A Comparison of Maps and Power Spectra Determined from South Pole Telescope and Planck Data

We study the consistency of 150 GHz data from the South Pole Telescope (SPT) and 143 GHz data from the Planck satellite over the patch of sky covered by the SPT-SZ survey. We first visually compare the maps and find that the residuals appear consistent with noise after accounting for differences in angular resolution and filtering. We then calculate (1) the cross-spectrum between two independent halves of SPT data, (2) the cross-spectrum between two independent halves of Planck data, and (3) the cross-spectrum between SPT and Planck data. We find the three cross-spectra are well-fit (PTE = 0.30) by the null hypothesis in which both experiments have measured the same sky map up to a single free calibration parameter---i.e., we find no evidence for systematic errors in either data set. As a by-product, we improve the precision of the SPT calibration by nearly an order of magnitude, from 2.6% to 0.3% in power. Finally, we compare all three cross-spectra to the full-sky Planck power spectrum and find marginal evidence for differences between the power spectra from the SPT-SZ footprint and the full sky. We model these differences as a power law in spherical harmonic multipole number. The best-fit value of this tilt is consistent among the three cross-spectra in the SPT-SZ footprint, implying that the source of this tilt is a sample variance fluctuation in the SPT-SZ region relative to the full sky. The consistency of cosmological parameters derived from these datasets is discussed in a companion paper.Comment: 15 pages, 9 figures. Published in The Astrophysical Journal. Current arxiv version matches published versio

A Comparison of Cosmological Parameters Determined from CMB Temperature Power Spectra from the South Pole Telescope and the Planck Satellite

The Planck cosmic microwave background (CMB) temperature data are best fit with a LCDM model that is in mild tension with constraints from other cosmological probes. The South Pole Telescope (SPT) 2540 $\text{deg}^2$ SPT-SZ survey offers measurements on sub-degree angular scales (multipoles $650 \leq \ell \leq 2500$) with sufficient precision to use as an independent check of the Planck data. Here we build on the recent joint analysis of the SPT-SZ and Planck data in \citet{hou17} by comparing LCDM parameter estimates using the temperature power spectrum from both data sets in the SPT-SZ survey region. We also restrict the multipole range used in parameter fitting to focus on modes measured well by both SPT and Planck, thereby greatly reducing sample variance as a driver of parameter differences and creating a stringent test for systematic errors. We find no evidence of systematic errors from such tests. When we expand the maximum multipole of SPT data used, we see low-significance shifts in the angular scale of the sound horizon and the physical baryon and cold dark matter densities, with a resulting trend to higher Hubble constant. When we compare SPT and Planck data on the SPT-SZ sky patch to Planck full-sky data but keep the multipole range restricted, we find differences in the parameters $n_s$ and $A_se^{-2\tau}$. We perform further checks, investigating instrumental effects and modeling assumptions, and we find no evidence that the effects investigated are responsible for any of the parameter shifts. Taken together, these tests reveal no evidence for systematic errors in SPT or Planck data in the overlapping sky coverage and multipole range and, at most, weak evidence for a breakdown of LCDM or systematic errors influencing either the Planck data outside the SPT-SZ survey area or the SPT data at $\ell >2000$.Comment: 14 pages, 7 figures. Updated 1 figure and expanded on the reasoning for fixing the affect of lensing on the power spectrum instead of varying Alen

Consistency of cosmic microwave background temperature measurements in three frequency bands in the 2500-square-degree SPT-SZ survey

We present an internal consistency test of South Pole Telescope (SPT) measurements of the cosmic microwave background (CMB) temperature anisotropy using three-band data from the SPT-SZ survey. These measurements are made from observations of ~2500 deg^2 of sky in three frequency bands centered at 95, 150, and 220 GHz. We combine the information from these three bands into six semi-independent estimates of the CMB power spectrum (three single-frequency power spectra and three cross-frequency spectra) over the multipole range 650 < l < 3000. We subtract an estimate of foreground power from each power spectrum and evaluate the consistency among the resulting CMB-only spectra. We determine that the six foreground-cleaned power spectra are consistent with the null hypothesis, in which the six cleaned spectra contain only CMB power and noise. A fit of the data to this model results in a chi-squared value of 236.3 for 235 degrees of freedom, and the probability to exceed this chi-squared value is 46%.Comment: 21 pages, 4 figures, current version matches version published in JCA

Genetic Analysis of Hematological Parameters in Incipient Lines of the Collaborative Cross

Hematological parameters, including red and white blood cell counts and hemoglobin concentration, are widely used clinical indicators of health and disease. These traits are tightly regulated in healthy individuals and are under genetic control. Mutations in key genes that affect hematological parameters have important phenotypic consequences, including multiple variants that affect susceptibility to malarial disease. However, most variation in hematological traits is continuous and is presumably influenced by multiple loci and variants with small phenotypic effects. We used a newly developed mouse resource population, the Collaborative Cross (CC), to identify genetic determinants of hematological parameters. We surveyed the eight founder strains of the CC and performed a mapping study using 131 incipient lines of the CC. Genome scans identified quantitative trait loci for several hematological parameters, including mean red cell volume (Chr 7 and Chr 14), white blood cell count (Chr 18), percent neutrophils/lymphocytes (Chr 11), and monocyte number (Chr 1). We used evolutionary principles and unique bioinformatics resources to reduce the size of candidate intervals and to view functional variation in the context of phylogeny. Many quantitative trait loci regions could be narrowed sufficiently to identify a small number of promising candidate genes. This approach not only expands our knowledge about hematological traits but also demonstrates the unique ability of the CC to elucidate the genetic architecture of complex traits

Ecological Invasion, Roughened Fronts, and a Competitor's Extreme Advance: Integrating Stochastic Spatial-Growth Models

Both community ecology and conservation biology seek further understanding of factors governing the advance of an invasive species. We model biological invasion as an individual-based, stochastic process on a two-dimensional landscape. An ecologically superior invader and a resident species compete for space preemptively. Our general model includes the basic contact process and a variant of the Eden model as special cases. We employ the concept of a "roughened" front to quantify effects of discreteness and stochasticity on invasion; we emphasize the probability distribution of the front-runner's relative position. That is, we analyze the location of the most advanced invader as the extreme deviation about the front's mean position. We find that a class of models with different assumptions about neighborhood interactions exhibit universal characteristics. That is, key features of the invasion dynamics span a class of models, independently of locally detailed demographic rules. Our results integrate theories of invasive spatial growth and generate novel hypotheses linking habitat or landscape size (length of the invading front) to invasion velocity, and to the relative position of the most advanced invader.Comment: The original publication is available at www.springerlink.com/content/8528v8563r7u2742

From Classical Genetics to Quantitative Genetics to Systems Biology: Modeling Epistasis

Gene expression data has been used in lieu of phenotype in both classical and quantitative genetic settings. These two disciplines have separate approaches to measuring and interpreting epistasis, which is the interaction between alleles at different loci. We propose a framework for estimating and interpreting epistasis from a classical experiment that combines the strengths of each approach. A regression analysis step accommodates the quantitative nature of expression measurements by estimating the effect of gene deletions plus any interaction. Effects are selected by significance such that a reduced model describes each expression trait. We show how the resulting models correspond to specific hierarchical relationships between two regulator genes and a target gene. These relationships are the basic units of genetic pathways and genomic system diagrams. Our approach can be extended to analyze data from a variety of experiments, multiple loci, and multiple environments

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals

Maps of the Southern Millimeter-wave Sky from Combined 2500 deg2^2 SPT-SZ and Planck Temperature Data

We present three maps of the millimeter-wave sky created by combining data from the South Pole Telescope (SPT) and the Planck satellite. We use data from the SPT-SZ survey, a survey of 2540 deg$^2$ of the the sky with arcminute resolution in three bands centered at 95, 150, and 220 GHz, and the full-mission Planck temperature data in the 100, 143, and 217 GHz bands. A linear combination of the SPT-SZ and Planck data is computed in spherical harmonic space, with weights derived from the noise of both instruments. This weighting scheme results in Planck data providing most of the large-angular-scale information in the combined maps, with the smaller-scale information coming from SPT-SZ data. A number of tests have been done on the maps. We find their angular power spectra to agree very well with theoretically predicted spectra and previously published results.Comment: 21 pages, 12 figure

Improving Cosmological Constraints from Galaxy Cluster Number Counts with CMB-cluster-lensing Data: Results from the SPT-SZ Survey and Forecasts for the Future

We show the improvement to cosmological constraints from galaxy cluster surveys with the addition of cosmic microwave background (CMB)-cluster lensing data. We explore the cosmological implications of adding mass information from the 3.1 sigma detection of gravitational lensing of the CMB by galaxy clusters to the Sunyaev-Zel'dovich (SZ) selected galaxy cluster sample from the 2500 deg(2) SPT-SZ survey and targeted optical and X-ray follow-up data. In the ACDM model, the combination of the cluster sample with the Planck power spectrum measurements prefers sigma(8) (Omega(m)/0.3)(0.5) = 0.831 +/- 0.020. Adding the cluster data reduces the uncertainty on this quantity by a factor of 1.4, which is unchanged whether the 3.1 sigma CMB-cluster lensing measurement is included or not. We then forecast the impact of CMB-cluster lensing measurements with future cluster catalogs. Adding CMB-cluster lensing measurements to the SZ cluster catalog of the ongoing SPT-3G survey is expected to improve the expected constraint on the dark energy equation of state w by a factor of 1.3 to sigma(w) = 0.19. We find the largest improvements from CMB-cluster lensing measurements to be for sigma(8), where adding CMB-cluster lensing data to the cluster number counts reduces the expected uncertainty on sigma(8) by respective factors of 2.4 and 3.6 for SPT-3G and CMB-S4