myVCF: a desktop application for high-throughput mutations data management

Abstract Summary Next-generation sequencing technologies have become the most powerful tool to discover genetic variants associated with human diseases. Although the dramatic reductions in the costs facilitate the use in the wet-lab and clinics, the huge amount of data generated renders their management by non-expert researchers and physicians extremely difficult. Therefore, there is an urgent need of novel approaches and tools aimed at getting the 'end-users' closer to the sequencing data, facilitating the access by non-bioinformaticians, and to speed-up the functional interpretation of genetic variants. We developed myVCF, a standalone, easy-to-use desktop application, which is based on a browser interface and is suitable for Windows, Mac and UNIX systems. myVCF is an efficient platform that is able to manage multiple sequencing projects created from VCF files within the system; stores genetic variants and samples genotypes from an annotated VCF files into a SQLite database; implements a flexible search engine for data exploration, allowing to query for chromosomal region, gene, single variant or dbSNP ID. Besides, myVCF generates a summary statistics report about mutations distribution across samples and across the genome/exome by aggregating the information within the VCF file. In summary, the myVCF platform allows end-users without strong programming and bioinformatics skills to explore, query, visualize and export mutations data in a simple and straightforward way. Availability and implementation https://apietrelli.github.io/myVCF/ Supplementary information Supplementary data are available at Bioinformatics online

Interaction between IL28B and PNPLA3 genotypes in the pathogenesis of steatosis in chronic hepatitis C non genotype-3 patients

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Quantum resonant activation

Quantum resonant activation is investigated for the archetype setup of an externally driven two-state (spin-boson) system subjected to strong dissipation by means of both analytical and extensive numerical calculations. The phenomenon of resonant activation emerges in the presence of either randomly fluctuating or deterministic periodically varying driving fields. Addressing the incoherent regime, a characteristic minimum emerges in the mean first passage time to reach an absorbing neighboring state whenever the intrinsic time scale of the modulation matches the characteristic time scale of the system dynamics. For the case of deterministic periodic driving, the first passage time probability density function (pdf) displays a complex, multi-peaked behavior, which depends crucially on the details of initial phase, frequency, and strength of the driving. As an interesting feature we find that the mean first passage time enters the resonant activation regime at a critical frequency $\nu^*$ which depends very weakly on the strength of the driving. Moreover, we provide the relation between the first passage time pdf and the statistics of residence times.Comment: 14 pages, 13 figure

Quantum dissipative dynamics of a bistable system in the sub-Ohmic to super-Ohmic regime

We investigate the quantum dynamics of a multilevel bistable system coupled to a bosonic heat bath beyond the perturbative regime. We consider different spectral densities of the bath, in the transition from sub-Ohmic to super-Ohmic dissipation, and different cutoff frequencies. The study is carried out by using the real-time path integral approach of the Feynman-Vernon influence functional. We find that, in the crossover dynamical regime characterized by damped \emph{intrawell} oscillations and incoherent tunneling, the short time behavior and the time scales of the relaxation starting from a nonequilibrium initial condition depend nontrivially on the spectral properties of the heat bath.Comment: 16 pages, 7 figure

A call to action for fatty liver disease

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Super-Soft CP Violation

Solutions of the Strong CP Problem based on the spontaneous breaking of CP must feature a non-generic structure and simultaneously explain a coincidence between a priori unrelated CP-even and CP-odd mass scales. We show that these properties can emerge from gauge invariance and a CP-conserving, but otherwise generic, physics at the Planck scale. In our scenarios no fundamental scalar is introduced beyond the Standard Model Higgs doublet, and CP is broken at naturally small scales by a confining non-abelian dynamics. This approach is remarkably predictive: robustness against uncontrollable UV corrections to the QCD topological angle requires one or more families of vector-like quarks below a few $10$'s of TeV, hence potentially accessible at colliders. Because CP violation is communicated to the SM at these super-soft scales, our solution of the Strong CP Problem is not spoiled by the presence of heavy new states motivated by other puzzles in physics beyond the Standard Model. In addition, these models generically predict a dark sector that may lead to interesting cosmological signatures.Comment: 19 pages. v2: matches the published versio

Finite-temperature geometric properties of the Kitaev honeycomb model

We study finite-temperature topological properties of the Kitaev’s spin-honeycomb model in the vortex-free sector with the use of the recently introduced mean Uhlmann curvature. We employ an appropriate fermionization procedure to study the system as a two-band p-wave superconductor described by a Bogoliubov–de Gennes Hamiltonian. This allows us to study relevant quantities such as Berry and mean Uhlmann curvatures in a simple setting. More specifically, we consider the spin honeycomb in the presence of an external magnetic field breaking time-reversal symmetry. The introduction of such an external perturbation opens up a gap in the phase of the system characterized by non-Abelian statistics. The resulting model belongs to a symmetry-protected class, so that the Uhlmann number can be analyzed. We first consider the Berry curvature on a particular evolution line over the phase diagram. The mean Uhlmann curvature and the Uhlmann number are then analyzed by assuming a thermal state. The mean Uhlmann curvature describes a crossover effect as temperature rises. In the trivial phase, a nonmonotonic dependence of the Uhlmann number, as temperature increases, is reported and explained