Definition of valid proteomic biomarkers: a bayesian solution

Clinical proteomics is suffering from high hopes generated by reports on apparent biomarkers, most of which could not be later substantiated via validation. This has brought into focus the need for improved methods of finding a panel of clearly defined biomarkers. To examine this problem, urinary proteome data was collected from healthy adult males and females, and analysed to find biomarkers that differentiated between genders. We believe that models that incorporate sparsity in terms of variables are desirable for biomarker selection, as proteomics data typically contains a huge number of variables (peptides) and few samples making the selection process potentially unstable. This suggests the application of a two-level hierarchical Bayesian probit regression model for variable selection which assumes a prior that favours sparseness. The classification performance of this method is shown to improve that of the Probabilistic K-Nearest Neighbour model

A combined PLC and CPU approach to multiprocessor control

A sophisticated multiprocessor control system has been developed for use in the E-Power Supply System Integrated Control (EPSSIC) on the DIII-D tokamak. EPSSIC provides control and interlocks for the ohmic heating coil power supply and its associated systems. Of particular interest is the architecture of this system: both a Programmable Logic Controller (PLC) and a Central Processor Unit (CPU) have been combined on a standard VME bus. The PLC and CPU input and output signals are routed through signal conditioning modules, which provide the necessary voltage and ground isolation. Additionally these modules adapt the signal levels to that of the VME I/O boards. One set of I/O signals is shared between the two processors. The resulting multiprocessor system provides a number of advantages: redundant operation for mission critical situations, flexible communications using conventional TCP/IP protocols, the simplicity of ladder logic programming for the majority of the control code, and an easily maintained and expandable non-proprietary system

Isospin-Violating Meson-Nucleon Vertices as an Alternate Mechanism of Charge-Symmetry Breaking

We compute isospin-violating meson-nucleon coupling constants and their consequent charge-symmetry-breaking nucleon-nucleon potentials. The couplings result from evaluating matrix elements of quark currents between nucleon states in a nonrelativistic constituent quark model; the isospin violations arise from the difference in the up and down constituent quark masses. We find, in particular, that isospin violation in the omega-meson--nucleon vertex dominates the class IV CSB potential obtained from these considerations. We evaluate the resulting spin-singlet--triplet mixing angles, the quantities germane to the difference of neutron and proton analyzing powers measured in elastic $\vec{n}-\vec{p}$ scattering, and find them commensurate to those computed originally using the on-shell value of the $\rho$-$\omega$ mixing amplitude. The use of the on-shell $\rho$-$\omega$ mixing amplitude at $q^2=0$ has been called into question; rather, the amplitude is zero in a wide class of models. Our model possesses no contribution from $\rho$-$\omega$ mixing at $q^2=0$, and we find that omega-meson exchange suffices to explain the measured $n-p$ analyzing power difference~at~183 MeV.Comment: 20 pages, revtex, 3 uuencoded PostScript figure

On the pion-nucleon coupling constant

In view of persisting misunderstanding about the determination of the pion-nucleon coupling constants in the Nijmegen multienergy partial-wave analyses of pp, np, and pbar-p scattering data, we present additional information which may clarify several points of discussion. We comment on several recent papers addressing the issue of the pion-nucleon coupling constant and criticizing the Nijmegen analyses.Comment: 19 pages, Nijmegen preprint THEF-NYM-92-0

The alpha-particle based on modern nuclear forces

The Faddeev-Yakubovsky equations for the alpha-particle are solved. Accurate results are obtained for several modern NN interaction models, which include charge-symmetry breaking effects in the NN force, nucleon mass dependences as well as the Coulomb interaction. These models are augmented by three-nucleon forces of different types and adjusted to the 3N binding energy. Our results are close to the experimental binding energy with a slight overbinding. Thus there is only little room left for the contribution of possible 4N interactions to the alpha-particle binding energy. We also discuss model dependences of the binding energies and the wave functions.Comment: 22 pages REVTeX 4, 12 figures, table with TM parameters added, typos corrected, version as published in PR

Tri-meson-mixing of π\pi-η\eta-η′\eta' and ρ\rho-ω\omega-ϕ\phi in the light-cone quark model

The radiative transition form factors of the pseudoscalar mesons {$\pi$, $\eta$, $\eta'$} and the vector mesons {$\rho$, $\omega$, $\phi$} are restudied with $\pi$-$\eta$-$\eta'$ and $\rho$-$\omega$-$\phi$ in tri-meson-mixing pattern, which is described by tri-mixing matrices in the light-cone constituent quark model. The experimental transition decay widths are better reproduced with tri-meson-mixing than previous results in a two-mixing-angle scenario of only two-meson $\eta$-$\eta'$ mixing and $\omega$-$\phi$ mixing.Comment: 8 pages, 6 figures, final version to appear in EPJ

Weak capture of protons by protons

The cross section for the proton weak capture reaction $^1H(p,e^+\nu_e)^2H$ is calculated with wave functions obtained from a number of modern, realistic high-precision interactions. To minimize the uncertainty in the axial two-body current operator, its matrix element has been adjusted to reproduce the measured Gamow-Teller matrix element of tritium $\beta$ decay in model calculations using trinucleon wave functions from these interactions. A thorough analysis of the ambiguities that this procedure introduces in evaluating the two-body current contribution to the pp capture is given. Its inherent model dependence is in fact found to be very weak. The overlap integral $\Lambda^2(E=0)$ for the pp capture is predicted to be in the range 7.05--7.06, including the axial two-body current contribution, for all interactions considered.Comment: 17 pages RevTeX (twocolumn), 5 postscript figure

Search for Neutrinoless Double-Beta Decay with the Upgraded EXO-200 Detector

Results from a search for neutrinoless double-beta decay (0νββ) of Xe136 are presented using the first year of data taken with the upgraded EXO-200 detector. Relative to previous searches by EXO-200, the energy resolution of the

Structure and functionality of a multimeric human COQ7:COQ9 complex.

Coenzyme Q (CoQ) is a redox-active lipid essential for core metabolic pathways and antioxidant defense. CoQ is synthesized upon the mitochondrial inner membrane by an ill-defined "complex Q" metabolon. Here, we present structure-function analyses of a lipid-, substrate-, and NADH-bound complex comprising two complex Q subunits: the hydroxylase COQ7 and the lipid-binding protein COQ9. We reveal that COQ7 adopts a ferritin-like fold with a hydrophobic channel whose substrate-binding capacity is enhanced by COQ9. Using molecular dynamics, we further show that two COQ7:COQ9 heterodimers form a curved tetramer that deforms the membrane, potentially opening a pathway for the CoQ intermediates to translocate from the bilayer to the proteins' lipid-binding sites. Two such tetramers assemble into a soluble octamer with a pseudo-bilayer of lipids captured within. Together, these observations indicate that COQ7 and COQ9 cooperate to access hydrophobic precursors within the membrane and coordinate subsequent synthesis steps toward producing CoQ