Use of Time Dependent Data in Bayesian Global 21cm Foreground and Signal Modelling

Global 21cm cosmology aims to investigate the cosmic dawn and epoch of reionisation by measuring the sky averaged HI absorption signal, which requires, accurate modelling of, or correction for, the bright radio foregrounds and distortions arising from chromaticity of the antenna beam. We investigate the effect of improving foreground modelling by fitting data sets from many observation times simultaneously in a single Bayesian analysis, fitting for the same parameter set by performing these fits on simulated data. We find that for a hexagonal dipole antenna, this simultaneous fitting produces a significant improvement in the accuracy of the recovered 21cm signal, relative to fitting a time average of the data. Furthermore, the recovered models of the foreground are also seen to become more accurate by up to a factor of $\sim$2-3 relative to time averaged fitting. For a less chromatic log spiral antenna, no significant improvement in signal recovery was found by this process. However, the modelling of the foregrounds was still significantly improved. We also investigate extending this technique to fit multiple data sets from different antennae simultaneously for the same parameters. This is also found to improve both 21cm signal and foreground modelling, to a higher degree than fitting data set from multiple times from the same antenna.Comment: 19 pages, 19 figure

Modelling a Hot Horizon in Global 21 cm Experimental Foregrounds

The 21 cm signal from cosmic hydrogen is one of the most propitious probes of the early Universe. The detection of this signal would reveal key information about the first stars, the nature of dark matter, and early structure formation. We explore the impact of an emissive and reflective, or `hot', horizon on the recovery of this signal for global 21 cm experiments. It is demonstrated that using physically motivated foreground models to recover the sky-averaged 21 cm signal one must accurately describe the horizon around the radiometer. We show that not accounting for the horizon will lead to a signal recovery with residuals an order of magnitude larger than the injected signal, with a log Bayesian evidence of almost 1600 lower than when one does account for the horizon. It is shown that signal recovery is sensitive to incorrect values of soil temperature and reflection coefficient in describing the horizon, with even a 10% error in reflectance causing twofold increases in the RMSE of a given fit. We also show these parameters may be fitted using Bayesian inference to mitigate for these issues without overfitting and mischaracterising a non-detection. We further demonstrate that signal recovery is sensitive to errors in measurements of the horizon projection onto the sky, but fitting for soil temperature and reflection coefficients with priors that extend beyond physical expectation can resolve these problems. We show that using an expanded prior range can reliably recover the signal even when the height of the horizon is mismeasured by up to 20%, decreasing the RMSE from the model that does not perform this fitting by a factor of 9.Comment: 12 pages, 11 figures, 5 table

A General Bayesian Framework to Account for Foreground Map Errors in Global 21-cm Experiments

Measurement of the global 21-cm signal during Cosmic Dawn (CD) and the Epoch of Reionization (EoR) is made difficult by bright foreground emission which is 2-5 orders of magnitude larger than the expected signal. Fitting for a physics-motivated parametric forward model of the data within a Bayesian framework provides a robust means to separate the signal from the foregrounds, given sufficient information about the instrument and sky. It has previously been demonstrated that, within such a modelling framework, a foreground model of sufficient fidelity can be generated by dividing the sky into $N$ regions and scaling a base map assuming a distinct uniform spectral index in each region. Using the Radio Experiment for the Analysis of Cosmic Hydrogen (REACH) as our fiducial instrument, we show that, if unaccounted-for, amplitude errors in low-frequency radio maps used for our base map model will prevent recovery of the 21-cm signal within this framework, and that the level of bias in the recovered 21-cm signal is proportional to the amplitude and the correlation length of the base-map errors in the region. We introduce an updated foreground model that is capable of accounting for these measurement errors by fitting for a monopole offset and a set of spatially-dependent scale factors describing the ratio of the true and model sky temperatures, with the size of the set determined by Bayesian evidence-based model comparison. We show that our model is flexible enough to account for multiple foreground error scenarios allowing the 21-cm sky-averaged signal to be detected without bias from simulated observations with a smooth conical log spiral antenna.Comment: 18 pages, 13 figure

Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics.

The incidence of Plasmodium vivax infection has declined markedly in Malaysia over the past decade despite evidence of high-grade chloroquine resistance. Here we investigate the genetic changes in a P. vivax population approaching elimination in 51 isolates from Sabah, Malaysia and compare these with data from 104 isolates from Thailand and 104 isolates from Indonesia. Sabah displays extensive population structure, mirroring that previously seen with the emergence of artemisinin-resistant P. falciparum founder populations in Cambodia. Fifty-four percent of the Sabah isolates have identical genomes, consistent with a rapid clonal expansion. Across Sabah, there is a high prevalence of loci known to be associated with antimalarial drug resistance. Measures of differentiation between the three countries reveal several gene regions under putative selection in Sabah. Our findings highlight important factors pertinent to parasite resurgence and molecular cues that can be used to monitor low-endemic populations at the end stages of P. vivax elimination

Observing America: what mass-observation reveals about British views of the USA

Since its foundation in 1937, the social research organisation Mass-Observation has systematically documented the opinions of a British public experiencing profound societal change. This includes the most extensive data available on grassroots attitudes towards the USA, from the outbreak of the Second World War to the final phase of the Cold War. Most of the scholarship on Anglo-American relations focuses on the political and diplomatic elites of Britain and the USA. The extent to which their interaction reflected and reinforced public opinion is seldom considered. This article uses the Mass-Observation archive to situate elite interaction within the broader context of public opinion. In so doing, it assesses the extent to which British political leaders have in their dealings with the USA represented the views of the electorate they serve

Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial

SummaryBackground Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatoryactions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.Methods In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospitalwith COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients wererandomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once perday by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatmentgroups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment andwere twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants andlocal study staff were not masked to the allocated treatment, but all others involved in the trial were masked to theoutcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treatpopulation. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.Findings Between April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) wereeligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomlyallocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall,561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days(rate ratio 0·97, 95% CI 0·87–1·07; p=0·50). No significant difference was seen in duration of hospital stay (median10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days(rate ratio 1·04, 95% CI 0·98–1·10; p=0·19). Among those not on invasive mechanical ventilation at baseline, nosignificant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilationor death (risk ratio 0·95, 95% CI 0·87–1·03; p=0·24).Interpretation In patients admitted to hospital with COVID-19, azithromycin did not improve survival or otherprespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restrictedto patients in whom there is a clear antimicrobial indication

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Data Analysis in Global 21cm Experiments: Physically Motivated Bayesian Modelling Techniques

21cm cosmology is a field in which the absorption and emission from the cosmic radio background by neutral hydrogen gas is used to probe cosmology and astrophysics of early epochs of the universe. In particular, this process is one of the most promising methods of measuring the Cosmic Dawn, when the first stars formed, and the Epoch of Reionisation, making it a key objective of modern radio cosmology. This thesis primarily investigates the application of Bayesian data analysis techniques to global 21cm cosmology, to aid in overcoming two of the most prominent difficulties in detecting a sky-averaged ('global') 21cm signal: the presence of foregrounds around four orders of magnitude brighter than the signal and systematic distortions that arise from chromaticity of the antenna's gain pattern. Therefore, in this thesis, the impact that these difficulties can have on experiments is investigated through simulations and the efficacy with which existing data analysis techniques in the field can manage them is quantified. Following this, a new data analysis pipeline is developed, utilising Bayesian processes, that is designed to overcome limitations with existing techniques. The primary concept of the pipeline developed in this thesis is to perform continuous physically motivated simulations of observations using parametrised models of the sky and antenna to explain and fit for systematic distortions in a physically understood manner. Throughout this thesis, this pipeline is developed and tested in simulations to quantify its performance and limitations. The core of this work was published in Anstey et al. (2021). This thesis also discusses the additional technique of utilising time- and antenna-dependencies in data, coupled with the developed pipeline, to improve the Bayesian modelling process, which is being written in Anstey et al. (in prep.), as well as a method by which simulated observations in the developed pipeline could be used to help guide the design of a global 21cm experiment, published in Anstey et al. (2022). The techniques developed in this thesis are generally applicable to any global 21cm experiment. However, they were developed with the primary intent of being utilised in the Radio Experiment for the Analysis of Cosmic Hydrogen (REACH) (de Lera Acedo et al. 2022)