Genetic Characterization of the Tick-Borne Orbiviruses

The International Committee for Taxonomy of Viruses (ICTV) recognizes four species of tick-borne orbiviruses (TBOs): Chenuda virus, Chobar Gorge virus, Wad Medani virus and Great Island virus (genus Orbivirus, family Reoviridae). Nucleotide (nt) and amino acid (aa) sequence comparisons provide a basis for orbivirus detection and classification, however full genome sequence data were only available for the Great Island virus species. We report representative genome-sequences for the three other TBO species (virus isolates: Chenuda virus (CNUV); Chobar Gorge virus (CGV) and Wad Medani virus (WMV)). Phylogenetic comparisons show that TBOs cluster separately from insect-borne orbiviruses (IBOs). CNUV, CGV, WMV and GIV share low level aa/nt identities with other orbiviruses, in 'conserved' Pol, T2 and T13 proteins/genes, identifying them as four distinct virus-species. The TBO genome segment encoding cell attachment, outer capsid protein 1 (OC1), is approximately half the size of the equivalent segment from insect-borne orbiviruses, helping to explain why tick-borne orbiviruses have a ~1 kb smaller genome

Inhomogeneous soliton ratchets under two ac forces

We extend our previous work on soliton ratchet devices [L. Morales-Molina et al., Eur. Phys. J. B 37, 79 (2004)] to consider the joint effect of two ac forces including non-harmonic drivings, as proposed for particle ratchets by Savele'v et al. [Europhys. Lett. 67}, 179 (2004); Phys. Rev. E {\bf 70} 066109 (2004)]. Current reversals due to the interplay between the phases, frequencies and amplitudes of the harmonics are obtained. An analysis of the effect of the damping coefficient on the dynamics is presented. We show that solitons give rise to non-trivial differences in the phenomenology reported for particle systems that arise from their extended character. A comparison with soliton ratchets in homogeneous systems with biharmonic forces is also presented. This ratchet device may be an ideal candidate for Josephson junction ratchets with intrinsic large damping

Random Costs in Combinatorial Optimization

The random cost problem is the problem of finding the minimum in an exponentially long list of random numbers. By definition, this problem cannot be solved faster than by exhaustive search. It is shown that a classical NP-hard optimization problem, number partitioning, is essentially equivalent to the random cost problem. This explains the bad performance of heuristic approaches to the number partitioning problem and allows us to calculate the probability distributions of the optimum and sub-optimum costs.Comment: 4 pages, Revtex, 2 figures (eps), submitted to PR

Fine and ultrafine particle number and size measurements from industrial combustion processes : primary emissions field data

This study is to our knowledge the first to present the results of on-line measurements of residual nanoparticle numbers downstream of the flue gas treatment systems of a wide variety of medium- and large-scale industrial installations. Where available, a semi-quantitative elemental composition of the sampled particles is carried out using a Scanning Electron Microscope coupled with an Energy Dispersive Spectrometer (SEM-EDS). The semi-quantitative elemental composition as a function of the particle size is presented. EU's Best Available Technology documents (BAT) show removal efficiencies of Electrostatic Precipitator (ESP) and bag filter dedusting systems exceeding 99% when expressed in terms of weight. Their efficiency decreases slightly for particles smaller than 1 mu m but when expressed in terms of weight, still exceeds 99% for bag filters and 96% for ESP. This study reveals that in terms of particle numbers, residual nanoparticles (NP) leaving the dedusting systems dominate by several orders of magnitude. In terms of weight, all installations respect their emission limit values and the contribution of NP to weight concentrations is negligible, despite their dominance in terms of numbers. Current World Health Organisation regulations are expressed in terms of PM2.5 wt concentrations and therefore do not reflect the presence or absence of a high number of NP. This study suggests that research is needed on possible additional guidelines related to NP given their possible toxicity and high potential to easily enter the blood stream when inhaled by humans

Number partitioning as random energy model

Number partitioning is a classical problem from combinatorial optimisation. In physical terms it corresponds to a long range anti-ferromagnetic Ising spin glass. It has been rigorously proven that the low lying energies of number partitioning behave like uncorrelated random variables. We claim that neighbouring energy levels are uncorrelated almost everywhere on the energy axis, and that energetically adjacent configurations are uncorrelated, too. Apparently there is no relation between geometry (configuration) and energy that could be exploited by an optimization algorithm. This ``local random energy'' picture of number partitioning is corroborated by numerical simulations and heuristic arguments.Comment: 8+2 pages, 9 figures, PDF onl

On the combination of omics data for prediction of binary outcomes

Enrichment of predictive models with new biomolecular markers is an important task in high-dimensional omic applications. Increasingly, clinical studies include several sets of such omics markers available for each patient, measuring different levels of biological variation. As a result, one of the main challenges in predictive research is the integration of different sources of omic biomarkers for the prediction of health traits. We review several approaches for the combination of omic markers in the context of binary outcome prediction, all based on double cross-validation and regularized regression models. We evaluate their performance in terms of calibration and discrimination and we compare their performance with respect to single-omic source predictions. We illustrate the methods through the analysis of two real datasets. On the one hand, we consider the combination of two fractions of proteomic mass spectrometry for the calibration of a diagnostic rule for the detection of early-stage breast cancer. On the other hand, we consider transcriptomics and metabolomics as predictors of obesity using data from the Dietary, Lifestyle, and Genetic determinants of Obesity and Metabolic syndrome (DILGOM) study, a population-based cohort, from Finland

Switching between different vortex states in 2-dimensional easy-plane magnets due to an ac magnetic field

Using a discrete model of 2-dimensional easy-plane classical ferromagnets, we propose that a rotating magnetic field in the easy plane can switch a vortex from one polarization to the opposite one if the amplitude exceeds a threshold value, but the backward process does not occur. Such switches are indeed observed in computer simulations.Comment: 4 pages, 4 figures, submitted to Phys. Rev. Let

Criticality of natural absorbing states

We study a recently introduced ladder model which undergoes a transition between an active and an infinitely degenerate absorbing phase. In some cases the critical behaviour of the model is the same as that of the branching annihilating random walk with $N\geq 2$ species both with and without hard-core interaction. We show that certain static characteristics of the so-called natural absorbing states develop power law singularities which signal the approach of the critical point. These results are also explained using random walk arguments. In addition to that we show that when dynamics of our model is considered as a minimum finding procedure, it has the best efficiency very close to the critical point.Comment: 6 page

Counting Lattice Animals in High Dimensions

We present an implementation of Redelemeier's algorithm for the enumeration of lattice animals in high dimensional lattices. The implementation is lean and fast enough to allow us to extend the existing tables of animal counts, perimeter polynomials and series expansion coefficients in $d$-dimensional hypercubic lattices for $3 \leq d\leq 10$. From the data we compute formulas for perimeter polynomials for lattice animals of size $n\leq 11$ in arbitrary dimension $d$. When amended by combinatorial arguments, the new data suffices to yield explicit formulas for the number of lattice animals of size $n\leq 14$ and arbitrary $d$. We also use the enumeration data to compute numerical estimates for growth rates and exponents in high dimensions that agree very well with Monte Carlo simulations and recent predictions from field theory.Comment: 18 pages, 7 figures, 6 tables; journal versio