Genome Reference and Sequence Variation in the Large Repetitive Central Exon of Human MUC5AC

Despite modern sequencing efforts, the difficulty in assembly of highly repetitive sequences has prevented resolution of human genome gaps, including some in the coding regions of genes with important biological functions. One such gene, MUC5AC, encodes a large, secreted mucin, which is one of the two major secreted mucins in human airways. The MUC5AC region contains a gap in the human genome reference (hg19) across the large, highly repetitive, and complex central exon. This exon is predicted to contain imperfect tandem repeat sequences and multiple conserved cysteine-rich (CysD) domains. To resolve the MUC5AC genomic gap, we used high-fidelity long PCR followed by single molecule real-time (SMRT) sequencing. This technology yielded long sequence reads and robust coverage that allowed for de novo sequence assembly spanning the entire repetitive region. Furthermore, we used SMRT sequencing of PCR amplicons covering the central exon to identify genetic variation in four individuals. The results demonstrated the presence of segmental duplications of CysD domains, insertions/deletions (indels) of tandem repeats, and single nucleotide variants. Additional studies demonstrated that one of the identified tandem repeat insertions is tagged by nonexonic single nucleotide polymorphisms. Taken together, these data illustrate the successful utility of SMRT sequencing long reads for de novo assembly of large repetitive sequences to fill the gaps in the human genome. Characterization of the MUC5AC gene and the sequence variation in the central exon will facilitate genetic and functional studies for this critical airway mucin

Massively parallel full-wave modeling of advanced packaging structures on BlueGene supercomputer

A parallel, distributed memory version of a full wave Method of Moments (MoM) solution combined with the Reduced Coupling approximation technique is presented on the largest parallel-server. Modeling results for product-level simulation of a single-chip module are correlated with time-domain measurements for validation of the technique. Scaling for this and other representative examples are shown for up to 16,384 compute nodes on IBM's BlueGene supercomputer, the largest parallel-platform ever reported for MoM based solutions. © 2008 IEEE.link_to_subscribed_fulltex

Monte Carlo Least-Squares Fitting of Experimental Signal Waveforms

This paper focuses on why the regular least–squares fitting technique is unstable when used to fit exponential functions to signal waveforms, since such functions are highly correlated. It talks about alternative approaches, such as the search method, which has a slow convergence rate of 1/N1/M, for M parameters, where N is the number of computations performed. We have used the Monte Carlo method, utilizing both search and random walk, to devise a stable least–squares fitting algorithm that converges rapidly at a rate 1/N1/2, regardless of the number of parameters used in fitting the waveforms. The Monte Carlo approach has been tested for computed data—with and without noise, and by fitting actual experimental signal waveforms associated with optogalvanic transitions recorded with a hollow cathode discharge tube containing a mixture of neon (Ne) and carbon monoxide (CO) gases, and has yielded excellent results, making the developed algorithm both stable and fast for today’s personal computers

ANALYSIS OF THE PERTURBATIONS IN THE A1ΠA^{1}\Pi STATE OF 13C18O^{13}C^{18}O

Author Institution: Department of physics and Physical Oceanography, Memorial University of Newfoundland; Department of physics and Physical Oceanography, Steacie Institute of Molecular Sciences; Department de Physique, Universit\'{e} de ToursThe vacuum ultraviolet spectrum of the fourth positive $(A^{1}\Pi-X^{1}\Sigma^{+})$ system of $^{13}C ^{18}O$ generated in emission in a jet discharge apparatus was photographed in the spectral region 1460-1670 {\AA} for the first time on a 10.6 m vacuum grating spectrograph. Detailed rotational analysis of nineteen bands involving seven vibrational levels ($v=0,1,2,4,6,7$, and 9) of the $A^{1}\Pi$ state was carried out. Several perturbations occurring in the $A^{1}\Pi$ state due to its neighbouring states $e^{3}\Sigma, a^{3} \Sigma^{+}, d^{3}\Delta_{i} I ^{1}\Sigma$ and $D^{1} \Delta$ were observed. The 1-0 band of the intercombination system $e^{3} \Sigma^{-} - X^{1} \Sigma^{\prime}$ was observed because of ``intensity borrowing” from the A-X system. From a deperturbation analysis, depertured molecular constants were obtained for the specified seven vibrational levels as well as for the perturbating states. Perturbation parameters and mixing coefficients which characterize the perturbations were also derived