Inference of Ancestral Recombination Graphs through Topological Data Analysis

The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Gal\'apagos Islands.Comment: 33 pages, 12 figures. The accompanying software, instructions and example files used in the manuscript can be obtained from https://github.com/RabadanLab/TARGe

Parallelization of a Monte Carlo Ray Tracing Algorithm for Channel Modelling in Underwater Wireless Optical Communications

AbstractIn this paper, an algorithm to calculate the underwater wireless optical impulse response is presented. It is based on a modified Monte Carlo Ray Tracing algorithm and takes into account the most significant phenomena of the underwater channel. In order to reduce the simulation time, two parallelization schemes are proposed, one based on a multiprocessor architecture and other based on the use of GPU (Graphics Processing Unit). Several simulation results are presented, including scenario channel simulations and calculation of time computation complexity for each algorithm implementation

Axion interpretation of the PVLAS data?

The PVLAS collaboration has recently reported the observation of a rotation of the polarization plane of light propagating through a transverse static magnetic field. Such an effect can arise from the production of a light, m_A ~ meV, pseudoscalar coupled to two photons with coupling strength g_{A\gamma} ~ 5x10^{-6} GeV^{-1}. Here, we review these experimental findings, discuss how astrophysical and helioscope bounds on this coupling can be evaded, and emphasize some experimental proposals to test the scenario.Comment: 4 pages, 1 figure, jpconf.cls, talk presented at the ninth International Conference on Topics in Astroparticle and Underground Physics, TAUP 2005, Zaragoza, Spain, September 10-14, 200

Unitarity, quasi-normal modes and the AdS_3/CFT_2 correspondence

In general, black-hole perturbations are governed by a discrete spectrum of complex eigen-frequencies (quasi-normal modes). This signals the breakdown of unitarity. In asymptotically AdS spaces, this is puzzling because the corresponding CFT is unitary. To address this issue in three dimensions, we replace the BTZ black hole by a wormhole, following a suggestion by Solodukhin [hep-th/0406130]. We solve the wave equation for a massive scalar field and find an equation for the poles of the propagator. This equation yields a rich spectrum of {\em real} eigen-frequencies. We show that the throat of the wormhole is $o(e^{-1/G})$, where $G$ is Newton's constant. Thus, the quantum effects which might produce the wormhole are non-perturbative.Comment: 9 page

Signs of the 2009 Influenza Pandemic in the New York-Presbyterian Hospital Electronic Health Records

Background In June of 2009, the World Health Organization declared the first influenza pandemic of the 21st century, and by July, New York City's New York-Presbyterian Hospital (NYPH) experienced a heavy burden of cases, attributable to a novel strain of the virus (H1N1pdm). Methods and Results We present the signs in the NYPH electronic health records (EHR) that distinguished the 2009 pandemic from previous seasonal influenza outbreaks via various statistical analyses. These signs include (1) an increase in the number of patients diagnosed with influenza, (2) a preponderance of influenza diagnoses outside of the normal flu season, and (3) marked vaccine failure. The NYPH EHR also reveals distinct age distributions of patients affected by seasonal influenza and the pandemic strain, and via available longitudinal data, suggests that the two may be associated with distinct sets of comorbid conditions as well. In particular, we find significantly more pandemic flu patients with diagnoses associated with asthma and underlying lung disease. We further observe that the NYPH EHR is capable of tracking diseases at a resolution as high as particular zip codes in New York City. Conclusion The NYPH EHR permits early detection of pandemic influenza and hypothesis generation via identification of those significantly associated illnesses. As data standards develop and databases expand, EHRs will contribute more and more to disease detection and the discovery of novel disease associations

Gravitational Approach to Tachyon Matter

We found a gravity solution of p+1 dimensional extended object with SO(p)xSO(9-p) symmetry which has zero pressure and zero dilaton charge. We expect that this object is a residual tachyon dust after tachyon condensation of brane and anti-brane system discussed by Sen, recently. We also discuss the Hawking temperature and some properties of this object.Comment: 14 pages, LaTeX, reference added and typos correcte