Likelihood Non-Gaussianity in Large-Scale Structure Analyses

Standard present day large-scale structure (LSS) analyses make a major assumption in their Bayesian parameter inference --- that the likelihood has a Gaussian form. For summary statistics currently used in LSS, this assumption, even if the underlying density field is Gaussian, cannot be correct in detail. We investigate the impact of this assumption on two recent LSS analyses: the Beutler et al. (2017) power spectrum multipole ($P_\ell$) analysis and the Sinha et al. (2017) group multiplicity function ($\zeta$) analysis. Using non-parametric divergence estimators on mock catalogs originally constructed for covariance matrix estimation, we identify significant non-Gaussianity in both the $P_\ell$ and $\zeta$ likelihoods. We then use Gaussian mixture density estimation and Independent Component Analysis on the same mocks to construct likelihood estimates that approximate the true likelihood better than the Gaussian $pseudo$-likelihood. Using these likelihood estimates, we accurately estimate the true posterior probability distribution of the Beutler et al. (2017) and Sinha et al. (2017) parameters. Likelihood non-Gaussianity shifts the $f\sigma_8$ constraint by $-0.44\sigma$, but otherwise, does not significantly impact the overall parameter constraints of Beutler et al. (2017). For the $\zeta$ analysis, using the pseudo-likelihood significantly underestimates the uncertainties and biases the constraints of Sinha et al. (2017) halo occupation parameters. For $\log M_1$ and $\alpha$, the posteriors are shifted by $+0.43\sigma$ and $-0.51\sigma$ and broadened by $42\%$ and $66\%$, respectively. The divergence and likelihood estimation methods we present provide a straightforward framework for quantifying the impact of likelihood non-Gaussianity and deriving more accurate parameter constraints.Comment: 33 pages, 7 figure

The clustering of Galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey : including covariance matrix errors

JP acknowledges support from the UK Science & Technology Facilities Council (STFC) through the consolidated grant ST/K0090X/1 and from the European Research Council through the ‘Starting Independent Research’ grant 202686, MDEPUGS. AGS acknowledges support from the Trans-regional Collaborative Research Centre TR33 ‘The Dark Universe’ of the German Research Foundation (DFG).We present improved methodology for including covariance matrices in the error budget of Baryon Oscillation Spectroscopic Survey (BOSS) galaxy clustering measurements, revisiting Data Release 9 (DR9) analyses, and describing a method that is used in DR10/11 analyses presented in companion papers. The precise analysis method adopted is becoming increasingly important, due to the precision that BOSS can now reach: even using as many as 600 mock catalogues to estimate covariance of two-point clustering measurements can still lead to an increase in the errors of ∼20 per cent, depending on how the cosmological parameters of interest are measured. In this paper, we extend previous work on this contribution to the error budget, deriving formulae for errors measured by integrating over the likelihood, and to the distribution of recovered best-fitting parameters fitting the simulations also used to estimate the covariance matrix. Both are situations that previous analyses of BOSS have considered. We apply the formulae derived to baryon acoustic oscillation (BAO) and redshift-space distortion (RSD) measurements from BOSS in our companion papers. To further aid these analyses, we consider the optimum number of bins to use for two-point measurements using the monopole power spectrum or correlation function for BAO, and the monopole and quadrupole moments of the correlation function for anisotropic-BAO and RSD measurements.Publisher PDFPeer reviewe

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey : cosmological implications of the full shape of the clustering wedges in the data release 10 and 11 galaxy samples

We explore the cosmological implications of the angle-averaged correlation function, ξ(s), and the clustering wedges, ξ⊥(s) and ξ∥(s), of the LOWZ and CMASS galaxy samples from Data Releases 10 and 11 of the Sloan Digital Sky Survey III (SDSS-III) Baryon Oscillation Spectroscopic Survey. Our results show no significant evidence for a deviation from the standard Λ cold dark matter model. The combination of the information from our clustering measurements with recent data from the cosmic microwave background is sufficient to constrain the curvature of the Universe to Ωk = 0.0010 ± 0.0029, the total neutrino mass to ∑mν < 0.23 eV (95 per cent confidence level), the effective number of relativistic species to Neff = 3.31 ± 0.27 and the dark energy equation of state to wDE = −1.051 ± 0.076. These limits are further improved by adding information from Type Ia supernovae and baryon acoustic oscillations from other samples. In particular, this data set combination is completely consistent with a time-independent dark energy equation of state, in which case we find wDE = −1.024 ± 0.052. We explore the constraints on the growth rate of cosmic structures assuming f(z) = Ωm(z)γ and obtain γ = 0.69 ± 0.15, consistent with the predictions of general relativity of γ = 0.55.Publisher PDFPeer reviewe

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: single-probe measurements from CMASS anisotropic galaxy clustering

With the largest spectroscopic galaxy survey volume drawn from the SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS), we can extract cosmological constraints from the measurements of redshift and geometric distortions at quasi-linear scales (e.g. above 50 $h^{-1}$Mpc). We analyze the broad-range shape of the monopole and quadrupole correlation functions of the BOSS Data Release 12 (DR12) CMASS galaxy sample, at the effective redshift $z=0.59$, to obtain constraints on the Hubble expansion rate $H(z)$, the angular-diameter distance $D_A(z)$, the normalized growth rate $f(z)\sigma_8(z)$, and the physical matter density $\Omega_mh^2$. We obtain robust measurements by including a polynomial as the model for the systematic errors, and find it works very well against the systematic effects, e.g., ones induced by stars and seeing. We provide accurate measurements $\{D_A(0.59)r_{s,fid}/r_s$ $\rm Mpc$, $H(0.59)r_s/r_{s,fid}$ $km s^{-1} Mpc^{-1}$, $f(0.59)\sigma_8(0.59)$, $\Omega_m h^2\}$ = $\{1427\pm26$, $97.3\pm3.3$, $0.488 \pm 0.060$, $0.135\pm0.016\}$, where $r_s$ is the comoving sound horizon at the drag epoch and $r_{s,fid}=147.66$ Mpc is the sound scale of the fiducial cosmology used in this study. The parameters which are not well constrained by our galaxy clustering analysis are marginalized over with wide flat priors. Since no priors from other data sets, e.g., cosmic microwave background (CMB), are adopted and no dark energy models are assumed, our results from BOSS CMASS galaxy clustering alone may be combined with other data sets, i.e., CMB, SNe, lensing or other galaxy clustering data to constrain the parameters of a given cosmological model. The uncertainty on the dark energy equation of state parameter, $w$, from CMB+CMASS is about 8 per cent. The uncertainty on the curvature fraction, $\Omega_k$, is 0.3 per cent. We do not find deviation from flat $\Lambda$CDM.Comment: 15 pages, 11 figures. The latest version matches and the accepted version by MNRAS. A bug in the first version has been identified and fixed in the new version. We have redone the analysis with newest data (BOSS DR12

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey : measuring DA and H at z = 0.57 from the baryon acoustic peak in the Data Release 9 spectroscopic Galaxy sample

We present measurements of the angular diameter distance to and Hubble parameter at z = 0.57 from the measurement of the baryon acoustic peak in the correlation of galaxies from the Sloan Digital Sky Survey III Baryon Oscillation Spectroscopic Survey. Our analysis is based on a sample from Data Release 9 of 264 283 galaxies over 3275 square degrees in the redshift range 0.43 < z < 0.70. We use two different methods to provide robust measurement of the acoustic peak position across and along the line of sight in order to measure the cosmological distance scale. We find DA(0.57) = 1408 ± 45 Mpc and H(0.57) = 92.9 ± 7.8 km s−1 Mpc−1 for our fiducial value of the sound horizon. These results from the anisotropic fitting are fully consistent with the analysis of the spherically averaged acoustic peak position presented in Anderson et al. Our distance measurements are a close match to the predictions of the standard cosmological model featuring a cosmological constant and zero spatial curvature.Publisher PDFPeer reviewe

SDSS-III Baryon Oscillation Spectroscopic Survey data release 12 : galaxy target selection and large-scale structure catalogues

The Baryon Oscillation Spectroscopic Survey (BOSS), part of the Sloan Digital Sky Survey (SDSS) III project, has provided the largest survey of galaxy redshifts available to date, in terms of both the number of galaxy redshifts measured by a single survey, and the effective cosmological volume covered. Key to analysing the clustering of these data to provide cosmological measurements is understanding the detailed properties of this sample. Potential issues include variations in the target catalogue caused by changes either in the targeting algorithm or properties of the data used, the pattern of spectroscopic observations, the spatial distribution of targets for which redshifts were not obtained, and variations in the target sky density due to observational systematics. We document here the target selection algorithms used to create the galaxy samples that comprise BOSS. We also present the algorithms used to create large-scale structure catalogues for the final Data Release (DR12) samples and the associated random catalogues that quantify the survey mask. The algorithms are an evolution of those used by the BOSS team to construct catalogues from earlier data, and have been designed to accurately quantify the galaxy sample. The code used, designated mksample, is released with this paper.Publisher PDFPeer reviewe

Incidence of Atazanavir-associated Hyperbilirubinemia in Korean HIV Patients: 30 Months Follow-up Results in a Population with Low UDP-glucuronosyltransferase1A1*28 Allele Frequency

Hyperbilirubinemia is frequently observed in Caucasian HIV patients treated with atazanavir. UDP-glucuronosyltransferase 1A1 polymorphism, UGT1A1*28, which is associated with atazanavir-induced hyperbilirubinemia, is less common in Asians than in Caucasians. However, little is known about the incidence of atazanavir-associated hyperbilirubinemia in Asian populations. Our objective was to investigate the incidence of and tolerability of atazanavir-associated hyperbilirubinemia in Korean HIV patients. The prevalence and cumulative incidence of atazanavir-associated hyperbilirubinemia and UGT1A1*28 allele frequency was investigated in 190 Korean HIV-infected patients treated with atazanavir 400 mg per day. The UGT1A1*28 were examined by direct sequencing of DNA from peripheral whole blood. The UGT1A1*28 allele frequency was 11%. The cumulative incidence of any grade of hyperbilirubinemia was 77%, 89%, 98%, and 100%, at 3, 12, 24, and 30 months, respectively. The cumulative incidence of severe (grade 3-4) hyperbilirubinemia was 21%, 41%, 66%, and 75%, at 3, 12, 24, and 30 months, respectively. However, the point prevalence of severe hyperbilirubinemia did not increase with time and remained around 25%. Our data suggest that atazanavir-associated hyperbilirubinemia is common but transient in a population with low UGT1A1*28 allele frequency

The large-scale 3-point correlation function of the SDSS BOSS DR12 CMASS galaxies

We report a measurement of the large-scale 3-point correlation function of galaxies using the largest dataset for this purpose to date, 777, 202 Luminous Red Galaxies in the Sloan Digital Sky Survey Baryon Acoustic Oscillation Spectroscopic Survey (SDSS BOSS) DR12 CMASS sample. This work exploits the novel algorithm of Slepian & Eisenstein (2015b) to compute the multipole moments of the 3PCF in O(N2) time, with N the number of galaxies. Leading-order perturbation theory models the data well in a compressed basis where one triangle side is integrated out. We also present an accurate and computationally efficient means of estimating the covariance matrix. With these techniques the redshift-space linear and non-linear bias are measured, with 2.6% precision on the former if σ8 is fixed. The data also indicates a 2.8σ preference for the BAO, confirming the presence of BAO in the 3-point function.PreprintNon peer reviewe

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey : baryon acoustic oscillations in the Data Releases 10 and 11 Galaxy samples

We present a one per cent measurement of the cosmic distance scale from the detections of the baryon acoustic oscillations (BAO) in the clustering of galaxies from the Baryon Oscillation Spectroscopic Survey, which is part of the Sloan Digital Sky Survey III. Our results come from the Data Release 11 (DR11) sample, containing nearly one million galaxies and covering approximately 8500 square degrees and the redshift range 0.2 < z < 0.7. We also compare these results with those from the publicly released DR9 and DR10 samples. Assuming a concordance Λ cold dark matter (ΛCDM) cosmological model, the DR11 sample covers a volume of 13 Gpc3 and is the largest region of the Universe ever surveyed at this density. We measure the correlation function and power spectrum, including density-field reconstruction of the BAO feature. The acoustic features are detected at a significance of over 7σ in both the correlation function and power spectrum. Fitting for the position of the acoustic features measures the distance relative to the sound horizon at the drag epoch, rd, which has a value of rd,fid = 149.28 Mpc in our fiducial cosmology. We find DV = (1264 ± 25 Mpc)(rd/rd,fid) at z = 0.32 and DV = (2056 ± 20 Mpc)(rd/rd,fid) at z = 0.57. At 1.0 per cent, this latter measure is the most precise distance constraint ever obtained from a galaxy survey. Separating the clustering along and transverse to the line of sight yields measurements at z = 0.57 of DA = (1421 ± 20 Mpc)(rd/rd,fid) and H = (96.8 ± 3.4 km s−1 Mpc−1)(rd,fid/rd). Our measurements of the distance scale are in good agreement with previous BAO measurements and with the predictions from cosmic microwave background data for a spatially flat CDM model with a cosmological constant.Publisher PDFPeer reviewe

A Plant-Derived Recombinant Human Glucocerebrosidase Enzyme—A Preclinical and Phase I Investigation

Gaucher disease is a progressive lysosomal storage disorder caused by the deficiency of glucocerebrosidase leading to the dysfunction in multiple organ systems. Intravenous enzyme replacement is the accepted standard of treatment. In the current report, we evaluate the safety and pharmacokinetics of a novel human recombinant glucocerebrosidase enzyme expressed in transformed plant cells (prGCD), administered to primates and human subjects. Short term (28 days) and long term (9 months) repeated injections with a standard dose of 60 Units/kg and a high dose of 300 Units/kg were administered to monkeys (n = 4/sex/dose). Neither clinical drug-related adverse effects nor neutralizing antibodies were detected in the animals. In a phase I clinical trial, six healthy volunteers were treated by intravenous infusions with escalating single doses of prGCD. Doses of up to 60 Units/kg were administered at weekly intervals. prGCD infusions were very well tolerated. Anti-prGCD antibodies were not detected. The pharmacokinetic profile of the prGCD revealed a prolonged half-life compared to imiglucerase, the commercial enzyme that is manufactured in a costly mammalian cell system. These studies demonstrate the safety and lack of immunogenicity of prGCD. Following these encouraging results, a pivotal phase III clinical trial for prGCD was FDA approved and is currently ongoing.ClinicalTrials.gov NCT00258778