The WiggleZ Dark Energy Survey: Galaxy Evolution at 0.25 ≤ z ≤ 0.75 Using the Second Red-Sequence Cluster Survey

We study the evolution of galaxy populations around the spectroscopic WiggleZ sample of star-forming galaxies at 0.25 ≤ z ≤ 0.75 using the photometric catalog from the Second Red-Sequence Cluster Survey (RCS2). We probe the optical photometric properties of the net excess neighbor galaxies. The key concept is that the marker galaxies and their neighbors are located at the same redshift, providing a sample of galaxies representing a complete census of galaxies in the neighborhood of star-forming galaxies. The results are compared with those using the RCS WiggleZ Spare-Fibre (RCS-WSF) sample as markers, representing galaxies in cluster environments at 0.25 ≤ z ≤ 0.45. By analyzing the stacked color-color properties of the WiggleZ neighbor galaxies, we find that their optical colors are not a strong function of indicators of star-forming activities such as EW([O II]) or Galaxy Evolution Explorer (GALEX) near-UV luminosity of the markers. The galaxies around the WiggleZ markers exhibit a bimodal distribution on the color-magnitude diagram, with most of them located in the blue cloud. The optical galaxy luminosity functions (GLFs) of the blue neighbor galaxies have a faint-end slope α of ~ –1.3, similar to that for galaxies in cluster environments drawn from the RCS-WSF sample. The faint-end slope of the GLF for the red neighbors, however, is ~ –0.4, significantly shallower than the ~ –0.7 found for those in cluster environments. This suggests that the buildup of the faint end of the red sequence in cluster environments is in a significantly more advanced stage than that in the star-forming and lower galaxy density WiggleZ neighborhoods. We find that the red galaxy fraction (f_red) around the star-forming WiggleZ galaxies has similar values from z ~ 0.3 to z ~ 0.6 with f_red ~ 0.28, but drops to f_red ~ 0.20 at z gsim 0.7. This change of f_red with redshift suggests that there is either a higher rate of star-forming galaxies entering the luminosity-limited sample at z ≳ 0.7, or a decrease in the quenching rate of star formation at that redshift. Comparing to that in a dense cluster environment, the f_red of the WiggleZ neighbors is both considerably smaller and has a more moderate change with redshift, pointing to the stronger and more prevalent environmental influences on galaxy evolution in high-density regions

Genetic Association Analysis of Complex Diseases Incorporating Intermediate Phenotype Information

Genetic researchers often collect disease related quantitative traits in addition to disease status because they are interested in understanding the pathophysiology of disease processes. In genome-wide association (GWA) studies, these quantitative phenotypes may be relevant to disease development and serve as intermediate phenotypes or they could be behavioral or other risk factors that predict disease risk. Statistical tests combining both disease status and quantitative risk factors should be more powerful than case-control studies, as the former incorporates more information about the disease. In this paper, we proposed a modified inverse-variance weighted meta-analysis method to combine disease status and quantitative intermediate phenotype information. The simulation results showed that when an intermediate phenotype was available, the inverse-variance weighted method had more power than did a case-control study of complex diseases, especially in identifying susceptibility loci having minor effects. We further applied this modified meta- analysis to a study of imputed lung cancer genotypes with smoking data in 1154 cases and 1137 matched controls. The most significant SNPs came from the CHRNA3-CHRNA5-CHRNB4 region on chromosome 15q24–25.1, which has been replicated in many other studies. Our results confirm that this CHRNA region is associated with both lung cancer development and smoking behavior. We also detected three significant SNPs—rs1800469, rs1982072, and rs2241714—in the promoter region of the TGFB1 gene on chromosome 19 (p = 1.46 X 10-5,1.18 X 10-5, and 6.57 X 10-6, respectively). The SNP rs1800469 is reported to be associated with chronic obstructive pulmonary disease and lung cancer in cigarette smokers. The present study is the first GWA study to replicate this result. Signals in the 3q26 region were also identified in the meta-analysis. We demonstrate the intermediate phenotype can potentially enhance the power of complex disease association analysis and the modified meta-analysis method is robust to incorporate intermediate phenotype or other quantitative risk factor in the analysis

Linearly and Circularly Polarized Emission in Sagittarius A*

We perform general relativistic ray-tracing calculations of the transfer of polarized synchrotron radiation through the relativistic accretion flow in Sagittarius (Sgr) A*. Based on a two-temperature magneto-rotational-instability (MRI) induced accretion mode, the birefringence effects are treated self-consistently. By fitting the spectrum and polarization of Sgr A* from millimeter to near-infrared bands, we are able to not only constrain the basic parameters related to the MRI and the electron heating rate, but also limit the orientation of the accretion torus. These constraints lead to unique polarimetric images, which may be compared with future millimeter and sub-millimeter VLBI observations. In combination with general relativistic MHD simulations, the model has the potential to test the MRI with observations of Sgr A*.Comment: 12 pages, 2 figures, ApJL accepte

Disparities in breast cancer characteristics and outcomes by race/ethnicity.

Disparities in breast cancer stage and mortality by race/ethnicity in the United States are persistent and well known. However, few studies have assessed differences across racial/ethnic subgroups of women broadly defined as Hispanic, Asian, or Pacific Islander, particularly using more recent data. Using data from 17 population-based cancer registries in the Surveillance, Epidemiology, and End Results (SEER) program, we evaluated the relationships between race/ethnicity and breast cancer stage, hormone receptor status, treatment, and mortality. The cohort consisted of 229,594 women 40-79 years of age diagnosed with invasive breast carcinoma between January 2000 and December 2006, including 176,094 non-Hispanic whites, 20,486 Blacks, 15,835 Hispanic whites, 14,951 Asians, 1,224 Pacific Islanders, and 1,004 American Indians/Alaska Natives. With respect to statistically significant findings, American Indian/Alaska Native, Asian Indian/Pakistani, Black, Filipino, Hawaiian, Mexican, Puerto Rican, and Samoan women had 1.3-7.1-fold higher odds of presenting with stage IV breast cancer compared to non-Hispanic white women. Almost all groups were more likely to be diagnosed with estrogen receptor-negative/progesterone receptor-negative (ER-/PR-) disease with Black and Puerto Rican women having the highest odds ratios (2.4 and 1.9-fold increases, respectively) compared to non-Hispanic whites. Lastly, Black, Hawaiian, Puerto Rican, and Samoan patients had 1.5-1.8-fold elevated risks of breast cancer-specific mortality. Breast cancer disparities persist by race/ethnicity, though there is substantial variation within subgroups of women broadly defined as Hispanic or Asian. Targeted, multi-pronged interventions that are culturally appropriate may be important means of reducing the magnitudes of these disparities

Hormone receptor status, tumor characteristics, and prognosis: a prospective cohort of breast cancer patients

BACKGROUND: Breast cancer patients with tumors that are estrogen receptor (ER)-positive and/or progesterone receptor (PR)-positive have lower risks of mortality after their diagnosis compared to women with ER- and/or PR-negative disease. However, few studies have evaluated variations in the risks of breast cancer-specific mortality across ER/PR status by either demographic or clinical characteristics. METHODS: Using data from 11 population-based cancer registries that participate in the SEER (Surveillance, Epidemiology, and End Results) program, 155,175 women at least 30 years old with a primary diagnosis of invasive breast carcinoma from 1990 to 2001 were included in the study. Associations between joint hormone receptor status and breast cancer mortality risk within categories of diagnosis age, diagnosis year, race/ethnicity, histologic tumor type, stage, grade, size, and axillary lymph node status were evaluated using the Cox proportional hazards model. RESULTS: Compared to ER+/PR+ cases, elevations in risk of mortality were observed across all subcategories of age at diagnosis, ranging from 1.2- to 1.5-fold differences for ER+/PR- cases, 1.5- to 2.1-fold differences for ER-/PR+ cases, and 2.1- to 2.6-fold differences for ER-/PR- cases. Greater differences were observed in analyses stratified by grade; among women with low-grade lesions, ER-/PR- patients had a 2.6-fold (95% confidence interval [CI] 1.7 to 3.9) to 3.1-fold (95% CI 2.8 to 3.4) increased risk of mortality compared to ER+/PR+ patients, but among women with high-grade lesions, they had a 2.1-fold (95% CI 1.9 to 2.2) to 2.3-fold (95% CI 1.8 to 2.8) increased risk. CONCLUSION: Compared to women with ER+/PR+ tumors, women with ER+/PR-, ER-/PR+, or ER-/PR- tumors experienced higher risks of mortality, which were largely independent of the various demographic and clinical tumor characteristics assessed in this study. The higher relative mortality risks identified among ER-/PR- patients with small or low-grade tumors raise the question of whether there may be a beneficial role for adjuvant chemotherapy in this population

Gene and Pathway-Based Analysis: Second Wave of Genome-wide Association Studies

Despite great success of GWAS in identification of common genetic variants associated with complex diseases, the current GWAS have focused on single SNP analysis. However, single SNP analysis often identifies a number of the most significant SNPs that account for only a small proportion of the genetic variants and offers limited understanding of complex diseases. To overcome these limitations, we propose gene and pathway-based association analysis as a new paradigm for GWAS. As a proof of concept, we performed a comprehensive gene and pathway-based association analysis for thirteen published GWAS. Our results showed that the proposed new paradigm for GWAS not only identified the genes that include significant SNPs found by single SNP analysis, but also detected new genes in which each single SNP conferred small disease risk, but their joint actions were implicated in the development of diseases. The results also demonstrated that the new paradigm for GWAS was able to identify biologically meaningful pathways associated with the diseases which were confirmed by gene-set rich analysis using gene expression data

Genetic variants in ELOVL2 and HSD17B12 predict melanoma‐specific survival

Fatty acids play a key role in cellular bioenergetics, membrane biosynthesis and intracellular signaling processes and thus may be involved in cancer development and progression. In the present study, we comprehensively assessed associations of 14,522 common single‐nucleotide polymorphisms (SNPs) in 149 genes of the fatty‐acid synthesis pathway with cutaneous melanoma disease‐specific survival (CMSS). The dataset of 858 cutaneous melanoma (CM) patients from a published genome‐wide association study (GWAS) by The University of Texas M.D. Anderson Cancer Center was used as the discovery dataset, and the identified significant SNPs were validated by a dataset of 409 CM patients from another GWAS from the Nurses’ Health and Health Professionals Follow‐up Studies. We found 40 noteworthy SNPs to be associated with CMSS in both discovery and validation datasets after multiple comparison correction by the false positive report probability method, because more than 85% of the SNPs were imputed. By performing functional prediction, linkage disequilibrium analysis, and stepwise Cox regression selection, we identified two independent SNPs of ELOVL2 rs3734398 T>C and HSD17B12 rs11037684 A>G that predicted CMSS, with an allelic hazards ratio of 0.66 (95% confidence interval = 0.51–0.84 and p = 8.34 × 10−4) and 2.29 (1.55–3.39 and p = 3.61 × 10−5), respectively. Finally, the ELOVL2 rs3734398 variant CC genotype was found to be associated with a significantly increased mRNA expression level. These SNPs may be potential markers for CM prognosis, if validated by additional larger and mechanistic studies

Sub-Alfvenic Non-Ideal MHD Turbulence Simulations with Ambipolar Diffusion: I. Turbulence Statistics

Most numerical investigations on the role of magnetic fields in turbulent molecular clouds (MCs) are based on ideal magneto-hydrodynamics (MHD). However, MCs are weakly ionized, so that the time scale required for the magnetic field to diffuse through the neutral component of the plasma by ambipolar diffusion (AD) can be comparable to the dynamical time scale. We have performed a series of 256^3 and 512^3 simulations on supersonic but sub-Alfvenic turbulent systems with AD using the Heavy-Ion Approximation developed in Li, McKee, & Klein (2006). Our calculations are based on the assumption that the number of ions is conserved, but we show that these results approximately apply to the case of time-dependent ionization in molecular clouds as well. Convergence studies allow us to determine the optimal value of the ionization mass fraction when using the heavy-ion approximation for low Mach number, sub-Alfvenic turbulent systems. We find that ambipolar diffusion steepens the velocity and magnetic power spectra compared to the ideal MHD case. Changes in the density PDF, total magnetic energy, and ionization fraction are determined as a function of the AD Reynolds number. The power spectra for the neutral gas properties of a strongly magnetized medium with a low AD Reynolds number are similar to those for a weakly magnetized medium; in particular, the power spectrum of the neutral velocity is close to that for Burgers turbulence.Comment: 37 pages, 11 figures, 4 table