A weighted q-gram method for glycan structure classification

<p>Abstract</p> <p>Background</p> <p>Glycobiology pertains to the study of carbohydrate sugar chains, or glycans, in a particular cell or organism. Many computational approaches have been proposed for analyzing these complex glycan structures, which are chains of monosaccharides. The monosaccharides are linked to one another by glycosidic bonds, which can take on a variety of comformations, thus forming branches and resulting in complex tree structures. The <it>q</it>-gram method is one of these recent methods used to understand glycan function based on the classification of their tree structures. This <it>q</it>-gram method assumes that for a certain <it>q</it>, different <it>q</it>-grams share no similarity among themselves. That is, that if two structures have completely different components, then they are completely different. However, from a biological standpoint, this is not the case. In this paper, we propose a weighted <it>q</it>-gram method to measure the similarity among glycans by incorporating the similarity of the geometric structures, monosaccharides and glycosidic bonds among <it>q</it>-grams. In contrast to the traditional <it>q</it>-gram method, our weighted <it>q</it>-gram method admits similarity among <it>q</it>-grams for a certain <it>q</it>. Thus our new kernels for glycan structure were developed and then applied in SVMs to classify glycans.</p> <p>Results</p> <p>Two glycan datasets were used to compare the weighted <it>q</it>-gram method and the original <it>q</it>-gram method. The results show that the incorporation of <it>q</it>-gram similarity improves the classification performance for all of the important glycan classes tested.</p> <p>Conclusion</p> <p>The results in this paper indicate that similarity among <it>q</it>-grams obtained from geometric structure, monosaccharides and glycosidic linkage contributes to the glycan function classification. This is a big step towards the understanding of glycan function based on their complex structures.</p

Standard Model Contributions to the Neutrino Index of Refraction in the Early Universe

With the standard electroweak interactions, the lowest-order coherent forward scattering amplitudes of neutrinos in a CP symmetric medium (such as the early universe) are zero, and the index of refraction of a propagating neutrino can only arise from the expansion of gauge boson propagators, from radiative corrections, and from new physics interactions. Motivated by nucleosynthesis constraints on a possible sterile neutrino (suggested by the solar neutrino deficit and a possible $17\ keV$ neutrino), we calculate the standard model contributions to the neutrino index of refraction in the early universe, focusing on the period when the temperature was of the order of a few $MeV$. We find sizable radiative corrections to the tree level result obtained by the expansion of the gauge boson propagator. For $\nu_e+e(\bar{e})\to \nu_e+e(\bar{e})$ the leading log correction is about $+10\%$, while for $\nu_e+\nu_e(\bar{\nu}_e)\to \nu_e+\nu_e(\bar{\nu}_e)$ the correction is about $+20\%$. Depending on the family mixing (if any), effects from different family scattering can be dominated by radiative corrections. The result for $\nu+\gamma\to\nu+\gamma$ is zero at one-loop level, even if neutrinos are massive. The cancellation of infrared divergence in a coherent process is also discussed.Comment: 46pp, 13 figures (not included), UPR-0495

Measurement of Inclusive Production of Neutral Pions from Upsilon(4S) Decays

Using the Belle detector operating at the KEKB e+e- storage ring, we have measured the mean multiplicity and the momentum spectrum of neutral pions from the decays of the Upsilon(4S) resonance. We measure a mean of 4.70 +/- 0.04 +/- 0.22 neutral pions per Upsilon(4S) decay.Comment: 15 pages, 4 figs. Submitted to Phys.Rev.

Astrometry and geodesy with radio interferometry: experiments, models, results

Summarizes current status of radio interferometry at radio frequencies between Earth-based receivers, for astrometric and geodetic applications. Emphasizes theoretical models of VLBI observables that are required to extract results at the present accuracy levels of 1 cm and 1 nanoradian. Highlights the achievements of VLBI during the past two decades in reference frames, Earth orientation, atmospheric effects on microwave propagation, and relativity.Comment: 83 pages, 19 Postscript figures. To be published in Rev. Mod. Phys., Vol. 70, Oct. 199

Measurement of B0d - B0d-bar mixing rate from the time evolution of dilepton events at the Upsilon(4S)

We report a determination of the B0d - B0d-bar mixing parameter Delta-m_d based on the time evolution of dilepton yields in Upsilon(4S) decays. The measurement is based on a 5.9 /fb data sample collected by the Belle detector at KEKB. The proper-time difference distributions for same-sign and opposite-sign dilepton events are simultaneously fitted to an expression containing Delta-m_d as a free parameter. Using both muons and electrons, we obtain Delta-m_d = 0.463 +- 0.008(stat.) +- 0.016(sys.) ps^{-1} This is the first determination of Delta-m_d from time evolution measurements at the Upsilon(4S). We also place limits on possible CPT violations.Comment: 12 pages, 2 figure

Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology

The study of the pearl oyster Pinctada fucata is key to increasing our understanding of the molecular mechanisms involved in pearl biosynthesis and biology of bivalve molluscs. We sequenced ∼1150-Mb genome at ∼40-fold coverage using the Roche 454 GS-FLX and Illumina GAIIx sequencers. The sequences were assembled into contigs with N50 = 1.6 kb (total contig assembly reached to 1024 Mb) and scaffolds with N50 = 14.5 kb. The pearl oyster genome is AT-rich, with a GC content of 34%. DNA transposons, retrotransposons, and tandem repeat elements occupied 0.4, 1.5, and 7.9% of the genome, respectively (a total of 9.8%). Version 1.0 of the P. fucata draft genome contains 23 257 complete gene models, 70% of which are supported by the corresponding expressed sequence tags. The genes include those reported to have an association with bio-mineralization. Genes encoding transcription factors and signal transduction molecules are present in numbers comparable with genomes of other metazoans. Genome-wide molecular phylogeny suggests that the lophotrochozoan represents a distinct clade from ecdysozoans. Our draft genome of the pearl oyster thus provides a platform for the identification of selection markers and genes for calcification, knowledge of which will be important in the pearl industry

A Measurement of the Branching Fraction for the Inclusive B --> X(s) gamma Decays with the Belle Detector

We have measured the branching fraction of the inclusive radiative B meson decay B --> X(s) gamma to be Br(B->X(s)gamma)=(3.36 +/- 0.53(stat) +/- 0.42(sys) +0.50-0.54(th)) x 10^{-4}. The result is based on a sample of 6.07 x 10^6 BBbar events collected at the Upsilon(4S) resonance with the Belle detector at the KEKB asymmetric e^+e^- storage ring.Comment: 14 pages, 6 Postsript figures, uses elsart.cl

Measurement of the CP Violation Parameter sin(2phi_1) in B^0_d Meson Decays

We present a measurement of the Standard Model CP violation parameter sin(2phi_1) based on a 10.5 fb^{-1} data sample collected at the Upsilon(4S) resonance with the Belle detector at the KEKB asymmetric e+e- collider. One neutral B meson is reconstructed in the J/psi K_S, psi(2S) K_S, chi_{c1} K_S, eta_c K_S, J/psi K_L or J/psi pi^0 CP-eigenstate decay channel and the flavor of the accompanying B meson is identified from its charged particle decay products. From the asymmetry in the distribution of the time interval between the two B-meson decay points, we determine sin(2phi_1) = 0.58 +0.32-0.34 (stat) +0.09-0.10 (syst).Comment: LaTex, 13 pages, 3 figures, submitted to P.R.

Identification of Genes Required for Neural-Specific Glycosylation Using Functional Genomics

Glycosylation plays crucial regulatory roles in various biological processes such as development, immunity, and neural functions. For example, α1,3-fucosylation, the addition of a fucose moiety abundant in Drosophila neural cells, is essential for neural development, function, and behavior. However, it remains largely unknown how neural-specific α1,3-fucosylation is regulated. In the present study, we searched for genes involved in the glycosylation of a neural-specific protein using a Drosophila RNAi library. We obtained 109 genes affecting glycosylation that clustered into nine functional groups. Among them, members of the RNA regulation group were enriched by a secondary screen that identified genes specifically regulating α1,3-fucosylation. Further analyses revealed that an RNA–binding protein, second mitotic wave missing (Swm), upregulates expression of the neural-specific glycosyltransferase FucTA and facilitates its mRNA export from the nucleus. This first large-scale genetic screen for glycosylation-related genes has revealed novel regulation of fucTA mRNA in neural cells