Prediction and testing of biological networks underlying intestinal cancer

Colorectal cancer progresses through an accumulation of somatic mutations, some of which reside in so-called driver genes that provide a growth advantage to the tumor. To identify points of intersection between driver gene pathways, we implemented a network analysis framework using protein interactions to predict likely connections - both precedented and novel - between key driver genes in cancer. We applied the framework to find significant connections between two genes, Apc and Cdkn1a (p21), known to be synergistic in tumorigenesis in mouse models. We then assessed the functional coherence of the resulting Apc-Cdkn1a network by engineering in vivo single node perturbations of the network: mouse models mutated individually at Apc (Apc1638N+/2) or Cdkn1a (Cdkn1a-/-), followed by measurements of protein and gene expression changes in intestinal epithelial tissue. We hypothesized that if the predicted network is biologically coherent (functional), then the predicted nodes should associate more specifically with dysregulated genes and proteins than stochastically selected genes and proteins. The predicted Apc-Cdkn1a network was significantly perturbed at the mRNAlevel by both single gene knockouts, and the predictions were also strongly supported based on physical proximity and mRNA coexpression of proteomic targets. These results support the functional coherence of the proposed Apc-Cdkn1a network and also demonstrate how network-based predictions can be statistically tested using high-throughput biological data. © 2010 Patel et al

Pionic Degrees of Freedom in Atomic Nuclei and Quasielastic Knockout of Pions by High-Energy Electrons

The nonlinear model of pionic condensate in nuclei by G. Preparata can be efficiently verified by investigation of the quasielastic knockout process of pions out of nuclei by high energy electrons. First, a momentum distribution (MD) of the collective pions has a bright maximum at q=0.3 Gev.Second the excitation spectrum of a recoil nucleus is concentrated at low energies E lesser than 1MeV. The results for the pion knockout from mesonic clouds of individual nucleons are absolutely different. The latter results are presented both for pion and rho-meson clouds localized on nucleons.Comment: 13 pages, 3 figure

Pion Form Factor in the NLC QCD SR approach

We present results of a calculation of the electromagnetic pion form factor within a framework of QCD Sum Rules with nonlocal condensates and using a perturbative spectral density which includes \mathcal{O}(\alpha_s) contributions.Comment: 9 pages, 2 figures (embedded). Talk presented by the second author at the Workshop on Physics of Fundamental Interactions, Institute of High Energy Physics, Protvino, Russia, 22--25 December 200

Branching Ratio and CP Violation of B to pi pi Decays in Perturbative QCD Approach

We calculate the branching ratios and CP asymmetries for B^0 to pi^+pi^-, B^+ to pi^+pi^0 and B^0 to pi^0pi^0 decays, in a perturbative QCD approach. In this approach, we calculate non-factorizable and annihilation type contributions, in addition to the usual factorizable contributions. We found that the annihilation diagram contributions are not very small as previous argument. Our result is in agreement with the measured branching ratio of B to pi^+pi^- by CLEO collaboration. With a non-negligible contribution from annihilation diagrams and a large strong phase, we predict a large direct CP asymmetry in B^0 to pi^+pi^-, and pi^0pi^0, which can be tested by the current running B factories.Comment: Latex, 28 pages including 11 figures; added contents and figures, corrected typo

Symmetry restoration of the soft pion corrections for the light sea quark distributions in the small xx region

The soft pion correction at high energy may play a crucial role in non-perturbative parts of sea quark distributions. In this paper, we show that, while the soft pion correction for the strange sea qaurk distribution is suppressed in the large and the medium $x$ region compared with that for the up and the down sea quark one, it can become large and SU(3) flavor symmetric in the very small $x$ region. This gives us a good reason for the symmetry restoration of light sea quark distributions required by the mean charge sum rule for the light sea quarks. Then, by estimating this sum rule with the help of the results obtained by the soft pion correction, it is argued that there is a large symmetry restoration of the strange sea quark in the region from $x=10^{-2}$ to $10^{-6}$ at $Q^2\sim 1$ GeV.Comment: 22 pages including 4 eps figures, ReVTeX, to appear in Phys. Rev.

Pomeron in diffractive processes γ∗(Q2)p→ρ0p\gamma^*(Q^2)p\to\rho^0 p and γ∗(Q2)p→γ∗(Q2)p\gamma^*(Q^2)p\to\gamma^*(Q^2) p at large Q^2: the onset of pQCD

We study the reactions $\gamma^*(Q^2)p\to\rho^0 p$ and $\gamma^*(Q^2)p\to\gamma^*(Q^2) p$ at large Q^2 and $W^2/Q^2$ and small momentum transfer, $\kappa^2_\perp$, to the nucleon where the pomeron exchange dominates. At large Q^2 the virtual photon selects a hard $q\bar q$ pair, thus selecting the hard pomeron component (the BFKL pomeron). The amplitudes for both transverse and longitudinal polarizations of the initial photon and outgoing $\rho$-meson (photon) are calculated in the framework of the BFKL pomeron exchange. Our calculations show that one cannot expect the early onset of the pure perturbative regime in the discussed diffractive processes: the small interquark distances, $\rho_{q\bar q} <0.2$ fm, start to dominate not earlier than at $Q^2 \simeq 100 GeV^2, W^2/Q^2 \simeq 10^7$ in $\gamma^*(Q^2)p\to\rho^0 p$ and $Q^2 \simeq 50 GeV^2, W^2/Q^2 \simeq 10^6$ in $\gamma^*(Q^2)p\to\gamma^*(Q^2) p$.Comment: 20 pages, LaTeX, epsfig.st

Skewed parton distributions and the scale dependence of the transverse size parameter

We discuss the scale dependence of a skewed parton distribution of the pion obtained from a generalized light-cone wave function overlap formula. Using a simple ansatz for the transverse momentum dependence of the light-cone wave function and restricting ourselves to the case of a zero skewedness parameter, the skewed parton distribution can be expressed through an ordinary parton distribution multiplied by an exponential function. Matching the generalized and ordinary DGLAP evolution equations of the skewed and ordinary parton distributions, respectively, we derive a constraint for the scale dependence of the transverse size parameter, which describes the width of the pion wave function in transverse momentum space. This constraint has implications for the Fock state probability and valence distribution. We apply our results to the pion form factor.Comment: 10 pages, 4 figures; version to appear in Phys. Rev. D; Refs. added, new discussion of results for pion form factor in view of new dat

Near infrared detectors for SNAP

Large format (1k x 1k and 2k x 2k) near infrared detectors manufactured by Rockwell Scientific Center and Raytheon Vision Systems are characterized as part of the near infrared R&amp;D effort for SNAP (the Super-Nova/Acceleration Probe). These are hybridized HgCdTe focal plane arrays with a sharp high wavelength cut-off at 1.7 um. This cut-off provides a sufficiently deep reach in redshift while it allows at the same time low dark current operation of the passively cooled detectors at 140 K. Here the baseline SNAP near infrared system is briefly described and the science driven requirements for the near infrared detectors are summarized. A few results obtained during the testing of engineering grade near infrared devices procured for the SNAP project are highlighted. In particular some recent measurements that target correlated noise between adjacent detector pixels due to capacitive coupling and the response uniformity within individual detector pixels are discussed

New Constraints on Dispersive Form Factor Parameterizations from the Timelike Region

We generalize a recent model-independent form factor parameterization derived from rigorous dispersion relations to include constraints from data in the timelike region. These constraints dictate the convergence properties of the parameterization and appear as sum rules on the parameters. We further develop a new parameterization that takes into account finiteness and asymptotic conditions on the form factor, and use it to fit to the elastic \pi electromagnetic form factor. We find that the existing world sample of timelike data gives only loose bounds on the form factor in the spacelike region, but explain how the acquisition of additional timelike data or fits to other form factors are expected to give much better results. The same parameterization is seen to fit spacelike data extremely well.Comment: 24 pages, latex (revtex), 3 eps figure