An Efficient Bayesian Model Selection Approach for Interacting Quantitative Trait Loci Models With Many Effects

We extend our Bayesian model selection framework for mapping epistatic QTL in experimental crosses to include environmental effects and gene–environment interactions. We propose a new, fast Markov chain Monte Carlo algorithm to explore the posterior distribution of unknowns. In addition, we take advantage of any prior knowledge about genetic architecture to increase posterior probability on more probable models. These enhancements have significant computational advantages in models with many effects. We illustrate the proposed method by detecting new epistatic and gene–sex interactions for obesity-related traits in two real data sets of mice. Our method has been implemented in the freely available package R/qtlbim (http://www.qtlbim.org) to facilitate the general usage of the Bayesian methodology for genomewide interacting QTL analysis

Direct reaction measurements with a 132Sn radioactive ion beam

The (d,p) neutron transfer and (d,d) elastic scattering reactions were measured in inverse kinematics using a radioactive ion beam of 132Sn at 630 MeV. The elastic scattering data were taken in a region where Rutherford scattering dominated the reaction, and nuclear effects account for less than 8% of the cross section. The magnitude of the nuclear effects was found to be independent of the optical potential used, allowing the transfer data to be normalized in a reliable manner. The neutron-transfer reaction populated a previously unmeasured state at 1363 keV, which is most likely the single-particle 3p1/2 state expected above the N=82 shell closure. The data were analyzed using finite range adiabatic wave calculations and the results compared with the previous analysis using the distorted wave Born approximation. Angular distributions for the ground and first excited states are consistent with the previous tentative spin and parity assignments. Spectroscopic factors extracted from the differential cross sections are similar to those found for the one neutron states beyond the benchmark doubly-magic nucleus 208Pb.Comment: 22 pages, 7 figure

Reactions of a Be-10 beam on proton and deuteron targets

The extraction of detailed nuclear structure information from transfer reactions requires reliable, well-normalized data as well as optical potentials and a theoretical framework demonstrated to work well in the relevant mass and beam energy ranges. It is rare that the theoretical ingredients can be tested well for exotic nuclei owing to the paucity of data. The halo nucleus Be-11 has been examined through the 10Be(d,p) reaction in inverse kinematics at equivalent deuteron energies of 12,15,18, and 21.4 MeV. Elastic scattering of Be-10 on protons was used to select optical potentials for the analysis of the transfer data. Additionally, data from the elastic and inelastic scattering of Be-10 on deuterons was used to fit optical potentials at the four measured energies. Transfers to the two bound states and the first resonance in Be-11 were analyzed using the Finite Range ADiabatic Wave Approximation (FR-ADWA). Consistent values of the spectroscopic factor of both the ground and first excited states were extracted from the four measurements, with average values of 0.71(5) and 0.62(4) respectively. The calculations for transfer to the first resonance were found to be sensitive to the size of the energy bin used and therefore could not be used to extract a spectroscopic factor.Comment: 16 Pages, 10 figure

Statistical Fluctuations of Electromagnetic Transition Intensities in pf-Shell Nuclei

We study the fluctuation properties of E2 and M1 transition intensities among T=0,1 states of A = 60 nuclei in the framework of the interacting shell model, using a realistic effective interaction for pf-shell nuclei with a Ni56 as a core. It is found that the B(E2) distributions are well described by the Gaussian orthogonal ensemble of random matrices (Porter-Thomas distribution) independently of the isobaric quantum number T_z. However, the statistics of the B(M1) transitions is sensitive to T_z: T_z=1 nuclei exhibit a Porter-Thomas distribution, while a significant deviation from the GOE statistics is observed for self-conjugate nuclei (T_z=0).Comment: 8 pages, latex, 3 figures (ps format

19Ne levels studied with the 18F(d,n)19Ne\u3csup\u3e*\u3c/sup\u3e(18F+p) reaction

A good understanding of the level structure of 19Ne around the proton threshold is critical to estimating the destruction of long-lived 18F in novae. Here we report the properties of levels in 19Ne in the excitation energy range of 6.9 ≤ Ex ≤ 8.4 MeV studied via the proton-transfer 18F(d,n)Ne* reaction at the Holifield Radioactive Ion Beam Facility. The populated 19Ne levels decay by breakup into p+18F and α+15O particles. The results presented in this manuscript are those of levels that are simultaneously observed from the breakup into both channels. An s-wave state is observed at 1468 keV above the proton threshold, which is a potential candidate for a predicted broad Jπ = 1/2+ state. The proton and α partial widths are deduced to be Γp = 228 ± 50 keV and Γα = 130 ± 30 keV for this state. © 2012 American Physical Society

Recombination rate and selection strength in HIV intra-patient evolution

The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the parameters governing genetic diversification and the strength of selection need to be known. While mutation rates can be measured in single replication cycles, the relevant effective recombination rate depends on the probability of coinfection of a cell with more than one virus and can only be inferred from population data. However, most population genetic estimators for recombination rates assume absence of selection and are hence of limited applicability to HIV, since positive and purifying selection are important in HIV evolution. Here, we estimate the rate of recombination and the distribution of selection coefficients from time-resolved sequence data tracking the evolution of HIV within single patients. By examining temporal changes in the genetic composition of the population, we estimate the effective recombination to be r=1.4e-5 recombinations per site and generation. Furthermore, we provide evidence that selection coefficients of at least 15% of the observed non-synonymous polymorphisms exceed 0.8% per generation. These results provide a basis for a more detailed understanding of the evolution of HIV. A particularly interesting case is evolution in response to drug treatment, where recombination can facilitate the rapid acquisition of multiple resistance mutations. With the methods developed here, more precise and more detailed studies will be possible, as soon as data with higher time resolution and greater sample sizes is available.Comment: to appear in PLoS Computational Biolog

The magic nature of 132Sn explored through the single-particle states of 133Sn

Atomic nuclei have a shell structure where nuclei with 'magic numbers' of neutrons and protons are analogous to the noble gases in atomic physics. Only ten nuclei with the standard magic numbers of both neutrons and protons have so far been observed. The nuclear shell model is founded on the precept that neutrons and protons can move as independent particles in orbitals with discrete quantum numbers, subject to a mean field generated by all the other nucleons. Knowledge of the properties of single-particle states outside nuclear shell closures in exotic nuclei is important for a fundamental understanding of nuclear structure and nucleosynthesis (for example the r-process, which is responsible for the production of about half of the heavy elements). However, as a result of their short lifetimes, there is a paucity of knowledge about the nature of single-particle states outside exotic doubly magic nuclei. Here we measure the single-particle character of the levels in 133Sn that lie outside the double shell closure present at the short-lived nucleus 132Sn. We use an inverse kinematics technique that involves the transfer of a single nucleon to the nucleus. The purity of the measured single-particle states clearly illustrates the magic nature of 132Sn.Comment: 19 pages, 5 figures and 4 table

Universal Predictions for Statistical Nuclear Correlations

We explore the behavior of collective nuclear excitations under a multi-parameter deformation of the Hamiltonian. The Hamiltonian matrix elements have the form $P(|H_{ij}|)\propto 1/\sqrt{|H_{ij}|}\exp(-|H_{ij}|/V)$, with a parametric correlation of the type $\log \langle H(x)H(y)\rangle\propto -|x-y|$. The studies are done in both the regular and chaotic regimes of the Hamiltonian. Model independent predictions for a wide variety of correlation functions and distributions which depend on wavefunctions and energies are found from parametric random matrix theory and are compared to the nuclear excitations. We find that our universal predictions are observed in the nuclear states. Being a multi-parameter theory, we consider general paths in parameter space and find that universality can be effected by the topology of the parameter space. Specifically, Berry's phase can modify short distance correlations, breaking certain universal predictions.Comment: Latex file + 12 postscript figure

Genetic Drift of HIV Populations in Culture

Populations of Human Immunodeficiency Virus type 1 (HIV-1) undergo a surprisingly large amount of genetic drift in infected patients despite very large population sizes, which are predicted to be mostly deterministic. Several models have been proposed to explain this phenomenon, but all of them implicitly assume that the process of virus replication itself does not contribute to genetic drift. We developed an assay to measure the amount of genetic drift for HIV populations replicating in cell culture. The assay relies on creation of HIV populations of known size and measurements of variation in frequency of a neutral allele. Using this assay, we show that HIV undergoes approximately ten times more genetic drift than would be expected from its population size, which we defined as the number of infected cells in the culture. We showed that a large portion of the increase in genetic drift is due to non-synchronous infection of target cells. When infections are synchronized, genetic drift for the virus is only 3-fold higher than expected from its population size. Thus, the stochastic nature of biological processes involved in viral replication contributes to increased genetic drift in HIV populations. We propose that appreciation of these effects will allow better understanding of the evolutionary forces acting on HIV in infected patients