Inference of Temporally Varying Bayesian Networks

When analysing gene expression time series data an often overlooked but crucial aspect of the model is that the regulatory network structure may change over time. Whilst some approaches have addressed this problem previously in the literature, many are not well suited to the sequential nature of the data. Here we present a method that allows us to infer regulatory network structures that may vary between time points, utilising a set of hidden states that describe the network structure at a given time point. To model the distribution of the hidden states we have applied the Hierarchical Dirichlet Process Hideen Markov Model, a nonparametric extension of the traditional Hidden Markov Model, that does not require us to fix the number of hidden states in advance. We apply our method to exisiting microarray expression data as well as demonstrating is efficacy on simulated test data

Regulation and Identity of Florigen: Flowering Locus T Moves Center Stage

The transition from vegetative to reproductive growth is controlled by day length in many plant species. Day length is perceived in leaves and induces a systemic signal, called florigen, that moves through the phloem to the shoot apex. At the shoot apical meristem (SAM), florigen causes changes in gene expression that reprogram the SAM to form flowers instead of leaves. Analysis of flowering of Arabidopsis thaliana placed the CONSTANS/FLOWERING LOCUS T (CO/FT) module at the core of a pathway that promotes flowering in response to changes in day length. We describe progress in defining the molecular mechanisms that activate this module in response to changing day length and the increasing evidence that FT protein is a major component of florigen. Finally, we discuss conservation of FT function in other species and how variation in its regulation could generate different flowering behaviors

The Influence of in-medium NN cross-sections, symmetry potential and impact parameter on the isospin observables

We explore the influence of in-medium nucleon-nucleon cross section, symmetry potential and impact parameter on isospin sensitive observables in intermediate-energy heavy-ion collisions with the ImQMD05 code, a modified version of Quantum Molecular Dynamics model. At incident velocities above the Fermi velocity, we find that the density dependence of symmetry potential plays a more important role on the double neutron to proton ratio $DR(n/p)$ and the isospin transport ratio $R_i$ than the in-medium nucleon-nucleon cross sections, provided that the latter are constrained to a fixed total NN collision rate. We also explore both $DR(n/p)$ and $R_i$ as a function of the impact parameter. Since the copious production of intermediate mass fragments is a distinguishing feature of intermediate-energy heavy-ion collisions, we examine the isospin transport ratios constructed from different groups of fragments. We find that the values of the isospin transport ratios for projectile rapidity fragments with $Z\ge20$ are greater than those constructed from the entire projectile rapidity source. We believe experimental investigations of this phenomenon can be performed. These may provide significant tests of fragmentation time scales predicted by ImQMD calculations.Comment: 24 pages, 9 figures, to be published in Phys. Rev.

Investigations of three, four, and five-particle exit channels of levels in light nuclei created using a 9C beam

The interactions of a E/A=70-MeV 9C beam with a Be target was used to populate levels in Be, B, and C isotopes which undergo decay into many-particle exit channels. The decay products were detected in the HiRA array and the level energies were identified from their invariant mass. Correlations between the decay products were examined to deduce the nature of the decays, specifically to what extent all the fragments were created in one prompt step or whether the disintegration proceeded in a sequential fashion through long-lived intermediate states. In the latter case, information on the spin of the level was also obtained. Of particular interest is the 5-body decay of the 8C ground state which was found to disintegrate in two steps of two-proton decay passing through the 6Beg.s. intermediate state. The isobaric analog of 8Cg.s. in 8B was also found to undergo two-proton decay to the isobaric analog of 6Beg.s. in 6Li. A 9.69-MeV state in 10C was found to undergo prompt 4-body decay to the 2p+2alpha exit channel. The two protons were found to have a strong enhancementin the diproton region and the relative energies of all four p-alpha pairs were consistent with the 5Lig.s. resonance

Correlations in intermediate-energy two-proton removal reactions

We report final-state-exclusive measurements of the light charged fragments in coincidence with 26Ne residual nuclei following the direct two-proton removal from a neutron-rich 28Mg secondary beam. A Dalitz-plot analysis and comparisons with simulations show that a majority of the triple- coincidence events with two protons display phase-space correlations consistent with the (two-body) kinematics of a spatially-correlated pair-removal mechanism. The fraction of such correlated events, 56(12) %, is consistent with the fraction of the calculated cross section, 64 %, arising from spin S = 0 two-proton configurations in the entrance-channel (shell-model) 28Mg ground state wave function. This result promises access to an additional and more specific probe of the spin and spatial correlations of valence nucleon pairs in exotic nuclei produced as fast secondary beams.Comment: accepted for publication in Physical Review Letter

Angular Dependence in Proton-Proton Correlation Functions in Central 40Ca+40Ca^{40}Ca+^{40}Ca and 48Ca+48Ca^{48}Ca+^{48}Ca Reactions

The angular dependence of proton-proton correlation functions is studied in central $^{40}Ca+^{40}Ca$ and $^{48}Ca+^{48}Ca$ nuclear reactions at E=80 MeV/A. Measurements were performed with the HiRA detector complemented by the 4$\pi$ Array at NSCL. A striking angular dependence in the laboratory frame is found within p-p correlation functions for both systems that greatly exceeds the measured and expected isospin dependent difference between the neutron-rich and neutron-deficient systems. Sources measured at backward angles reflect the participant zone of the reaction, while much larger sources observed at forward angles reflect the expanding, fragmenting and evaporating projectile remnants. The decrease of the size of the source with increasing momentum is observed at backward angles while a weaker trend in the opposite direction is observed at forward angles. The results are compared to the theoretical calculations using the BUU transport model.Comment: 8 pages, 3 figures, submitted to PR