Finite mixtures of matrix-variate Poisson-log normal distributions for three-way count data

Three-way data structures, characterized by three entities, the units, the variables and the occasions, are frequent in biological studies. In RNA sequencing, three-way data structures are obtained when high-throughput transcriptome sequencing data are collected for n genes across p conditions at r occasions. Matrix-variate distributions offer a natural way to model three-way data and mixtures of matrix-variate distributions can be used to cluster three-way data. Clustering of gene expression data is carried out as means to discovering gene co-expression networks. In this work, a mixture of matrix-variate Poisson-log normal distributions is proposed for clustering read counts from RNA sequencing. By considering the matrix-variate structure, full information on the conditions and occasions of the RNA sequencing dataset is simultaneously considered, and the number of covariance parameters to be estimated is reduced. A Markov chain Monte Carlo expectation-maximization algorithm is used for parameter estimation and information criteria are used for model selection. The models are applied to both real and simulated data, giving favourable clustering results

Non-Relativistic Gravitation: From Newton to Einstein and Back

We present an improvement to the Classical Effective Theory approach to the non-relativistic or Post-Newtonian approximation of General Relativity. The "potential metric field" is decomposed through a temporal Kaluza-Klein ansatz into three NRG-fields: a scalar identified with the Newtonian potential, a 3-vector corresponding to the gravito-magnetic vector potential and a 3-tensor. The derivation of the Einstein-Infeld-Hoffmann Lagrangian simplifies such that each term corresponds to a single Feynman diagram providing a clear physical interpretation. Spin interactions are dominated by the exchange of the gravito-magnetic field. Leading correction diagrams corresponding to the 3PN correction to the spin-spin interaction and the 2.5PN correction to the spin-orbit interaction are presented.Comment: 10 pages, 3 figures. v2: published version. v3: Added a computation of Einstein-Infeld-Hoffmann in higher dimensions within our improved ClEFT which partially confirms and partially corrects a previous computation. See notes added at end of introductio

Gene expression during preimplantation mouse development

To develop a resource for the identification and isolation of genes expressed in the early mammalian embryo, large and representative cDNA libraries were constructed from unfertilized eggs, and two-cell, eight-cell, and blastocyst-stage mouse embryos. Using these libraries, we now report the first stages at which the cytokines interleukin (IL)-6, IL-1 beta, and interferon (IFN)-gamma are transcribed in the developing embryo and the presence of IL-7 transcripts in the unfertilized egg. Transcripts for IL-1 alpha, -2, -3, -4, or -5 were not detected at these stages. To identify novel genes expressed on activation of the embryonic genome, the egg and eight-cell stage-specific cDNA libraries were subtracted from the two-cell library, yielding a specialized cDNA library enriched for transcripts expressed at the two-cell stage. Sequence and Southern blot analysis of several of these cDNAs expressed predominantly at the two-cell stage of embryogenesis revealed them to be from novel genes, thereby providing the first molecular tools with which to approach the study of gene expression in the early mammalian embryo

High Energy Field Theory in Truncated AdS Backgrounds

In this letter we show that, in five-dimensional anti-deSitter space (AdS) truncated by boundary branes, effective field theory techniques are reliable at high energy (much higher than the scale suggested by the Kaluza-Klein mass gap), provided one computes suitable observables. We argue that in the model of Randall and Sundrum for generating the weak scale from the AdS warp factor, the high energy behavior of gauge fields can be calculated in a {\em cutoff independent manner}, provided one restricts Green's functions to external points on the Planck brane. Using the AdS/CFT correspondence, we calculate the one-loop correction to the Planck brane gauge propagator due to charged bulk fields. These effects give rise to non-universal logarithmic energy dependence for a range of scales above the Kaluza-Klein gap.Comment: LaTeX, 7 pages; minor typos fixe

Finite Mixtures of Multivariate Poisson-Log Normal Factor Analyzers for Clustering Count Data

A mixture of multivariate Poisson-log normal factor analyzers is introduced by imposing constraints on the covariance matrix, which resulted in flexible models for clustering purposes. In particular, a class of eight parsimonious mixture models based on the mixtures of factor analyzers model are introduced. Variational Gaussian approximation is used for parameter estimation, and information criteria are used for model selection. The proposed models are explored in the context of clustering discrete data arising from RNA sequencing studies. Using real and simulated data, the models are shown to give favourable clustering performance. The GitHub R package for this work is available at https://github.com/anjalisilva/mixMPLNFA and is released under the open-source MIT license.Comment: 29 pages, 2 figure

Next to leading order spin-orbit effects in the motion of inspiralling compact binaries

Using effective field theory (EFT) techniques we calculate the next-to-leading order (NLO) spin-orbit contributions to the gravitational potential of inspiralling compact binaries. We use the covariant spin supplementarity condition (SSC), and explicitly prove the equivalence with previous results by Faye et al. in arXiv:gr-qc/0605139. We also show that the direct application of the Newton-Wigner SSC at the level of the action leads to the correct dynamics using a canonical (Dirac) algebra. This paper then completes the calculation of the necessary spin dynamics within the EFT formalism that will be used in a separate paper to compute the spin contributions to the energy flux and phase evolution to NLO.Comment: 25 pages, 4 figures, revtex4. v2: minor changes, refs. added. To appear in Class. Quant. Gra

Finite size corrections to the radiation reaction force in classical electrodynamics

We introduce an effective field theory approach that describes the motion of finite size objects under the influence of electromagnetic fields. We prove that leading order effects due to the finite radius $R$ of a spherically symmetric charge is order $R^2$ rather than order $R$ in any physical model, as widely claimed in the literature. This scaling arises as a consequence of Poincar\'e and gauge symmetries, which can be shown to exclude linear corrections. We use the formalism to calculate the leading order finite size correction to the Abraham-Lorentz-Dirac force.Comment: 4 pages, 2 figure

Precision Measurements of Stretching and Compression in Fluid Mixing

The mixing of an impurity into a flowing fluid is an important process in many areas of science, including geophysical processes, chemical reactors, and microfluidic devices. In some cases, for example periodic flows, the concepts of nonlinear dynamics provide a deep theoretical basis for understanding mixing. Unfortunately, the building blocks of this theory, i.e. the fixed points and invariant manifolds of the associated Poincare map, have remained inaccessible to direct experimental study, thus limiting the insight that could be obtained. Using precision measurements of tracer particle trajectories in a two-dimensional fluid flow producing chaotic mixing, we directly measure the time-dependent stretching and compression fields. These quantities, previously available only numerically, attain local maxima along lines coinciding with the stable and unstable manifolds, thus revealing the dynamical structures that control mixing. Contours or level sets of a passive impurity field are found to be aligned parallel to the lines of large compression (unstable manifolds) at each instant. This connection appears to persist as the onset of turbulence is approached.Comment: 5 pages, 5 figure