A model-based circular binary segmentation algorithm for the analysis of array CGH data

<p>Abstract</p> <p>Background</p> <p>Circular Binary Segmentation (CBS) is a permutation-based algorithm for array Comparative Genomic Hybridization (aCGH) data analysis. CBS accurately segments data by detecting change-points using a maximal-<it>t </it>test; but extensive computational burden is involved for evaluating the significance of change-points using permutations. A recent implementation utilizing a hybrid method and early stopping rules (hybrid CBS) to improve the performance in speed was subsequently proposed. However, a time analysis revealed that a major portion of computation time of the hybrid CBS was still spent on permutation. In addition, what the hybrid method provides is an approximation of the significance upper bound or lower bound, not an approximation of the significance of change-points itself.</p> <p>Results</p> <p>We developed a novel model-based algorithm, extreme-value based CBS (eCBS), which limits permutations and provides robust results without loss of accuracy. Thousands of aCGH data under null hypothesis were simulated in advance based on a variety of non-normal assumptions, and the corresponding maximal-<it>t </it>distribution was modeled by the Generalized Extreme Value (GEV) distribution. The modeling results, which associate characteristics of aCGH data to the GEV parameters, constitute lookup tables (eXtreme model). Using the eXtreme model, the significance of change-points could be evaluated in a constant time complexity through a table lookup process.</p> <p>Conclusions</p> <p>A novel algorithm, eCBS, was developed in this study. The current implementation of eCBS consistently outperforms the hybrid CBS 4× to 20× in computation time without loss of accuracy. Source codes, supplementary materials, supplementary figures, and supplementary tables can be found at <url>http://ntumaps.cgm.ntu.edu.tw/eCBSsupplementary</url>.</p

PmoB subunit of particulate methane monooxygenase (pMMO) in Methylococcus capsulatus (Bath): The Cu^I sponge and its function

In this study, we describe efforts to clarify the role of the copper cofactors associated with subunit B (PmoB) of the particulate methane monooxygenase (pMMO) from Methylococcus capsulatus (Bath) (M. capsulatus). This subunit exhibits strong affinity toward Cu^I ions. To elucidate the high copper affinity of the subunit, the full-length PmoB, and the N-terminal truncated mutants PmoB_(33–414) and PmoB_(55–414), each fused to the maltose-binding protein (MBP), are cloned and over-expressed into Escherichia coli (E. coli) K12 TB1 cells. The Y374F, Y374S and M300L mutants of these protein constructs are also studied. When this E. coli is grown with the pmoB gene in 1.0 mM Cu^(II), it behaves like M. capsulatus (Bath) cultured under high copper stresswith abundant membrane accumulation and high CuI content. The recombinantPmoB proteins are verified by Western blotting of antibodies directed against the MBP sub-domain in each of the copper-enriched PmoB proteins. Cu K-edge X-rayabsorption near edge spectroscopy (XANES) of the copper ions confirms that all the PmoB recombinants are Cu^I proteins. All the PmoB proteins show evidence of a “dicopper site” according to analysis of the Cu extended X-ray absorption edge fine structure (EXAFS) of the membranes. No specific activities toward methane and propene oxidation are observed with the recombinant membrane-bound PmoB proteins. However, significant production of hydrogen peroxide is observed in the case of the PmoB_(33–414) mutant. Reaction of the dicopper site with dioxygenproduces hydrogen peroxide and leads to oxidation of the CuI ions residing in the C-terminal sub-domain of the PmoB subunit

A Close Binary Star Resolved from Occultation by 87 Sylvia

The star BD+29 1748 was resolved to be a close binary from its occultation by the asteroid 87 Sylvia on 2006 December 18 UT. Four telescopes were used to observe this event at two sites separated by some 80 km apart. Two flux drops were observed at one site, whereas only one flux drop was detected at the other. From the long-term variation of Sylvia, we inferred the probable shape of the shadow during the occultation, and this in turn constrains the binary parameters: the two components of BD+29 1748 have a projected separation of 0.097" to 0.110" on the sky with a position angle 104 deg to 107 deg. The asteroid was clearly resolved with a size scale ranging from 130 to 290 km, as projected onto the occultation direction. No occultation was detected for either of the two known moonlets of 87 Sylvia.Comment: 12 pages, 4 figures, 2 tables; submitted to the PAS

Ultra-broadband Light Absorption by a Sawtooth Anisotropic Metamaterial Slab

We present an ultra broadband thin-film infrared absorber made of saw-toothed anisotropic metamaterial. Absorbtivity of higher than 95% at normal incidence is supported in a wide range of frequencies, where the full absorption width at half maximum is about 86%. Such property is retained well at a very wide range of incident angles too. Light of shorter wavelengths are harvested at upper parts of the sawteeth of smaller widths, while light of longer wavelengths are trapped at lower parts of larger tooth widths. This phenomenon is explained by the slowlight modes in anisotropic metamaterial waveguide. Our study can be applied in the field of designing photovoltaic devices and thermal emitters.Comment: 12 pages, 4 picture

Water-Gated Charge Doping of Graphene Induced by Mica Substrates

We report on the existence of water-gated charge doping of graphene deposited on atomically flat mica substrates. Molecular films of water in units of ~0.4 nm-thick bilayers were found to be present in regions of the interface of graphene/mica hetero-stacks prepared by micromechanical exfoliation of kish graphite. The spectral variation of the G and 2D bands, as visualized by Raman mapping, shows that mica substrates induce strong p-type doping in graphene, with hole densities of $(9 \pm 2) \times 1012 cm${-2}$. The ultrathin water films, however, effectively block interfacial charge transfer, rendering graphene significantly less hole-doped. Scanning Kelvin probe microscopy independently confirmed a water-gated modulation of the Fermi level by 0.35 eV, in agreement with the optically determined hole density. The manipulation of the electronic properties of graphene demonstrated in this study should serve as a useful tool in realizing future graphene applications.Comment: 15 pages, 4 figures; Nano Letters, accepted (2012

Composite Dirac Neutrinos

We present a mechanism that naturally produces light Dirac neutrinos. The basic idea is that the right-handed neutrinos are composite. Any realistic composite model must involve `hidden flavor' chiral symmetries. In general some of these symmetries may survive confinement, and in particular, one of them manifests itself at low energy as an exact $B-L$ symmetry. Dirac neutrinos are therefore produced. The neutrinos are naturally light due to compositeness. In general, sterile states are present in the model, some of them can naturally be warm dark matter candidates.Comment: 12 pages; Sec. IIC updated; minor corrections; published versio

Electromagnetic Meson Production in the Nucleon Resonance Region

Recent experimental and theoretical advances in investigating electromagnetic meson production reactions in the nucleon resonance region are reviewed.Comment: 75 pages, 42 figure

Rare B decays and Tevatron top-pair asymmetry

The recent Tevatron result on the top quark forward-backward asymmetry, which deviates from its standard model prediction by 3.4$\sigma$, has prompted many authors to build new models to account for this anomaly. Among the various proposals, we find that those mechanisms which produce $t\bar t$ via $t$- or $u$-channel can have a strong correlation to the rare B decays. We demonstrate this link by studying a model with a new charged gauge boson, $W'$. In terms of the current measurements on $B\to \pi K$ decays, we conclude that the branching ratio for $B^-\to \pi^- \bar K^0$ is affected most by the new effects. Furthermore, using the world average branching ratio for the exclusive B decays at $2\sigma$ level, we discuss the allowed values for the new parameters. Finally, we point out that the influence of the new physics effects on the direct CP asymmetry in B decays is insignificant.Comment: 15 page, 6 figures, typos corrected and references added, final version to appear journa

Semiclassical theory of shot-noise suppression

The Boltzmann-Langevin equation is used to relate the shot-noise power of a mesoscopic conductor to classical transmission probabilities at the Fermi level. This semiclassical theory is applied to tunneling through n barriers in series. For n -> infinity the shot noise approaches one third of the Poisson noise, independent of the transparency of the barriers. This confirms that the one-third suppression known to occur in diffusive conductors does not require phase coherence.Comment: pages, RevTeX, 1 figur