Biomarkers of oxidative stress: methods and measures of oxidative DNA damage (COMET assay) and telomere shortening

Oxidative stress is fast becoming the nutritional and medical buzzword for the twenty-first century. The theoretical importance of oxidative stress in diabetes is highlighted by its potential double impact on metabolic dysfunction on one hand and the vascular system on the other hand. The new concept of oxidative stress, being an important trigger in the onset and progression of diabetes and its complications, emphasizes the need for measurement of markers of oxidation to assess the degree of oxidative stress. While we have been routinely measuring biomarkers in our molecular epidemiology projects, here we discuss the utility of two assays, (a) DNA damage assessment by COMET measurement and (b) telomere length measurement. As DNA damage is efficiently repaired by cellular enzymes, its measurement gives a snapshot view of the level of oxidative stress. The protocol allows for measurement of oxidative DNA damage (FPG-sensitive DNA strand breaks). Telomere length measured by Southern blotting technique allows one to estimate the chronic burden of oxidative stress at the molecular level and is now considered as biomarker of biological aging

Optimal correction of concatenated fault-tolerant quantum codes

We present a method of concatenated quantum error correction in which improved classical processing is used with existing quantum codes and fault-tolerant circuits to more reliably correct errors. Rather than correcting each level of a concatenated code independently, our method uses information about the likelihood of errors having occurred at lower levels to maximize the probability of correctly interpreting error syndromes. Results of simulations of our method applied to the [[4,1,2]] subsystem code indicate that it can correct a number of discrete errors up to half of the distance of the concatenated code, which is optimal.Comment: 7 pages, 2 figures, published versio

Study of Neutron-Induced Ionization in Helium and Argon Chamber Gases

Ion chambers used to monitor the secondary hadron and tertiary muon beam in the NuMI neutrino beamline will be exposed to background particles, including low energy neutrons produced in the beam dump. To understand these backgrounds, we have studied Helium- and Argon-filled ionization chambers exposed to intense neutron fluxes from PuBe neutron sources ($E_n=1-10$ MeV). The sources emit about 10$^8$ neutrons per second. The number of ion pairs in the chamber gas volume per incident neutron is derived. While limited in precision because of a large gamma ray background from the PuBe sources, our results are consistent with the expectation that the neutrons interact purely elastically in the chamber gas.Comment: accepted for publication in NIM

A Paraconsistent Higher Order Logic

Classical logic predicts that everything (thus nothing useful at all) follows from inconsistency. A paraconsistent logic is a logic where an inconsistency does not lead to such an explosion, and since in practice consistency is difficult to achieve there are many potential applications of paraconsistent logics in knowledge-based systems, logical semantics of natural language, etc. Higher order logics have the advantages of being expressive and with several automated theorem provers available. Also the type system can be helpful. We present a concise description of a paraconsistent higher order logic with countable infinite indeterminacy, where each basic formula can get its own indeterminate truth value (or as we prefer: truth code). The meaning of the logical operators is new and rather different from traditional many-valued logics as well as from logics based on bilattices. The adequacy of the logic is examined by a case study in the domain of medicine. Thus we try to build a bridge between the HOL and MVL communities. A sequent calculus is proposed based on recent work by Muskens.Comment: Originally in the proceedings of PCL 2002, editors Hendrik Decker, Joergen Villadsen, Toshiharu Waragai (http://floc02.diku.dk/PCL/). Correcte

NGN, QCD_2 and chiral phase transition from string theory

We construct a D2-D8-$\bar{D8}$ configuration in string theory, it can be described at low energy by two dimensional field theory. In the weak coupling region, the low energy theory is a nonlocal generalization of Gross-Neveu(GN) model which dynamically breaks the chiral flavor symmetry $U(N_f)_L \times U(N_f)_R$ at large $N_c$ and finite $N_f$. However, in the strong coupling region, we can use the SUGRA/Born-Infeld approximation to describe the low energy dynamics of the system. Also, we analyze the low energy dynamics about the configuration of wrapping the one direction of D2 brane on a circle with anti-periodic boundary condition of fermions. The fermions and scalars on D2 branes get mass and decouple from the low energy theory. The IR dynamics is described by the $QCD_2$ at weak coupling. In the opposite region, the dynamics has a holographic dual description. And we have discussed the phase transition of chiral symmetry breaking at finite temperature. Finally, after performing T-duality, this configuration is related to some other brane configurations.Comment: 30 pages, 3 figures, minor change

Parity Violation in Proton-Proton Scattering

Measurements of parity-violating longitudinal analyzing powers (normalized asymmetries) in polarized proton-proton scattering provide a unique window on the interplay between the weak and strong interactions between and within hadrons. Several new proton-proton parity violation experiments are presently either being performed or are being prepared for execution in the near future: at TRIUMF at 221 MeV and 450 MeV and at COSY (Kernforschungsanlage Juelich) at 230 MeV and near 1.3 GeV. These experiments are intended to provide stringent constraints on the set of six effective weak meson-nucleon coupling constants, which characterize the weak interaction between hadrons in the energy domain where meson exchange models provide an appropriate description. The 221 MeV is unique in that it selects a single transition amplitude (3P2-1D2) and consequently constrains the weak meson-nucleon coupling constant h_rho{pp}. The TRIUMF 221 MeV proton-proton parity violation experiment is described in some detail. A preliminary result for the longitudinal analyzing power is Az = (1.1 +/-0.4 +/-0.4) x 10^-7. Further proton-proton parity violation experiments are commented on. The anomaly at 6 GeV/c requires that a new multi-GeV proton-proton parity violation experiment be performed.Comment: 13 Pages LaTeX, 5 PostScript figures, uses espcrc1.sty. Invited talk at QULEN97, International Conference on Quark Lepton Nuclear Physics -- Nonperturbative QCD Hadron Physics & Electroweak Nuclear Processes --, Osaka, Japan May 20--23, 199

Genetic variation at MECOM, TERT, JAK2 and HBS1L-MYB predisposes to myeloproliferative neoplasms

Clonal proliferation in myeloproliferative neoplasms (MPN) is driven by somatic mutations in JAK2, CALR or MPL, but the contribution of inherited factors is poorly characterized. Using a three-stage genome-wide association study of 3,437 MPN cases and 10,083 controls, we identify two SNPs with genome-wide significance in JAK2V617F-negative MPN: rs12339666 (JAK2; meta-analysis P=1.27 × 10−10) and rs2201862 (MECOM; meta-analysis P=1.96 × 10−9). Two additional SNPs, rs2736100 (TERT) and rs9376092 (HBS1L/MYB), achieve genome-wide significance when including JAK2V617F-positive cases. rs9376092 has a stronger effect in JAK2V617F-negative cases with CALR and/or MPL mutations (Breslow–Day P=4.5 × 10−7), whereas in JAK2V617F-positive cases rs9376092 associates with essential thrombocythemia (ET) rather than polycythemia vera (allelic χ2 P=7.3 × 10−7). Reduced MYB expression, previously linked to development of an ET-like disease in model systems, associates with rs9376092 in normal myeloid cells. These findings demonstrate that multiple germline variants predispose to MPN and link constitutional differences in MYB expression to disease phenotype

Dynamical modelling of the elliptical galaxy NGC 2974

In this paper we analyse the relations between a previously described oblate Jaffe model for an ellipsoidal galaxy and the observed quantities for NGC 2974, and obtain the length and velocity scales for a relevant elliptical galaxy model. We then derive the finite total mass of the model from these scales, and finally find a good fit of an isotropic oblate Jaffe model by using the Gauss-Hermite fit parameters and the observed ellipticity of the galaxy NGC 2974. The model is also used to predict the total luminous mass of NGC 2974, assuming that the influence of dark matter in this galaxy on the image, ellipticity and Gauss-Hermite fit parameters of this galaxy is negligible within the central region, of radius $0.5R_{\rm e}.$Comment: 7 figure

Jamming at Zero Temperature and Zero Applied Stress: the Epitome of Disorder

We have studied how 2- and 3- dimensional systems made up of particles interacting with finite range, repulsive potentials jam (i.e., develop a yield stress in a disordered state) at zero temperature and applied stress. For each configuration, there is a unique jamming threshold, $\phi_c$, at which particles can no longer avoid each other and the bulk and shear moduli simultaneously become non-zero. The distribution of $\phi_c$ values becomes narrower as the system size increases, so that essentially all configurations jam at the same $\phi$ in the thermodynamic limit. This packing fraction corresponds to the previously measured value for random close-packing. In fact, our results provide a well-defined meaning for "random close-packing" in terms of the fraction of all phase space with inherent structures that jam. The jamming threshold, Point J, occurring at zero temperature and applied stress and at the random close-packing density, has properties reminiscent of an ordinary critical point. As Point J is approached from higher packing fractions, power-law scaling is found for many quantities. Moreover, near Point J, certain quantities no longer self-average, suggesting the existence of a length scale that diverges at J. However, Point J also differs from an ordinary critical point: the scaling exponents do not depend on dimension but do depend on the interparticle potential. Finally, as Point J is approached from high packing fractions, the density of vibrational states develops a large excess of low-frequency modes. All of these results suggest that Point J may control behavior in its vicinity-perhaps even at the glass transition.Comment: 21 pages, 20 figure

On non-local variational problems with lack of compactness related to non-linear optics

We give a simple proof of existence of solutions of the dispersion manage- ment and diffraction management equations for zero average dispersion, respectively diffraction. These solutions are found as maximizers of non-linear and non-local vari- ational problems which are invariant under a large non-compact group. Our proof of existence of maximizer is rather direct and avoids the use of Lions' concentration compactness argument or Ekeland's variational principle.Comment: 30 page