Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with arXiv:1103.434

Bounds on OPE coefficients in 4D Conformal Field Theories

We numerically study the crossing symmetry constraints in 4D CFTs, using previously introduced algorithms based on semidefinite programming. We study bounds on OPE coefficients of tensor operators as a function of their scaling dimension and extend previous studies of bounds on OPE coefficients of conserved vector currents to the product groups SO(N) 7SO(M). We also analyze the bounds on the OPE coefficients of the conserved vector currents associated with the groups SO(N), SU(N) and SO(N) 7SO(M) under the assumption that in the singlet channel no scalar operator has dimension less than four, namely that the CFT has no relevant deformations. This is motivated by applications in the context of composite Higgs models, where the strongly coupled sector is assumed to be a spontaneously broken CFT with a global symmetry. \ua9 The Authors

The effective bootstrap

We study the numerical bounds obtained using a conformal-bootstrap method - advocated in ref. [1] but never implemented so far - where different points in the plane of conformal cross ratios z and z¯ are sampled. In contrast to the most used method based on derivatives evaluated at the symmetric point z=z¯=1/2, we can consistently "integrate out" higher-dimensional operators and get a reduced simpler, and faster to solve, set of bootstrap equations. We test this "effective" bootstrap by studying the 3D Ising and O(n) vector models and bounds on generic 4D CFTs, for which extensive results are already available in the literature. We also determine the scaling dimensions of certain scalar operators in the O(n) vector models, with n=2,3,4, which have not yet been computed using bootstrap techniques. ArXI

HIV-associated neurocognitive disorders in sub-Saharan Africa: a pilot study in Cameroon

<p>Abstract</p> <p>Background</p> <p>The disease burden of human immunodeficiency virus (HIV) - acquired immunodeficiency syndrome (AIDS) is highest in sub-Saharan Africa but there are few studies on the associated neurocognitive disorders in this region. The objectives of this study were to determine whether Western neuropsychological (NP) methods are appropriate for use in Cameroon, and to evaluate cognitive function in a sample of HIV-infected adults.</p> <p>Methods</p> <p>We used a battery of 19 NP measures in a cross-sectional study with 44 HIV+ adults and 44 demographically matched HIV- controls, to explore the validity of these NP measures in Cameroon, and evaluate the effect of viral infection on seven cognitive ability domains.</p> <p>Results</p> <p>In this pilot study, the global mean z-score on the NP battery showed worse overall cognition in the HIV+ individuals. Significantly lower performance was seen in the HIV+ sample on tests of executive function, speed of information processing, working memory, and psychomotor speed. HIV+ participants with AIDS performed worse than those with less advanced HIV disease.</p> <p>Conclusions</p> <p>Similar to findings in Western cohorts, our results in Cameroon suggest that HIV infection, particularly in advanced stages, is associated with worse performance on standardized, Western neurocognitive tests. The tests used here appear to be promising for studying NeuroAIDS in sub-Saharan Africa.</p

Populations of planets in multiple star systems

Astronomers have discovered that both planets and binaries are abundant throughout the Galaxy. In combination, we know of over 100 planets in binary and higher-order multi-star systems, in both circumbinary and circumstellar configurations. In this chapter we review these findings and some of their implications for the formation of both stars and planets. Most of the planets found have been circumstellar, where there is seemingly a ruinous influence of the second star if sufficiently close (<50 AU). Hosts of hot Jupiters have been a particularly popular target for binary star studies, showing an enhanced rate of stellar multiplicity for moderately wide binaries (>100 AU). This was thought to be a sign of Kozai-Lidov migration, however recent studies have shown this mechanism to be too inefficient to account for the majority of hot Jupiters. A couple of dozen circumbinary planets have been proposed around both main sequence and evolved binaries. Around main sequence binaries there are preliminary indications that the frequency of gas giants is as high as those around single stars. There is however a conspicuous absence of circumbinary planets around the tightest main sequence binaries with periods of just a few days, suggesting a unique, more disruptive formation history of such close stellar pairs.Comment: Invited review chapter, accepted for publication in "Handbook of Exoplanets", ed. H. Deeg & J. A. Belmont