Likelihood Inference for Models with Unobservables: Another View

There have been controversies among statisticians on (i) what to model and (ii) how to make inferences from models with unobservables. One such controversy concerns the difference between estimation methods for the marginal means not necessarily having a probabilistic basis and statistical models having unobservables with a probabilistic basis. Another concerns likelihood-based inference for statistical models with unobservables. This needs an extended-likelihood framework, and we show how one such extension, hierarchical likelihood, allows this to be done. Modeling of unobservables leads to rich classes of new probabilistic models from which likelihood-type inferences can be made naturally with hierarchical likelihood.Comment: This paper discussed in: [arXiv:1010.0804], [arXiv:1010.0807], [arXiv:1010.0810]. Rejoinder at [arXiv:1010.0814]. Published in at http://dx.doi.org/10.1214/09-STS277 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Detection of a low-eccentricity and super-massive planet to the subgiant HD 38801

We report the detection of a large mass planet orbiting around the K0 metal-rich subgiant HD38801 ($V=8.26$) by precise radial velocity (RV) measurements from the Subaru Telescope and the Keck Telescope. The star has a mass of $1.36M_{\odot}$ and metallicity of [Fe/H]= +0.26. The RV variations are consistent with a circular orbit with a period of 696.0 days and a velocity semiamplitude of 200.0\mps, which yield a minimum-mass for the companion of 10.7\mjup and semimajor axis of 1.71 AU. Such super-massive objects with very low-eccentricities and hundreds of days period are uncommon among the ensemble of known exoplanets

Models of X-ray Photoionization in LMC X-4: Slices of a Stellar Wind

We show that the orbital variation in the UV P Cygni lines of the X-ray binary LMC X-4 results when X-rays photoionize nearly the entire region outside of the X-ray shadow of the normal star. We fit models to HST GHRS observations of N V and C IV P Cygni line profiles. Analytic methods assuming a spherically symmetric wind show that the wind velocity law is well-fit by v~(1-1/r)^beta, where beta is likely 1.4-1.6 and definitely <2.5. Escape probability models can fit the observed P Cygni profiles, and provide measurements of the stellar wind parameters. The fits determine Lx/Mdot=2.6+/-0.1 x10^43 erg/s/Msun yr, where Lx is the X-ray luminosity and Mdot is the mass-loss rate of the star. Allowing an inhomogeneous wind improves the fits. IUE spectra show greater P Cygni absorption during the second half of the orbit than during the first. We discuss possible causes of this effect.Comment: 56 pages, 12 figures, to be published in the Astrophysical Journa

The SEGUE Stellar Parameter Pipeline. I. Description and Initial Validation Tests

We describe the development and implementation of the SEGUE (Sloan Extension for Galactic Exploration and Understanding) Stellar Parameter Pipeline (SSPP). The SSPP derives, using multiple techniques, radial velocities and the fundamental stellar atmospheric parameters (effective temperature, surface gravity, and metallicity) for AFGK-type stars, based on medium-resolution spectroscopy and $ugriz$ photometry obtained during the course of the original Sloan Digital Sky Survey (SDSS-I) and its Galactic extension (SDSS-II/SEGUE). The SSPP also provides spectral classification for a much wider range of stars, including stars with temperatures outside of the window where atmospheric parameters can be estimated with the current approaches. This is Paper I in a series of papers on the SSPP; it provides an overview of the SSPP, and initial tests of its performance using multiple data sets. Random and systematic errors are critically examined for the current version of the SSPP, which has been used for the sixth public data release of the SDSS (DR-6).Comment: 64 pages, 8 tables, 12 figures, submitted to the Astronomical Journa

The ACS Virgo Cluster Survey X. Half-light Radii of Globular Clusters in Early-Type Galaxies: Environmental Dependencies and a Standard Ruler for Distance Estimation

We have measured half-light radii, r_h, for globular clusters (GCs) belonging to the 100 early-type galaxies observed in the ACS Virgo Cluster Survey and the elliptical galaxy NGC 4697. An analysis of the dependencies of the measured r_h on both the properties of the GCs themselves and their host galaxies reveals that the average r_h increases with increasing galactocentric distance or, alternatively, with decreasing galaxy surface brightness. For the first time, we find that the average r_h decreases with the host galaxy color. We also show that there is no evidence for a variation of r_h with the luminosity of the GCs. Finally, we find in agreement with previous observations that the average r_h depends on the color of GCs, with red GCs being ~17% smaller than their blue counterparts. We show that this difference is probably a consequence of an intrinsic mechanism, rather than projection effects, and that it is in good agreement with the mechanism proposed in Jordan (2004). We discuss these findings in light of two simple pictures for the origin of the r_h of GCs and show that both lead to a behavior in rough agreement with the observations. After accounting for the dependencies found we show that the average GC half-light radii can be successfully used as a standard ruler for distance estimation. We outline the methodology, and provide a calibration for its use. We find = 2.7 +- 0.35 pc for GCs with (g-z)=1.2 mag in a galaxy with color (g-z)_{gal}=1.5 mag and at an underlying surface z-band brightness of mu_z = 21 mag arcsec^{-2}. Using this technique, we place an upper limit of 3.4 Mpc on the 1-sigma line-of-sight depth of the Virgo Cluster. Finally, we examine the form of the r_h distribution for our sample galaxies and provide an analytic expression which successfully describes this distribution. (Abridged)Comment: 18 pages, 13 figures. Accepted for publication in ApJ. Also available at http://www.physics.rutgers.edu/~pcote/acs/publications.htm

Statistical learning techniques applied to epidemiology: a simulated case-control comparison study with logistic regression

<p>Abstract</p> <p>Background</p> <p>When investigating covariate interactions and group associations with standard regression analyses, the relationship between the response variable and exposure may be difficult to characterize. When the relationship is nonlinear, linear modeling techniques do not capture the nonlinear information content. Statistical learning (SL) techniques with kernels are capable of addressing nonlinear problems without making parametric assumptions. However, these techniques do not produce findings relevant for epidemiologic interpretations. A simulated case-control study was used to contrast the information embedding characteristics and separation boundaries produced by a specific SL technique with logistic regression (LR) modeling representing a parametric approach. The SL technique was comprised of a kernel mapping in combination with a perceptron neural network. Because the LR model has an important epidemiologic interpretation, the SL method was modified to produce the analogous interpretation and generate odds ratios for comparison.</p> <p>Results</p> <p>The SL approach is capable of generating odds ratios for main effects and risk factor interactions that better capture nonlinear relationships between exposure variables and outcome in comparison with LR.</p> <p>Conclusions</p> <p>The integration of SL methods in epidemiology may improve both the understanding and interpretation of complex exposure/disease relationships.</p

Incorporating Prediction in Models for Two-Dimensional Smooth Pursuit

A predictive component can contribute to the command signal for smooth pursuit. This is readily demonstrated by the fact that low frequency sinusoidal target motion can be tracked with zero time delay or even with a small lead. The objective of this study was to characterize the predictive contributions to pursuit tracking more precisely by developing analytical models for predictive smooth pursuit. Subjects tracked a small target moving in two dimensions. In the simplest case, the periodic target motion was composed of the sums of two sinusoidal motions (SS), along both the horizontal and the vertical axes. Motions following the same or similar paths, but having a richer spectral composition, were produced by having the target follow the same path but at a constant speed (CS), and by combining the horizontal SS velocity with the vertical CS velocity and vice versa. Several different quantitative models were evaluated. The predictive contribution to the eye tracking command signal could be modeled as a low-pass filtered target acceleration signal with a time delay. This predictive signal, when combined with retinal image velocity at the same time delay, as in classical models for the initiation of pursuit, gave a good fit to the data. The weighting of the predictive acceleration component was different in different experimental conditions, being largest when target motion was simplest, following the SS velocity profiles

The Sloan Digital Sky Survey DR7 Spectroscopic M Dwarf Catalog II: Statistical Parallax Analysis

We present a statistical parallax analysis of low-mass dwarfs from the Sloan Digital Sky Survey (SDSS). We calculate absolute r-band magnitudes (M_r) as a function of color and spectral type, and investigate changes in M_r with location in the Milky Way. We find that magnetically active M dwarfs are intrinsically brighter in M_r than their inactive counterparts at the same color or spectral type. Metallicity, as traced by the proxy zeta, also affects M_r, with metal poor stars having fainter absolute magnitudes than higher metallicity M dwarfs at the same color or spectral type. Additionally, we measure the velocity ellipsoid and solar reflex motion for each subsample of M dwarfs. We find good agreement between our measured solar peculiar motion and previous results for similar populations, as well as some evidence for differing motions of early and late M type populations in U and W velocities that cannot be attributed to asymmetric drift. The reflex solar motion and the velocity dispersions both show that younger populations, as traced by magnetic activity and location near the Galactic plane, have experienced less dynamical heating. We introduce a new parameter, the independent position altitude (IPA), to investigate populations as a function of vertical height from the Galactic plane. M dwarfs at all types exhibit an increase in velocity dispersion when analyzed in comparable IPA subgroups.Comment: Accepted by AJ. 13 pages, 6 figures, emulate apj forma

The ACS Virgo Cluster Survey. VI. Isophotal Analysis and the Structure of Early-Type Galaxies

(Abridged) We present a detailed analysis of the morphology, isophotal parameters and surface brightness profiles for 100 early-type members of the Virgo Cluster, from dwarfs (M_B = -15.1 mag) to giants (M_B = -21.8 mag). Each galaxy has been imaged in two filters, closely resembling the Sloan g and z passbands, using the Advanced Camera for Surveys on board the Hubble Space Telescope. Dust and complex morphological structures are common, with kiloparsec-scale stellar disks, bars, and nuclear stellar disks seen in 60% of galaxies with intermediate luminosity (-20 < M_B < -17), and dust seen in 42% of galaxies brighter than M_B = -18.9 mag. Dust morphologies range from faint wisps and patches on tens of parsec scales, to regular, highly organized kpc-scale dust disks, often showing evidence of recent star formation. Surface brightness profiles and isophotal parameters are derived typically within 8 kpc from the center for the brightest galaxies, and 1.5 kpc for the faintest systems, with a resolution (FWHM) of 7 pc. Based on a parametrization of the surface brightness profiles in terms of a Sersic or core-Sersic model, we find that 1) there is no evidence of a bimodal behavior of the slope, gamma, of the profile in the innermost regions; 2) although the brightest galaxies have shallow inner profiles, the shallowest profiles (lowest gamma values) are found in faint dwarf systems; 3) the widely adopted separation of early-type galaxies between "core" and "power-law" types, which had originally been prompted by the claim of a clear bimodal distribution of gamma values, is untenable; and 4) there is no evidence of a structural dichothomy between dwarf and regular ellipticals.Comment: Accepted by The Astrophysical Journal Supplement Series. This submission contains low resolution figures; we strongly recommend downloading the original version of the paper from the ACSVCS project website: http://www.cadc.hia.nrc.gc.ca/community/ACSVCS/publications.html#acsvcs

High-throughput mapping of regulatory DNA

Quantifying the effects of cis-regulatory DNA on gene expression is a major challenge. Here, we present the multiplexed editing regulatory assay (MERA), a high-throughput CRISPR-Cas9–based approach that analyzes the functional impact of the regulatory genome in its native context. MERA tiles thousands of mutations across ~40 kb of cis-regulatory genomic space and uses knock-in green fluorescent protein (GFP) reporters to read out gene activity. Using this approach, we obtain quantitative information on the contribution of cis-regulatory regions to gene expression. We identify proximal and distal regulatory elements necessary for expression of four embryonic stem cell–specific genes. We show a consistent contribution of neighboring gene promoters to gene expression and identify unmarked regulatory elements (UREs) that control gene expression but do not have typical enhancer epigenetic or chromatin features. We compare thousands of functional and nonfunctional genotypes at a genomic location and identify the base pair–resolution functional motifs of regulatory elements.National Institutes of Health (U.S.) (1U01HG007037