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

A study of the antioxidant capacity of oak wood used in wine ageing and the correlation with polyphenol composition

The antioxidant capacity of oak wood used in the ageing of wine was studied by four different methods: measurement of scavenging capacity against a given radical (ABTS, DPPH), oxygen radical absorbance capacity (ORAC) and the ferric reducing antioxidant power (FRAP). Although, the four methods tested gave comparable results for the antioxidant capacity measured in oak wood extracts, the ORAC method gave results with some differences from the other methods. Non-toasted oak wood samples displayed more antioxidant power than toasted ones due to differences in the polyphenol compositon. A correlation analysis revealed that ellagitannins were the compounds mainly responsible for the antioxidant capacity of oak wood. Some phenolic acids, mainly gallic acid, also showed a significant correlation with antioxidant capacity

Dynamical coupled-channels analysis of 1H(e,e'pi)N reactions

We have performed a dynamical coupled-channels analysis of available p(e,e'pi)N data in the region of W < 1.6 GeV and Q^2 < 1.45 (GeV/c)^2. The channels included are gamma^* N, pi N, eta N, and pi pi N which has pi Delta, rho N, and sigma N components. With the hadronic parameters of the model determined in our previous investigations of pi N --> pi N, pi pi N reactions, we have found that the available data in the considered W < 1.6 GeV region can be fitted well by only adjusting the bare gamma^* N --> N^* helicity amplitudes for the lowest N^* states in P33, P11, S11 and D13 partial waves. The sensitivity of the resulting parameters to the amount of data included in the analysis is investigated. The importance of coupled-channels effect on the p(e,e' pi)N cross sections is demonstrated. The meson cloud effects, as required by the unitarity conditions, on the gamma^* N --> N^* form factors are also examined. Necessary future developments, both experimentally and theoretically, are discussed.Comment: 14 pages, 11 figures. Version to appear in PR

A graceful multiversal link of particle physics to cosmology

In this paper we work out a multiverse scenario whose physical characteristics enable us to advance the following the conjecture that whereas the physics of particles and fields is confined to live in the realm of the whole multiverse formed by finite-time single universes, that for our observable universe must be confined just in one of the infinite number of universes of the multiverse when such a universe is consistently referred to an infinite cosmic time. If this conjecture is adopted then some current fundamental problems that appear when one tries to make compatible particle physics and cosmology- such as that for the cosmological constant, the arrow of time and the existence of a finite proper size of the event horizon- can be solved.Comment: 10 pages, LaTe

A dark energy multiverse

We present cosmic solutions corresponding to universes filled with dark and phantom energy, all having a negative cosmological constant. All such solutions contain infinite singularities, successively and equally distributed along time, which can be either big bang/crunchs or big rips singularities. Classicaly these solutions can be regarded as associated with multiverse scenarios, being those corresponding to phantom energy that may describe the current accelerating universe

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

Statistical analysis of Ni nanowires breaking processes: a numerical simulation study

A statistical analysis of the breaking behavior of Ni nanowires is presented. Using molecular dynamic simulations, we have determined the time evolution of both the nanowire atomic structure and its minimum cross section (Sm(t)). Accumulating thousands of independent breaking events, Sm histograms are built and used to study the influence of the temperature, the crystalline stretching direction and the initial nanowire size. The proportion of monomers, dimers and more complex structures at the latest stages of the breaking process are calculated, finding important differences among results obtained for different nanowire orientations and sizes. Three main cases have been observed. (A) [111] stretching direction and large nanowire sizes: the wire evolves from more complex structures to monomers and dimers prior its rupture; well ordered structures is presented during the breaking process. (B) Large nanowires stretched along the [100] and [110] directions: the system mainly breaks from complex structures (low probability of finding monomers and dimers), having disordered regions during their breakage; at room temperature, a huge histogram peak around Sm=5 appears, showing the presence of long staggered pentagonal Ni wires with ...-5-1-5-... structure. (C) Initial wire size is small: strong size effects independently on the temperature and stretching direction. Finally, the local structure around monomers and dimmers do not depend on the stretching direction. These configurations differ from those usually chosen in static studies of conductance.Comment: 18 pages, 13 figure

Directed percolation depinning models: Evolution equations

We present the microscopic equation for the growing interface with quenched noise for the model first presented by Buldyrev et al. [Phys. Rev. A 45, R8313 (1992)]. The evolution equation for the height, the mean height, and the roughness are reached in a simple way. The microscopic equation allows us to express these equations in two contributions: the contact and the local one. We compare this two contributions with the ones obtained for the Tang and Leschhorn model [Phys. Rev A 45, R8309 (1992)] by Braunstein et al. [Physica A 266, 308 (1999)]. Even when the microscopic mechanisms are quiet different in both model, the two contribution are qualitatively similar. An interesting result is that the diffusion contribution, in the Tang and Leschhorn model, and the contact one, in the Buldyrev model, leads to an increase of the roughness near the criticality.Comment: 10 pages and 4 figures. To be published in Phys. Rev.

A tabu search heuristic for the Equitable Coloring Problem

The Equitable Coloring Problem is a variant of the Graph Coloring Problem where the sizes of two arbitrary color classes differ in at most one unit. This additional condition, called equity constraints, arises naturally in several applications. Due to the hardness of the problem, current exact algorithms can not solve large-sized instances. Such instances must be addressed only via heuristic methods. In this paper we present a tabu search heuristic for the Equitable Coloring Problem. This algorithm is an adaptation of the dynamic TabuCol version of Galinier and Hao. In order to satisfy equity constraints, new local search criteria are given. Computational experiments are carried out in order to find the best combination of parameters involved in the dynamic tenure of the heuristic. Finally, we show the good performance of our heuristic over known benchmark instances

Dynamical coupled-channel approach to hadronic and electromagnetic production of kaon-hyperon on the proton

A dynamical coupled-channel formalism for processes $\pi N \to KY$ and $\gamma N \to KY$ is presented which provides a comprehensive investigation of recent data on the $\gamma p \to K^+ \Lambda$ reaction. The non-resonant interactions within the subspace $KY\oplus\pi N$ are derived from effective Lagrangians, using a unitary transformation method. The calculations of photoproduction amplitudes are simplified by casting the coupled-channel equations into a form such that the empirical $\gamma N \to \pi N$ amplitudes are input and only the parameters associated with the $KY$ channel are determined by performing $\chi^2$-fits to all of the available data for $\pi^- p \to K^\circ\Lambda, K^\circ\Sigma^\circ$ and $\gamma p \to K^+\Lambda$. Good agreement between our models and those data are obtained. In the fits to $\pi N \to KY$ channels, most of the parameters are constrained within $\pm 20$ of the values given by the Particle Data Group and/or quark model predictions, while for $\gamma p \to K^+ \Lambda$ parameters, ranges compatible with broken $SU(6)\otimes O(3)$ symmetry are imposed. The main reaction mechanisms in $K^+ \Lambda$ photoproduction are singled out and issues related to newly suggested resonances $S_{11}$, $P_{13}$, and $D_{13}$ are studied. Results illustrating the importance of using a coupled-channel treatment are reported. Meson cloud effects on the $\gamma N \to N^*$ transitions are also discussed.Comment: Accepted Physical Review