iTriplet, a rule-based nucleic acid sequence motif finder

<p>Abstract</p> <p>Background</p> <p>With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete identification a computationally challenging problem. Many attempts in using statistical or combinatorial approaches have been made with great success in the past. However, identifying highly degenerate and long (>20 nucleotides) motifs still remains an unmet challenge as high degeneracy will diminish statistical significance of biological signals and increasing motif size will cause combinatorial explosion. In this report, we present a novel rule-based method that is focused on finding degenerate and long motifs. Our proposed method, named iTriplet, avoids costly enumeration present in existing combinatorial methods and is amenable to parallel processing.</p> <p>Results</p> <p>We have conducted a comprehensive assessment on the performance and sensitivity-specificity of iTriplet in analyzing artificial and real biological sequences in various genomic regions. The results show that iTriplet is able to solve challenging cases. Furthermore we have confirmed the utility of iTriplet by showing it accurately predicts polyA-site-related motifs using a dual Luciferase reporter assay.</p> <p>Conclusion</p> <p>iTriplet is a novel rule-based combinatorial or enumerative motif finding method that is able to process highly degenerate and long motifs that have resisted analysis by other methods. In addition, iTriplet is distinguished from other methods of the same family by its parallelizability, which allows it to leverage the power of today's readily available high-performance computing systems.</p

Micro–Raman Spectroscopy of Diamonds from JaH 054 and Sahara 98505 Ureilites, Statistic Research

In this paper Raman spectra of diamonds from two different ureilites, JaH 054 and Sahara 98505, were measured. Obtained results for both ureilites showed the Raman shift ranged between 1321 cm -1 and 1336 cm -1 for JaH 054 and between 1329 cm -1 and 1336 cm -1 for Sahara 98505. FWHM parameter (full width at half maximum) varied also in wide range especially for Sahara 98505. Raman imaging was done for JaH 054 sample and diamonds of different Raman shifts (1321 cm-1, 1328 cm-1, 1330 cm-1) were found in few tens (im sized area of carbon vein. Raman peaks of ureilitic diamonds were compared with literature data of laboratory diamonds produced under high pressure, under low pressure with MW PACVD method and with other ureilites. Presented research showed that even in highly shocked ureilites Raman shift versus FWHM parameter plots are similar with CVD diamonds for ureilites. However, the origin of diamonds in ureilites is not explained based on the obtained results, close coexistence of different diamonds in investigated ureilites suggests that the mechanism of diamond creation in meteorites was very complex and could be multi-step process

Effect of resonant magnetic perturbations on low collisionality discharges in MAST and a comparison with ASDEX Upgrade

Sustained ELM mitigation has been achieved on MAST and AUG using RMPs with a range of toroidal mode numbers over a wide region of low to medium collisionality discharges. The ELM energy loss and peak heat loads at the divertor targets have been reduced. The ELM mitigation phase is typically associated with a drop in plasma density and overall stored energy. In one particular scenario on MAST, by carefully adjusting the fuelling it has been possible to counteract the drop in density and to produce plasmas with mitigated ELMs, reduced peak divertor heat flux and with minimal degradation in pedestal height and confined energy. While the applied resonant magnetic perturbation field can be a good indicator for the onset of ELM mitigation on MAST and AUG there are some cases where this is not the case and which clearly emphasise the need to take into account the plasma response to the applied perturbations. The plasma response calculations show that the increase in ELM frequency is correlated with the size of the edge peeling-tearing like response of the plasma and the distortions of the plasma boundary in the X-point region.Comment: 31 pages, 28 figures. This is an author-created, un-copyedited version of an article submitted for publication in Nuclear Fusion. IoP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from i

Search for a Scalar Bottom Quark with Mass 3.5-4.5 GeV/c2c^{2}

We report on a search for a supersymmetric $\tilde{B}$ meson with mass between 3.5 and 4.5 GeV/$c^2$ using 4.52 ${\rm fb}^{-1}$ of integrated luminosity produced at $\sqrt{s}=10.52$ GeV, just below the $e^+e^-\to B\bar{B}$ threshold, and collected with the CLEO detector. We find no evidence for a light scalar bottom quark.Comment: 10 pages postscript, also available through http://w4.lns.cornell.edu/public/CLN

Multiscale Systems, Homogenization, and Rough Paths:VAR75 2016: Probability and Analysis in Interacting Physical Systems

In recent years, substantial progress was made towards understanding convergence of fast-slow deterministic systems to stochastic differential equations. In contrast to more classical approaches, the assumptions on the fast flow are very mild. We survey the origins of this theory and then revisit and improve the analysis of Kelly-Melbourne [Ann. Probab. Volume 44, Number 1 (2016), 479-520], taking into account recent progress in $p$-variation and c\`adl\`ag rough path theory.Comment: 27 pages. Minor corrections. To appear in Proceedings of the Conference in Honor of the 75th Birthday of S.R.S. Varadha

Study of e+e- --> pi+ pi- pi0 process using initial state radiation with BABAR

The process e+e- --> pi+ pi- pi0 gamma has been studied at a center-of-mass energy near the Y(4S) resonance using a 89.3 fb-1 data sample collected with the BaBar detector at the PEP-II collider. From the measured 3pi mass spectrum we have obtained the products of branching fractions for the omega and phi mesons, B(omega --> e+e-)B(omega --> 3pi)=(6.70 +/- 0.06 +/- 0.27)10-5 and B(phi --> e+e-)B(phi --> 3pi)=(4.30 +/- 0.08 +/- 0.21)10-5, and evaluated the e+e- --> pi+ pi- pi0 cross section for the e+e- center-of-mass energy range 1.05 to 3.00 GeV. About 900 e+e- --> J/psi gamma --> pi+ pi- pi0 gamma events have been selected and the branching fraction B(J/psi --> pi+ pi- pi0)=(2.18 +/- 0.19)% has been measured.Comment: 21 pages, 37 postscript figues, submitted to Phys. Rev.