Modeling influenza seasonality in the tropics and subtropics

Climate drivers such as humidity and temperature may play a key role in influenza seasonal transmission dynamics. Such a relationship has been well defined for temperate regions. However, to date no models capable of capturing the diverse seasonal pattern in tropical and subtropical climates exist. In addition, multiple influenza viruses could cocirculate and shape epidemic dynamics. Here we construct seven mechanistic epidemic models to test the effect of two major climate drivers (humidity and temperature) and multi-strain co-circulation on influenza transmission in Hong Kong, an influenza epidemic center located in the subtropics. Based on model fit to long-term influenza surveillance data from 1998 to 2018, we found that a simple model incorporating the effect of both humidity and temperature best recreated the influenza epidemic patterns observed in Hong Kong. The model quantifies a bimodal effect of absolute humidity on influenza transmission where both low and very high humidity levels facilitate transmission quadratically; the model also quantifies the monotonic but nonlinear relationship with temperature. In addition, model results suggest that, at the population level, a shorter immunity period can approximate the co-circulation of influenza virus (sub)types. The basic reproductive number R0 estimated by the best-fit model is also consistent with laboratory influenza survival and transmission studies under various combinations of humidity and temperature levels. Overall, our study has developed a simple mechanistic model capable of quantifying the impact of climate drivers on influenza transmission in (sub)tropical regions. This model can be applied to improve influenza forecasting in the (sub)tropics in the future

Growth rate degeneracies in kinematic dynamos

We consider the classical problem of kinematic dynamo action in simple steady flows. Due to the adjointness of the induction operator, we show that the growth rate of the dynamo will be exactly the same for two types of magnetic boundary conditions: the magnetic field can be normal (infinite magnetic permeability, also called pseudovacuum) or tangent (perfect electrical conductor) to the boundaries of the domain. These boundary conditions correspond to well-defined physical limits often used in numerical models and relevant to laboratory experiments. The only constraint is for the velocity field u to be reversible, meaning there exists a transformation changing u into −u. We illustrate this surprising property using S2T2 type of flows in spherical geometry inspired by [Dudley and James, Proc. R. Soc. London A 425, 407 (1989)]. Using both types of boundary conditions, it is shown that the growth rates of the dynamos are identical, although the corresponding magnetic eigenmodes are drastically different

Effects of Large-Scale Convection on p-mode Frequencies

We describe an approach for finding the eigenfrequencies of solar acoustic modes (p modes) in a convective envelope in the WKB limit. This approximation restricts us to examining the effects of fluid motions which are large compared to the mode wavelength, but allows us to treat the three-dimensional mode as a localized ray. The method of adiabatic switching is then used to investigate the frequency shifts resulting from simple perturbations to a polytropic model of the convection zone as well as from two basic models of a convective cell. We find that although solely depth-dependent perturbations can give frequency shifts which are first order in the strength of the perturbation, models of convective cells generate downward frequency shifts which are second order in the perturbation strength. These results may have implications for resolving the differences between eigenfrequencies derived from solar models and those found from helioseismic observations.Comment: 27 pages + 6 figures; accepted for publication in Ap

A Spherical Plasma Dynamo Experiment

We propose a plasma experiment to be used to investigate fundamental properties of astrophysical dynamos. The highly conducting, fast-flowing plasma will allow experimenters to explore systems with magnetic Reynolds numbers an order of magnitude larger than those accessible with liquid-metal experiments. The plasma is confined using a ring-cusp strategy and subject to a toroidal differentially rotating outer boundary condition. As proof of principle, we present magnetohydrodynamic simulations of the proposed experiment. When a von K\'arm\'an-type boundary condition is specified, and the magnetic Reynolds number is large enough, dynamo action is observed. At different values of the magnetic Prandtl and Reynolds numbers the simulations demonstrate either laminar or turbulent dynamo action

Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data

Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing, expression profiles, proteomics, and electronic health records are some examples of such technologies. Extracting meaningful information from those technologies requires careful analysis of the large volumes of data they produce. In this note, we present a set of distributions that commonly appear in the analysis of such data. These distributions present some interesting features: they are discontinuous in the rational numbers, but continuous in the irrational numbers, and possess a certain self-similar (fractal-like) structure. The first set of examples which we present here are drawn from a high-throughput sequencing experiment. Here, the self-similar distributions appear as part of the evaluation of the error rate of the sequencing technology and the identification of tumorogenic genomic alterations. The other examples are obtained from risk factor evaluation and analysis of relative disease prevalence and co-mordbidity as these appear in electronic clinical data. The distributions are also relevant to identification of subclonal populations in tumors and the study of the evolution of infectious diseases, and more precisely the study of quasi-species and intrahost diversity of viral populations

Hall magnetohydrodynamics of partially ionized plasmas

The Hall effect arises in a plasma when electrons are able to drift with the magnetic field but ions cannot. In a fully-ionized plasma this occurs for frequencies between the ion and electron cyclotron frequencies because of the larger ion inertia. Typically this frequency range lies well above the frequencies of interest (such as the dynamical frequency of the system under consideration) and can be ignored. In a weakly-ionized medium, however, the Hall effect arises through a different mechanism -- neutral collisions preferentially decouple ions from the magnetic field. This typically occurs at much lower frequencies and the Hall effect may play an important role in the dynamics of weakly-ionised systems such as the Earth's ionosphere and protoplanetary discs. To clarify the relationship between these mechanisms we develop an approximate single-fluid description of a partially ionized plasma that becomes exact in the fully-ionized and weakly-ionized limits. Our treatment includes the effects of ohmic, ambipolar, and Hall diffusion. We show that the Hall effect is relevant to the dynamics of a partially ionized medium when the dynamical frequency exceeds the ratio of ion to bulk mass density times the ion-cyclotron frequency, i.e. the Hall frequency. The corresponding length scale is inversely proportional to the ion to bulk mass density ratio as well as to the ion-Hall beta parameter.Comment: 11 page, 1 figure, typos removed, numbers in tables revised; accepted for publication in MNRA

Stellar Hydrodynamics in Radiative Regions

We present an analysis of the response of a radiative region to waves generated by a convective region of the star; this wave treatment of the classical problem of ``overshooting'' gives extra mixing relative to the treatment traditionally used in stellar evolutionary codes. The interface between convectively stable and unstable regions is dynamic and nonspherical, so that the nonturbulent material is driven into motion, even in the absence of ``penetrative overshoot.'' These motions may be described by the theory of nonspherical stellar pulsations, and are related to motion measured by helioseismology. Multi-dimensional numerical simulations of convective flow show puzzling features which we explain by this simplified physical model. Gravity waves generated at the interface are dissipated, resulting in slow circulation and mixing seen outside the formal convection zone. The approach may be extended to deal with rotation and composition gradients. Tests of this description in the stellar evolution code TYCHO produce carbon stars on the asymptotic giant branch (AGB), an isochrone age for the Hyades and three young clusters with lithium depletion ages from brown dwarfs, and lithium and beryllium depletion consistent with observations of the Hyades and Pleiades, all without tuning parameters. The insight into the different contributions of rotational and hydrodynamic mixing processes could have important implications for realistic simulation of supernovae and other questions in stellar evolution.Comment: 27 pages, 5 figures, accepted to the Astrophysical Journa

Observation of a Turbulence-Induced Large Scale Magnetic Field

An axisymmetric magnetic field is applied to a spherical, turbulent flow of liquid sodium. An induced magnetic dipole moment is measured which cannot be generated by the interaction of the axisymmetric mean flow with the applied field, indicating the presence of a turbulent electromotive force. It is shown that the induced dipole moment should vanish for any axisymmetric laminar flow. Also observed is the production of toroidal magnetic field from applied poloidal magnetic field (the omega-effect). Its potential role in the production of the induced dipole is discussed.Comment: 5 pages, 4 figures Revisions to accomodate peer-reviewer concerns; changes to main text including simplification of a proof, Fig. 2 updated, and minor typos and clarifications; Added refrences. Resubmitted to Phys. Rev. Let

Hand hygiene and risk of influenza virus infections in the community: a systematic review and meta-analysis

Community-based prevention strategies for seasonal and pandemic influenza are essential to minimize their potential threat to public health. Our aim was to evaluate the efficacy of hand hygiene interventions in reducing influenza transmission in the community and to investigate the possible modifying effects of latitude, temperature and humidity on hand hygiene efficacy. We identified 979 articles in the initial search and 10 randomized controlled trials met our inclusion criteria. The combination of hand hygiene with facemasks was found to have statistically significant efficacy against laboratory-confirmed influenza while hand hygiene alone did not. Our meta-regression model did not identify statistically significant effects of latitude, temperature or humidity on the efficacy of hand hygiene. Our findings highlight the potential importance of interventions that protect against multiple modes of influenza transmission, and the modest efficacy of hand hygiene suggests that additional measures besides hand hygiene may also be important to control influenza

Numerical simulations of current generation and dynamo excitation in a mechanically-forced, turbulent flow

The role of turbulence in current generation and self-excitation of magnetic fields has been studied in the geometry of a mechanically driven, spherical dynamo experiment, using a three dimensional numerical computation. A simple impeller model drives a flow which can generate a growing magnetic field, depending upon the magnetic Reynolds number, Rm, and the fluid Reynolds number. When the flow is laminar, the dynamo transition is governed by a simple threshold in Rm, above which a growing magnetic eigenmode is observed. The eigenmode is primarily a dipole field tranverse to axis of symmetry of the flow. In saturation the Lorentz force slows the flow such that the magnetic eigenmode becomes marginally stable. For turbulent flow, the dynamo eigenmode is suppressed. The mechanism of suppression is due to a combination of a time varying large-scale field and the presence of fluctuation driven currents which effectively enhance the magnetic diffusivity. For higher Rm a dynamo reappears, however the structure of the magnetic field is often different from the laminar dynamo; it is dominated by a dipolar magnetic field which is aligned with the axis of symmetry of the mean-flow, apparently generated by fluctuation-driven currents. The fluctuation-driven currents have been studied by applying a weak magnetic field to laminar and turbulent flows. The magnetic fields generated by the fluctuations are significant: a dipole moment aligned with the symmetry axis of the mean-flow is generated similar to those observed in the experiment, and both toroidal and poloidal flux expulsion are observed.Comment: 14 pages, 14 figure