Bayesian Variational Regularisation for Dark Matter Reconstruction with Uncertainty Quantification

Despite the great wealth of cosmological knowledge accumulated since the early 20th century, the nature of dark-matter, which accounts for ~85% of the matter content of the universe, remains illusive. Unfortunately, though dark-matter is scientifically interesting, with implications for our fundamental understanding of the Universe, it cannot be directly observed. Instead, dark-matter may be inferred from e.g. the optical distortion (lensing) of distant galaxies which, at linear order, manifests as a perturbation to the apparent magnitude (convergence) and ellipticity (shearing). Ensemble observations of the shear are collected and leveraged to construct estimates of the convergence, which can directly be related to the universal dark-matter distribution. Imminent stage IV surveys are forecast to accrue an unprecedented quantity of cosmological information; a discriminative partition of which is accessible through the convergence, and is disproportionately concentrated at high angular resolutions, where the echoes of cosmological evolution under gravity are most apparent. Capitalising on advances in probability concentration theory, this thesis merges the paradigms of Bayesian inference and optimisation to develop hybrid convergence inference techniques which are scalable, statistically principled, and operate over the Euclidean plane, celestial sphere, and 3-dimensional ball. Such techniques can quantify the plausibility of inferences at one-millionth the computational overhead of competing sampling methods. These Bayesian techniques are applied to the hotly debated Abell-520 merging cluster, concluding that observational catalogues contain insufficient information to determine the existence of dark-matter self-interactions. Further, these techniques were applied to all public lensing catalogues, recovering the then largest global dark-matter mass-map. The primary methodological contributions of this thesis depend only on posterior log-concavity, paving the way towards a, potentially revolutionary, complete hybridisation with artificial intelligence techniques. These next-generation techniques are the first to operate over the full 3-dimensional ball, laying the foundations for statistically principled universal dark-matter cartography, and the cosmological insights such advances may provide

Collapse of a molecular cloud core to stellar densities: the radiative impact of stellar core formation on the circumstellar disc

We present results from the first three-dimensional radiation hydrodynamical calculations to follow the collapse of a molecular cloud core beyond the formation of the stellar core. We find the energy released by the formation of the stellar core, within the optically-thick first hydrostatic core, is comparable to the binding energy of the disc-like first core. This heats the inner regions of the disc, drives a shock wave through the disc, dramatically decreases the accretion rate on to the stellar core, and launches a temporary bipolar outflow perpendicular to the rotation axis that travels in excess of 50 AU into the infalling envelope. This outburst may assist the young protostar in launching a conventional magnetic jet. Furthermore, if these events are cyclic, they may provide a mechanism for intense bursts of accretion separated by long periods of relatively quiescent accretion which can potentially solve both the protostellar luminosity problem and the apparent age spread of stars in young clusters. Such outbursts may also provide a formation mechanism for the chondrules found in meteorites, with the outflow transporting them to large distances in the circumstellar disc.Comment: Accepted by MNRAS Letters. 6 pages, 4 figures. Animations can be found at http://www.astro.ex.ac.uk/people/mbate/Animations/Stellar

A Full-Ocean-Depth Rated Modular Lander and Pressure-Retaining Sampler Capable of Collecting Hadal-Endemic Microbes Under \u3ci\u3ein situ\u3c/i\u3e Conditions

The hadal zone remains one of the least studied environments because of its inaccessibility, in part because of hydrostatic pressures extending to 110 MPa. Few instruments are capable of sampling from such great depths. We have developed a full-ocean-depth-capable lander that can be fit with sampling packages for the collection of still images, video, motile megafauna, and hadal seawater. One payload includes a pressure-retaining sampler (PRS) able to maintain seawater samples under in situ pressure during recovery. We describe the technical specifications of the lander and the PRS and preliminary results from three deployments at depths in excess of 10,700 m in the Mariana Trench. Seawater from full-ocean depth was recovered at 81% of the in situ pressure. This facilitated the collection of microbial genomes affiliated with the family Flavobacteriaceae within the Bacteroidetes and the phylum Marinimicrobia. We show that these microbes are specifically enriched in hadal zones, representing novel trench lineages, and describe their adaptations for living in hadal environments. These findings highlight the utility of this lander system, which facilitates scientific inquiry at depths greater than 6000 m

The growth and hydrodynamic collapse of a protoplanet envelope

We have conducted three-dimensional self-gravitating radiation hydrodynamical models of gas accretion onto high mass cores (15-33 Earth masses) over hundreds of orbits. Of these models, one case accretes more than a third of a Jupiter mass of gas, before eventually undergoing a hydrodynamic collapse. This collapse causes the density near the core to increase by more than an order of magnitude, and the outer envelope to evolve into a circumplanetary disc. A small reduction in the mass within the Hill radius (R_H) accompanies this collapse as a shock propagates outwards. This collapse leads to a new hydrostatic equilibrium for the protoplanetary envelope, at which point 97 per cent of the mass contained within the Hill radius is within the inner 0.03 R_H which had previously contained less than 40 per cent. Following this collapse the protoplanet resumes accretion at its prior rate. The net flow of mass towards this dense protoplanet is predominantly from high latitudes, whilst at the outer edge of the circumplanetary disc there is net outflow of gas along the midplane. We also find a turnover of gas deep within the bound envelope that may be caused by the establishment of convection cells.Comment: 16 pages, 16 figures. Accepted for publication in MNRA

Exploring the conditions required to form giant planets via gravitational instability in massive protoplanetary discs

We carry out global three-dimensional radiation hydrodynamical simulations of self-gravitating accretion discs to determine if, and under what conditions, a disc may fragment to form giant planets. We explore the parameter space (in terms of the disc opacity, temperature and size) and include the effect of stellar irradiation. We find that the disc opacity plays a vital role in determining whether a disc fragments. Specifically, opacities that are smaller than interstellar Rosseland mean values promote fragmentation (even at small radii, R < 25AU) since low opacities allow a disc to cool quickly. This may occur if a disc has a low metallicity or if grain growth has occurred. With specific reference to the HR 8799 planetary system, given its star is metal-poor, our results suggest that the formation of its imaged planetary system could potentially have occurred by gravitational instability. We also find that the presence of stellar irradiation generally acts to inhibit fragmentation (since the discs can only cool to the temperature defined by stellar irradiation). However, fragmentation may occur if the irradiation is sufficiently weak that it allows the disc to attain a low Toomre stability parameter.Comment: Accepted for publication by MNRAS. 11 pages, 12 figures

Circumplanetary disc properties obtained from radiation hydrodynamical simulations of gas accretion by protoplanets

We investigate the properties of circumplanetary discs formed in three-dimensional, self-gravitating radiation hydrodynamical models of gas accretion by protoplanets. We determine disc sizes, scaleheights, and density and temperature profiles for different protoplanet masses, in solar nebulae of differing grain opacities. We find that the analytical prediction of circumplanetary disc radii in an evacuated gap (R_Hill/3) from Quillen & Trilling (1998) yields a good estimate for discs formed by high mass protoplanets. The radial density profiles of the circumplanetary discs may be described by power-laws between r^-2 and r^-3/2. We find no evidence for the ring-like density enhancements that have been found in some previous models of circumplanetary discs. Temperature profiles follow a ~r^-7/10 power-law regardless of protoplanet mass or nebula grain opacity. The discs invariably have large scaleheights (H/r > 0.2), making them thick in comparison with their encompassing circumstellar discs, and they show no flaring.Comment: 9 pages, 6 figures, accepted for publication in MNRA

Planet migration: self-gravitating radiation hydrodynamical models of protoplanets with surfaces

We calculate radial migration rates of protoplanets in laminar minimum mass solar nebula discs using three-dimensional self-gravitating radiation hydrodynamical (RHD) models. The protoplanets are free to migrate, whereupon their migration rates are measured. For low mass protoplanets (10-50 M_\oplus) we find increases in the migration timescales of up to an order of magnitude between locally-isothermal and RHD models. In the high-mass regime the migration rates are changed very little. These results are arrived at by calculating migration rates in locally-isothermal models, before sequentially introducing self-gravity, and radiative transfer, allowing us to isolate the effects of the additional physics. We find that using a locally-isothermal equation of state, without self-gravity, we reproduce the migration rates obtained by previous analytic and numerical models. We explore the impact of different protoplanet models, and changes to their assumed radii, upon migration. The introduction of self-gravity gives a slight reduction of the migration rates, whilst the inertial mass problem, which has been proposed for high mass protoplanets with circumplanetary discs, is reproduced. Upon introducing radiative transfer to models of low mass protoplanets (\approx 10 M_\oplus), modelled as small radius accreting point masses, we find outward migration with a rate of approximately twice the analytic inward rate. However, when modelling such a protoplanet in a more realistic manner, with a surface which enables the formation of a deep envelope, this outward migration is not seen.Comment: 21 pages, 21 figure

Collapse of a molecular cloud core to stellar densities: the formation and evolution of pre-stellar discs

We report results from radiation hydrodynamical simulations of the collapse of molecular cloud cores to form protostars. The calculations follow the formation and evolution of the first hydrostatic core/disc, the collapse to form a stellar core, and effect of stellar core formation on the surrounding disc and envelope. Past barotropic calculations have shown that rapidly-rotating first cores evolve into `pre-stellar discs' with radii up to ~100 AU that may last thousands of years before a stellar core forms. We investigate how the inclusion of a realistic equation of state and radiative transfer alters this behaviour, finding that the qualitative behaviour is similar, but that the pre-stellar discs may last 1.5-3 times longer in the more realistic calculations. The masses, radii, and lifetimes of the discs increase for initial molecular cloud cores with faster rotation rates. In the most extreme case we model, a pre-stellar disc with a mass of 0.22 Msun and a radius of ~100 AU can form in a solar-mass cloud and last several thousand years before a stellar core is formed. Such large, massive objects may be imaged using ALMA. Fragmentation of these massive discs may also provide an effective route to binary and multiple star formation, before radiative feedback from accretion onto the stellar core can inhibit fragmentation. Once collapse to form a stellar core occurs within the pre-stellar disc, the radiation hydrodynamical simulations produce qualitatively different behaviour from the barotropic calculations due to the accretion energy released. This drives a shock wave through the circumstellar disc and launches a bipolar outflow even in the absence of magnetic fields.Comment: Accepted for publication in MNRAS, 22 pages, 18 figure

CD4+ T Cell Depletion during all Stages of HIV Disease Occurs Predominantly in the Gastrointestinal Tract

The mechanisms underlying CD4+ T cell depletion in human immunodeficiency virus (HIV) infection are not well understood. Comparative studies of lymphoid tissues, where the vast majority of T cells reside, and peripheral blood can potentially illuminate the pathogenesis of HIV-associated disease. Here, we studied the effect of HIV infection on the activation and depletion of defined subsets of CD4+ and CD8+ T cells in the blood, gastrointestinal (GI) tract, and lymph node (LN). We also measured HIV-specific T cell frequencies in LNs and blood, and LN collagen deposition to define architectural changes associated with chronic inflammation. The major findings to emerge are the following: the GI tract has the most substantial CD4+ T cell depletion at all stages of HIV disease; this depletion occurs preferentially within CCR5+ CD4+ T cells; HIV-associated immune activation results in abnormal accumulation of effector-type T cells within LNs; HIV-specific T cells in LNs do not account for all effector T cells; and T cell activation in LNs is associated with abnormal collagen deposition. Taken together, these findings define the nature and extent of CD4+ T cell depletion in lymphoid tissue and point to mechanisms of profound depletion of specific T cell subsets related to elimination of CCR5+ CD4+ T cell targets and disruption of T cell homeostasis that accompanies chronic immune activation

Specialist Respiratory Outreach : a case-finding initiative for identifying undiagnosed COPD in primary care

Acknowledgments This report is independent research funded by the National Institute for Health Research Wessex ARC. The views expressed in this publication are those of the author(s) and not necessarily those of the National Institute for Health Research or the Department of Health and Social Care. We are very grateful to Optimum Patient care and their team for their help and support with the data extraction and application of the case-finding risk score. We would also like to thank: The participants, Mark Stafford-Watson (PPI) in memorial, Colin Newell, Dr Fiona McKenna, Dr Andy Powell, Dr Helen Myers, Dr Stuart McKinnes, Dr Mark Williams, Dr Louisa Egbe, Dr Richard Baxter, Dr Sarah A’Court, Dr Elisabeth Willows, Dr Gareth Morris, Dr Ford, Dr Kate Lippiett, Wessex Clinical Research Network, West Hampshire CCG and Southampton City CCGPeer reviewedPublisher PD