Untangling the physical components of galaxies using infrared spectra

The two main physical processes that underpin galaxy evolution are star formation and accretion of mass in active galactic nuclei (AGN). Understanding how contributions from these processes vary across cosmic time requires untangling their relative contributions. The infrared part of the electromagnetic spectrum contains a number of AGN and star formation diagnostics e.g. emission lines from ionised gas or polyaromatic hydrocarbons (PAHs), and the shape of the continuum. Despite the higher resolution of data from Spitzer’s IRS spectrograph, separating out emission from star formation and AGN is carried out using limited spectral features or simplistic templates. In the first part of this thesis, I show how sophisticated data analysis techniques can make full use of the wealth of spectral data. I demonstrate how the popular multivariate technique, Principal Component Analysis (PCA), can classify different types of ultra luminous infrared galaxies (ULIRGs), whilst providing a simple set of spectral components that provide better fits than state-of-the art radiative transfer models. I show how an alternative multivariate technique, Non-Negative Matrix Factorisation (NMF) is more appropriate by applying it to over 700 extragalactic spectra from the CASSIS database and demonstrating its capability in producing spectral components that are physically intuitive, allowing the processes of star formation and AGN activity to be clearly untangled. Finally, I show how rotational transition lines from carbon monoxide and water, observed by the Herschel Space Observatory, provides constraints on the physical conditions within galaxies. By coupling the radiative transfer code, RADEX, with the nested sampling routine, Multinest, I carry out Bayesian inference on the CO spectral line energy distribution ladder of the nearby starburst galaxy, IC342. I also show that water emission lines provide important constraints the conditions of the ISM of on one of the most distant starburst galaxies ever detected, HFLS3

Creating longitudinal datasets and cleaning existing data identifiers in a cystic fibrosis registry using a novel Bayesian probabilistic approach from astronomy

Patient registry data are commonly collected as annual snapshots that need to be amalgamated to understand the longitudinal progress of each patient. However, patient identifiers can either change or may not be available for legal reasons when longitudinal data are collated from patients living in different countries. Here, we apply astronomical statistical matching techniques to link individual patient records that can be used where identifiers are absent or to validate uncertain identifiers. We adopt a Bayesian model framework used for probabilistically linking records in astronomy. We adapt this and validate it across blinded, annually collected data. This is a high-quality (Danish) sub-set of data held in the European Cystic Fibrosis Society Patient Registry (ECFSPR). Our initial experiments achieved a precision of 0.990 at a recall value of 0.987. However, detailed investigation of the discrepancies uncovered typing errors in 27 of the identifiers in the original Danish sub-set. After fixing these errors to create a new gold standard our algorithm correctly linked individual records across years achieving a precision of 0.997 at a recall value of 0.987 without recourse to identifiers. Our Bayesian framework provides the probability of whether a pair of records belong to the same patient. Unlike other record linkage approaches, our algorithm can also use physical models, such as body mass index curves, as prior information for record linkage. We have shown our framework can create longitudinal samples where none existed and validate pre-existing patient identifiers. We have demonstrated that in this specific case this automated approach is better than the existing identifiers

SDSS J124602.54+011318.8: A Highly Luminous Optical Transient at z=0.385

We report the discovery of a highly luminous optical transient (OT), SDSS J124602.54+011318.8, associated with a galaxy at a redshift of 0.385. In this paper we consider the possibility that the OT may be a GRB afterglow. Three sets of images and two sets of spectra were obtained as part of the normal operations of the Sloan Digital Sky Survey (SDSS). In the first two image sets, observed two nights apart, the object appears as a point source at $r^{*}\approx 17$. The third image set, observed about 410 days later, shows an extended source which is more than 2.5 magnitudes fainter. The spectra were observed about 400 and 670 days after the first two image sets, and both show an apparently normal galaxy at a redshift of 0.385. Associating the OT with the galaxy, the absolute magnitude was $M_{r^*}=-24.8$, which is over 4 magnitudes brighter than the most luminous supernova ever measured. The spectral energy distributions of the galaxy-subtracted OT derived from the first two image sets are well-fit by single power-laws with indices of $\beta_{\nu}=-0.92$ and -1.29 respectively, similar to most GRB afterglows. Based upon the luminosity of the OT, non-detections in contemporaneous ROTSE-I images, and the change in spectral slope, the OT, if an afterglow, was likely discovered early during a ``plateau'' or slowly-fading phase. The discovery of a GRB afterglow at this stage of the SDSS is consistent with expectations, but only if the optical emission is much less strongly beamed than the gamma-rays. We emphasize that other explanations for the OT cannot be ruled out; a recent follow-up study by [galyam02] provides strong evidence that this source is in fact an unusual AGN.Comment: Updated version to appear in Ap

GRB Afterglows and Other Transients in the SDSS

The Sloan Digital Sky Survey (SDSS) will image one quarter of the sky centered on the northern galactic cap and produce a 3‐D map of galaxies and quasars found in the sample. An additional 225 deg2 southern survey will be imaged repeatedly on varying timescales. Here we discuss both archival searches in the SDSS catalog (such as SDSS J24602.54+011318.8) and active searches with the SDSS instruments (such as for GRB 010222) for GRB afterglows and other transient objects. © 2003 American Institute of PhysicsPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87288/2/349_1.pd

Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

Background Suicide is a leading cause of death worldwide, and nonfatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders. Methods We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium (ISGC). The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via multitrait-based conditional and joint analysis, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders, and other known risk factors. Results Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, the latter of which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking behavior, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking behavior, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status, and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with nonpsychiatric traits remained largely unchanged. Conclusions Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.Peer reviewe

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

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

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome

Histogram of the match probabilities for the false positives for first run of algorithm (in green) and final run with cleaned links (in blue).

<p>For the first run, our algorithm had assigned a ‘high probability of being a match’ to a significant number of false positives, the majority of which turned out to have incorrect IDs.</p