We develop a cross-platform open-source Java application (BACOM2) with graphic user interface (GUI), and users also can use a XML file to set the parameters of algorithm model, file paths and the dataset of paired samples. BACOM2 implements the new e
ntire pipeline of copy number change analysis for heterogeneous cancer tissues, including extraction of raw copy number signals from CEL files of paired samples, attenuation correction, identification of balanced AB-genotype loci, copy number detection and segmentation, global baseline calculation and absolute normalization, differentiation of deletion types, estimation of the normal tissue fraction and correction of normal tissue contamination. BACOM2 focuses on the common tools for data preparation and absolute normalization for copy number analysis of heterogeneous cancer tissues. The software provides an additional choice for scientists who require a user-friendly, high-speed processing, cross-platform computing environment for large copy number data analysis.
The BICEP2 collaboration reports a detection of primordial cosmic microwave background (CMB) B-mode with a tensor-scalar ratio $r=0.20^{+0.07}_{-0.05}$ (68% C.L.). However, this result is in tension with the recent Planck limit, $r<0.11$ (95% C.L.),
on constraining inflation models. In this Letter we consider an inflationary cosmology with a preceding nonsingular bounce which gives rise to observable signatures on primordial perturbations. One interesting phenomenon is that both the primordial scalar and tensor modes can have a step feature on their power spectra, which nicely cancels the tensor excess power on the CMB temperature power spectrum. By performing a global analysis, we obtain the 68% C.L. constraints on the parameters of the model from the Planck+WP and BICEP2 data together: the jump scale $log_{10}(k_{rm b}/{rm Mpc}^{-1})=-2.4pm0.2$ and the spectrum amplitude ratio of bounce-to-inflation $r_Bequiv P_{rm m} / A_{rm s} = 0.71pm0.09$. Our result reveals that the bounce inflation scenario can simultaneously explain the Planck and BICEP2 observations better than the standard $Lambda$CDM model, and can be verified by the future CMB polarization measurements.
BACOM is a statistically principled and unsupervised method that detects copy number deletion types (homozygous versus heterozygous), estimates normal cell fraction, and recovers cancer specific copy number profiles, using allele specific copy number
signals. In a subsequent analysis of TCGA ovarian cancer dataset, the average normal cell fraction estimated by BACOM was found higher than expected. In this letter, we first discuss the advantages of the BACOM in relation to alternative approaches. Then, we show that this elevated estimate of normal cell fraction is the combined result of inaccurate signal modeling and normalization. Lastly, we describe an allele specific signal modeling and normalization scheme that can enhance BACOM applications in many biological contexts. An open source MATLAB program was developed to implement our extended method and it is publically available.
We show that the f(T) gravitational paradigm, in which gravity is described by an arbitrary function of the torsion scalar, can provide a mechanism for realizing bouncing cosmologies, thereby avoiding the Big Bang singularity. After constructing the
simplest version of an f(T) matter bounce, we investigate the scalar and tensor modes of cosmological perturbations. Our results show that metric perturbations in the scalar sector lead to a background-dependent sound speed, which is a distinguishable feature from Einstein gravity. Additionally, we obtain a scale-invariant primordial power spectrum, which is consistent with cosmological observations, but suffers from the problem of a large tensor-to-scalar ratio. However, this can be avoided by introducing extra fields, such as a matter bounce curvaton.
In this letter, we propose a model of inflationary cosmology with a bounce preceded and study its primordial curvature perturbations. Our model gives rise to a primordial power spectrum with a feature of oscillation on large scales compared with the
nearly scale-invariant spectrum generated by the traditional slow rolling inflation model. We will show this effect changes the Cosmic Microwave Background (CMB) temperature power spectrum and the Large Scale Structure (LSS) matter power spectrum. And further with a detailed simulation we will point out this signal is detectable to the forthcoming observations, such as PLANCK and LAMOST.
In this paper, we study the possibility of building a model of the oscillating universe with quintom matter in the framework of 4-dimensional Friedmann-Robertson-Walker background. Taking the two-scalar-field quintom model as an example, we find in t
he model parameter space there are five different types of solutions which correspond to: (I) a cyclic universe with the minimal and maximal values of the scale factor remaining the same in every cycle, (II) an oscillating universe with its minimal and maximal values of the scale factor increasing cycle by cycle, (III) an oscillating universe with its minimal and maximal values of the scale factor decreasing cycle by cycle, (IV) an oscillating universe with its scale factor always increasing, and (V) an oscillating universe with its scale factor always decreasing.
