Bayesian DNA copy number analysis

BACKGROUND: Some diseases, like tumors, can be related to chromosomal aberrations, leading to changes of DNA copy number. The copy number of an aberrant genome can be represented as a piecewise constant function, since it can exhibit regions of deletions or gains. Instead, in a healthy cell the copy number is two because we inherit one copy of each chromosome from each our parents. Bayesian Piecewise Constant Regression (BPCR) is a Bayesian regression method for data that are noisy observations of a piecewise constant function. The method estimates the unknown segment number, the endpoints of the segments and the value of the segment levels of the underlying piecewise constant function. The Bayesian Regression Curve (BRC) estimates the same data with a smoothing curve. However, in the original formulation, some estimators failed to properly determine the corresponding parameters. For example, the boundary estimator did not take into account the dependency among the boundaries and succeeded in estimating more than one breakpoint at the same position, losing segments. RESULTS: We derived an improved version of the BPCR (called mBPCR) and BRC, changing the segment number estimator and the boundary estimator to enhance the fitting procedure. We also proposed an alternative estimator of the variance of the segment levels, which is useful in case of data with high noise. Using artificial data, we compared the original and the modified version of BPCR and BRC with other regression methods, showing that our improved version of BPCR generally outperformed all the others. Similar results were also observed on real data. CONCLUSION: We propose an improved method for DNA copy number estimation, mBPCR, which performed very well compared to previously published algorithms. In particular, mBPCR was more powerful in the detection of the true position of the breakpoints and of small aberrations in very noisy data. Hence, from a biological point of view, our method can be very useful, for example, to find targets of genomic aberrations in clinical cancer samples

NIEL Dose Dependence for Solar Cells Irradiated with Electrons and Protons

The investigation of solar cells degradation and the prediction of its end-of-life performance is of primary importance in the preparation of a space mission. In the present work, we investigate the reduction of solar-cells' maximum power resulting from irradiations with electrons and protons. Both GaAs single junction and GaInP/GaAs/Ge triple junction solar cells were studied. The results obtained indicate how i) the dominant radiation damaging mechanism is due to atomic displacements, ii) the relative maximum power degradation is almost independent of the type of incoming particle, i.e., iii) to a first approximation, the fitted semi-empirical function expressing the decrease of maximum power depends only on the absorbed NIEL dose, and iv) the actual displacement threshold energy value (Ed=21 eV) accounts for annealing treatments, mostly due to self-annealing induced effects. Thus, for a given type of solar cell, a unique maximum power degradation curve can be determined as a function of the absorbed NIEL dose. The latter expression allows one to predict the performance of those solar cells in space radiation environment.Comment: To appear on the Proceedings of the 13th ICATPP Conference on Astroparticle, Particle, Space Physics and Detectors for Physics Applications, Villa Olmo (Como, Italy), 23--27 October, 2013, to be published by World Scientific (Singapore

Pulsar Wind Nebulae as a source of the observed electron and positron excess at high energy: the case of Vela-X

We investigate, in terms of production from pulsars and their nebulae, the cosmic ray positron and electron fluxes above $\sim10$ GeV, observed by the AMS-02 experiment up to 1 TeV. We concentrate on the Vela-X case. Starting from the gamma-ray photon spectrum of the source, generated via synchrotron and inverse Compton processes, we estimated the electron and positron injection spectra. Several features are fixed from observations of Vela-X and unknown parameters are borrowed from the Crab nebula. The particle spectra produced in the pulsar wind nebula are then propagated up to the Solar System, using a diffusion model. Differently from previous works, the omnidirectional intensity excess for electrons and positrons is obtained as a difference between the AMS-02 data and the corresponding local interstellar spectrum. An equal amount of electron and positron excess is observed and we interpreted this excess (above $\sim$100 GeV in the AMS-02 data) as a supply coming from Vela-X. The particle contribution is consistent with models predicting the gamma-ray emission at the source. The input of a few more young pulsars is also allowed, while below $\sim$100 GeV more aged pulsars could be the main contributors.Comment: Accepted for publication in Journal of High Energy Astrophysics (2015

FAST FRONT-END ELECTRONICS FOR EXPERIMENTS USING SILICON CALORIMETERS AT SSC /LHC COLLIDERS

Abstract A fast VLSI preamplifier using HF2CMOS technology was designed and built. The preamplifier meets the requirements for silicon calorimetry application in experiments at hadron colliders SSC/LHC. The overall power consumption is less than 45 mW for a maximum output voltage swing of 5 V (≈ 7 ns rise time). The slew rate is about 700 V/μs for an input capacitance of 150 pF. The measured value of ENC (equivalent noise charge), for an RC-CR shaping time of 20 ns and an input capacitance of 150 pF, is 17 ke RMS

Antiproton modulation in the Heliosphere and AMS-02 antiproton over proton ratio prediction

We implemented a quasi time-dependent 2D stochastic model of solar modulation describing the transport of cosmic rays (CR) in the heliosphere. Our code can modulate the Local Interstellar Spectrum (LIS) of a generic charged particle (light cosmic ions and electrons), calculating the spectrum at 1AU. Several measurements of CR antiparticles have been performed. Here we focused our attention on the CR antiproton component and the antiproton over proton ratio. We show that our model, using the same heliospheric parameters for both particles, fit the observed anti-p/p ratio. We show a good agreement with BESS-97 and PAMELA data and make a prediction for the AMS-02 experiment

Monolithic read-out electronics for the silicon calorimeters at SSC/LHC colliders

Abstract A very fast monolithic charge sensitive preamplifier using HF2CMOS technology featuring less than 45mW power dissipation for a 5V maximum output voltage swing, with a slew rate about 700V/μsec for 150pF input capacitance (≈ 7nsec rise time), has been realized. A front-end set up for the read out of more detectors and the shaping of the signal with a 20nsec RC-CR filter employing only monolithic preamplifiers is described and tested. The measured value of ENC (Electronic Noise Charge) for the arrangement with 150pF input capacitance is 17keRMS. The preamplifier meets the requirements for silicon calorimetry application for experiments at the hadron colliders SSC/LHC

Nuclear and Non-Ionizing Energy-Loss for Coulomb Scattered Particles from Low Energy up to Relativistic Regime in Space Radiation Environment

In the space environment, instruments onboard of spacecrafts can be affected by displacement damage due to radiation. The differential scattering cross section for screened nucleus--nucleus interactions - i.e., including the effects due to screened Coulomb nuclear fields -, nuclear stopping powers and non-ionization energy losses are treated from about 50 keV/nucleon up to relativistic energies.Comment: Accepted for publication in the Proceedings of the ICATPP Conference on Cosmic Rays for Particle and Astroparticle Physics, Villa Olmo (Como, Italy), 7--8 October, 2010, to be published by World Scientifi

Proton Modulation in the Heliosphere for Different Solar Conditions and Prediction for AMS-02

Spectra of Galactic Cosmic Rays (GCRs) measured at the Earth are the combination of several processes: sources production and acceleration, propagation in the interstellar medium and propagation in the heliosphere. Inside the solar cavity the flux of GCRs is reduced due to the solar modulation, the interaction which they have with the interplanetary medium. We realized a 2D stochastic simulation of solar modulation to reproduce CR spectra at the Earth, and evaluated the importance in our results of the Local Interstellar Spectrum (LIS) model and its agreement with data at high energy. We show a good agreement between our model and the data taken by AMS-01 and BESS experiments during periods with different solar activity conditions. Furthermore we made a prediction for the flux which will be measured by AMS-02 experiment.Comment: Accepted for publication in the Proceedings of the ICATPP Conference on Cosmic Rays for Particle and Astroparticle Physics, Villa Olmo (Como, Italy), 7-8 October, 2010, to be published by World Scientific (Singapore