Integrative Model-based clustering of microarray methylation and expression data

In many fields, researchers are interested in large and complex biological processes. Two important examples are gene expression and DNA methylation in genetics. One key problem is to identify aberrant patterns of these processes and discover biologically distinct groups. In this article we develop a model-based method for clustering such data. The basis of our method involves the construction of a likelihood for any given partition of the subjects. We introduce cluster specific latent indicators that, along with some standard assumptions, impose a specific mixture distribution on each cluster. Estimation is carried out using the EM algorithm. The methods extend naturally to multiple data types of a similar nature, which leads to an integrated analysis over multiple data platforms, resulting in higher discriminating power.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS533 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Evidence of Reduced Global Processing in Autism Spectrum Disorder

Frith’s original notion of ‘weak central coherence’ suggested that increased local processing in autism spectrum disorder (ASD) resulted from reduced global processing. More recent accounts have emphasised superior local perception and suggested intact global integration. However, tasks often place local and global processing in direct trade-off, making it difficult to determine whether group differences reflect reduced global processing, increased local processing, or both. We present two measures of global integration in which poor performance could not reflect increased local processing. ASD participants were slower to identify fragmented figures and less sensitive to global geometric impossibility than IQ-matched controls. These findings suggest that reduced global integration comprises one important facet of weak central coherence in ASD

Is U3Ni3Sn4 best described as near a quantum critical point?

Although most known non-Fermi liquid (NFL) materials are structurally or chemically disordered, the role of this disorder remains unclear. In particular, very few systems have been discovered that may be stoichiometric and well ordered. To test whether U3Ni3Sn4 belongs in this latter class, we present measurements of the x-ray absorption fine structure (XAFS) of polycrystalline and single-crystal U3Ni3Sn4 samples that are consistent with no measurable local structural disorder. We also present temperature-dependent specific heat data in applied magnetic fields as high as 8 T that show features that are inconsistent with the antiferromagnetic Griffiths' phase model, but do support the conclusion that a Fermi liquid/NFL crossover temperature increases with applied field. These results are inconsistent with theoretical explanations that require strong disorder effects, but do support the view that U3Ni3Sn4 is a stoichiometric, ordered material that exhibits NFL behavior, and is best described as being near an antiferromagnetic quantum critical point.Comment: 9 pages, 8 figures, in press with PR

Quantifying structural damage from self-irradiation in a plutonium superconductor

The 18.5 K superconductor PuCoGa5 has many unusual properties, including those due to damage induced by self-irradiation. The superconducting transition temperature decreases sharply with time, suggesting a radiation-induced Frenkel defect concentration much larger than predicted by current radiation damage theories. Extended x-ray absorption fine-structure measurements demonstrate that while the local crystal structure in fresh material is well ordered, aged material is disordered much more strongly than expected from simple defects, consistent with strong disorder throughout the damage cascade region. These data highlight the potential impact of local lattice distortions relative to defects on the properties of irradiated materials and underscore the need for more atomic-resolution structural comparisons between radiation damage experiments and theory.Comment: 7 pages, 5 figures, to be published in PR

Monte Carlo Determination of Multiple Extremal Eigenpairs

We present a Monte Carlo algorithm that allows the simultaneous determination of a few extremal eigenpairs of a very large matrix without the need to compute the inner product of two vectors or store all the components of any one vector. The new algorithm, a Monte Carlo implementation of a deterministic one we recently benchmarked, is an extension of the power method. In the implementation presented, we used a basic Monte Carlo splitting and termination method called the comb, incorporated the weight cancellation method of Arnow {\it et al.}, and exploited a new sampling method, the sewing method, that does a large state space sampling as a succession of small state space samplings. We illustrate the effectiveness of the algorithm by its determination of the two largest eigenvalues of the transfer matrices for variously-sized two-dimensional, zero field Ising models. While very likely useful for other transfer matrix problems, the algorithm is however quite general and should find application to a larger variety of problems requiring a few dominant eigenvalues of a matrix.Comment: 22 pages, no figure

Horizon energy and angular momentum from a Hamiltonian perspective

Classical black holes and event horizons are highly non-local objects, defined in terms of the causal past of future null infinity. Alternative, (quasi)local definitions are often used in mathematical, quantum, and numerical relativity. These include apparent, trapping, isolated, and dynamical horizons, all of which are closely associated to two-surfaces of zero outward null expansion. In this paper we show that three-surfaces which can be foliated with such two-surfaces are suitable boundaries in both a quasilocal action and a phase space formulation of general relativity. The resulting formalism provides expressions for the quasilocal energy and angular momentum associated with the horizon. The values of the energy and angular momentum are in agreement with those derived from the isolated and dynamical horizon frameworks.Comment: 39 pages, 3 figures, Final Version : content essentially unchanged but many small improvements made in response to referees, a few references adde

Probing 5f-state configurations in URu2Si2 with U L3-edge resonant x-ray emission spectroscopy

Resonant x-ray emission spectroscopy (RXES) was employed at the U L3 absorption edge and the La1 emission line to explore the 5f occupancy, nf, and the degree of 5f orbital delocalization in the hidden order compound URu2Si2. By comparing to suitable reference materials such as UF4, UCd11, and alpha-U, we conclude that the 5f orbital in URu2Si2 is at least partially delocalized with nf = 2.87 +/- 0.08, and does not change with temperature down to 10 K within the estimated error. These results place further constraints on theoretical explanations of the hidden order, especially those requiring a localized f2 ground state.Comment: 11 pages,7 figure

Quasinormal modes for the charged Vaidya metric

The scalar wave equation is considered in the background of a charged Vaidya metric in double null coordinates $(u,v)$ describing a non-stationary charged black hole with varying mass $m(v)$ and charge $q(v)$. The resulting time-dependent quasinormal modes are presented and analyzed. We show, in particular, that it is possible to identify some signatures in the quasinormal frequencies from the creation of a naked singularity.Comment: 4 pages. Prepared for the proceedings of the Spanish Relativity meeting (ERE2010), Granada, Spain, September 6-10, 201