Realizing surface driven flows in the primitive equations

© Copyright 2015 American Meteorological Society (AMS). Permission to use figures, tables, and brief excerpts from this work in scientific and educational works is hereby granted provided that the source is acknowledged. Any use of material in this work that is determined to be “fair use” under Section 107 of the U.S. Copyright Act September 2010 Page 2 or that satisfies the conditions specified in Section 108 of the U.S. Copyright Act (17 USC §108, as revised by P.L. 94-553) does not require the AMS’s permission. Republication, systematic reproduction, posting in electronic form, such as on a web site or in a searchable database, or other uses of this material, except as exempted by the above statement, requires written permission or a license from the AMS. Additional details are provided in the AMS Copyright Policy, available on the AMS Web site located at (https://www.ametsoc.org/) or from the AMS at 617-227-2425 or [email protected] surface quasigeostrophic (SQG) model describes flows with surface buoyancy perturbations with no interior quasigeostrophic potential vorticity at small Rossby number Ro and O(1) Burger number, where quasigeostrophic dynamics are expected to hold. Numerical simulations of SQG dynamics have shown that vortices are frequently generated at small scales, which may have O(1) Rossby numbers and therefore may be beyond the limits of SQG. This paper examines the dynamics of an initially geostrophically balanced elliptical surface buoyancy perturbation in both the SQG model and the nonhydrostatic Boussinesq primitive equations (PE). In the case of very small Rossby number, it is confirmed that both models agree, as expected. For larger Ro, non-SQG effects emerge and as a result the solution of the PE deviates significantly from that of SQG. In particular, an increase in the Rossby number has the following effects: (i) the buoyancy filaments at the surface are stabilized in that they generate fewer secondary vortices; (ii) the core of the vortex experiences inertial instability, which results in a uniform buoyancy profile in its interior; (iii) the divergent part of the energy spectrum increases in magnitude; (iv) the PE model has significantly more gravity waves that are radiated from the vortex; (v) the magnitude of the vertical velocity increases; and (vi) in the mature stages of evolution, there are gravitational instabilities that develop because of the complicated dynamics inside the vortex. It is demonstrated that significant non-SQG effects are evident when the large-scale Rossby number of the initial flow is about 0.05 and the local Rossby number is O(1).Natural Sciences and Engineering Research Council || RGPIN/386456-201

Parametric instability in oscillatory shear flows

Author Posting. © Cambridge University Press, 2003. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Journal of Fluid Mechanics 481 (2003): 329-353, doi:10.1017/S0022112003004051.In this article we investigate time-periodic shear flows in the context of the two-dimensional vorticity equation, which may be applied to describe certain large-scale atmospheric and oceanic flows. The linear stability analyses of both discrete and continuous profiles demonstrate that parametric instability can arise even in this simple model: the oscillations can stabilize (destabilize) an otherwise unstable (stable) shear flow, as in Mathieu's equation (Stoker 1950). Nonlinear simulations of the continuous oscillatory basic state support the predictions from linear theory and, in addition, illustrate the evolution of the instability process and thereby show the structure of the vortices that emerge. The discovery of parametric instability in this model suggests that this mechanism can occur in geophysical shear flows and provides an additional means through which turbulent mixing can be generated in large-scale flows.F.P.’s and G.F.’s research was supported by grants from NSF, OPP- 9910052 and OCE-0137023. J.P.’s research is supported in part by a grant from NSF, OCE-9901654

The baroclinic adjustment of time-dependent shear flows

Author Posting. © American Meteorological Society, 2010. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 40 (2010): 1851-1865, doi:10.1175/2010JPO4217.1.Motivated by the fact that time-dependent currents are ubiquitous in the ocean, this work studies the two-layer Phillips model on the beta plane with baroclinic shear flows that are steady, periodic, or aperiodic in time to understand their nonlinear evolution better. When a linearly unstable basic state is slightly perturbed, the primary wave grows exponentially until nonlinear advection adjusts the growth. Even though for long time scales these nearly two-dimensional motions predominantly cascade energy to large scales, for relatively short times the wave–mean flow and wave–wave interactions cascade energy to smaller horizontal length scales. The authors demonstrate that the manner through which these mechanisms excite the harmonics depends significantly on the characteristics of the basic state. Time-dependent basic states can excite harmonics very rapidly in comparison to steady basic states. Moreover, in all the simulations of aperiodic baroclinic shear flows, the barotropic component of the primary wave continues to grow after the adjustment by the nonlinearities. Furthermore, the authors find that the correction to the zonal mean flow can be much larger when the basic state is aperiodic compared to the periodic or steady limits. Finally, even though time-dependent baroclinic shear on an f plane is linearly stable, the authors show that perturbations can grow algebraically in the linear regime because of the erratic variations in the aperiodic flow. Subsequently, baroclinicity adjusts the growing wave and creates a final state that is more energetic than the nonlinear adjustment of any of the unstable steady baroclinic shears that are considered.FJP was supported by NSERC and JP was supported by NSF OCE 0925061 during the research and writing of this manuscript

Risk maps for range expansion of the Lyme disease vector, Ixodes scapularis, in Canada now and with climate change

<p>Abstract</p> <p>Background</p> <p>Lyme disease is the commonest vector-borne zoonosis in the temperate world, and an emerging infectious disease in Canada due to expansion of the geographic range of the tick vector <it>Ixodes scapularis</it>. Studies suggest that climate change will accelerate Lyme disease emergence by enhancing climatic suitability for <it>I. scapularis</it>. Risk maps will help to meet the public health challenge of Lyme disease by allowing targeting of surveillance and intervention activities.</p> <p>Results</p> <p>A risk map for possible Lyme endemicity was created using a simple risk algorithm for occurrence of <it>I. scapularis </it>populations. The algorithm was calculated for each census sub-division in central and eastern Canada from interpolated output of a temperature-driven simulation model of <it>I. scapularis </it>populations and an index of tick immigration. The latter was calculated from estimates of tick dispersion distances by migratory birds and recent knowledge of the current geographic range of endemic <it>I. scapularis </it>populations. The index of tick immigration closely predicted passive surveillance data on <it>I. scapularis </it>occurrence, and the risk algorithm was a significant predictor of the occurrence of <it>I. scapularis </it>populations in a prospective field study. Risk maps for <it>I. scapularis </it>occurrence in Canada under future projected climate (in the 2020s, 2050s and 2080s) were produced using temperature output from the Canadian Coupled Global Climate Model 2 with greenhouse gas emission scenario enforcing '<it>A2</it>' of the Intergovernmental Panel on Climate Change.</p> <p>Conclusion</p> <p>We have prepared risk maps for the occurrence of <it>I. scapularis </it>in eastern and central Canada under current and future projected climate. Validation of the risk maps provides some confidence that they provide a useful first step in predicting the occurrence of <it>I. scapularis </it>populations, and directing public health objectives in minimizing risk from Lyme disease. Further field studies are needed, however, to continue validation and refinement of the risk maps.</p

Assessing the Validity of Sexual Behaviour Reports in a Whole Population Survey in Rural Malawi

Background: Sexual behaviour surveys are widely used, but under-reporting of particular risk behaviours is common, especially by women. Surveys in whole populations provide an unusual opportunity to understand the extent and nature of such under-reporting.Methods: All consenting individuals aged between 15 and 59 within a demographic surveillance site in northern Malawi were interviewed about their sexual behaviour. Validity of responses was assessed by analysis of probing questions; by comparison of results with in-depth interviews and with Herpes simplex type-2 (HSV-2) seropositivity; by comparing reports to same sex and opposite sex interviewers; and by quantifying the partnerships within the local community reported by men and by women, adjusted for response rates.Results: 6,796 women and 5,253 men (83% and 72% of those eligible) consented and took part in sexual behaviour interviews. Probing questions and HSV-2 antibody tests in those who denied sexual activity identified under-reporting for both men and women. Reports varied little by sex or age of the interviewer. The number of marital partnerships reported was comparable for men and women, but men reported about 4 times as many non-marital partnerships. The discrepancy in reporting of non-marital partnerships was most marked for married women (men reported about 7 times as many non-marital partnerships with married women as were reported by married women themselves), but was only apparent in younger married women.Conclusions: We have shown that the under-reporting of non-marital partnerships by women was strongly age-dependent. The extent of under-reporting of sexual activity by young men was surprisingly high. The results emphasise the importance of triangulation, including biomarkers, and the advantages of considering a whole population

Helminth burden and ecological factors associated with alterations in wild host gastrointestinal microbiota

Infection by gastrointestinal helminths of humans, livestock and wild animals is common, but the impact of such endoparasites on wild hosts and their gut microbiota represents an important overlooked component of population dynamics. Wild host gut microbiota and endoparasites occupy the same physical niche spaces with both affecting host nutrition and health. However, associations between the two are poorly understood. Here we used the commonly parasitized European shag (Phalacrocorax aristotelis) as a model wild host. Forty live adults from the same colony were sampled. Endoscopy was employed to quantify helminth infection in situ. Microbiota from the significantly distinct proventriculus (site of infection), cloacal and faecal gastrointestinal tract microbiomes were characterised using 16S rRNA gene-targeted high-throughput sequencing. We found increasingly strong associations between helminth infection and microbiota composition progressing away from the site of infection, observing a pronounced dysbiosis in microbiota when samples were partitioned into high- and low-burden groups. We posit this dysbiosis is predominately explained by helminths inducing an anti-inflammatory environment in the proventriculus, diverting host immune responses away from themselves. This study, within live wild animals, provides a vital foundation to better understand the mechanisms that underpin the three-way relationship between helminths, microbiota and hosts

Physiological Correlates of Volunteering

We review research on physiological correlates of volunteering, a neglected but promising research field. Some of these correlates seem to be causal factors influencing volunteering. Volunteers tend to have better physical health, both self-reported and expert-assessed, better mental health, and perform better on cognitive tasks. Research thus far has rarely examined neurological, neurochemical, hormonal, and genetic correlates of volunteering to any significant extent, especially controlling for other factors as potential confounds. Evolutionary theory and behavioral genetic research suggest the importance of such physiological factors in humans. Basically, many aspects of social relationships and social activities have effects on health (e.g., Newman and Roberts 2013; Uchino 2004), as the widely used biopsychosocial (BPS) model suggests (Institute of Medicine 2001). Studies of formal volunteering (FV), charitable giving, and altruistic behavior suggest that physiological characteristics are related to volunteering, including specific genes (such as oxytocin receptor [OXTR] genes, Arginine vasopressin receptor [AVPR] genes, dopamine D4 receptor [DRD4] genes, and 5-HTTLPR). We recommend that future research on physiological factors be extended to non-Western populations, focusing specifically on volunteering, and differentiating between different forms and types of volunteering and civic participation