MPT64 patch test for the diagnosis of active pulmonary tuberculosis: a randomised controlled trial in Peru.

SETTING: There remains a lack of effective and inexpensive diagnostic tools for active tuberculosis (TB) disease. Testing immune responses to proteins secreted by Mycobacterium tuberculosis, such as MPT64, may be a diagnostic option. OBJECTIVE: To evaluate the sensitivity and specificity of a patch test using MPT64 for the diagnosis of active TB disease. DESIGN: This randomised, double-blind, placebo-controlled, prospective study in Lima, Peru, involved 55 healthy controls and 457 symptomatic individuals referred for routine TB testing by the National TB Control Programme. All subjects underwent a comprehensive diagnostic workup, and received an active patch on one arm and a placebo patch on the opposite arm, which were read after 4 days. RESULTS: Eighty-one (18%) of the symptomatic participants were classified as having definite TB, while an additional 98 (21%) had probable TB. The patch tests performed the same in both groups, with a sensitivity of 27% and specificity of 74%. The area under the receiver operating characteristic curve was 0.495 (95%CI 0.425-0.565). CONCLUSIONS: Contrary to existing literature, the MPT64 patch was not sensitive and specific to detect active TB. Given the potential of the test, understanding possible differences in the protein source or underlying genetic factors should be explored further

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers are, how the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times or rate constants, and the hierarchical relationship among basins, complete the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, the dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.Comment: PLoS Computational Biology (in press

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

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

The clustering of galaxies in the completed SDSS-III Baryon Oscillation Spectroscopic Survey: cosmological implications of the Fourier space wedges of the final sample

Citation: Grieb, J. N., Sanchez, A. G., Salazar-Albornoz, S., Scoccimarro, R., Crocce, M., Dalla Vecchia, C., . . . Zhao, G. B. (2017). The clustering of galaxies in the completed SDSS-III Baryon Oscillation Spectroscopic Survey: cosmological implications of the Fourier space wedges of the final sample. Monthly Notices of the Royal Astronomical Society, 467(2), 2085-2112. doi:10.1093/mnras/stw3384We extract cosmological information from the anisotropic power-spectrummeasurements from the recently completed Baryon Oscillation Spectroscopic Survey (BOSS), extending the concept of clustering wedges to Fourier space. Making use of new fast-Fourier-transform-based estimators, we measure the power-spectrum clustering wedges of the BOSS sample by filtering out the information of Legendre multipoles l > 4. Our modelling of these measurements is based on novel approaches to describe non-linear evolution, bias and redshift-space distortions, which we test using synthetic catalogues based on large-volume N-body simulations. We are able to include smaller scales than in previous analyses, resulting in tighter cosmological constraints. Using three overlapping redshift bins, we measure the angular-diameter distance, the Hubble parameter and the cosmic growth rate, and explore the cosmological implications of our full-shape clustering measurements in combination with cosmic microwave background and Type Ia supernova data. Assuming a Lambda cold dark matter (Lambda CDM) cosmology, we constrain the matter density to Omega M = 0.311(-0.010)(+ 0.009) and the Hubble parameter to H-0 = 67.6(-0.6)(+0.7) km s(-1) Mpc(-1), at a confidence level of 68 per cent. We also allow for nonstandard dark energy models and modifications of the growth rate, finding good agreement with the Lambda CDM paradigm. For example, we constrain the equation-of-state parameter to omega =-1.019(-0.039)(+0.048) . This paper is part of a set that analyses the final galaxy-clustering data set from BOSS. The measurements and likelihoods presented here are combined with others in Alam et al. to produce the final cosmological constraints from BOSS

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: Analysis of potential systematics

We analyze the density field of galaxies observed by the Sloan Digital Sky Survey (SDSS)-III Baryon Oscillation Spectroscopic Survey (BOSS) included in the SDSS Data Release Nine (DR9). DR9 includes spectroscopic redshifts for over 400,000 galaxies spread over a footprint of 3,275 deg^2. We identify, characterize, and mitigate the impact of sources of systematic uncertainty on large-scale clustering measurements, both for angular moments of the redshift-space correlation function and the spherically averaged power spectrum, P(k), in order to ensure that robust cosmological constraints will be obtained from these data. A correlation between the projected density of stars and the higher redshift (0.43 < z < 0.7) galaxy sample (the `CMASS' sample) due to imaging systematics imparts a systematic error that is larger than the statistical error of the clustering measurements at scales s > 120h^-1Mpc or k < 0.01hMpc^-1. We find that these errors can be ameliorated by weighting galaxies based on their surface brightness and the local stellar density. We use mock galaxy catalogs that simulate the CMASS selection function to determine that randomly selecting galaxy redshifts in order to simulate the radial selection function of a random sample imparts the least systematic error on correlation function measurements and that this systematic error is negligible for the spherically averaged correlation function. The methods we recommend for the calculation of clustering measurements using the CMASS sample are adopted in companion papers that locate the position of the baryon acoustic oscillation feature (Anderson et al. 2012), constrain cosmological models using the full shape of the correlation function (Sanchez et al. 2012), and measure the rate of structure growth (Reid et al. 2012). (abridged)Comment: Matches version accepted by MNRAS. Clarifications and references have been added. See companion papers that share the "The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey:" titl

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: Baryon Acoustic Oscillations in the Data Release 9 Spectroscopic Galaxy Sample

We present measurements of galaxy clustering from the Baryon Oscillation Spectroscopic Survey (BOSS), which is part of the Sloan Digital Sky Survey III (SDSS-III). These use the Data Release 9 (DR9) CMASS sample, which contains 264,283 massive galaxies covering 3275 square degrees with an effective redshift z=0.57 and redshift range 0.43 < z < 0.7. Assuming a concordance Lambda-CDM cosmological model, this sample covers an effective volume of 2.2 Gpc^3, and represents the largest sample of the Universe ever surveyed at this density, n = 3 x 10^-4 h^-3 Mpc^3. We measure the angle-averaged galaxy correlation function and power spectrum, including density-field reconstruction of the baryon acoustic oscillation (BAO) feature. The acoustic features are detected at a significance of 5\sigma in both the correlation function and power spectrum. Combining with the SDSS-II Luminous Red Galaxy Sample, the detection significance increases to 6.7\sigma. Fitting for the position of the acoustic features measures the distance to z=0.57 relative to the sound horizon DV /rs = 13.67 +/- 0.22 at z=0.57. Assuming a fiducial sound horizon of 153.19 Mpc, which matches cosmic microwave background constraints, this corresponds to a distance DV(z=0.57) = 2094 +/- 34 Mpc. At 1.7 per cent, this is the most precise distance constraint ever obtained from a galaxy survey. We place this result alongside previous BAO measurements in a cosmological distance ladder and find excellent agreement with the current supernova measurements. We use these distance measurements to constrain various cosmological models, finding continuing support for a flat Universe with a cosmological constant.Comment: 33 page

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: cosmological implications of the large-scale two-point correlation function

We obtain constraints on cosmological parameters from the spherically averaged redshift-space correlation function of the CMASS Data Release 9 (DR9) sample of the Baryonic Oscillation Spectroscopic Survey (BOSS). We combine this information with additional data from recent CMB, SN and BAO measurements. Our results show no significant evidence of deviations from the standard flat-Lambda CDM model, whose basic parameters can be specified by Omega_m = 0.285 +- 0.009, 100 Omega_b = 4.59 +- 0.09, n_s = 0.96 +- 0.009, H_0 = 69.4 +- 0.8 km/s/Mpc and sigma_8 = 0.80 +- 0.02. The CMB+CMASS combination sets tight constraints on the curvature of the Universe, with Omega_k = -0.0043 +- 0.0049, and the tensor-to-scalar amplitude ratio, for which we find r < 0.16 at the 95 per cent confidence level (CL). These data show a clear signature of a deviation from scale-invariance also in the presence of tensor modes, with n_s <1 at the 99.7 per cent CL. We derive constraints on the fraction of massive neutrinos of f_nu < 0.049 (95 per cent CL), implying a limit of sum m_nu < 0.51 eV. We find no signature of a deviation from a cosmological constant from the combination of all datasets, with a constraint of w_DE = -1.033 +- 0.073 when this parameter is assumed time-independent, and no evidence of a departure from this value when it is allowed to evolve as w_DE(a) = w_0 + w_a (1 - a). The achieved accuracy on our cosmological constraints is a clear demonstration of the constraining power of current cosmological observations.Comment: 26 pages, 15 figures. Minor changes to match version accepted by MNRA

Descriptive epidemiology of somatising tendency: findings from the CUPID study.

Somatising tendency, defined as a predisposition to worry about common somatic symptoms, is importantly associated with various aspects of health and health-related behaviour, including musculoskeletal pain and associated disability. To explore its epidemiological characteristics, and how it can be specified most efficiently, we analysed data from an international longitudinal study. A baseline questionnaire, which included questions from the Brief Symptom Inventory about seven common symptoms, was completed by 12,072 participants aged 20-59 from 46 occupational groups in 18 countries (response rate 70%). The seven symptoms were all mutually associated (odds ratios for pairwise associations 3.4 to 9.3), and each contributed to a measure of somatising tendency that exhibited an exposure-response relationship both with multi-site pain (prevalence rate ratios up to six), and also with sickness absence for non-musculoskeletal reasons. In most participants, the level of somatising tendency was little changed when reassessed after a mean interval of 14 months (75% having a change of 0 or 1 in their symptom count), although the specific symptoms reported at follow-up often differed from those at baseline. Somatising tendency was more common in women than men, especially at older ages, and varied markedly across the 46 occupational groups studied, with higher rates in South and Central America. It was weakly associated with smoking, but not with level of education. Our study supports the use of questions from the Brief Symptom Inventory as a method for measuring somatising tendency, and suggests that in adults of working age, it is a fairly stable trait

The DESI One-Percent Survey: Modelling the clustering and halo occupation of all four DESI tracers with Uchuu

We present results from a set of high-fidelity simulated lightcones for the DESI One-Percent Survey, created from the Uchuu simulation. This 8 (Gpc/h)^3 N-body simulation comprises 2.1 trillion particles and provides high-resolution dark matter (sub)haloes in the framework of the Planck base-LCDM cosmology. Employing the subhalo abundance matching (SHAM) technique, we populate the Uchuu (sub)haloes with all four DESI tracers (BGS, LRG, ELG and QSO) to z = 2.1. Our method accounts for redshift evolution as well as the clustering dependence on luminosity and stellar mass. The two-point clustering statistics of the DESI One-Percent Survey align reasonably well with our predictions from Uchuu across scales ranging from 0.1 Mpc/h to 100 Mpc/h. Some discrepancies arise due to cosmic variance, incompleteness in the massive end of the stellar mass function, and a simplified galaxy-halo connection model. We find that the Uchuu BGS and LRG samples are adequately described using the standard 5-parameter halo occupation distribution model, while the ELGs and QSOs show agreement with an adopted Gaussian distribution for central halos with a power law for satellites. We observe a fair agreement in the large-scale bias measurements between data and mock samples, although the data exhibits smaller bias values, likely due to cosmic variance. The bias dependence on absolute magnitude, stellar mass and redshift aligns with that of previous surveys. These results improve simulated lightcone construction from cosmological models and enhance our understanding of the galaxy-halo connection, with pivotal insights from the first DESI data for the success of the final survey.Comment: 23 pages, 15 figures, 5 tables, submitted to MNRAS. The Uchuu-DESI lightcones will be available at https://data.desi.lbl.go