"last_name":"Groenen","full_name":"Groenen, Martien A. M.","first_name":"Martien A. M."},{"first_name":"Marcel E.","last_name":"Visser","full_name":"Visser, Marcel E."},{"first_name":"Ben C.","full_name":"Sheldon, Ben C.","last_name":"Sheldon"},{"last_name":"Slate","full_name":"Slate, Jon","first_name":"Jon"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"month":"12","status":"public","oa_version":"Published Version","date_created":"2020-04-30T10:51:01Z","publication_status":"published"},{"oa_version":"Published Version","author":[{"last_name":"Adams","full_name":"Adams, Mark James","first_name":"Mark James"},{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard"},{"first_name":"Maria-Elena","last_name":"Mannarelli","full_name":"Mannarelli, Maria-Elena"},{"last_name":"Hatchwell","full_name":"Hatchwell, Ben J.","first_name":"Ben J."}],"title":"Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird","date_updated":"2021-01-12T08:15:12Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","doi":"10.1098/rspb.2015.0689","day":"07","oa":1,"intvolume":" 282","date_published":"2015-07-07T00:00:00Z","article_number":"20150689","article_type":"original","year":"2015","publication_identifier":{"issn":["0962-8452","1471-2954"]},"publication":"Proceedings of the Royal Society B: Biological Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2020-04-30T10:58:07Z","external_id":{"pmid":["26063846"]},"_id":"7741","month":"07","issue":"1810","pmid":1,"extern":"1","abstract":[{"text":"Phenotypes expressed in a social context are not only a function of the individual, but can also be shaped by the phenotypes of social partners. These social effects may play a major role in the evolution of cooperative breeding if social partners differ in the quality of care they provide and if individual carers adjust their effort in relation to that of other carers. When applying social effects models to wild study systems, it is also important to explore sources of individual plasticity that could masquerade as social effects. We studied offspring provisioning rates of parents and helpers in a wild population of long-tailed tits Aegithalos caudatus using a quantitative genetic framework to identify these social effects and partition them into genetic, permanent environment and current environment components. Controlling for other effects, individuals were consistent in their provisioning effort at a given nest, but adjusted their effort based on who was in their social group, indicating the presence of social effects. However, these social effects differed between years and social contexts, indicating a current environment effect, rather than indicating a genetic or permanent environment effect. While this study reveals the importance of examining environmental and genetic sources of social effects, the framework we present is entirely general, enabling a greater understanding of potentially important social effects within any ecological population.","lang":"eng"}],"type":"journal_article","citation":{"ama":"Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 2015;282(1810). doi:10.1098/rspb.2015.0689","ieee":"M. J. Adams, M. R. Robinson, M.-E. Mannarelli, and B. J. Hatchwell, “Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird,” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810. The Royal Society, 2015.","apa":"Adams, M. J., Robinson, M. R., Mannarelli, M.-E., & Hatchwell, B. J. (2015). Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2015.0689","mla":"Adams, Mark James, et al. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810, 20150689, The Royal Society, 2015, doi:10.1098/rspb.2015.0689.","chicago":"Adams, Mark James, Matthew Richard Robinson, Maria-Elena Mannarelli, and Ben J. Hatchwell. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2015.0689.","ista":"Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. 2015. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 282(1810), 20150689.","short":"M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings of the Royal Society B: Biological Sciences 282 (2015)."},"quality_controlled":"1","volume":282,"publisher":"The Royal Society","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rspb.2015.0689"}]},{"date_published":"2015-10-29T00:00:00Z","abstract":[{"text":"The fact that a disordered material is not constrained in its properties in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential for novel material design. However, unlike their crystalline\r\ncounterparts, disordered solids are not well understood. One of the primary\r\nobstacles is the lack of a theoretical framework for thinking about disorder\r\nand its relation to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition with diverging length scales and clean power-law\r\nsignatures. This critical point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the potential to provide the essential theoretical\r\nfoundation necessary for a unified understanding of the mechanics of disordered\r\nsolids. We begin by showing that jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact nonlinearities.\" We then investigate\r\nthe critical nature of the transition, focusing on diverging length scales and\r\nfinite-size effects. Next, we argue that jamming plays the same role for\r\ndisordered solids as the perfect crystal plays for crystalline solids. Not only\r\ncan it be considered an idealized starting point for understanding disordered\r\nmaterials, but it can even influence systems that have a relatively high amount\r\nof crystalline order. The behavior of solids can thus be thought of as existing\r\non a spectrum, with the perfect crystal and the jamming transition at opposing\r\nends. Finally, we introduce a new principle wherein the contribution of an\r\nindividual bond to one global property is independent of its contribution to\r\nanother. This principle allows the different global responses of a disordered\r\nsystem to be manipulated independently and provides a great deal of flexibility\r\nin designing materials with unique, textured and tunable properties.","lang":"eng"}],"day":"29","doi":"10.48550/arXiv.1510.08820","type":"preprint","extern":"1","citation":{"short":"C.P. Goodrich, ArXiv (n.d.).","apa":"Goodrich, C. P. (n.d.). Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv. https://doi.org/10.48550/arXiv.1510.08820","ama":"Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv. doi:10.48550/arXiv.1510.08820","ieee":"C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response of disordered solids,” arXiv. .","mla":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv, 1510.08820, doi:10.48550/arXiv.1510.08820.","ista":"Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv, 1510.08820.","chicago":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1510.08820."},"oa":1,"year":"2015","article_number":"1510.08820","publication":"arXiv","arxiv":1,"OA_type":"green","main_file_link":[{"url":"https://arxiv.org/abs/1510.08820","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-30T12:16:18Z","oa_version":"Preprint","publication_status":"submitted","external_id":{"arxiv":["1510.08820"]},"_id":"7779","date_updated":"2025-06-26T10:26:40Z","author":[{"orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter"}],"title":"Unearthing the anticrystal: Criticality in the linear response of disordered solids","article_processing_charge":"No","month":"10","status":"public","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"last_name":"Kopinsky","full_name":"Kopinsky, Justin","first_name":"Justin"},{"first_name":"Petr","last_name":"Kuznetsov","full_name":"Kuznetsov, Petr"},{"full_name":"Ravi, Srivatsan","last_name":"Ravi","first_name":"Srivatsan"},{"first_name":"Nir","full_name":"Shavit, Nir","last_name":"Shavit"}],"title":"Inherent limitations of hybrid transactional memory","date_updated":"2023-02-23T13:17:35Z","page":"185 - 199","publist_id":"6880","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"acknowledgement":"P. Kuznetsov-The author is supported by the Agence Nationale de la Recherche, ANR-14-CE35-0010-01, project DISCMAT. N. Shavit-Support is gratfeully acknowledgedfrom the National Science Foundation under grants CCF-1217921, CCF-1201926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.","year":"2015","day":"01","doi":"10.1007/978-3-662-48653-5_13","oa":1,"intvolume":" 9363","date_published":"2015-01-01T00:00:00Z","month":"01","_id":"778","conference":{"name":"DISC: Distributed Computing"},"alternative_title":["LNCS"],"external_id":{"arxiv":["1405.5689"]},"publication_status":"published","date_created":"2018-12-11T11:48:27Z","publisher":"Springer","main_file_link":[{"url":"https://arxiv.org/abs/1405.5689","open_access":"1"}],"volume":9363,"abstract":[{"text":"Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed to complement the fast, but best-effort nature of Hardware Transactional Memory (HTM) with a slow, reliable software backup. However, the costs of providing concurrency between hardware and software transactions in HyTM are still not well understood. In this paper, we propose a general model for HyTM implementations, which captures the ability of hardware transactions to buffer memory accesses. The model allows us to formally quantify and analyze the amount of overhead (instrumentation) caused by the potential presence of software transactions.We prove that (1) it is impossible to build a strictly serializable HyTM implementation that has both uninstrumented reads and writes, even for very weak progress guarantees, and (2) the instrumentation cost incurred by a hardware transaction in any progressive opaque HyTM is linear in the size of the transaction’s data set.We further describe two implementations which exhibit optimal instrumentation costs for two different progress conditions. In sum, this paper proposes the first formal HyTM model and captures for the first time the trade-off between the degree of hardware-software TM concurrency and the amount of instrumentation overhead.","lang":"eng"}],"type":"conference","extern":"1","citation":{"ieee":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, and N. Shavit, “Inherent limitations of hybrid transactional memory,” presented at the DISC: Distributed Computing, 2015, vol. 9363, pp. 185–199.","apa":"Alistarh, D.-A., Kopinsky, J., Kuznetsov, P., Ravi, S., & Shavit, N. (2015). Inherent limitations of hybrid transactional memory (Vol. 9363, pp. 185–199). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-662-48653-5_13","ama":"Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. Inherent limitations of hybrid transactional memory. In: Vol 9363. Springer; 2015:185-199. doi:10.1007/978-3-662-48653-5_13","mla":"Alistarh, Dan-Adrian, et al. Inherent Limitations of Hybrid Transactional Memory. Vol. 9363, Springer, 2015, pp. 185–99, doi:10.1007/978-3-662-48653-5_13.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Petr Kuznetsov, Srivatsan Ravi, and Nir Shavit. “Inherent Limitations of Hybrid Transactional Memory,” 9363:185–99. Springer, 2015. https://doi.org/10.1007/978-3-662-48653-5_13.","ista":"Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. 2015. Inherent limitations of hybrid transactional memory. DISC: Distributed Computing, LNCS, vol. 9363, 185–199.","short":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer, 2015, pp. 185–199."},"quality_controlled":"1"},{"_id":"780","page":"479 - 491","date_updated":"2023-02-23T13:18:11Z","title":"Polylogarithmic-time leader election in population protocols","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"},{"first_name":"Rati","full_name":"Gelashvili, Rati","last_name":"Gelashvili"}],"language":[{"iso":"eng"}],"month":"01","status":"public","date_created":"2018-12-11T11:48:28Z","publist_id":"6877","oa_version":"Preprint","publication_status":"published","external_id":{"arxiv":["1502.05745"]},"conference":{"name":"ICALP: International Colloquium on Automota, Languages and Programming"},"arxiv":1,"volume":9135,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.05745"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","intvolume":" 9135","date_published":"2015-01-01T00:00:00Z","type":"conference","day":"01","doi":"10.1007/978-3-662-47666-6_38","abstract":[{"lang":"eng","text":"Population protocols are networks of finite-state agents, interacting randomly, and updating their states using simple rules. Despite their extreme simplicity, these systems have been shown to cooperatively perform complex computational tasks, such as simulating register machines to compute standard arithmetic functions. The election of a unique leader agent is a key requirement in such computational constructions. Yet, the fastest currently known population protocol for electing a leader only has linear convergence time, and it has recently been shown that no population protocol using a constant number of states per node may overcome this linear bound. In this paper, we give the first population protocol for leader election with polylogarithmic convergence time, using polylogarithmic memory states per node. The protocol structure is quite simple: each node has an associated value, and is either a leader (still in contention) or a minion (following some leader). A leader keeps incrementing its value and “defeats” other leaders in one-to-one interactions, and will drop from contention and become a minion if it meets a leader with higher value. Importantly, a leader also drops out if it meets a minion with higher absolute value. While these rules are quite simple, the proof that this algorithm achieves polylogarithmic convergence time is non-trivial. In particular, the argument combines careful use of concentration inequalities with anti-concentration bounds, showing that the leaders’ values become spread apart as the execution progresses, which in turn implies that straggling leaders get quickly eliminated. We complement our analysis with empirical results, showing that our protocol converges extremely fast, even for large network sizes."}],"extern":"1","oa":1,"citation":{"short":"D.-A. Alistarh, R. Gelashvili, in:, Springer, 2015, pp. 479–491.","ieee":"D.-A. Alistarh and R. Gelashvili, “Polylogarithmic-time leader election in population protocols,” presented at the ICALP: International Colloquium on Automota, Languages and Programming, 2015, vol. 9135, pp. 479–491.","apa":"Alistarh, D.-A., & Gelashvili, R. (2015). Polylogarithmic-time leader election in population protocols (Vol. 9135, pp. 479–491). Presented at the ICALP: International Colloquium on Automota, Languages and Programming, Springer. https://doi.org/10.1007/978-3-662-47666-6_38","ama":"Alistarh D-A, Gelashvili R. Polylogarithmic-time leader election in population protocols. In: Vol 9135. Springer; 2015:479-491. doi:10.1007/978-3-662-47666-6_38","ista":"Alistarh D-A, Gelashvili R. 2015. Polylogarithmic-time leader election in population protocols. ICALP: International Colloquium on Automota, Languages and Programming vol. 9135, 479–491.","chicago":"Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader Election in Population Protocols,” 9135:479–91. Springer, 2015. https://doi.org/10.1007/978-3-662-47666-6_38.","mla":"Alistarh, Dan-Adrian, and Rati Gelashvili. Polylogarithmic-Time Leader Election in Population Protocols. Vol. 9135, Springer, 2015, pp. 479–91, doi:10.1007/978-3-662-47666-6_38."},"acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.”","year":"2015"},{"publication_status":"published","publist_id":"6875","oa_version":"None","date_created":"2018-12-11T11:48:28Z","conference":{"name":"PODC: Principles of Distributed Computing"},"author":[{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gelashvili, Rati","last_name":"Gelashvili","first_name":"Rati"},{"last_name":"Vladu","full_name":"Vladu, Adrian","first_name":"Adrian"}],"title":"How to elect a leader faster than a tournament","_id":"783","date_updated":"2023-02-23T13:18:55Z","page":"365 - 374","status":"public","month":"07","language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"citation":{"chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Adrian Vladu. “How to Elect a Leader Faster than a Tournament,” 2015–July:365–74. ACM, 2015. https://doi.org/10.1145/2767386.2767420.","ista":"Alistarh D-A, Gelashvili R, Vladu A. 2015. How to elect a leader faster than a tournament. PODC: Principles of Distributed Computing vol. 2015–July, 365–374.","mla":"Alistarh, Dan-Adrian, et al. How to Elect a Leader Faster than a Tournament. Vol. 2015–July, ACM, 2015, pp. 365–74, doi:10.1145/2767386.2767420.","apa":"Alistarh, D.-A., Gelashvili, R., & Vladu, A. (2015). How to elect a leader faster than a tournament (Vol. 2015–July, pp. 365–374). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767420","ieee":"D.-A. Alistarh, R. Gelashvili, and A. Vladu, “How to elect a leader faster than a tournament,” presented at the PODC: Principles of Distributed Computing, 2015, vol. 2015–July, pp. 365–374.","ama":"Alistarh D-A, Gelashvili R, Vladu A. How to elect a leader faster than a tournament. In: Vol 2015-July. ACM; 2015:365-374. doi:10.1145/2767386.2767420","short":"D.-A. Alistarh, R. Gelashvili, A. Vladu, in:, ACM, 2015, pp. 365–374."},"doi":"10.1145/2767386.2767420","extern":"1","abstract":[{"lang":"eng","text":"The problem of electing a leader from among n contenders is one of the fundamental questions in distributed computing. In its simplest formulation, the task is as follows: given n processors, all participants must eventually return a win or lose indication, such that a single contender may win. Despite a considerable amount of work on leader election, the following question is still open: can we elect a leader in an asynchronous fault-prone system faster than just running a Θ(log n)-time tournament, against a strong adaptive adversary? In this paper, we answer this question in the affirmative, improving on a decades-old upper bound. We introduce two new algorithmic ideas to reduce the time complexity of electing a leader to O(log∗ n), using O(n2) point-to-point messages. A non-trivial application of our algorithm is a new upper bound for the tight renaming problem, assigning n items to the n participants in expected O(log2 n) time and O(n2) messages. We complement our results with lower bound of Ω(n2) messages for solving these two problems, closing the question of their message complexity."}],"day":"21","type":"conference","date_published":"2015-07-21T00:00:00Z","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926,\r\nand IIS-1447786, the Department of Energy under grant\r\nER26116/DE-SC0008923, and the Oracle and Intel corporations.\r\nThe authors would like to thank Prof. Nir Shavit for ad-\r\nvice and encouragement during this work, and the anonymous reviewers for their very useful suggestions.","year":"2015","volume":"2015-July","publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.1001"}]},{"extern":"1","abstract":[{"lang":"eng","text":"The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments."}],"type":"journal_article","citation":{"ieee":"P. Ma et al., “Observing the overall rocking motion of a protein in a crystal,” Nature Communications, vol. 6. Springer Nature, 2015.","ama":"Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361","apa":"Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda, P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms9361","chicago":"Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361.","ista":"Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 6, 8361.","mla":"Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015, doi:10.1038/ncomms9361.","short":"P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii, D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 6 (2015)."},"quality_controlled":"1","volume":6,"OA_type":"gold","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.1038/ncomms9361","open_access":"1"}],"publication_status":"published","date_created":"2020-09-18T10:07:36Z","_id":"8456","month":"10","scopus_import":"1","day":"05","doi":"10.1038/ncomms9361","oa":1,"intvolume":" 6","date_published":"2015-10-05T00:00:00Z","article_number":"8361","article_type":"original","publication_identifier":{"issn":["2041-1723"]},"year":"2015","publication":"Nature Communications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","oa_version":"Published Version","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"author":[{"full_name":"Ma, Peixiang","last_name":"Ma","first_name":"Peixiang"},{"last_name":"Xue","full_name":"Xue, Yi","first_name":"Yi"},{"first_name":"Nicolas","full_name":"Coquelle, Nicolas","last_name":"Coquelle"},{"last_name":"Haller","full_name":"Haller, Jens D.","first_name":"Jens D."},{"first_name":"Tairan","last_name":"Yuwen","full_name":"Yuwen, Tairan"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"last_name":"Mikhailovskii","full_name":"Mikhailovskii, Oleg","first_name":"Oleg"},{"first_name":"Dieter","full_name":"Willbold, Dieter","last_name":"Willbold"},{"full_name":"Colletier, Jacques-Philippe","last_name":"Colletier","first_name":"Jacques-Philippe"},{"first_name":"Nikolai R.","last_name":"Skrynnikov","full_name":"Skrynnikov, Nikolai R."},{"first_name":"Paul","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"title":"Observing the overall rocking motion of a protein in a crystal","date_updated":"2025-01-22T14:39:22Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"Yes"},{"month":"05","issue":"4","scopus_import":"1","_id":"9057","external_id":{"pmid":["26601175"],"arxiv":["1505.05111"]},"tmp":{"short":"CC BY-NC (4.0)","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)"},"publication_status":"published","date_created":"2021-02-02T13:15:02Z","publisher":"American Association for the Advancement of Science ","volume":1,"citation":{"short":"J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg, D.J. Pine, P.M. Chaikin, Science Advances 1 (2015).","apa":"Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances. American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214","ama":"Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science Advances. 2015;1(4). doi:10.1126/sciadv.1400214","ieee":"J. A. Palacci et al., “Artificial rheotaxis,” Science Advances, vol. 1, no. 4. American Association for the Advancement of Science , 2015.","mla":"Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:10.1126/sciadv.1400214.","chicago":"Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” Science Advances. American Association for the Advancement of Science , 2015. https://doi.org/10.1126/sciadv.1400214.","ista":"Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ, Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214."},"pmid":1,"type":"journal_article","abstract":[{"text":"Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes.","lang":"eng"}],"extern":"1","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2021-02-02T13:22:19Z","author":[{"first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","full_name":"Palacci, Jérémie A"},{"full_name":"Sacanna, Stefano","last_name":"Sacanna","first_name":"Stefano"},{"first_name":"Anaïs","full_name":"Abramian, Anaïs","last_name":"Abramian"},{"last_name":"Barral","full_name":"Barral, Jérémie","first_name":"Jérémie"},{"first_name":"Kasey","full_name":"Hanson, Kasey","last_name":"Hanson"},{"first_name":"Alexander Y.","last_name":"Grosberg","full_name":"Grosberg, Alexander Y."},{"last_name":"Pine","full_name":"Pine, David J.","first_name":"David J."},{"first_name":"Paul M.","last_name":"Chaikin","full_name":"Chaikin, Paul M."}],"title":"Artificial rheotaxis","date_updated":"2023-02-23T13:47:52Z","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","ddc":["530"],"arxiv":1,"publication":"Science Advances","article_number":"e1400214","publication_identifier":{"issn":["2375-2548"]},"year":"2015","article_type":"original","oa":1,"file":[{"date_created":"2021-02-02T13:22:19Z","file_name":"2015_ScienceAdvances_Palacci.pdf","success":1,"creator":"cziletti","file_size":2416780,"access_level":"open_access","date_updated":"2021-02-02T13:22:19Z","file_id":"9058","content_type":"application/pdf","checksum":"b97d62433581875c1b85210c5f6ae370","relation":"main_file"}],"doi":"10.1126/sciadv.1400214","day":"01","date_published":"2015-05-01T00:00:00Z","intvolume":" 1"},{"oa_version":"Published Version","page":"4760-4777","date_updated":"2022-01-24T13:45:41Z","title":"A three-dimensional map of tidal dissipation over abyssal hills","author":[{"first_name":"Adrien","last_name":"Lefauve","full_name":"Lefauve, Adrien"},{"full_name":"Muller, Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","first_name":"Caroline J"},{"first_name":"Angélique","last_name":"Melet","full_name":"Melet, Angélique"}],"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_published":"2015-06-08T00:00:00Z","intvolume":" 120","oa":1,"doi":"10.1002/2014jc010598","day":"08","article_type":"original","publication_identifier":{"issn":["2169-9275"]},"year":"2015","publication":"Journal of Geophysical Research: Oceans","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2021-02-15T14:21:49Z","publication_status":"published","_id":"9141","issue":"7","month":"06","quality_controlled":"1","citation":{"short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.","mla":"Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.","chicago":"Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598.","ista":"Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.","ama":"Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777. doi:10.1002/2014jc010598","ieee":"A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” Journal of Geophysical Research: Oceans, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.","apa":"Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2014jc010598"},"type":"journal_article","extern":"1","abstract":[{"text":"The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere.","lang":"eng"}],"volume":120,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2014JC010598"}],"publisher":"American Geophysical Union"},{"article_number":"e09206","year":"2015","file":[{"file_name":"2015_eLife_Sehring.pdf","date_created":"2018-12-20T15:50:56Z","file_size":7202224,"creator":"dernst","access_level":"open_access","file_id":"5769","date_updated":"2020-07-14T12:48:15Z","relation":"main_file","content_type":"application/pdf","checksum":"1e4024b3161adcae4a53a0b3dc8a946e"}],"oa":1,"day":"21","doi":"10.7554/eLife.09206","date_published":"2015-10-21T00:00:00Z","intvolume":" 4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by/4.0/","ddc":["539","570"],"publication":"eLife","publist_id":"6512","oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:48:15Z","author":[{"last_name":"Sehring","full_name":"Sehring, Ivonne","first_name":"Ivonne"},{"first_name":"Pierre","last_name":"Recho","full_name":"Recho, Pierre"},{"full_name":"Denker, Elsa","last_name":"Denker","first_name":"Elsa"},{"first_name":"Matthew","last_name":"Kourakis","full_name":"Kourakis, Matthew"},{"first_name":"Birthe","last_name":"Mathiesen","full_name":"Mathiesen, Birthe"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Dong","full_name":"Dong, Bo","first_name":"Bo"},{"full_name":"Jiang, Di","last_name":"Jiang","first_name":"Di"}],"title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","date_updated":"2021-01-12T08:21:58Z","citation":{"short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015).","ista":"Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206.","chicago":"Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/eLife.09206.","mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications, 2015, doi:10.7554/eLife.09206.","ama":"Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206","apa":"Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206","ieee":"I. Sehring et al., “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences Publications, 2015."},"extern":"1","abstract":[{"lang":"eng","text":"The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events."}],"type":"journal_article","quality_controlled":"1","publisher":"eLife Sciences Publications","volume":4,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2018-12-11T11:49:15Z","month":"10","_id":"928"},{"quality_controlled":"1","citation":{"short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","apa":"García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112","ieee":"S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov, “Physics of active jamming during collective cellular motion in a monolayer,” PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015.","ama":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319. doi:10.1073/pnas.1510973112","ista":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 112(50), 15314–15319.","chicago":"García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan, and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112.","mla":"García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:10.1073/pnas.1510973112."},"extern":"1","type":"journal_article","pmid":1,"abstract":[{"text":"Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data.","lang":"eng"}],"volume":112,"main_file_link":[{"url":"https://www.pnas.org/content/pnas/112/50/15314.full.pdf","open_access":"1"}],"publisher":"National Academy of Sciences","date_created":"2018-12-11T11:49:16Z","publication_status":"published","external_id":{"pmid":["26627719"]},"_id":"933","issue":"50","month":"12","date_published":"2015-12-15T00:00:00Z","intvolume":" 112","oa":1,"day":"15","doi":"10.1073/pnas.1510973112","year":"2015","publication":"PNAS","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publist_id":"6511","page":"15314 - 15319","date_updated":"2021-01-12T08:22:01Z","title":"Physics of active jamming during collective cellular motion in a monolayer","author":[{"first_name":"Simón","full_name":"García, Simón","last_name":"García"},{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"first_name":"Jens","full_name":"Elgeti, Jens","last_name":"Elgeti"},{"full_name":"Joanny, Jean","last_name":"Joanny","first_name":"Jean"},{"first_name":"Pascal","last_name":"Silberzan","full_name":"Silberzan, Pascal"},{"last_name":"Gov","full_name":"Gov, Nir","first_name":"Nir"}],"language":[{"iso":"eng"}],"status":"public"},{"oa_version":"Published Version","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2021-06-08T09:55:10Z","title":"Evolution and function of genomic imprinting in plants","author":[{"last_name":"Rodrigues","full_name":"Rodrigues, Jessica A.","first_name":"Jessica A."},{"first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"date_updated":"2021-12-14T07:58:15Z","page":"2517–2531","article_type":"review","publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"year":"2015","file":[{"file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","success":1,"date_created":"2021-06-08T09:55:10Z","creator":"asandaue","file_size":1116846,"access_level":"open_access","date_updated":"2021-06-08T09:55:10Z","file_id":"9533","checksum":"086a88cfca4677646da26ed960cb02e9","content_type":"application/pdf","relation":"main_file"}],"oa":1,"day":"15","doi":"10.1101/gad.269902.115","date_published":"2015-12-15T00:00:00Z","intvolume":" 29","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["570"],"publication":"Genes and Development","external_id":{"pmid":["26680300"]},"tmp":{"short":"CC BY-NC (4.0)","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)"},"publication_status":"published","date_created":"2021-06-08T09:56:24Z","month":"12","issue":"24","scopus_import":"1","_id":"9532","citation":{"ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","apa":"Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.269902.115","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531."},"extern":"1","type":"journal_article","pmid":1,"abstract":[{"text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.","lang":"eng"}],"quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory Press","volume":29,"department":[{"_id":"DaZi"}]},{"oa_version":"Preprint","title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","author":[{"first_name":"Michael","last_name":"Krivelevich","full_name":"Krivelevich, Michael"},{"orcid":"0000-0002-4003-7567","last_name":"Kwan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan"},{"full_name":"Sudakov, Benny","last_name":"Sudakov","first_name":"Benny"}],"page":"181-187","date_updated":"2023-02-23T14:01:28Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","doi":"10.1016/j.endm.2015.06.027","day":"01","oa":1,"intvolume":" 49","date_published":"2015-11-01T00:00:00Z","article_type":"original","publication_identifier":{"issn":["1571-0653"]},"year":"2015","publication":"Electronic Notes in Discrete Mathematics","arxiv":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publication_status":"published","date_created":"2021-06-21T06:40:34Z","external_id":{"arxiv":["1501.04816"]},"_id":"9575","month":"11","scopus_import":"1","type":"journal_article","abstract":[{"text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.","lang":"eng"}],"extern":"1","citation":{"chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier, 2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics, vol. 49. Elsevier, pp. 181–187, 2015.","apa":"Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187. doi:10.1016/j.endm.2015.06.027","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187."},"quality_controlled":"1","volume":49,"publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.04816"}]},{"intvolume":" 92","date_published":"2015-11-01T00:00:00Z","doi":"10.1103/physrevb.92.180102","day":"01","oa":1,"year":"2015","publication_identifier":{"issn":["1098-0121"],"eissn":["1550-235X"]},"article_type":"original","article_number":"180102","arxiv":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Preprint","date_updated":"2021-08-09T12:38:49Z","author":[{"full_name":"Cheng, Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing"},{"full_name":"Tribello, Gareth A.","last_name":"Tribello","first_name":"Gareth A."},{"first_name":"Michele","full_name":"Ceriotti, Michele","last_name":"Ceriotti"}],"title":"Solid-liquid interfacial free energy out of equilibrium","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","extern":"1","type":"journal_article","abstract":[{"lang":"eng","text":"The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification."}],"citation":{"short":"B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015).","ista":"Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 92(18), 180102.","chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102.","mla":"Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102.","apa":"Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18. American Physical Society, 2015.","ama":"Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 2015;92(18). doi:10.1103/physrevb.92.180102"},"volume":92,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.08668"}],"publisher":"American Physical Society","date_created":"2021-07-19T10:07:22Z","publication_status":"published","external_id":{"arxiv":["1511.08668"]},"_id":"9688","scopus_import":"1","issue":"18","month":"11"},{"year":"2015","oa":1,"citation":{"short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects of allogrooming on disease transmission in ant societies, Dryad, 10.5061/dryad.dj2bf.","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Dryad, 2015. https://doi.org/10.5061/dryad.dj2bf.","mla":"Theis, Fabian, et al. Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies. Dryad, 2015, doi:10.5061/dryad.dj2bf.","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects of allogrooming on disease transmission in ant societies.” Dryad, 2015.","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming on disease transmission in ant societies. 2015. doi:10.5061/dryad.dj2bf","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Data from: Opposing effects of allogrooming on disease transmission in ant societies. Dryad. https://doi.org/10.5061/dryad.dj2bf"},"doi":"10.5061/dryad.dj2bf","type":"research_data_reference","abstract":[{"lang":"eng","text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems."}],"day":"29","date_published":"2015-12-29T00:00:00Z","publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.5061/dryad.dj2bf","open_access":"1"}],"department":[{"_id":"SyCr"}],"oa_version":"Published Version","date_created":"2021-07-26T09:38:36Z","month":"12","status":"public","article_processing_charge":"No","author":[{"last_name":"Theis","full_name":"Theis, Fabian","first_name":"Fabian"},{"first_name":"Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","full_name":"Ugelvig, Line V"},{"first_name":"Carsten","full_name":"Marr, Carsten","last_name":"Marr"},{"first_name":"Sylvia","full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"title":"Data from: Opposing effects of allogrooming on disease transmission in ant societies","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1830"}]},"_id":"9721","date_updated":"2025-09-23T09:44:52Z"}]