High-throughput next-generation RNA sequencing has matured into a viable and powerful method for detecting variations in transcript expression and regulation. Proactive quality control is of critical ...importance as unanticipated biases, artifacts, or errors can potentially drive false associations and lead to flawed results.
We have developed the Quality of RNA-Seq Toolset, or QoRTs, a comprehensive, multifunction toolset that assists in quality control and data processing of high-throughput RNA sequencing data.
QoRTs generates an unmatched variety of quality control metrics, and can provide cross-comparisons of replicates contrasted by batch, biological sample, or experimental condition, revealing any outliers and/or systematic issues that could drive false associations or otherwise compromise downstream analyses. In addition, QoRTs simultaneously replaces the functionality of numerous other data-processing tools, and can quickly and efficiently generate quality control metrics, coverage counts (for genes, exons, and known/novel splice-junctions), and browser tracks. These functions can all be carried out as part of a single unified data-processing/quality control run, greatly reducing both the complexity and the total runtime of the analysis pipeline. The software, source code, and documentation are available online at http://hartleys.github.io/QoRTs.
We measure new estimates for the galaxy stellar mass function and star formation rates for samples of galaxies at z ∼ 4, 5, 6 and 7 using data in the CANDELS GOODS South field. The deep near-infrared ...observations allow us to construct the stellar mass function at z ≥ 6 directly for the first time. We estimate stellar masses for our sample by fitting the observed spectral energy distributions with synthetic stellar populations, including nebular line and continuum emission. The observed UV luminosity functions for the samples are consistent with previous observations; however, we find that the observed M
UV-M
* relation has a shallow slope more consistent with a constant mass-to-light ratio and a normalization which evolves with redshift. Our stellar mass functions have steep low-mass slopes (α ≈ −1.9), steeper than previously observed at these redshifts and closer to that of the UV luminosity function. Integrating our new mass functions, we find the observed stellar mass density evolves from
$\log _{10} \rho _{*} = 6.64^{+0.58}_{-0.89}$
at z ∼ 7 to 7.36 ± 0.06 M⊙ Mpc− 3 at z ∼ 4. Finally, combining the measured UV continuum slopes (β) with their rest-frame UV luminosities, we calculate dust-corrected star formation rates (SFR) for our sample. We find the specific SFR for a fixed stellar mass increases with redshift whilst the global SFR density falls rapidly over this period. Our new SFR density estimates are higher than previously observed at this redshift.
In this work, we present the first cosmology results from large-scale structure using the full 5000 deg2 of imaging data from the Dark Energy Survey (DES) Data Release 1. We perform an analysis of ...large-scale structure combining three two-point correlation functions ( 3×2pt ): (i) cosmic shear using 100 million source galaxies, (ii) galaxy clustering, and (iii) the cross-correlation of source galaxy shear with lens galaxy positions, galaxy–galaxy lensing. To achieve the cosmological precision enabled by these measurements has required updates to nearly every part of the analysis from DES Year 1, including the use of two independent galaxy clustering samples, modeling advances, and several novel improvements in the calibration of gravitational shear and photometric redshift inference. The analysis was performed under strict conditions to mitigate confirmation or observer bias; we describe specific changes made to the lens galaxy sample following unblinding of the results and tests of the robustness of our results to this decision. We model the data within the flat Λ CDM and wCDM cosmological models, marginalizing over 25 nuisance parameters. We find consistent cosmological results between the three two-point correlation functions; their combination yields clustering amplitude S8=0.776-0.017+0.017 and matter density Ω m =0.339-0.031+0.032 in Λ CDM , mean with 68% confidence limits; S8=0.775-0.024+0.026 , Ω m =0.352-0.041+0.035 , and dark energy equation-of-state parameter w=-0.98-0.20+0.32 in wCDM . These constraints correspond to an improvement in signal-to-noise of the DES Year 3 3×2pt data relative to DES Year 1 by a factor of 2.1, about 20% more than expected from the increase in observing area alone. This combination of DES data is consistent with the prediction of the model favored by the Planck 2018 cosmic microwave background (CMB) primary anisotropy data, which is quantified with a probability-to-exceed p=0.13 –0.48. We find better agreement between DES 3×2pt and Planck than in DES Y1, despite the significantly improved precision of both. When combining DES 3×2pt data with available baryon acoustic oscillation, redshift-space distortion, and type Ia supernovae data, we find p=0.34 . Combining all of these datasets with Planck CMB lensing yields joint parameter constraints of S8=0.812-0.008+0.008 , Ω m =0.306-0.005+0.004 , h=0.680-0.003+0.004 , and Σmν<0.13 eV (95% C.L.) in Λ CDM ; S8=0.812-0.008+0.008 , Ω m =0.302-0.006+0.006 , h=0.687-0.007+0.006 , and w=-1.031-0.027+0.030 in wCDM .
Abstract
We present a new constraint on the Hubble constant
H
0
using a sample of well-localized gravitational-wave (GW) events detected during the first three LIGO/Virgo observing runs as dark ...standard sirens. In the case of dark standard sirens, a unique host galaxy is not identified, and the redshift information comes from the distribution of potential host galaxies. From the third LIGO/Virgo observing run detections, we add the asymmetric-mass binary black hole GW190412 and the high-confidence GW candidates S191204r, S200129m, and S200311bg to the sample of dark standard sirens analyzed in Palmese et al. Our sample contains the top 20% (based on localization) GW events and candidates to date with significant coverage by the Dark Energy Spectroscopic Instrument Legacy Survey. We combine the
H
0
posterior for eight dark siren events, finding
H
0
=
79.8
−
12.8
+
19.1
km
s
−
1
Mpc
−
1
(68% highest density interval) for a prior in
H
0
uniform between 20, 140 km s
−1
Mpc
−1
. This result shows that a combination of eight well-localized dark sirens combined with an appropriate galaxy catalog is able to provide an
H
0
constraint that is competitive (∼20% versus 18% precision) with a single bright standard siren analysis (i.e., assuming the electromagnetic counterpart) using GW170817. When combining the posterior with that from GW170817, we obtain
H
0
=
72.77
−
7.55
+
11.0
km
s
−
1
Mpc
−
1
. This result is broadly consistent with recent
H
0
estimates from both the cosmic microwave background and supernovae.
Like most complex phenotypes, exceptional longevity is thought to reflect a combined influence of environmental (e.g., lifestyle choices, where we live) and genetic factors. To explore the genetic ...contribution, we undertook a genome-wide association study of exceptional longevity in 801 centenarians (median age at death 104 years) and 914 genetically matched healthy controls. Using these data, we built a genetic model that includes 281 single nucleotide polymorphisms (SNPs) and discriminated between cases and controls of the discovery set with 89% sensitivity and specificity, and with 58% specificity and 60% sensitivity in an independent cohort of 341 controls and 253 genetically matched nonagenarians and centenarians (median age 100 years). Consistent with the hypothesis that the genetic contribution is largest with the oldest ages, the sensitivity of the model increased in the independent cohort with older and older ages (71% to classify subjects with an age at death>102 and 85% to classify subjects with an age at death>105). For further validation, we applied the model to an additional, unmatched 60 centenarians (median age 107 years) resulting in 78% sensitivity, and 2863 unmatched controls with 61% specificity. The 281 SNPs include the SNP rs2075650 in TOMM40/APOE that reached irrefutable genome wide significance (posterior probability of association = 1) and replicated in the independent cohort. Removal of this SNP from the model reduced the accuracy by only 1%. Further in-silico analysis suggests that 90% of centenarians can be grouped into clusters characterized by different "genetic signatures" of varying predictive values for exceptional longevity. The correlation between 3 signatures and 3 different life spans was replicated in the combined replication sets. The different signatures may help dissect this complex phenotype into sub-phenotypes of exceptional longevity.
We investigate galactic-scale outflows in the redshift range 0.71 ≤ z ≤ 1.63, using 413 K-band selected galaxies observed in the spectroscopic follow-up of the UKIDSS Ultra-Deep Survey (UDSz). The ...galaxies have an average stellar mass of ∼109.5 M and span a wide range in rest-frame colours, representing typical star-forming galaxies at this epoch. We stack the spectra by various galaxy properties, including stellar mass, O ii equivalent width, star formation rate, specific star formation rate and rest-frame spectral indices. We find that outflows are present in virtually all spectral stacks, with velocities ranging from 100 to 1000 km s−1, indicating that large-scale outflowing winds are a common property at these redshifts. The highest velocity outflows (>500 km s−1) are found in galaxies with the highest stellar masses and the youngest stellar populations. Our findings suggest that high-velocity galactic outflows are mostly driven by star-forming processes rather than active galactic nuclei, with implied mass outflow rates comparable to the rates of star formation. Such behaviour is consistent with models required to reproduce the high-redshift mass-metallicity relation.
This work and its companion paper, Amon et al. Phys. Rev. D 105, 023514 (2022), present cosmic shear measurements and cosmological constraints from over 100 million source galaxies in the Dark Energy ...Survey (DES) Year 3 data. We constrain the lensing amplitude parameter S8≡σ8 Ω m / 0.3 at the 3% level in Λ CDM : S8=0.759-0.023+0.025 (68% CL). Our constraint is at the 2% level when using angular scale cuts that are optimized for the Λ CDM analysis: S8=0.772-0.017+0.018 (68% CL). With cosmic shear alone, we find no statistically significant constraint on the dark energy equation-of-state parameter at our present statistical power. We carry out our analysis blind, and compare our measurement with constraints from two other contemporary weak lensing experiments: the Kilo-Degree Survey (KiDS) and Hyper-Suprime Camera Subaru Strategic Program (HSC). We additionally quantify the agreement between our data and external constraints from the Cosmic Microwave Background (CMB). Our DES Y3 result under the assumption of Λ CDM is found to be in statistical agreement with Planck 2018, although favors a lower S8 than the CMB-inferred value by 2.3σ (a p -value of 0.02). This paper explores the robustness of these cosmic shear results to modeling of intrinsic alignments, the matter power spectrum and baryonic physics. We additionally explore the statistical preference of our data for intrinsic alignment models of different complexity. The fiducial cosmic shear model is tested using synthetic data, and we report no biases greater than 0.3σ in the plane of S8× Ω m caused by uncertainties in the theoretical models.
We explore the redshift evolution of a curious correlation between the star formation properties of central galaxies and their satellites (‘galactic conformity’) at intermediate to high redshift (0.4 ...< z < 1.9). Using an extremely deep near-infrared survey, we study the distribution and properties of satellite galaxies with stellar masses, log(M
*/M⊙) > 9.7, around central galaxies at the characteristic Schechter function mass, M ∼ M*. We fit the radial profiles of satellite number densities with simple power laws, finding slopes in the range −1.1 to −1.4 for mass-selected satellites, and −1.3 to −1.6 for passive satellites. We confirm the tendency for passive satellites to be preferentially located around passive central galaxies at 3σ significance and show that it exists to at least z ∼ 2. Meanwhile, the quenched fraction of satellites around star-forming galaxies is consistent with field galaxies of equal stellar masses. We find no convincing evidence for a redshift-dependent evolution of these trends. One simple interpretation of these results is that only passive central galaxies occupy an environment that is capable of independently shutting off star formation in satellite galaxies. By examining the satellites of higher stellar mass star-forming galaxies (log(M
*/M⊙) > 11), we conclude that the origin of galactic conformity is unlikely to be exclusively due to the host dark matter halo mass. A halo-mass-independent correlation could be established by either formation bias or a more physical connection between central and satellite star formation histories. For the latter, we argue that a star formation (or active galactic nucleus) related outburst event from the central galaxy could establish a hot halo environment which is then capable of quenching both central and satellite galaxies.
We report the first results of AS2UDS, an 870 m continuum survey with the Atacama Large Millimeter/Submillimeter Array (ALMA) of a total area of ∼50 arcmin2 comprising a complete sample of 716 ...submillimeter sources drawn from the SCUBA-2 Cosmology Legacy Survey (S2CLS) map of the UKIDSS/UDS field. The S2CLS parent sample covers a 0.96 degree2 field at 850 = 0.90 0.05 mJy beam−1. Our deep, high-resolution ALMA observations with 870 ∼ 0.25 mJy and a 0 15-0 30 FWHM synthesized beam, provide precise locations for 695 submillimeter galaxies (SMGs) responsible for the submillimeter emission corresponding to 606 sources in the low-resolution, single-dish map. We measure the number counts of SMGs brighter than S870 ≥ 4 mJy, free from the effects of blending and show that the normalization of the counts falls by 28% 2% in comparison with the SCUBA-2 published counts, but that the shape remains unchanged. We determine that 44 − 14 + 16 % of the brighter single-dish sources with S850 ≥ 9 mJy consist of a blend of two or more ALMA-detectable SMGs brighter than S870 ∼ 1 mJy (corresponding to a galaxy with a total-infrared luminosity of LIR 1012 L ), in comparison with 28% 2% for the single-dish sources at S850 ≥ 5 mJy. Using the 46 single-dish submillimeter sources that contain two or more ALMA-detected SMGs with photometric redshifts, we show that there is a significant statistical excess of pairs of SMGs with similar redshifts (<1% probability of occurring by chance), suggesting that at least 30% of these blends arise from physically associated pairs of SMGs.
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