Genetic Parameters and Responses of Linear Type, Yield Traits, and Somatic Cell Scores to Divergent Selection for Predicted Transmitting Ability for Type in Holsteins

The objective was to examine the direct and correlated responses of linear type, yield traits, and somatic cell scores (SCS) to divergent selection for predicted transmitting ability for type (PTAT) in Holsteins, while maintaining selection for yield traits across lines. For four generations, one-half of the University of Nebraska research Holstein herd was bred to Holstein sires with PTAT -1.50 and the other half to sires with PTAT - 1.25, with nearly equal predicted transmitting abilities for yield traits for both groups. Estimates of genetic and residual correlations and heritabilities were obtained from REML estimates of (co)variance components. Model for type traits included fixed effect of date cows were classified, effects of age in days at freshening, and stage of lactation at classification. Year-season when cows freshened was fixed effect in model for yield and SCS. Animal genetic and residual effects were random. Final score, milk, fat, and protein yields, and SCS had heritability estimates of 0.38, 0.13, 0.22, 0.09, and 0.38, respectively. Heritability estimates for type traits ranged from 0.04 to 0.52. Estimates of genetic correlations of final score with SCS and milk, fat, and protein yields were -0.64, 0.01, -0.18, and 0.06, respectively. Estimates of genetic correlations among linear type traits ranged from -0.77 to 1.00. Means of estimated breeding values for final score, stature, strength, body depth, fore udder attachment, rear udder height and width, udder cleft, udder depth, and front teat placement were significantly different between lines in the third generation. Milk, fat, and protein yields were not significantly different between lines in third generation, whereas SCS was significantly different. Estimate of genetic correlation between final score and SCS suggest that selection on PTAT would result in a change for SCS. In this study, divergent selection on PTAT of sires had a significant effect on udder and body traits, but little or no effect on feet and leg traits

Majority Dynamics and Aggregation of Information in Social Networks

Consider n individuals who, by popular vote, choose among q >= 2 alternatives, one of which is "better" than the others. Assume that each individual votes independently at random, and that the probability of voting for the better alternative is larger than the probability of voting for any other. It follows from the law of large numbers that a plurality vote among the n individuals would result in the correct outcome, with probability approaching one exponentially quickly as n tends to infinity. Our interest in this paper is in a variant of the process above where, after forming their initial opinions, the voters update their decisions based on some interaction with their neighbors in a social network. Our main example is "majority dynamics", in which each voter adopts the most popular opinion among its friends. The interaction repeats for some number of rounds and is then followed by a population-wide plurality vote. The question we tackle is that of "efficient aggregation of information": in which cases is the better alternative chosen with probability approaching one as n tends to infinity? Conversely, for which sequences of growing graphs does aggregation fail, so that the wrong alternative gets chosen with probability bounded away from zero? We construct a family of examples in which interaction prevents efficient aggregation of information, and give a condition on the social network which ensures that aggregation occurs. For the case of majority dynamics we also investigate the question of unanimity in the limit. In particular, if the voters' social network is an expander graph, we show that if the initial population is sufficiently biased towards a particular alternative then that alternative will eventually become the unanimous preference of the entire population.Comment: 22 page

Classical Equations for Quantum Systems

The origin of the phenomenological deterministic laws that approximately govern the quasiclassical domain of familiar experience is considered in the context of the quantum mechanics of closed systems such as the universe as a whole. We investigate the requirements for coarse grainings to yield decoherent sets of histories that are quasiclassical, i.e. such that the individual histories obey, with high probability, effective classical equations of motion interrupted continually by small fluctuations and occasionally by large ones. We discuss these requirements generally but study them specifically for coarse grainings of the type that follows a distinguished subset of a complete set of variables while ignoring the rest. More coarse graining is needed to achieve decoherence than would be suggested by naive arguments based on the uncertainty principle. Even coarser graining is required in the distinguished variables for them to have the necessary inertia to approach classical predictability in the presence of the noise consisting of the fluctuations that typical mechanisms of decoherence produce. We describe the derivation of phenomenological equations of motion explicitly for a particular class of models. Probabilities of the correlations in time that define equations of motion are explicitly considered. Fully non-linear cases are studied. Methods are exhibited for finding the form of the phenomenological equations of motion even when these are only distantly related to those of the fundamental action. The demonstration of the connection between quantum-mechanical causality and causalty in classical phenomenological equations of motion is generalized. The connections among decoherence, noise, dissipation, and the amount of coarse graining necessary to achieve classical predictability are investigated quantitatively.Comment: 100pages, 1 figur

Bose-Einstein Condensation in a Harmonic Potential

We examine several features of Bose-Einstein condensation (BEC) in an external harmonic potential well. In the thermodynamic limit, there is a phase transition to a spatial Bose-Einstein condensed state for dimension D greater than or equal to 2. The thermodynamic limit requires maintaining constant average density by weakening the potential while increasing the particle number N to infinity, while of course in real experiments the potential is fixed and N stays finite. For such finite ideal harmonic systems we show that a BEC still occurs, although without a true phase transition, below a certain ``pseudo-critical'' temperature, even for D=1. We study the momentum-space condensate fraction and find that it vanishes as 1/N^(1/2) in any number of dimensions in the thermodynamic limit. In D less than or equal to 2 the lack of a momentum condensation is in accord with the Hohenberg theorem, but must be reconciled with the existence of a spatial BEC in D=2. For finite systems we derive the N-dependence of the spatial and momentum condensate fractions and the transition temperatures, features that may be experimentally testable. We show that the N-dependence of the 2D ideal-gas transition temperature for a finite system cannot persist in the interacting case because it violates a theorem due to Chester, Penrose, and Onsager.Comment: 34 pages, LaTeX, 6 Postscript figures, Submitted to Jour. Low Temp. Phy

Minding impacting events in a model of stochastic variance

We introduce a generalisation of the well-known ARCH process, widely used for generating uncorrelated stochastic time series with long-term non-Gaussian distributions and long-lasting correlations in the (instantaneous) standard deviation exhibiting a clustering profile. Specifically, inspired by the fact that in a variety of systems impacting events are hardly forgot, we split the process into two different regimes: a first one for regular periods where the average volatility of the fluctuations within a certain period of time is below a certain threshold and another one when the local standard deviation outnumbers it. In the former situation we use standard rules for heteroscedastic processes whereas in the latter case the system starts recalling past values that surpassed the threshold. Our results show that for appropriate parameter values the model is able to provide fat tailed probability density functions and strong persistence of the instantaneous variance characterised by large values of the Hurst exponent is greater than 0.8, which are ubiquitous features in complex systems.Comment: 18 pages, 5 figures, 1 table. To published in PLoS on

Comparative analysis of homology models of the Ah receptor ligand binding domain: Verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor

The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates the biological and toxic effects of a wide variety of structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). While significant interspecies differences in AHR ligand binding specificity, selectivity, and response have been observed, the structural determinants responsible for those differences have not been determined, and homology models of the AHR ligand-binding domain (LBD) are available for only a few species. Here we describe the development and comparative analysis of homology models of the LBD of 16 AHRs from 12 mammalian and nonmammalian species and identify the specific residues contained within their ligand binding cavities. The ligand-binding cavity of the fish AHR exhibits differences from those of mammalian and avian AHRs, suggesting a slightly different TCDD binding mode. Comparison of the internal cavity in the LBD model of zebrafish (zf) AHR2, which binds TCDD with high affinity, to that of zfAHR1a, which does not bind TCDD, revealed that the latter has a dramatically shortened binding cavity due to the side chains of three residues (Tyr296, Thr386, and His388) that reduce the amount of internal space available to TCDD. Mutagenesis of two of these residues in zfAHR1a to those present in zfAHR2 (Y296H and T386A) restored the ability of zfAHR1a to bind TCDD and to exhibit TCDD-dependent binding to DNA. These results demonstrate the importance of these two amino acids and highlight the predictive potential of comparative analysis of homology models from diverse species. The availability of these AHR LBD homology models will facilitate in-depth comparative studies of AHR ligand binding and ligand-dependent AHR activation and provide a novel avenue for examining species-specific differences in AHR responsiveness. © 2013 American Chemical Society

Mean Field Calculations of Bose-Einstein Condensation of 7Li Atoms In a Harmonic Trap

A self-consistent mean-field theory for bosons for T>0 is used to reconcile predictions of collapse with recent observations of Bose-Einstein condensation of 7Li. Eigenfunctions of a (non-separable) Hamiltonian that includes the anisotropic external trap field and atom-atom interactions are obtained by an iteration process. A sum over the Bose distribution, and the ``alternating direction implicit'' algorithm are used. Near Tc, the ensemble exhibits a localized condensate composed of atoms in the few lowest states. For lower T, numerical instability indicates collapse to a more dense phase.Comment: 11 pages + 4 figure

An optimization principle for deriving nonequilibrium statistical models of Hamiltonian dynamics

A general method for deriving closed reduced models of Hamiltonian dynamical systems is developed using techniques from optimization and statistical estimation. As in standard projection operator methods, a set of resolved variables is selected to capture the slow, macroscopic behavior of the system, and the family of quasi-equilibrium probability densities on phase space corresponding to these resolved variables is employed as a statistical model. The macroscopic dynamics of the mean resolved variables is determined by optimizing over paths of these probability densities. Specifically, a cost function is introduced that quantifies the lack-of-fit of such paths to the underlying microscopic dynamics; it is an ensemble-averaged, squared-norm of the residual that results from submitting a path of trial densities to the Liouville equation. The evolution of the macrostate is estimated by minimizing the time integral of the cost function. The value function for this optimization satisfies the associated Hamilton-Jacobi equation, and it determines the optimal relation between the statistical parameters and the irreversible fluxes of the resolved variables, thereby closing the reduced dynamics. The resulting equations for the macroscopic variables have the generic form of governing equations for nonequilibrium thermodynamics, and they furnish a rational extension of the classical equations of linear irreversible thermodynamics beyond the near-equilibrium regime. In particular, the value function is a thermodynamic potential that extends the classical dissipation function and supplies the nonlinear relation between thermodynamics forces and fluxes

Time resolution of the plastic scintillator strips with matrix photomultiplier readout for J-PET tomograph

Recent tests of a single module of the Jagiellonian Positron Emission Tomography system (J-PET) consisting of 30 cm long plastic scintillator strips have proven its applicability for the detection of annihilation quanta (0.511 MeV) with a coincidence resolving time (CRT) of 0.266 ns. The achieved resolution is almost by a factor of two better with respect to the current TOF-PET detectors and it can still be improved since, as it is shown in this article, the intrinsic limit of time resolution for the determination of time of the interaction of 0.511 MeV gamma quanta in plastic scintillators is much lower. As the major point of the article, a method allowing to record timestamps of several photons, at two ends of the scintillator strip, by means of matrix of silicon photomultipliers (SiPM) is introduced. As a result of simulations, conducted with the number of SiPM varying from 4 to 42, it is shown that the improvement of timing resolution saturates with the growing number of photomultipliers, and that the 2 x 5 configuration at two ends allowing to read twenty timestamps, constitutes an optimal solution. The conducted simulations accounted for the emission time distribution, photon transport and absorption inside the scintillator, as well as quantum efficiency and transit time spread of photosensors, and were checked based on the experimental results. Application of the 2 x 5 matrix of SiPM allows for achieving the coincidence resolving time in positron emission tomography of $\approx$ 0.170 ns for 15 cm axial field-of-view (AFOV) and $\approx$ 0.365 ns for 100 cm AFOV. The results open perspectives for construction of a cost-effective TOF-PET scanner with significantly better TOF resolution and larger AFOV with respect to the current TOF-PET modalities.Comment: To be published in Phys. Med. Biol. (26 pages, 17 figures

The Quantum Vlasov Equation and its Markov Limit

The adiabatic particle number in mean field theory obeys a quantum Vlasov equation which is nonlocal in time. For weak, slowly varying electric fields this particle number can be identified with the single particle distribution function in phase space, and its time rate of change is the appropriate effective source term for the Boltzmann-Vlasov equation. By analyzing the evolution of the particle number we exhibit the time structure of the particle creation process in a constant electric field, and derive the local form of the source term due to pair creation. In order to capture the secular Schwinger creation rate, the source term requires an asymptotic expansion which is uniform in time, and whose longitudinal momentum dependence can be approximated by a delta function only on long time scales. The local Vlasov source term amounts to a kind of Markov limit of field theory, where information about quantum phase correlations in the created pairs is ignored and a reversible Hamiltonian evolution is replaced by an irreversible kinetic one. This replacement has a precise counterpart in the density matrix description, where it corresponds to disregarding the rapidly varying off-diagonal terms in the adiabatic number basis and treating the more slowly varying diagonal elements as the probabilities of creating pairs in a stochastic process. A numerical comparison between the quantum and local kinetic approaches to the dynamical backreaction problem shows remarkably good agreement, even in quite strong electric fields, over a large range of times.Comment: 49 pages, RevTex/LaTeX2e, 8 .eps figures included in 404KB .gz file (~3MB total uncompressed). Replacement added \tightenpages command to reduce from 67 to 49 p