Estimation of pedigree errors in the UK dairy population using microsatellite markers and the impact on selection

The proportion of cows in the UK dairy herd whose sires were misidentified was estimated using DNA markers. Genetic marker genotypes were determined on 568 cows (from 168 milk samples and 400 hair samples) and 96 putative sires (from semen samples). The estimated pedigree error rate from the hair samples was 8.8%, and from the milk samples, 13.1%, giving an overall estimate of the error rate of 10%. This level of pedigree errors will have a relatively large impact on the efficiency of progeny testing and the accuracy of cow predicted breeding values. We predict a loss of response to selection of approximately 2 to 3% given this error rate

FORC+ Analysis of Perpendicular Magnetic Tunnel Junctions

We have studied magnetic tunnel junction (MTJ) thin-film stacks using the First Order Reversal Curve (FORC) method. These have very sharp structures in the FORC distribution, unlike most particulate systems or patterned films. These structures are hard to study using conventional FORC analysis programs that require smoothing, because this washes out the structure. We have used a new analysis program (FORC+) that is designed to distinguish fine-scale structure from noise without the use of smoothing, to identify these structures and gain information about the switching mechanism of the stack

A Comparison of Near-Infrared Photometry and Spectra for Y Dwarfs with a New Generation of Cool Cloudy Models

We present YJHK photometry, or a subset, for the six Y dwarfs discovered in WISE data by Cushing et al.. The data were obtained using NIRI on the Gemini North telescope. We also present a far-red spectrum obtained using GMOS-North for WISEPC J205628.90+145953.3. We compare the data to Morley et al. (2012) models, which include cloud decks of sulfide and chloride condensates. We find that the models with these previously neglected clouds can reproduce the energy distributions of T9 to Y0 dwarfs quite well, other than near 5um where the models are too bright. This is thought to be because the models do not include departures from chemical equilibrium caused by vertical mixing, which would enhance the abundance of CO, decreasing the flux at 5um. Vertical mixing also decreases the abundance of NH_3, which would otherwise have strong absorption features at 1.03um and 1.52um that are not seen in the Y0 WISEPC J205628.90+145953.3. We find that the five Y0 to Y0.5 dwarfs have 300 < T_eff K < 450, 4.0 < log g < 4.5 and f_sed ~ 3. These temperatures and gravities imply a mass range of 5 - 15 M_Jupiter and ages around 5 Gyr. We suggest that WISEP J182831.08+265037.8 is a binary system, as this better explains its luminosity and color. We find that the data can be made consistent with observed trends, and generally consistent with the models, if the system is composed of a T_eff = 325 K and log g ~ 4.0 secondary, corresponding to masses of 10 and 7 M_Jupiter and an age around 2 Gyr. If our deconvolution is correct, then the T_eff = 300 K cloud-free model fluxes at K and W2 are too faint by 0.5 - 1.0 magnitudes. We will address this discrepancy in our next generation of models, which will incorporate water clouds and mixing.Comment: 39 pages, 10 Figures, 8 Tables. Accepted by ApJ. This revision replaces Figures 9 and 10 with B & W versions, corrects figure captions for color online only, corrects references. Text is unchanged. Tables 3, 4 and 8 are available at http://www.gemini.edu/staff/sleggett, other model data are available at http://www.ucolick.org/~cmorley/cmorley/Data.htm

Estimation of linkage disequilibrium in a sample of the United Kingdom dairy cattle population using unphased genotypes

The association between genetic marker alleles was estimated for two regions of the bovine genome from a random sample of 50 young dairy bulls born in the United Kingdom between 1988 and 1995. Microsatellite marker genotypes were obtained for six markers on chromosome 2 and seven markers on chromosome 6, spanning 38 and 20 cM, respectively. Two different methods, which do not require family information, were used to estimate population haplotype frequencies. Haplotype frequencies were estimated for pairs of loci using the expectation-maximization algorithm and for all linked loci using a Bayesian approach via a Markov chain-Monte Carlo algorithm. Significant (P = 0.0007) linkage disequilibrium was detected between pairs of loci in syntenic groups (that is, loci in the same linkage group), extending to about 10 cM. No significant linkage disequilibrium was detected between markers in nonsyntenic regions. Given the observed level of linkage disequilibrium, mapping methods based on population-wide association might provide a better resolution than traditional quantitative trait loci mapping methods in the U.K. dairy cattle population and may reduce the required sample sizes of the experiments

Spin-torque switching: Fokker-Planck rate calculation

We describe a new approach to understanding and calculating magnetization switching rates and noise in the recently observed phenomenon of "spin-torque switching". In this phenomenon, which has possible applications to information storage, a large current passing from a pinned ferromagnetic (FM) layer to a free FM layer switches the free layer. Our main result is that the spin-torque effect increases the Arrhenius factor $\exp(-E/kT)$ in the switching rate, not by lowering the barrier $E$, but by raising the effective spin temperature $T$. To calculate this effect quantitatively, we extend Kramers' 1940 treatment of reaction rates, deriving and solving a Fokker-Planck equation for the energy distribution including a current-induced spin torque of the Slonczewski type. This method can be used to calculate slow switching rates without long-time simulations; in this Letter we calculate rates for telegraph noise that are in good qualitative agreement with recent experiments. The method also allows the calculation of current-induced magnetic noise in CPP (current perpendicular to plane) spin valve read heads.Comment: 11 pages, 8 figures, 1 appendix Original version in Nature format, replaced by Phys. Rev. Letters format. No substantive change

Is Random Close Packing of Spheres Well Defined?

Despite its long history, there are many fundamental issues concerning random packings of spheres that remain elusive, including a precise definition of random close packing (RCP). We argue that the current picture of RCP cannot be made mathematically precise and support this conclusion via a molecular dynamics study of hard spheres using the Lubachevsky-Stillinger compression algorithm. We suggest that this impasse can be broken by introducing the new concept of a maximally random jammed state, which can be made precise.Comment: 6 pages total, 2 figure

Landing together: how flocks arrive at a coherent action in time and space in the presence of perturbations

Collective motion is abundant in nature, producing a vast amount of phenomena which have been studied in recent years, including the landing of flocks of birds. We investigate the collective decision making scenario where a flock of birds decides the optimal time of landing in the absence of a global leader. We introduce a simple phenomenological model in the spirit of the statistical mechanics-based self-propelled particles (SPP-s) approach to interpret this process. We expect that our model is applicable to a larger class of spatiotemporal decision making situations than just the landing of flocks (which process is used as a paradigmatic case). In the model birds are only influenced by observable variables, like position and velocity. Heterogeneity is introduced in the flock in terms of a depletion time after which a bird feels increasing bias to move towards the ground. Our model demonstrates a possible mechanism by which animals in a large group can arrive at an egalitarian decision about the time of switching from one activity to another in the absence of a leader. In particular, we show the existence of a paradoxical effect where noise enhances the coherence of the landing process.Comment: 15 pages, 7 figure