Z_N x Z_M orientifolds with and without discrete torsion

We discuss compact four-dimensional Z_N x Z_M type IIB orientifolds. We take a systematic approach to classify the possible models and construct them explicitely. The supersymmetric orientifolds of this type have already been constructed some time ago. We find that there exist several consistent orientifolds for each of the discrete groups Z_2 x Z_2, Z_2 x Z_4, Z_4 x Z_4, Z_2 x Z_6, Z_2 x Z_6' and Z_6 x Z_6 if anti-D5-branes are introduced. Supersymmetry is broken by the open strings ending on antibranes. The rank of the gauge group is reduced by a factor two if the underlying orbifold space has discrete torsion.Comment: Latex, 61 page

Photon Regeneration from Pseudoscalars at X-ray Laser Facilities

Recently, the PVLAS collaboration has reported an anomalously large rotation of the polarization of light in the presence of a magnetic field. As a possible explanation they consider the existence of a light pseudoscalar particle coupled to two photons. In this note, we propose a method of independently testing this result by using a high-energy photon regeneration experiment (the X-ray analogue of "invisible light shining through walls") using the synchrotron X-rays from a free-electron laser (FEL). With such an experiment the region of parameter space implied by PVLAS could be probed in a matter of minutes.Comment: 3 pages, 2 figure

Evolution of the Influenza A Virus: Some New Advances

Influenza is an RNA virus that causes mild to severe respiratory symptoms in humans and other hosts. Every year approximately half a million people around the world die from seasonal Influenza. But this number is substantially larger in the case of pandemics, with the most dramatic instance being the 1918 “Spanish flu” that killed more than 50 million people worldwide. In the last few years, thousands of Influenza genomic sequences have become publicly available, including the 1918 pandemic strain and many isolates from non-human hosts. Using these data and developing adequate bioinformatic and statistical tools, some of the major questions surrounding Influenza evolution are becoming tractable. Are the mutations and reassortments random? What are the patterns behind the virus’s evolution? What are the necessary and sufficient conditions for a virus adapted to one host to infect a different host? Why is Influenza seasonal? In this review, we summarize some of the recent progress in understanding the evolution of the virus

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