Abstract:
Mammals have a large cohort of endo- and ecto- symbiotic microorganisms (the microbiome) that potentially influence host phenotypes. There have been numerous exploratory studies of these symbiotic organisms in humans and other animals, often with the aim of relating the microbiome to a complex phenotype such as body mass index (BMI) or disease state. Here, we describe an efficient methodology for predicting complex traits from quantitative microbiome profiles. The method was demonstrated by predicting inflammatory bowel disease (IBD) status and BMI from human microbiome data, and enteric greenhouse gas production from dairy cattle rumen microbiome profiles. The method uses unassembled massively parallel sequencing (MPS) data to form metagenomic relationship matrices (analogous to genomic relationship matrices used in genomic predictions) to predict IBD, BMI and methane production phenotypes with useful accuracies (r = 0.423, 0.422 and 0.466 respectively). Our results show that microbiome profiles derived from MPS can be used to predict complex phenotypes of the host. Although the number of biological replicates used here limits the accuracy that can be achieved, preliminary results suggest this approach may surpass current prediction accuracies that are based on the host genome. This is especially likely for traits that are largely influenced by the gut microbiota, for example digestive tract disorders or metabolic functions such as enteric methane production in cattle.

Abstract:
Rather than focusing on individual organisms within the rumen, our method used MPS data to generate quantitative rumen micro-biome profiles, regardless of taxonomic classifications. The method requires a previously assembled reference metagenome. A number of such reference metagenomes were considered, including two rumen derived metagenomes, a human faecal microflora metagenome and a reference metagenome made up of publically available prokaryote sequences. Sequence reads from each test sample were aligned to these references. The “rumen metagenome profile” was generated from the number of the reads that aligned to each contig in the database. We used this method to test the hypothesis that rumen fluid microbial community profiles vary more between cows than within multiple samples from the same cow. Rumen fluid samples were taken from three cows, at three locations within the rumen. DNA from the samples was sequenced on the Illumina GAIIx. When the reads were aligned to a rumen metagenome reference, the rumen metagenome profiles were repeatable (P？<？0.00001) by cow regardless of location of sampling rumen fluid. The repeatability was estimated at 9%, albeit with a high standard error, reflecting the small number of animals in the study. Finally, we compared rumen microbial profiles to faecal microbial profiles. Our hypothesis, that there would be a stronger correlation between faeces and rumen fluid from the same cow than between faeces and rumen fluid from different cows, was not supported by our data (with much greater significance of rumen versus faeces effect than animal effect in mixed linear model).We have presented a simple and high throughput method of metagenome profiling to assess the similarity of whole metagenomes, and illustrated its use on two novel datasets. This method utilises widely used freeware. The method should be useful in the exploration and comparison of metagenomes.

Abstract:
Photoassociation (PA) of ultracold metastable helium to the 2s2p manifold is theoretically investigated using a non-perturbative close-coupled treatment in which the laser coupling is evaluated without assuming the dipole approximation. The results are compared with our previous study [Cocks and Whittingham, Phys. Rev. A 80, 023417 (2009)] that makes use of the dipole approximation. The approximation is found to strongly affect the PA spectra because the photoassociated levels are weakly bound, and a similar impact is predicted to occur in other systems of a weakly bound nature. The inclusion or not of the approximation does not affect the resonance positions or widths, however significant differences are observed in the background of the spectra and the maximum laser intensity at which resonances are discernable. Couplings not satisfying the dipole selection rule |J-1| <= J' <= |J+1| do not lead to observable resonances.

Abstract:
Photoassociation of spin-polarized metastable helium to the three lowest rovibrational levels of the J=1, $0_u^+$ state asymptoting to 2$s {}^{3}$S$_{1}+2p {}^{3}$P$_{0}$ is studied using a second-order perturbative treatment of the line shifts valid for low laser intensities, and two variants of a non-perturbative close-coupled treatment, one based upon dressed states of the matter plus laser system, and the other on a modified radiative coupling which vanishes asymptotically, thus simulating experimental conditions. These non-perturbative treatments are valid for arbitrary laser intensities and yield the complete photoassociation resonance profile. Both variants give nearly identical results for the line shifts and widths of the resonances and show that their dependence upon laser intensity is very close to linear and quadratic respectively for the two lowest levels. The resonance profiles are superimposed upon a significant background loss, a feature for this metastable helium system not present in studies of photoassociation in other systems, which is due to the very shallow nature of the excited state $0_u^+$ potential. The results for the line shifts from the close-coupled and perturbative calculations agree very closely at low laser intensities.

Abstract:
The effects of non-adiabatic and Coriolis couplings on the bound states of the He(2 ^3S_1)+He(2 ^3P_j) system, where j=0,1,2, are investigated using the recently available ab initio short-range $^{1,3,5}\Sigma^+_{g,u}$ and $^{1,3,5}\Pi_{g,u}$ potentials computed by Deguilhem et al. (J. Phys. B: At. Mol. Opt. Phys. 42 (2009) 015102). Three sets of calculations have been undertaken: single-channel, multichannel without Coriolis couplings and full multichannel with Coriolis couplings. We find that non-adiabatic effects are negligible for $0^-_u,0^{\pm}_g,1_u,2_g,2_u,3_g$ Hund case (c) sets of levels in the j=2 asymptote but can be up to 15% for some of the $0^+_u$ and $1_g$ sets of levels where near degeneracies are present in the single-channel diagonalized potentials. Coriolis couplings are most significant for weakly bound levels, ranging from 1-5% for total angular momenta J=1,2 and up to 10% for J=3. Levels near the j=1 and j=0 asymptotes agree closely with previous multichannel calculations based upon long-range potentials constructed from retarded resonance dipole and dispersion interactions. Assignment of theoretical levels to experimental observations using criteria based upon the short-range character of each level and their coupling to metastable ground states produces well matched assignments for the majority of observations. After a 1% increase in the slope of the $^5\Sigma^+_{g,u}$ and $^5\Pi_{g,u}$ input potentials near the classical turning point is applied, improved matching of previous assignments is obtained and further assignments can be made, reproducing very closely the number of experimental observations.

Abstract:
Long-range bound states of the excited heteronuclear 3He*--4He* system that dissociate to either 3He(1s2s 3S_1) + 4He(1s2p 3P_j) or 3He(1s2p 3P_j) + 4He(1s2s 3S_1), where j=0, 1, 2, are investigated using both single-channel and multichannel calculations in order to analyse the effects of Coriolis and non-adiabatic couplings. The multichannel calculations predict two groups of resonances above the lowest asymptotic energy. One of these groups dissociates to an atomic pair with the 2p excitation on the fermionic atom and the other dissociates to two asymptotes which correspond to the 2p excitation on either atom. Many of these resonances could be identified with levels in the single-channel calculation although the differences in energies were large. The total parity was found to have a significant influence on the ability to make these identifications. No purely bound states were found, although several resonances with line widths smaller than 1 MHz were obtained.

Abstract:
The bound states of the fermionic ^3He(2 ^3S_1)+ ^3He(2 ^3P_j)system, where j=0,1,2, are investigated using the recently available ab initio short-range ${}^{1,3,5}\Sigma^{+}_{g,u}$ and ${}^{1,3,5}\Pi_{g,u}$ potentials computed by Deguilhem et al. (J. Phys. B: At. Mol. Opt. Phys., 2009, 42, 015102). Single-channel and multichannel calculations have been undertaken in order to investigate the effects of Coriolis and non-adiabatic couplings. The possible experimental observability of the theoretical levels is assessed using criteria based upon the short-range character of each level and their coupling to metastable ground states. Purely long-range levels have been identified and 30 short-range levels near five asymptotes are suggested for experimental investigation.

Abstract:
The transport of excess electrons in liquid argon driven out of equilibrium by an applied electric field is revisited using a multi-term solution of Boltzmann's equation together with ab initio liquid phase cross-sections calculated using the Dirac-Fock scattering equations. The calculation of liquid phase cross-sections extends previous treatments to consider multipole polarisabilities and a non-local treatment of exchange while the accuracy of the electron-argon potential is validated through comparison of the calculated gas phase cross-section with experiment. The results presented highlight the inadequacy of local treatments of exchange that are commonly used in liquid and cluster phase cross-section calculations. The multi-term Boltzmann equation framework accounting for coherent scattering enables the inclusion of the full anisotropy in the differential cross-section arising from the interaction and the structure factor, without an a priori assumption of quasi-isotropy in the velocity distribution function. The model, which contains no free parameters and accounts for both coherent scattering and liquid phase screening effects, was found to reproduce well the experimental drift velocities and characteristic energies.

Abstract:
We generalize a simple Monte Carlo (MC) model for dilute gases to consider the transport behavior of positrons and electrons in Percus-Yevick model liquids under highly non-equilibrium conditions, accounting rigorously for coherent scattering processes. The procedure extends an existing technique [Wojcik and Tachiya, Chem. Phys. Lett. 363, 3--4 (1992)], using the static structure factor to account for the altered anisotropy of coherent scattering in structured material. We identify the effects of the approximation used in the original method, and develop a modified method that does not require that approximation. We also present an enhanced MC technique that has been designed to improve the accuracy and flexibility of simulations in spatially-varying electric fields. All of the results are found to be in excellent agreement with an independent multi-term Boltzmann equation solution, providing benchmarks for future transport models in liquids and structured systems.