Knowledge-based variable selection for learning rules from proteomic data

<p>Abstract</p> <p>Background</p> <p>The incorporation of biological knowledge can enhance the analysis of biomedical data. We present a novel method that uses a proteomic knowledge base to enhance the performance of a rule-learning algorithm in identifying putative biomarkers of disease from high-dimensional proteomic mass spectral data. In particular, we use the Empirical Proteomics Ontology Knowledge Base (EPO-KB) that contains previously identified and validated proteomic biomarkers to select <it>m/z</it>s in a proteomic dataset prior to analysis to increase performance.</p> <p>Results</p> <p>We show that using EPO-KB as a pre-processing method, specifically selecting all biomarkers found only in the biofluid of the proteomic dataset, reduces the dimensionality by 95% and provides a statistically significantly greater increase in performance over no variable selection and random variable selection.</p> <p>Conclusion</p> <p>Knowledge-based variable selection even with a sparsely-populated resource such as the EPO-KB increases overall performance of rule-learning for disease classification from high-dimensional proteomic mass spectra.</p

Exclusive Lambda_b -> Lambda l^+ l^- decay in two Higgs doublet model

Rare Lambda_b -> Lambda l^+ l^- decay is investigated in framework of general two Higgs doublet model, in which a new source of CP violation exists (model III). The polarization parameter, CP asymmetry and decay width are calculated. It is shown that CP asymmetry is a very sensitive tool for establishing model III.Comment: 16 pages, 3 figures, LaTeX formatte

Enhancing the top signal at Tevatron using Neural Nets

We show that Neural Nets can be useful for top analysis at Tevatron. The main features of $t\bar t$ and background events on a mixed sample are projected in a single output, which controls the efficiency and purity of the $t\bar t$ signal.Comment: 11 pages, 6 figures (not included and available from the authors), Latex, UB-ECM-PF 94/1

The Neutron Electric Dipole Moment and CP-violating Couplings in the Supersymmetric Standard Model without R-parity

We analyze the neutron electric dipole moment (EDM) in the Minimal Supersymmetric Model with explicit R-parity violating terms. The leading contribution to the EDM occurs at the 2-loop level and is dominated by the chromoelectric dipole moments of quarks, assuming there is no tree-level mixings between sleptons and Higgs bosons or between leptons and gauginos. Based on the experimental constraint on the neutron EDM, we set limits on the imaginary parts of complex couplings ${\lambda'}_{ijk}$ and ${\lambda}_{ijk}$ due to the virtual b-loop or tau-loop.Comment: final manuscript to appear in Phys. Rev. D, 15 pages, latex, 4 figures include

Detection of the heavy Higgs boson at γγ\gamma\gamma colliders

We consider the possibility of detecting a heavy Higgs boson ($m_H>2m_Z$) in proposed $\gamma\gamma$ colliders through the semi-leptonic mode $\gamma\gamma \rightarrow H \rightarrow ZZ \rightarrow q\bar q \ell^+\ell^-$. We show that due to the non-monochromatic nature of the photon beams produced by the laser-backscattering method, the resultant cross section for Higgs production is much smaller than the on-resonance cross section and generally {\it decreases} with increasing collider energy. Although continuum $ZZ$ production is expected to be negligible, we demonstrate the presence of and calculate sizeable backgrounds from $\gamma\gamma\rightarrow \ell^+\ell^-Z,\,q\bar qZ$, with $Z\rightarrow q\bar q,\,\ell^+\ell^-$, respectively, and $\gamma\gamma\rightarrow t\bar t\rightarrow b\bar b\ell^+\ell^-\nu\bar\nu$. This channel may be used to detect a Higgs of mass $m_H$ up to around 350~GeV at a 0.5~TeV $e^+e^-$ collider, assuming a nominal yearly luminosity of 10--20~fb$^{-1}$.Comment: 18 pages (in RevTeX) plus Postscript figures (available by email or FAX), NUHEP-TH-92-29 and DOE-309-CPP-47. (Revised version: NO CHANGES to the manuscript, simply removed corrupted figure files

The CP asymmetry for B--> K^* l^+ l^- decay in the general two Higgs doublet model

We study CP asymmetry for the exclusive decay B --> K^* l^+ l^- in the two Higgs doublet model with three level flavor changing neutral currents (model III). We analyse the dependency of this quantity to the new phase coming from the complex Yukawa couplings in the theory and we find that there exist a considerable CP violation for the relevant process. Further, we see that the sign of the Wilson coefficient C_7^{eff} can be determined by fixing dilepton mass. Therefore, the future measurements of CP asymmetry for B --> K^* l^+ l^- decay will give a powerful information about the sign of Wilson coefficient C_{7}^{eff} and the new physics beyond the SM.Comment: 22 pages, 8 figure

Aspects of Soft and Spontaneous CP Violation

We study four different models for CP violation: the standard (KM) model, the aspon model of spontaneous breaking and two models of soft breaking. In all except the standard model, the strong CP problem is addressed and solved. Testable predictions for the area of the unitarity triangle and for (epsilon'/epsilon)_K are emphasized. The issue of CP violation may well become the first place where the standard model of particle theory is shown definitively to be deficient. There are two reasons for expecting this to happen: (1) the strong CP problem is still not understood in the unadorned standard model and (2) the KM mechanism, although unquestionably present, may not provide the full explanation of epsilon_K and (epsilon'/epsilon)_K.Comment: 24 pages LaTeX including 4 figures. Minor modification to analysis of lower bound for d_n, summarized in new Table I

Novel CP-violating Effects in B decays from Charged-Higgs in a Two-Higgs Doublet Model for the Top Quark

We explore charged-Higgs cp-violating effects in a specific type III two-Higgs doublet model which is theoretically attractive as it accommodates the large mass of the top quark in a natural fashion. Two new CP-violating phases arise from the right-handed up quark sector. We consider CP violation in both neutral and charged B decays. Some of the important findings are as follows. 1) Large direct-CP asymmetry is found to be possible for B+- to psi/J K+-. 2) Sizable D-anti-D mixing effect at the percent level is found to be admissible despite the stringent constraints from the data on K-anti-K mixing, b to s gamma and B to tau nu decays. 3) A simple but distinctive CP asymmetry pattern emerges in decays of B_d and B_s mesons, including B_d to psi/J K_S, D+ D-, and B_s to D_s+ D_s-, psi eta/eta^prime, psi/J K_S. 4) The effect of D-anti-D mixing on the CP asymmetry in B+- to D/anti-D K+- and on the extraction of the angle gamma of the unitarity triangle from such decays can be significant.Comment: 32 pages, 5 figures, section V.A revised, version to appear in PR

High-throughput sequencing of Astrammina rara: Sampling the giant genome of a giant foraminiferan protist

<p>Abstract</p> <p>Background</p> <p>Foraminiferan protists, which are significant players in most marine ecosystems, are also genetic innovators, harboring unique modifications to proteins that make up the basic eukaryotic cell machinery. Despite their ecological and evolutionary importance, foraminiferan genomes are poorly understood due to the extreme sequence divergence of many genes and the difficulty of obtaining pure samples: exogenous DNA from ingested food or ecto/endo symbionts often vastly exceed the amount of "native" DNA, and foraminiferans cannot be cultured axenically. Few foraminiferal genes have been sequenced from genomic material, although partial sequences of coding regions have been determined by EST studies and mass spectroscopy. The lack of genomic data has impeded evolutionary and cell-biology studies and has also hindered our ability to test ecological hypotheses using genetic tools.</p> <p>Results</p> <p>454 sequence analysis was performed on a library derived from whole genome amplification of microdissected nuclei of the Antarctic foraminiferan <it>Astrammina rara</it>. Xenogenomic sequence, which was shown not to be of eukaryotic origin, represented only 12% of the sample. The first foraminiferal examples of important classes of genes, such as tRNA genes, are reported, and we present evidence that sequences of mitochondrial origin have been translocated to the nucleus. The recovery of a 3' UTR and downstream sequence from an actin gene suggests that foraminiferal mRNA processing may have some unusual features. Finally, the presence of a co-purified bacterial genome in the library also permitted the first calculation of the size of a foraminiferal genome by molecular methods, and statistical analysis of sequence from different genomic sources indicates that low-complexity tracts of the genome may be endoreplicated in some stages of the foraminiferal life cycle.</p> <p>Conclusions</p> <p>These data provide the first window into genomic organization and genetic control in these organisms, and also complement and expands upon information about foraminiferal genes based on EST projects. The genomic data obtained are informative for environmental and cell-biological studies, and will also be useful for efforts to understand relationships between foraminiferans and other protists.</p