Discovery of Multi-Phase Cold Accretion in a Massive Galaxy at z=0.7

We present detailed photo+collisional ionization models and kinematic models of the multi-phase absorbing gas, detected within the HST/COS, HST/STIS, and Keck/HIRES spectra of the background quasar TON 153, at 104 kpc along the projected minor axis of a star-forming spiral galaxy (z=0.6610). Complementary g'r'i'Ks photometry and stellar population models indicate that the host galaxy is dominated by a 4 Gyr stellar population with slightly greater than solar metallicity and has an estimated log(M*)=11 and a log(Mvir)=13. Photoionization models of the low ionization absorption, (MgI, SiII, MgII and CIII) which trace the bulk of the hydrogen, constrain the multi-component gas to be cold (logT=3.8-5.2) and metal poor (-1.68<[X/H]<-1.64). A lagging halo model reproduces the low ionization absorption kinematics, suggesting gas coupled to the disk angular momentum, consistent with cold accretion mode material in simulations. The CIV and OVI absorption is best modeled in a separate collisionally ionized metal-poor (-2.50<[X/H]<-1.93) warm phase with logT=5.3. Although their kinematics are consistent with a wind model, given the 2-2.5dex difference between the galaxy stellar metallicity and the absorption metallicity indicates the gas cannot arise from galactic winds. We discuss and conclude that although the quasar sight-line passes along the galaxy minor axis at projected distance of 0.3 virial radii, well inside its virial shock radius, the combination of the relative kinematics, temperatures, and relative metallicities indicated that the multi-phase absorbing gas arises from cold accretion around this massive galaxy. Our results appear to contradict recent interpretations that absorption probing the projected minor axis of a galaxy is sampling winds.Comment: 16 pages, 11 figures, accepted for publication in MNRA

Prediction performance of linear models and gradient boosting machine on complex phenotypes in outbred mice.

We compared the performance of linear (GBLUP, BayesB, and elastic net) methods to a nonparametric tree-based ensemble (gradient boosting machine) method for genomic prediction of complex traits in mice. The dataset used contained genotypes for 50,112 SNP markers and phenotypes for 835 animals from 6 generations. Traits analyzed were bone mineral density, body weight at 10, 15, and 20 weeks, fat percentage, circulating cholesterol, glucose, insulin, triglycerides, and urine creatinine. The youngest generation was used as a validation subset, and predictions were based on all older generations. Model performance was evaluated by comparing predictions for animals in the validation subset against their adjusted phenotypes. Linear models outperformed gradient boosting machine for 7 out of 10 traits. For bone mineral density, cholesterol, and glucose, the gradient boosting machine model showed better prediction accuracy and lower relative root mean squared error than the linear models. Interestingly, for these 3 traits, there is evidence of a relevant portion of phenotypic variance being explained by epistatic effects. Using a subset of top markers selected from a gradient boosting machine model helped for some of the traits to improve the accuracy of prediction when these were fitted into linear and gradient boosting machine models. Our results indicate that gradient boosting machine is more strongly affected by data size and decreased connectedness between reference and validation sets than the linear models. Although the linear models outperformed gradient boosting machine for the polygenic traits, our results suggest that gradient boosting machine is a competitive method to predict complex traits with assumed epistatic effects

Adding gene transcripts into genomic prediction improves accuracy and reveals sampling time dependence.

Recent developments allowed generating multiple high-quality \u27omics\u27 data that could increase the predictive performance of genomic prediction for phenotypes and genetic merit in animals and plants. Here, we have assessed the performance of parametric and nonparametric models that leverage transcriptomics in genomic prediction for 13 complex traits recorded in 478 animals from an outbred mouse population. Parametric models were implemented using the best linear unbiased prediction, while nonparametric models were implemented using the gradient boosting machine algorithm. We also propose a new model named GTCBLUP that aims to remove between-omics-layer covariance from predictors, whereas its counterpart GTBLUP does not do that. While gradient boosting machine models captured more phenotypic variation, their predictive performance did not exceed the best linear unbiased prediction models for most traits. Models leveraging gene transcripts captured higher proportions of the phenotypic variance for almost all traits when these were measured closer to the moment of measuring gene transcripts in the liver. In most cases, the combination of layers was not able to outperform the best single-omics models to predict phenotypes. Using only gene transcripts, the gradient boosting machine model was able to outperform best linear unbiased prediction for most traits except body weight, but the same pattern was not observed when using both single nucleotide polymorphism genotypes and gene transcripts. Although the GTCBLUP model was not able to produce the most accurate phenotypic predictions, it showed the highest accuracies for breeding values for 9 out of 13 traits. We recommend using the GTBLUP model for prediction of phenotypes and using the GTCBLUP for prediction of breeding values

The Spatial, Ionization, and Kinematic Conditions of the z=1.39 Damped Ly-alpha Absorber in Q0957+561 A,B

We examined the sizes of the absorption clouds in a z=1.3911 damped Ly-alpha absorber (DLA) in the double image lensed quasar Q0957+561 A,B (separation 135 pc at the absorber redshift). Using HIRES/Keck spectra, we studied the MgII 2796,2803 doublet, FeII multiplet, and MgI 2853 transition in absorption. We defined six "clouds" in the system of sightline A and seven clouds in the system of sightline B. An examination of the N(v) profiles, using the apparent optical depth method, reveals no clear physical connection between the clouds in A and those in B. The observed column density ratios of all clouds is log[N(MgI)/N(FeII)] ~ -2 across the full velocity range in both systems and also spatially (in both sightlines). This is a remarkable uniformity not seen in Lyman limit systems. The uniformity of the cloud properties suggests that the multiple clouds are not part of a "halo". Based upon photoionization modeling, we constrain the ionization parameters in the range -6.2 < log(U) < -5.1, where the range brackets known abundance ratio and dust depletion patterns. The inferred cloud properties are densities of 2 < n_H < 20 cm^-3, and line of sight sizes of 1 < D < 25 pc. The masses of the clouds in system A are 10 < M/M_sun < 1000 and in system B are 1 < M/M_sun < 60 for spherical clouds. For planar clouds, the upper limits are 400 M_sun and 160 M_sun for A and B, respectively. We favor a model of the absorber in which the DLA region itself is a single cloud in thiscomplex, which could be a parcel of gas in a galactic ISM. A spherical cloud of ~10 pc would be limited to one of the sightlines (A) and imply a covering factor less than 0.1 for the DLA complex. We infer that the DLA cloud properties are consistent with those of lower density, cold clouds in the Galactic interstellar medium.Comment: Accepted for publication in the Astrophysical Journal; final versio

Analytic approach to bifurcation cascades in a class of generalized H\'enon-Heiles potentials

We derive stability traces of bifurcating orbits in H\'enon-Heiles potentials near their saddlesComment: LaTeX revtex4, 38 pages, 7 PostScript figures, 2 table

A Search for Time Variation of the Fine Structure Constant

A method offering an order of magnitude sensitivity gain is described for using quasar spectra to investigate possible time or space variation in the fine structure constant, alpha. Applying the technique to a sample of 30 absorption systems, spanning redshifts 0.5 < z< 1.6, obtained with the Keck I telescope, we derive limits on variations in alpha over a wide range of epochs. For the whole sample Delta(alpha)/alpha = -1.1 +/- 0.4 x 10^{-5}. This deviation is dominated by measurements at z > 1, where Delta(alpha)/alpha = -1.9 +/- 0.5 x 10^{-5}. For z < 1, Delta(alpha)/alpha = -0.2 +/- 0.4 x 10^{-5}, consistent with other known constraints. Whilst these results are consistent with a time-varying alpha, further work is required to explore possible systematic errors in the data, although careful searches have so far not revealed any.Comment: 4 pages, 1 figure, accepted for publication in Physical Review Letter

Further Evidence for Cosmological Evolution of the Fine Structure Constant

We describe the results of a search for time variability of the fine structure constant, alpha, using absorption systems in the spectra of distant quasars. Three large optical datasets and two 21cm/mm absorption systems provide four independent samples, spanning 23% to 87% of the age of the universe. Each sample yields a smaller alpha in the past and the optical sample shows a 4-sigma deviation: da/a = -0.72 +/- 0.18 x 10^{-5} over the redshift range 0.5 < z < 3.5. We find no systematic effects which can explain our results. The only potentially significant systematic effects push da/a towards positive values, i.e. our results would become more significant were we to correct for them.Comment: 5 pages, 1 figure. Published in Phys. Rev. Lett. Small changes to discussion, added an acknowledgement and a referenc

Occurrence of periodic Lam\'e functions at bifurcations in chaotic Hamiltonian systems

We investigate cascades of isochronous pitchfork bifurcations of straight-line librating orbits in some two-dimensional Hamiltonian systems with mixed phase space. We show that the new bifurcated orbits, which are responsible for the onset of chaos, are given analytically by the periodic solutions of the Lam\'e equation as classified in 1940 by Ince. In Hamiltonians with C_${2v}$ symmetry, they occur alternatingly as Lam\'e functions of period 2K and 4K, respectively, where 4K is the period of the Jacobi elliptic function appearing in the Lam\'e equation. We also show that the two pairs of orbits created at period-doubling bifurcations of touch-and-go type are given by two different linear combinations of algebraic Lam\'e functions with period 8K.Comment: LaTeX2e, 22 pages, 14 figures. Version 3: final form of paper, accepted by J. Phys. A. Changes in Table 2; new reference [25]; name of bifurcations "touch-and-go" replaced by "island-chain

Study protocol: Reporting characteristics of intervention trials of animals published in the Journal of Dairy Science in 2017

Objectives The scope of this cross-sectional observational study is to evaluate prevalence of reporting the 19 objective items of the REFLECT statement checklist (Sargeant et al., 2010), with the primary outcome being prevalence of sample size calculation, in clinical trials published in the Journal of Dairy Science from January to December of 2017. We will also determine risk of bias in individual studies using the Cochrane Risk of Bias 2.0 tools for individually randomized, parallel group trials; cluster randomized, parallel group trials; and individually randomized, cross-over trials (Higgins et al., 2016)