Microbiome datasets are compositional: and this is not optional

Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers, metagenomes or metatranscriptomes are commonplace and being used to study human disease states, ecological differences between sites, and the built environment. There is increasing awareness that microbiome datasets generated by HTS are compositional because they have an arbitrary total imposed by the instrument. However, many investigators are either unaware of this or assume specific properties of the compositional data. The purpose of this review is to alert investigators to the dangers inherent in ignoring the compositional nature of the data, and point out that HTS datasets derived from microbiome studies can and should be treated as compositions at all stages of analysis. We briefly introduce compositional data, illustrate the pathologies that occur when compositional data are analyzed inappropriately, and finally give guidance and point to resources and examples for the analysis of microbiome datasets using compositional data analysis.Peer ReviewedPostprint (published version

Noise suppression due to long-range Coulomb interaction: Crossover between diffusive and ballistic transport regimes

We present a Monte Carlo analysis of shot-noise suppression due to long-range Coulomb interaction in semiconductor samples under a crossover between diffusive and ballistic transport regimes. By varying the mean time between collisions we find that the strong suppression observed under the ballistic regime persists under quasi-ballistic conditions, before being washed out when a complete diffusive regime is reached.Comment: RevTex, 3 pages, 4 figures, minor correction

Model of correlated sequential adsorption of colloidal particles

We present results of a new model of sequential adsorption in which the adsorbing particles are correlated with the particles attached to the substrate. The strength of the correlations is measured by a tunable parameter $\sigma$. The model interpolates between free ballistic adsorption in the limit $\sigma\to\infty$ and a strongly correlated phase, appearing for $\sigma\to0$ and characterized by the emergence of highly ordered structures. The phenomenon is manifested through the analysis of several magnitudes, as the jamming limit and the particle-particle correlation function. The effect of correlations in one dimension manifests in the increased tendency to particle chaining in the substrate. In two dimensions the correlations induce a percolation transition, in which a spanning cluster of connected particles appears at a certain critical value $\sigma_c$. Our study could be applicable to more general situations in which the coupling between correlations and disorder is relevant, as for example, in the presence of strong interparticle interactions.Comment: 6 pages, 8 EPS figures. Phys. Rev. E (in press

Adsorption of colloidal particles in the presence of external field

We present a new class of sequential adsorption models in which the adsorbing particles reach the surface following an inclined direction (shadow models). Capillary electrophoresis, adsorption in the presence of a shear or on an inclined substrate are physical manifestations of these models. Numerical simulations are carried out to show how the new adsorption mechanisms are responsible for the formation of more ordered adsorbed layers and have important implications in the kinetics, in particular modifying the jamming limit.Comment: LaTex file, 3 figures available upon request, to appear in Phys.Rev.Let

Influence of Hydrodynamic Interactions on the Adsorption Process of Large Particles

We have studied the adsorption process of non-Brownian particles on a line incorporating hydrodynamic interactionsa and we have numerically analyzed their effect on typical relevant quantities. We compare our model to the ballistic deposition model (BM) and address the limitations of BM in experimental situations. The results obtained can explain some differences observed between recent experiments and BM predictions.Comment: 10 pages, LaTeX. 4 Figures upon reques

Shot-noise spectroscopy of energy-resolved ballistic currents

We investigate the shot noise of nonequilibrium carriers injected into a ballistic conductor and interacting via long-range Coulomb forces. Coulomb interactions are shown to act as an energy analyzer of the profile of injected electrons by means of the fluctuations of the potential barrier at the emitter contact. We show that the details in the energy profile can be extracted from shot-noise measurements in the Coulomb interaction regime, but cannot be obtained from time-averaged quantities or shot-noise measurements in the absence of interactions.Comment: 7 pages, 4 figure

Noise suppression by noise

We have analyzed the interplay between an externally added noise and the intrinsic noise of systems that relax fast towards a stationary state, and found that increasing the intensity of the external noise can reduce the total noise of the system. We have established a general criterion for the appearance of this phenomenon and discussed two examples in detail.Comment: 4 pages, 4 figure

Stochastic Resonance in a Dipole

We show that the dipole, a system usually proposed to model relaxation phenomena, exhibits a maximum in the signal-to-noise ratio at a non-zero noise level, thus indicating the appearance of stochastic resonance. The phenomenon occurs in two different situations, i.e. when the minimum of the potential of the dipole remains fixed in time and when it switches periodically between two equilibrium points. We have also found that the signal-to-noise ratio has a maximum for a certain value of the amplitude of the oscillating field.Comment: 4 pages, RevTex, 6 PostScript figures available upon request; to appear in Phys. Rev.

Stochastic Resonance in Nonpotential Systems

We propose a method to analytically show the possibility for the appearance of a maximum in the signal-to-noise ratio in nonpotential systems. We apply our results to the FitzHugh-Nagumo model under a periodic external forcing, showing that the model exhibits stochastic resonance. The procedure that we follow is based on the reduction to a one-dimensional dynamics in the adiabatic limit, and in the topology of the phase space of the systems under study. Its application to other nonpotential systems is also discussed.Comment: Submitted to Phys. Rev.

Stochastic Resonance in Noisy Non-Dynamical Systems

We have analyzed the effects of the addition of external noise to non-dynamical systems displaying intrinsic noise, and established general conditions under which stochastic resonance appears. The criterion we have found may be applied to a wide class of non-dynamical systems, covering situations of different nature. Some particular examples are discussed in detail.Comment: 4 pages, RevTex, 3 PostScript figures available upon reques