A tractable inhomogeneous closure theory for flow over mean topography

The quasi-diagonal direct interaction approximation (QDIA) is shown to be a computationally tractable closure theory for inhomogeneous two-dimensional turbulent flow over mean (single-realization) topography. In this paper numerical results for the QDIA are compared to direct numerical simulation (DNS) at moderate Reynolds number for two cases with quite different topographic and mean field amplitudes. The QDIA is found to be in excellent agreement with DNS for cases where the small-scale topographic amplitude is significant. For cases where the small-scale topography is weak, the QDIA closely reproduces the evolving mean field and large-scale energy containing transients but under represents the amplitudes of the small-scale transients in a similar way to the homogeneous DIA. We discuss the prospects of ameliorating the small-scale deficiencies using a regularization of the interaction coefficients

Systematic attribution of observed Southern Hemisphere circulation trends to external forcing and internal variability

A critical question in the global warming debate concerns the causes of the observed trends of the Southern Hemisphere (SH) atmospheric circulation over recent decades. Secular trends have been identified in the frequency of occurrence of circulation regimes, namely the positive phase of the Southern Annular Mode (SAM) and the hemispheric wave-3 pattern which is associated with blocking. Previous studies into the causes of these secular trends have either been purely model based, have not included observational forcing data or have mixed external forcing with indices of internal climate variability impeding a systematic and unbiased attribution of the causes of the secular trends. Most model studies also focused mainly on the austral summer season. However, the changes to the storm tracks have occurred in all seasons and particularly in the austral winter and early spring when midlatitude blocking is most active and stratospheric ozone should not play a role. Here we systematically attribute the secular trends over the recent decades using a non-stationary clustering method applied to both reanalysis and observational forcing data from all seasons. While most previous studies emphasized the importance of stratospheric ozone depletion in causing austral summer SH circulation trends, we show observational evidence that anthropogenic greenhouse gas concentrations have been the major driver of these secular trends in the SAM and blocking when all seasons are considered. Our results suggest that the recovery of the ozone hole might delay the signal of global warming less strongly than previously thought and that effects from all seasons are likely crucial in understanding the causes of the secular trends

Integro-differential closure equations for inhomogeneous turbulence

We present numerical and computational techniques to solve systems of integro-differential closure equations for inhomogeneous two-dimensional turbulent flow. The closure equations, representing the first tractable closure theory for inhomogeneous flow over mean (single realization) topography, are based on a quasi-diagonal direct interaction approximation derived via renormalization techniques. The equations are computationally challenging due to the potentially long time history integrals. In order to reduce the computational cost we have implemented a formal restart procedure for the two and three point cumulant terms. The restart procedure is shown to be in good agreement with the closure without restarts and results are compared to direct numerical simulation of the barotropic vorticity equation

Tuberculosis immunopathology: the neglected role of extracellular matrix destruction

The extracellular matrix in the lung must be destroyed for Mycobacterium tuberculosis—the agent that causes tuberculosis (TB)—to spread. The current paradigm proposes that this destruction occurs as a result of the action of proinflammatory cytokines, chemokines, immune cells, and lipids that mediate TB-associated necrosis in the lung. However, this view neglects the fact that lung matrix can only be degraded by proteases. We propose an original conceptual framework of TB immunopathology that may lead directly to treatments that involve inhibition of matrix metalloproteinase activity to hinder matrix destruction and reduce the morbidity and mortality associated with T

The scale of population structure in Arabidopsis thaliana

The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales