Accurate reconstruction of viral quasispecies spectra through improved estimation of strain richness

Background Estimating the number of different species (richness) in a mixed microbial population has been a main focus in metagenomic research. Existing methods of species richness estimation ride on the assumption that the reads in each assembled contig correspond to only one of the microbial genomes in the population. This assumption and the underlying probabilistic formulations of existing methods are not useful for quasispecies populations where the strains are highly genetically related. The lack of knowledge on the number of different strains in a quasispecies population is observed to hinder the precision of existing Viral Quasispecies Spectrum Reconstruction (QSR) methods due to the uncontrolled reconstruction of a large number of in silico false positives. In this work, we formulated a novel probabilistic method for strain richness estimation specifically targeting viral quasispecies. By using this approach we improved our recently proposed spectrum reconstruction pipeline ViQuaS to achieve higher levels of precision in reconstructed quasispecies spectra without compromising the recall rates. We also discuss how one other existing popular QSR method named ShoRAH can be improved using this new approach. Results On benchmark data sets, our estimation method provided accurate richness estimates (< 0.2 median estimation error) and improved the precision of ViQuaS by 2%-13% and F-score by 1%-9% without compromising the recall rates. We also demonstrate that our estimation method can be used to improve the precision and F-score of ShoRAH by 0%-7% and 0%-5% respectively. Conclusions The proposed probabilistic estimation method can be used to estimate the richness of viral populations with a quasispecies behavior and to improve the accuracy of the quasispecies spectra reconstructed by the existing methods ViQuaS and ShoRAH in the presence of a moderate level of technical sequencing errors

The fine-tuning price of the early LHC

LHC already probed and excluded half of the parameter space of the Constrained Minimal Supersymmetric Standard Model allowed by previous experiments. Only about 0.3% of the CMSSM parameter space survives. This fraction rises to about 0.9% if the bound on the Higgs mass can be circumvented.Comment: 7 pages. v3: updated with new bounds from ATLAS and CMS at 1.1/fb presented at the EPS-HEP-2011 conferenc

A Geometric Approach to CP Violation: Applications to the MCPMFV SUSY Model

We analyze the constraints imposed by experimental upper limits on electric dipole moments (EDMs) within the Maximally CP- and Minimally Flavour-Violating (MCPMFV) version of the MSSM. Since the MCPMFV scenario has 6 non-standard CP-violating phases, in addition to the CP-odd QCD vacuum phase \theta_QCD, cancellations may occur among the CP-violating contributions to the three measured EDMs, those of the Thallium, neutron and Mercury, leaving open the possibility of relatively large values of the other CP-violating observables. We develop a novel geometric method that uses the small-phase approximation as a starting point, takes the existing EDM constraints into account, and enables us to find maximal values of other CP-violating observables, such as the EDMs of the Deuteron and muon, the CP-violating asymmetry in b --> s \gamma decay, and the B_s mixing phase. We apply this geometric method to provide upper limits on these observables within specific benchmark supersymmetric scenarios, including extensions that allow for a non-zero \theta_QCD.Comment: 34 pages, 16 eps figures, to appear in JHE

Low-temperature muon spin rotation studies of the monopole charges and currents in Y doped Ho2Ti2O7

In the ground state of Ho2Ti2O7 spin ice, the disorder of the magnetic moments follows the same rules as the proton disorder in water ice. Excitations take the form of magnetic monopoles that interact via a magnetic Coulomb interaction. Muon spin rotation has been used to probe the low-temperature magnetic behaviour in single crystal Ho2−xYxTi2O7 (x = 0, 0.1, 1, 1.6 and 2). At very low temperatures, a linear field dependence for the relaxation rate of the muon precession λ(B), that in some previous experiments on Dy2Ti2O7 spin ice has been associated with monopole currents, is observed in samples with x = 0, and 0.1. A signal from the magnetic fields penetrating into the silver sample plate due to the magnetization of the crystals is observed for all the samples containing Ho allowing us to study the unusual magnetic dynamics of Y doped spin ice

CP Violation in Supersymmetry with Effective Minimal Flavour Violation

We analyze CP violation in supersymmetry with Effective Minimal Flavour Violation, as recently proposed in arXiv:1011.0730. Unlike the case of standard Minimal Flavour Violation, we show that all the phases allowed by the flavour symmetry can be sizable without violating existing Electric Dipole Moment constraints, thus solving the SUSY CP problem. The EDMs at one and two loops are precisely analyzed as well as their correlations with the expected CP asymmetries in B physics.Comment: 22 pages, 7 figures. v2: Discussion in section 2 extended, conclusions unchanged. Matches published versio

A Comprehensive Analysis of Electric Dipole Moment Constraints on CP-violating Phases in the MSSM

We analyze the constraints placed on individual, flavor diagonal CP-violating phases in the minimal supersymmetric extension of the Standard Model (MSSM) by current experimental bounds on the electric dipole moments (EDMs) of the neutron, Thallium, and Mercury atoms. We identify the four CP-violating phases that are individually highly constrained by current EDM bounds, and we explore how these phases and correlations among them are constrained by current EDM limits. We also analyze the prospective implications of the next generation of EDM experiments. We point out that all other CP-violating phases in the MSSM are not nearly as tightly constrained by limits on the size of EDMs. We emphasize that a rich set of phenomenological consequences is potentially associated with these generically large EDM-allowed phases, ranging from B physics, electroweak baryogenesis, and signals of CP-violation at the CERN Large Hadron Collider and at future linear colliders. Our numerical study takes into account the complete set of contributions from one- and two-loop EDMs of the electron and quarks, one- and two-loop Chromo-EDMs of quarks, the Weinberg 3-gluon operator, and dominant 4-fermion CP-odd operator contributions, including contributions which are both included and not included yet in the CPsuperH2.0 package. We also introduce an open-source numerical package, 2LEDM, which provides the complete set of two-loop electroweak diagrams contributing to the electric dipole moments of leptons and quarks.Comment: 23 pages, 11 figures; v2: references added, minor change