Asymptotic Dynamics of High Dynamic Range Stratified Turbulence.

Direct numerical simulations of homogeneous sheared and stably stratified turbulence are considered to probe the asymptotic high dynamic range regime suggested by Gargett et al. J. Fluid Mech. 144, 231 (1984)10.1017/S0022112084001592 and Shih et al. J. Fluid Mech. 525, 193 (1999)10.1017/S0022112004002587. We consider statistically stationary configurations of the flow that span three decades in dynamic range defined by the separation between the Ozmidov length scale L_{O}=sqrt[ε/N^{3}] and the Kolmogorov length scale L_{K}=(ν^{3}/ε)^{1/4}, up to Re_{b}≡(L_{O}/L_{K})^{4/3}=ε/(νN^{2})∼O(1000), where ε is the mean turbulent kinetic energy dissipation rate, ν is the kinematic viscosity, and N is the buoyancy frequency. We isolate the effects of Re_{b}, particularly on irreversible mixing, from the effects of other flow parameters of stratified and sheared turbulence. Specifically, we evaluate the influence of dynamic range independent of initial conditions. We present evidence that the flow approaches an asymptotic state for Re_{b}⪆300, characterized both by an asymptotic partitioning between the potential and kinetic energies and by the approach of components of the dissipation rate to their expected values under the assumption of isotropy. As Re_{b} increases above 100, there is a slight decrease in the turbulent flux coefficient Γ=χ/ε, where χ is the dissipation rate of buoyancy variance, but, for this flow, there is no evidence of the commonly suggested Γ∝Re_{b}^{-1/2} dependence when 100≤Re_{b}≤1000.This work was funded by the U.S. Office of Naval Research via grant N00014-15-1-2248. High performance computing resources were provided through the U.S. Department of Defense High Performance Computing Modernization Program by the Army Engineer Research and Development Center, the Army Research Laboratory and the Navy DSRC under Frontier Project FP-CFD-FY14- 007. The research activity of C.P.C. is supported by EPSRC Programme Grant EP/K034529/1 entitled `Mathematical Underpinnings of Stratified Turbulence'

Testing the assumptions underlying ocean mixing methodologies using direct numerical simulations

AbstractDirect numerical simulations of stratified turbulence are used to test several fundamental assumptions involved in the Osborn, Osborn–Cox, and Thorpe methods commonly used to estimate the turbulent diffusivity from field measurements. The forced simulations in an idealized triply periodic computational domain exhibit characteristic features of stratified turbulence including intermittency and layer formation. When calculated using the volume-averaged dissipation rates from the simulations, the vertical diffusivities inferred from the Osborn and Osborn–Cox methods are within 40% of the value diagnosed using the volume-averaged buoyancy flux for all cases, while the Thorpe-scale method performs similarly well in the simulation with a relatively large buoyancy Reynolds number (Reb ≃ 240) but significantly overestimates the vertical diffusivity in simulations with Reb &lt; 60. The methods are also tested using a limited number of vertical profiles randomly selected from the computational volume. The Osborn, Osborn–Cox, and Thorpe-scale methods converge to their respective estimates based on volume-averaged statistics faster than the vertical diffusivity calculated directly from the buoyancy flux, which is contaminated with reversible contributions from internal waves. When applied to a small number of vertical profiles, several assumptions underlying the Osborn and Osborn–Cox methods are not well supported by the simulation data. However, the vertical diffusivity inferred from these methods compares reasonably well to the exact value from the simulations and outperforms the assumptions underlying these methods in terms of the relative error. Motivated by a recent theoretical development, it is speculated that the Osborn method might provide a reasonable approximation to the diffusivity associated with the irreversible buoyancy flux.</jats:p

Robust identification of dynamically distinct regions in stratified turbulence

We present a new robust method for identifying three dynamically distinct regions in a stratified turbulent flow, which we characterise as quiescent flow, intermittent layers and turbulent patches. The method uses the cumulative filtered distribution function of the local density gradient to identify each region. We apply it to data from direct numerical simulations of homogeneous stratified turbulence, with unity Prandtl number, resolved on up to $8192\times 8192\times 4096$ grid points. In addition to classifying regions consistently with contour plots of potential enstrophy, our method identifies quiescent regions as regions where \unicode[STIX]{x1D716}/\unicode[STIX]{x1D708}N^{2}\sim O(1), layers as regions where \unicode[STIX]{x1D716}/\unicode[STIX]{x1D708}N^{2}\sim O(10) and patches as regions where \unicode[STIX]{x1D716}/\unicode[STIX]{x1D708}N^{2}\sim O(100). Here, \unicode[STIX]{x1D716} is the dissipation rate of turbulence kinetic energy, \unicode[STIX]{x1D708} is the kinematic viscosity and $N$ is the (overall) buoyancy frequency. By far the highest local dissipation and mixing rates, and the majority of dissipation and mixing, occur in patch regions, even when patch regions occupy only 5 % of the flow volume. We conjecture that treating stratified turbulence as an instantaneous assemblage of these different regions in varying proportions may explain some of the apparently highly scattered flow dynamics and statistics previously reported in the literature.The research activities of G.D.P. and S.dB.K. were funded by the US Office of Naval Research via grant N00014-15-1-2248. Additional support to G.D.P. and S.dB.K. was provided from the UK Engineering and Physical Sciences Research Council grant EP/K034529/1 entitled ‘Mathematical Underpinnings of Stratified Turbulence’, which also funds the research activity of J.R.T. and C.P.C. H.S. gratefully acknowledges the award of a Crighton Fellowship at the Department of Applied Mathematics & Theoretical Physics, University of Cambridge. High-performance computing resources were provided through the US Department of Defense High Performance Computing Modernization Program by the Army Engineer Research and Development Center and the Army Research Laboratory under Frontier Project FP-CFD-FY14-007.This is the author accepted manuscript. The final version is available from Cambridge University Press via https://doi.org/10.1017/jfm.2016.61

Circumcision for prevention against HIV: marked seasonal variation in demand and potential public sector readiness in Soweto, South Africa

The public sector delivery of male circumcision in the only public sector hospital in Soweto, South Africa was examined to gauge local capacity to deliver this procedure as an intervention for prevention of HIV acquisition. During the period from July 1998 to March 2006, approximately 360 procedures were performed per annum. Striking seasonal variations and the relatively few procedures performed may create challenges for program planning, if male circumcision is increased to a level required to have an impact on the incidence of HIV among this population

Desmodium mottle virus, the first legumovirus (genus Begomovirus) from East Africa

A novel bipartite legumovirus (genus Begomovirus, family Geminiviridae), that naturally infects the wild leguminous plant Desmodium sp. in Uganda, was molecularly characterized and named Desmodium mottle virus. The highest nucleotide identities for DNA-A, obtained from two field-collected samples, were 79.9% and 80.1% with the legumovirus, soybean mild mottle virus. DNA-B had the highest nucleotide identities (65.4% and 66.4%) with a typical non-legumovirus Old World begomovirus, African cassava mosaic virus. This is the first report of a legumovirus in East Africa and extends the known diversity of begomoviruses found infecting wild plants in this continent

Huntington's disease: a clinical review

Huntington disease (HD) is a rare neurodegenerative disorder of the central nervous system characterized by unwanted choreatic movements, behavioral and psychiatric disturbances and dementia. Prevalence in the Caucasian population is estimated at 1/10,000-1/20,000. Mean age at onset of symptoms is 30-50 years. In some cases symptoms start before the age of 20 years with behavior disturbances and learning difficulties at school (Juvenile Huntington's disease; JHD). The classic sign is chorea that gradually spreads to all muscles. All psychomotor processes become severely retarded. Patients experience psychiatric symptoms and cognitive decline. HD is an autosomal dominant inherited disease caused by an elongated CAG repeat (36 repeats or more) on the short arm of chromosome 4p16.3 in the Huntingtine gene. The longer the CAG repeat, the earlier the onset of disease. In cases of JHD the repeat often exceeds 55. Diagnosis is based on clinical symptoms and signs in an individual with a parent with proven HD, and is confirmed by DNA determination. Pre-manifest diagnosis should only be performed by multidisciplinary teams in healthy at-risk adult individuals who want to know whether they carry the mutation or not. Differential diagnoses include other causes of chorea including general internal disorders or iatrogenic disorders. Phenocopies (clinically diagnosed cases of HD without the genetic mutation) are observed. Prenatal diagnosis is possible by chorionic villus sampling or amniocentesis. Preimplantation diagnosis with in vitro fertilization is offered in several countries. There is no cure. Management should be multidisciplinary and is based on treating symptoms with a view to improving quality of life. Chorea is treated with dopamine receptor blocking or depleting agents. Medication and non-medical care for depression and aggressive behavior may be required. The progression of the disease leads to a complete dependency in daily life, which results in patients requiring full-time care, and finally death. The most common cause of death is pneumonia, followed by suicide

Weak Polygyny in California Sea Lions and the Potential for Alternative Mating Tactics

Female aggregation and male territoriality are considered to be hallmarks of polygynous mating systems. The development of genetic parentage assignment has called into question the accuracy of behavioral traits in predicting true mating systems. In this study we use 14 microsatellite markers to explore the mating system of one of the most behaviorally polygynous species, the California sea lion (Zalophus californianus). We sampled a total of 158 female-pup pairs and 99 territorial males across two breeding rookeries (San Jorge and Los Islotes) in the Gulf of California, Mexico. Fathers could be identified for 30% of pups sampled at San Jorge across three breeding seasons and 15% of sampled pups at Los Islotes across two breeding seasons. Analysis of paternal relatedness between the pups for which no fathers were identified (sampled over four breeding seasons at San Jorge and two at Los Islotes) revealed that few pups were likely to share a father. Thirty-one percent of the sampled males on San Jorge and 15% of the sampled males on Los Islotes were assigned at least one paternity. With one exception, no male was identified as the father of more than two pups. Furthermore, at Los Islotes rookery there were significantly fewer pups assigned paternity than expected given the pool of sampled males (p<0.0001). Overall, we found considerably lower variation in male reproductive success than expected in a species that exhibits behavior associated with strongly polygynous mating. Low variation in male reproductive success may result from heightened mobility among receptive females in the Gulf of California, which reduces the ability of males to monopolize groups of females. Our results raise important questions regarding the adaptive role of territoriality and the potential for alternative mating tactics in this species

Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax

The complex climatic and geological history of Southeast Asia has shaped this region’s high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have shaped the distribution of biota within this region, and whether such patterns show evidence of isolation within palaeodrainage basins. Our analyses revealed three major mitochondrial clades within A. panchax. The basal divergence of A. panchax mitochondrial lineages was approximately 3.5 Ma, whilst the subsequent divergence timings of these clades occurred early Pleistocene (~2.6 Ma), proceeding through the Pleistocene. Continuous phylogeographic analysis showed a clear west-east dispersal followed by rapid radiation across Southeast Asia. Individuals from Krabi, just north of the Isthmus of Kra, were more closely related to the Indian lineages, providing further evidence for a freshwater faunal disjunction at the Isthmus of Kra biogeographic barrier. Our results suggest that Sulawesi, across the Wallace Line, was colonised relatively recently (~30 ka). Nuclear DNA is less geographically structured, although Mantel tests indicated that nuclear genetic distances were correlated with geographic proximity. Overall, these results imply that recent gene flow, as opposed to historical isolation, has been the key factor determining patterns of nuclear genetic variation in A. panchax, however, some evidence of historical isolation is retained within the mitochondrial genome. Our study further validates the existence of a major biogeographic boundary at the Kra Isthmus, and also demonstrates the use of widely distributed fresh/brackishwater species in phylogeographic studies, and their ability to disperse across major marine barriers in relatively recent time periods