Next-generation sequencing of dsRNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO.

dsRNA is the genetic material of important viruses and a key component of RNA interference-based immunity in eukaryotes. Previous studies have noted difficulties in determining the sequence of dsRNA molecules that have affected studies of immune function and estimates of viral diversity in nature. DMSO has been used to denature dsRNA prior to the reverse-transcription stage to improve reverse transcriptase PCR and Sanger sequencing. We systematically tested the utility of DMSO to improve the sequencing yield of a dsRNA virus (Φ6) in a short-read next-generation sequencing platform. DMSO treatment improved sequencing read recovery by over two orders of magnitude, even when RNA and cDNA concentrations were below the limit of detection. We also tested the effects of DMSO on a mock eukaryotic viral community and found that dsRNA virus reads increased with DMSO treatment. Furthermore, we provide evidence that DMSO treatment does not adversely affect recovery of reads from a ssRNA viral genome (influenza A/California/07/2009). We suggest that up to 50 % DMSO treatment be used prior to cDNA synthesis when samples of interest are composed of or may contain dsRNA

Enhanced Parallel Generation of Tree Structures for the Recognition of 3D Images

Segmentations of a digital object based on a connectivity criterion at n-xel or sub-n-xel level are useful tools in image topological analysis and recognition. Working with cell complex analogous of digital objects, an example of this kind of segmentation is that obtained from the combinatorial representation so called Homological Spanning Forest (HSF, for short) which, informally, classifies the cells of the complex as belonging to regions containing the maximal number of cells sharing the same homological (algebraic homology with coefficient in a field) information. We design here a parallel method for computing a HSF (using homology with coefficients in Z/2Z) of a 3D digital object. If this object is included in a 3D image of m1 × m2 × m3 voxels, its theoretical time complexity order is near O(log(m1 + m2 + m3)), under the assumption that a processing element is available for each voxel. A prototype implementation validating our results has been written and several synthetic, random and medical tridimensional images have been used for testing. The experiments allow us to assert that the number of iterations in which the homological information is found varies only to a small extent from the theoretical computational time.Ministerio de Economía y Competitividad MTM2016-81030-

Catalogue of the morphological features in the Spitzer Survey of Stellar Structure in Galaxies (S4^4G)

A catalogue of the morphological features for the complete Spitzer Survey of Stellar Structure in Galaxies (S$^4$G), including 2352 nearby galaxies, is presented. The measurements are made using 3.6 $\mu$m images, largely tracing the old stellar population; at this wavelength the effects of dust are also minimal. The measured features are the sizes, ellipticities, and orientations of bars, rings, ringlenses, and lenses. Measured in a similar manner are also barlenses (lens-like structures embedded in the bars), which are not lenses in the usual sense, being rather the more face-on counterparts of the boxy/peanut structures in the edge-on view. In addition, pitch angles of spiral arm segments are measured for those galaxies where they can be reliably traced. More than one pitch angle may appear for a single galaxy. All measurements are made in a human-supervised manner so that attention is paid to each galaxy. We used isophotal analysis, unsharp masking, and fitting ellipses to measured structures. We find that the sizes of the inner rings and lenses normalized to barlength correlate with the galaxy mass: the normalized sizes increase toward the less massive galaxies; it has been suggested that this is related to the larger dark matter content in the bar region in these systems. Bars in the low mass galaxies are also less concentrated, likely to be connected to the mass cut-off in the appearance of the nuclear rings and lenses. We also show observational evidence that barlenses indeed form part of the bar, and that a large fraction of the inner lenses in the non-barred galaxies could be former barlenses in which the thin outer bar component has dissolved.Comment: 17 pages, 12 figures, accepted for publication in A&

Tissue-nonspecific alkaline phosphatase promotes axonal growth of hippocampal neurons

Axonal growth is essential for establishing neuronal circuits during brain development and for regenerative processes in the adult brain. Unfortunately, the extracellular signals controlling axonal growth are poorly understood. Here we report that a reduction in extracellular ATP levels by tissue-nonspecific alkaline phosphatase (TNAP) is essential for the development of neuritic processes by cultured hippocampal neurons. Selective blockade of TNAP activity with levamisole or specific TNAP knockdown with short hairpin RNA interference inhibited the growth and branching of principal axons, whereas addition of alkaline phosphatase (ALP) promoted axonal growth. Neither activation nor inhibition of adenosine receptors affected the axonal growth, excluding the contribution of extracellular adenosine as a potential hydrolysis product of extracellular ATP to the TNAP-mediated effects. TNAP was colocalized at axonal growth cones with ionotropic ATP receptors (P2X7 receptor), whose activation inhibited axonal growth. Additional analyses suggested a close functional interrelation of TNAP and P2X7 receptors whereby TNAP prevents P2X7 receptor activation by hydrolyzing ATP in the immediate environment of the receptor. Furthermore inhibition of P2X7 receptor reduced TNAP expression, whereas addition of ALP enhanced P2X7 receptor expression. Our results demonstrate that TNAP, regulating both ligand availability and protein expression of P2X7 receptor, is essential for axonal development

Feynman-Jackson integrals

We introduce perturbative Feynman integrals in the context of q-calculus generalizing the Gaussian q-integrals introduced by Diaz and Teruel. We provide analytic as well as combinatorial interpretations for the Feynman-Jackson integrals.Comment: Final versio

Extraction of P11 Resonance from pi-N Data and Its Stability

An important question about resonance extraction is how much resonance poles and residues extracted from data depend on a model used for the extraction, and on the precision of data. We address this question with the dynamical coupled-channel (DCC) model developed in Excited Baryon Analysis Center (EBAC) at JLab. We focus on the P11 pi-N scattering. We examine the model-dependence of the poles by varying parameters to a large extent within the EBAC-DCC model. We find that two poles associated with the Roper resonance are fairly stable against the variation. We also develop a model with a bare nucleon, thereby examining the stability of the Roper poles against different analytic structure of the P11 amplitude below pi-N threshold. We again find a good stability of the Roper poles.Comment: 6 pages, 8 figures, Contribution to the proceedings of 24th International Nuclear Physics Conference (INPC), Vancouver, Canada, 4-9 July 201

Double and single pion photoproduction within a dynamical coupled-channels model

Within a dynamical coupled-channels model which has already been fixed from analyzing the data of the pi N -> pi N and gamma N -> pi N reactions, we present the predicted double pion photoproduction cross sections up to the second resonance region, W< 1.7 GeV. The roles played by the different mechanisms within our model in determining both the single and double pion photoproduction reactions are analyzed, focusing on the effects due to the direct gamma N -> pi pi N mechanism, the interplay between the resonant and non-resonant amplitudes, and the coupled-channels effects. The model parameters which can be determined most effectively in the combined studies of both the single and double pion photoproduction data are identified for future studies.Comment: Version to appear in PRC. 16 pages, 13 figure

The little-studied cluster Berkeley 90. II. The foreground ISM

Context: Nearly one century after their discovery, the carrier(s) of Diffuse Interstellar Bands is/are still unknown and there are few sightlines studied in detail for a large number of DIBs. Aims: We want to study the ISM sightlines towards LS III +46 11 and LS III +46 12, two early-O-type stellar systems, and LS III +46 11 B, a mid-B-type star. The three targets are located in the stellar cluster Berkeley 90 and have a high extinction. Methods: We use the multi-epoch high-S/N optical spectra presented in paper I (Ma\'iz Apell\'aniz et al. 2015), the extinction results derived there, and additional spectra. Results: We have measured equivalent widths, velocities, and FWHMs for a large number of absorption lines in the rich ISM spectrum in front of Berkeley 90. The absorbing ISM has at least two clouds at different velocities, one with a lower column density (thinner) in the K I lines located away from Berkeley 90 and another one with a higher column density (thicker) associated with the cluster. The first cloud has similar properties for both O-star sightlines but the second one is thicker for LS III +46 11. The comparison between species indicate that the cloud with a higher column density has a denser core, allowing us to classify the DIBs in a sigma-zeta scale, some of them for the first time. The LS III +46 12 sightline also has a high-velocity redshifted component.Comment: Accepted for publication in A&

Testing models with non-minimal Higgs sector through the decay t->q+WZ

We study the contribution of charged Higgs boson to the rare decay of the top quark t->q+WZ (q=d,s,b) in models with Higgs sector that includes doublets and triplets. Higgs doublets are needed to couple charged Higgs with quarks, whereas the Higgs triplets are required to generate the non-standard vertex HWZ at tree-level. It is found that within a model that respect the custodial SU(2) symmetry and avoids flavour changing neutral currents by imposing discrete symmetries, the decay mode t->b+WZ, can reach a branching ratio of order 0.0178, whereas the decay modes t->(d,s)+WZ, can reach a similar branching ratio in models where flavour changing neutral currents are suppressed by flavour symmetries.Comment: Typeset using REVTEX and EPSF, 5 pag, 2 figure