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  • 1
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    Perturbation of fetal liver hematopoietic stem and progenitor cell development by trisomy 21 (2012)
    National Academy of Sciences
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    Publication Date: 2012-10-08
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    A hydrodynamical halo model for weak-lensing cross correlations (2020)
    EDP Sciences
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    Publication Date: 2020-09-01
    Description: On the scale of galactic haloes, the distribution of matter in the cosmos is affected by energetic, non-gravitational processes, the so-called baryonic feedback. A lack of knowledge about the details of how feedback processes redistribute matter is a source of uncertainty for weak-lensing surveys, which accurately probe the clustering of matter in the Universe over a wide range of scales. We developed a cosmology-dependent model for the matter distribution that simultaneously accounts for the clustering of dark matter, gas, and stars. We informed our model by comparing it to power spectra measured from the BAHAMAS suite of hydrodynamical simulations. In addition to considering matter power spectra, we also considered spectra involving the electron-pressure field, which directly relates to the thermal Sunyaev-Zel’dovich (tSZ) effect. We fitted parameters in our model so that it can simultaneously model both matter and pressure data and such that the distribution of gas as inferred from tSZ has an influence on the matter spectrum predicted by our model. We present two variants, one that matches the feedback-induced suppression seen in the matter–matter power spectrum at the percent level and a second that matches the matter–matter data to a slightly lesser degree (≃2%). However, the latter is able to simultaneously model the matter–electron pressure spectrum at the ≃15% level. We envisage our models being used to simultaneously learn about cosmological parameters and the strength of baryonic feedback using a combination of tSZ and lensing auto- and cross-correlation data.
    Print ISSN: 0004-6361
    Electronic ISSN: 1432-0746
    Topics: Physics
    Published by EDP Sciences
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  • 3
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    Rapid simulation rescaling from standard to modified gravity models (2015)
    Oxford University Press
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    Publication Date: 2015-08-13
    Description: We develop and test an algorithm to rescale a simulated dark-matter particle distribution or halo catalogue from a standard gravity model to that of a modified gravity model. This method is based on that of Angulo & White but with some additional ingredients to account for (i) scale-dependent growth of linear density perturbations and (ii) screening mechanisms that are generic features of viable modified gravity models. We attempt to keep the method as general as possible, so that it may plausibly be applied to a wide range of modified theories, although tests against simulations are restricted to a subclass of f ( R ) models at this stage. We show that rescaling allows the power spectrum of matter to be reproduced at the ~3 per cent level in both real and redshift space up to k  = 0.1 h Mpc –1 if we change the box size and alter the particle displacement field; this limit can be extended to k  = 1 h Mpc –1 if we additionally alter halo internal structure. We simultaneously develop an algorithm that can be applied directly to a halo catalogue, in which case the halo mass function and clustering can be reproduced at the ~5 per cent level. Finally, we investigate the clustering of halo particle distributions, generated from rescaled halo catalogues, and find that a similar accuracy can be reached.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    An accurate halo model for fitting non-linear cosmological power spectra and baryonic feedback models (2015)
    Oxford University Press
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    Publication Date: 2015-10-15
    Description: We present an optimized variant of the halo model, designed to produce accurate matter power spectra well into the non-linear regime for a wide range of cosmological models. To do this, we introduce physically motivated free parameters into the halo-model formalism and fit these to data from high-resolution N -body simulations. For a variety of cold dark matter (CDM) and w CDM models, the halo-model power is accurate to ~= 5 per cent for k  ≤ 10 h Mpc –1 and z  ≤ 2. An advantage of our new halo model is that it can be adapted to account for the effects of baryonic feedback on the power spectrum. We demonstrate this by fitting the halo model to power spectra from the OWLS (OverWhelmingly Large Simulations) hydrodynamical simulation suite via parameters that govern halo internal structure. We are able to fit all feedback models investigated at the 5 per cent level using only two free parameters, and we place limits on the range of these halo parameters for feedback models investigated by the OWLS simulations. Accurate predictions to high k are vital for weak-lensing surveys, and these halo parameters could be considered nuisance parameters to marginalize over in future analyses to mitigate uncertainty regarding the details of feedback. Finally, we investigate how lensing observables predicted by our model compare to those from simulations and from halofit for a range of k -cuts and feedback models and quantify the angular scales at which these effects become important. Code to calculate power spectra from the model presented in this paper can be found at https://github.com/alexander-mead/hmcode .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Application of single-cell genomics in cancer: promise and challenges (2015)
    Oxford University Press
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    Publication Date: 2015-09-17
    Description: Recent advances in single-cell genomics are opening up unprecedented opportunities to transform cancer genomics. While bulk tissue genomic analysis across large populations of tumour cells has provided key insights into cancer biology, this approach does not provide the resolution that is critical for understanding the interaction between different genetic events within the cellular hierarchy of the tumour during disease initiation, evolution, relapse and metastasis. Single-cell genomic approaches are uniquely placed to definitively unravel complex clonal structures and tissue hierarchies, account for spatiotemporal cell interactions and discover rare cells that drive metastatic disease, drug resistance and disease progression. Here we present five challenges that need to be met for single-cell genomics to fulfil its potential as a routine tool alongside bulk sequencing. These might be thought of as being challenges related to samples (processing and scale for analysis), sensitivity and specificity of mutation detection, sources of heterogeneity (biological and technical), synergies (from data integration) and systems modelling. We discuss these in the context of recent advances in technologies and data modelling, concluding with implications for moving cancer research into the clinic.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Remapping simulated halo catalogues in redshift space (2014)
    Oxford University Press
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    Publication Date: 2014-10-31
    Description: We discuss the extension to redshift space of a rescaling algorithm, designed to alter the effective cosmology of a pre-existing simulated particle distribution or catalogue of dark matter haloes. The rescaling approach was initially developed by Angulo & White and was adapted and applied to halo catalogues in real space in our previous work. This algorithm requires no information other than the initial and target cosmological parameters, and it contains no tuned parameters. It is shown here that the rescaling method also works well in redshift space, and that the rescaled simulations can reproduce the growth rate of cosmological density fluctuations appropriate for the target cosmology. Even when rescaling a grossly non-standard model with  = 0 and zero baryons, the redshift-space power spectrum of standard cold dark matter can be reproduced to about 5 per cent error for k  〈 0.2 h Mpc –1 . The ratio of quadrupole-to-monopole power spectra remains correct to the same tolerance up to k  = 1 h Mpc –1 , provided that the input halo catalogue contains measured internal velocity dispersions.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    Remapping dark matter halo catalogues between cosmological simulations (2014)
    Oxford University Press
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    Publication Date: 2014-04-15
    Description: We present and test a method for modifying the catalogue of dark matter haloes produced from a given cosmological simulation, so that it resembles the result of a simulation with an entirely different set of parameters. This extends the method of Angulo & White, which rescales the full particle distribution from a simulation. Working directly with the halo catalogue offers an advantage in speed, and also allows modifications of the internal structure of the haloes to account for non-linear differences between cosmologies. Our method can be used directly on a halo catalogue in a self-contained manner without any additional information about the overall density field; although the large-scale displacement field is required by the method, this can be inferred from the halo catalogue alone. We show proof of concept of our method by rescaling a matter-only simulation with no baryon acoustic oscillation (BAO) features to a more standard cold dark matter model containing a cosmological constant and a BAO signal. In conjunction with the halo occupation approach, this method provides a basis for the rapid generation of mock galaxy samples spanning a wide range of cosmological parameters.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Accurate halo-model matter power spectra with dark energy, massive neutrinos and modified gravitational forces (2016)
    Oxford University Press
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    Publication Date: 2016-04-23
    Description: We present an accurate non-linear matter power spectrum prediction scheme for a variety of extensions to the standard cosmological paradigm, which uses the tuned halo model previously developed in Mead et al. We consider dark energy models that are both minimally and non-minimally coupled, massive neutrinos and modified gravitational forces with chameleon and Vainshtein screening mechanisms. In all cases, we compare halo-model power spectra to measurements from high-resolution simulations. We show that the tuned halo-model method can predict the non-linear matter power spectrum measured from simulations of parametrized w ( a ) dark energy models at the few per cent level for k  〈 10 h Mpc –1 , and we present theoretically motivated extensions to cover non-minimally coupled scalar fields, massive neutrinos and Vainshtein screened modified gravity models that result in few per cent accurate power spectra for k  〈 10 h Mpc –1 . For chameleon screened models, we achieve only 10 per cent accuracy for the same range of scales. Finally, we use our halo model to investigate degeneracies between different extensions to the standard cosmological model, finding that the impact of baryonic feedback on the non-linear matter power spectrum can be considered independently of modified gravity or massive neutrino extensions. In contrast, considering the impact of modified gravity and massive neutrinos independently results in biased estimates of power at the level of 5 per cent at scales k  〉 0.5 h Mpc –1 . An updated version of our publicly available hmcode can be found at https://github.com/alexander-mead/hmcode .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Spherical collapse, formation hysteresis and the deeply non-linear cosmological power spectrum (2016)
    Oxford University Press
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    Publication Date: 2016-10-27
    Description: I examine differences in non-linear structure formation between cosmological models that share a z  = 0 linear power spectrum in both shape and amplitude, but that differ via their growth history. N -body simulations of these models display an approximately identical large-scale-structure skeleton, but reveal deeply non-linear differences in the demographics and properties of haloes. I investigate to what extent the spherical-collapse model can help in understanding these differences, in both real and redshift space. I discuss how this is difficult to do if one attempts to identify haloes directly, because in that case one is subject to the vagaries of halo-finding algorithms. However, I demonstrate that the halo model of structure formation provides an accurate non-linear response in the power spectrum, but only if results from spherical collapse that include formation hysteresis are properly incorporated. I comment on how this fact can be used to provide per cent level accurate matter power-spectrum predictions for dark energy models for k ≤ 5 h Mpc –1 by using the halo model as a correction to accurate CDM simulations. In the Appendix, I provide some fitting functions for the linear-collapse threshold ( c ) and virialized overdensity ( v ) that are valid for a wide range of dark energy models. I also make my spherical-collapse code available at https://github.com/alexander-mead/collapse .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Trisomy 21 hematopoietic stem and progenitor cells [Medical Sciences] (2012)
    National Academy of Sciences
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    Publication Date: 2012-10-24
    Description: The 40-fold increase in childhood megakaryocyte-erythroid and B-cell leukemia in Down syndrome implicates trisomy 21 (T21) in perturbing fetal hematopoiesis. Here, we show that compared with primary disomic controls, primary T21 fetal liver (FL) hematopoietic stem cells (HSC) and megakaryocyte-erythroid progenitors are markedly increased, whereas granulocyte-macrophage progenitors are reduced. Commensurately,...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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