School of Physics - Research Publications
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ItemStatistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis(BMC, 2006-11-22)BACKGROUND: Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for these technologies on a whole-array basis. RESULTS: A methodology is described for evaluating the precision and sensitivity of whole-genome gene expression technologies such as microarrays. The method consists of an easy-to-construct titration series of RNA samples and an associated statistical analysis using non-linear regression. The method evaluates the precision and responsiveness of each microarray platform on a whole-array basis, i.e., using all the probes, without the need to match probes across platforms. An experiment is conducted to assess and compare four widely used microarray platforms. All four platforms are shown to have satisfactory precision but the commercial platforms are superior for resolving differential expression for genes at lower expression levels. The effective precision of the two-color platforms is improved by allowing for probe-specific dye-effects in the statistical model. The methodology is used to compare three data extraction algorithms for the Affymetrix platforms, demonstrating poor performance for the commonly used proprietary algorithm relative to the other algorithms. For probes which can be matched across platforms, the cross-platform variability is decomposed into within-platform and between-platform components, showing that platform disagreement is almost entirely systematic rather than due to measurement variability. CONCLUSION: The results demonstrate good precision and sensitivity for all the platforms, but highlight the need for improved probe annotation. They quantify the extent to which cross-platform measures can be expected to be less accurate than within-platform comparisons for predicting disease progression or outcome.
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ItemStringent constraints on cosmological neutrino-antineutrino asymmetries from synchronized flavor transformation(AMER PHYSICAL SOC, 2002-07-01)We assess a mechanism which can transform neutrino-antineutrino asymmetries between flavors in the early universe, and confirm that such transformation is unavoidable in the near bi-maximal framework emerging for the neutrino mixing matrix. We show that the process is a standard Mikheyev-Smirnov-Wolfenstein flavor transformation dictated by a synchronization of momentum states. We also show that flavor ``equilibration'' is a special feature of maximal mixing, and carefully examine new constraints placed on neutrino asymmetries. In particular, the big bang nucleosynthesis limit on electron neutrino degeneracy xi_e < 0.04 does not apply directly to all flavors, yet confirmation of the large-mixing-angle solution to the solar neutrino problem will eliminate the possibility of degenerate big bang nucleosynthesis.
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ItemRecovering physical parameters from galaxy spectra using MOPED(BLACKWELL SCIENCE LTD, 2001-11-01)We derive physical parameters of galaxies from their observed spectrum, using MOPED, the optimized data compression algorithm of Heavens, Jimenez & Lahav 2000. Here we concentrate on parametrising galaxy properties, and apply the method to the NGC galaxies in Kennicutt's spectral atlas. We focus on deriving the star formation history, metallicity and dust content of galaxies. The method is very fast, taking a few seconds of CPU time to estimate 17 parameters, and so specially suited to study of large data sets, such as the Anglo-Australian 2 degree field galaxy survey and the Sloan Digital Sky Survey. Without the power of MOPED, the recovery of star formation histories in these surveys would be impractical. In the Kennicutt atlas, we find that for the spheroidals a small recent burst of star formation is required to provide the best fit to the spectrum. There is clearly a need for theoretical stellar atmospheric models with spectral resolution better than 1\AA if we are to extract all the rich information that large redshift surveys contain in their galaxy spectra.
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ItemEnergy transfer up-conversion in Tm3+-doped silica fiber(ELSEVIER SCIENCE BV, 2006-02-01)A study of the mechanisms responsible for the infra-red to near infra-red up-conversion in Tm3+-doped silica fibers is presented. Upconversion luminescence was observed from the 3H4 level of Tm3+ under 1586 nm pumping into the 3F4 level. The quadratic dependence of the up-conversion luminescence at 800 nm on the 1800 nm luminescence from the 3F4 level confirms that the 3H4 level is populated by a two photon process. Two possible processes are proposed as mechanisms responsible for the up-conversion: excited state absorption and energy transfer up-conversion. The decay characteristics of the luminescence from the 3H4 level were studied under direct and indirect pumping at 786 and 1586 nm, respectively. By comparing the decay waveforms to the solution of a simple set of rate equations, the energy transfer up-conversion process (3F4, 3F4 ! 3H4, 3H6) was established at Tm2O3 concentrations greater than 200 ppm.
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ItemCharge and low-frequency response of normal-superconducting heterostructures -: art. no. 045321(AMER PHYSICAL SOC, 2002-01-15)
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ItemNonlinear hole transport through a submicron-size channel(AMER INST PHYSICS, 2003-02-10)We investigate hole transport through a submicron-size channel fabricated from a modulation-doped p-type GaAs/(AlGa)As single-quantum-well heterostructure. The intense electric field in the channel accelerates the holes beyond the inflection point of the lowest energy subband dispersion curve. This leads to current saturation and negative differential conduction effects in the current–voltage characteristics.
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ItemModel for the voltage steps in the breakdown of the integer quantum Hall effect(AMERICAN PHYSICAL SOC, 2003-09-19)In samples used to maintain the U.S. resistance standard the breakdown of the dissipationless integer quantum Hall effect occurs as a series of dissipative voltage steps. A mechanism for this type of breakdown is proposed, based on the generation of magnetoexcitons when the quantum Hall fluid flows past an ionized impurity above a critical velocity. The calculated generation rate gives a voltage step height in good agreement with measurements on both electron and hole gases. We also compare this model to a hydrodynamic description of breakdown.
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ItemCreation of solitons and vortices by Bragg reflection of Bose-Einstein condensates in an optical lattice(AMERICAN PHYSICAL SOC, 2003-03-21)We study the dynamics of Bose-Einstein condensates in an optical lattice and harmonic trap. The condensates are set in motion by displacing the trap and initially follow simple semiclassical paths, shaped by the lowest energy band. Above a critical displacement, the condensate undergoes Bragg reflection. For high atom densities, the first Bragg reflection generates a train of solitons and vortices, which destabilize the condensate and trigger explosive expansion. At lower densities, soliton and vortex formation requires multiple Bragg reflections, and damps the center-of-mass motion.
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ItemTransport and disruption of Bose-Einstein condensates in optical lattices(AMER PHYSICAL SOC, 2004-03)
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ItemEffect of soliton and vortex geometry on the transport of Bose-Einstein condensates in optical lattices(AMER PHYSICAL SOC, 2004-06)