851 research outputs found
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 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 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 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
- …