Faculty and Staff

This paper studies the effect of targeted observations on state and parameter estimates determined with Kalman filter data assimilation (DA) techniques. We first provide an analytical result demonstrating that targeting observations within the Kalman filter for a linear model can significantly reduce state estimation error as opposed to fixed or randomly located observations. We next conduct observing system simulation experiments for a chaotic model of meteorological interest, where we demonstrate that the local ensemble transform Kalman filter (LETKF) with targeted observations based on largest ensemble variance is skillful in providing more accurate state estimates than the LETKF with randomly located observations. Additionally, we find that a hybrid ensemble Kalman filter parameter estimation method accurately updates model parameters within the targeted observation context to further improve state estimation.

The effects of urbanization on ozone levels have been widely investigated over cities primarily located in temperate and/or humid regions. In this study, nested WRF-Chem simulations with a finest grid resolution of 1 km are conducted to investigate ozone concentrations O₃ due to urbanization within cities in arid/semi-arid environments. First, a method based on a shape preserving Monotonic Cubic Interpolation (MCI) is developed and used to downscale anthropogenic emissions from the 4 km resolution 2005 National Emissions Inventory (NEI05) to the finest model resolution of 1 km. Using the rapidly expanding Phoenix metropolitan region as the area of focus, we demonstrate the proposed MCI method achieves ozone simulation results with appreciably improved correspondence to observations relative to the default interpolation method of the WRF-Chem system. Next, two additional sets of experiments are conducted, with the recommended MCI approach, to examine impacts of urbanization on ozone production: (1) the urban land cover is included (i.e., urbanization experiments) and, (2) the urban land cover is replaced with the region's native shrubland. Impacts due to the presence of the built environment on O₃ are highly heterogeneous across the metropolitan area. Increased near surface O₃ due to urbanization of 10–20 ppb is predominantly a nighttime phenomenon while simulated impacts during daytime are negligible. Urbanization narrows the daily O₃ range (by virtue of increasing nighttime minima), an impact largely due to the region's urban heat island. Our results demonstrate the importance of the MCI method for accurate representation of the diurnal profile of ozone, and highlight its utility for high-resolution air quality simulations for urban areas.

The emergence of the disease chytridiomycosis caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd) has been implicated in dramatic global amphibian declines. Although many species have undergone catastrophic declines and/or extinctions, others appear to be unaffected or persist at reduced frequencies after Bd outbreaks. The reasons behind this variance in disease outcomes are poorly understood: differences in host immune responses have been proposed, yet previous studies suggest a lack of robust immune responses to Bd in susceptible species. Here, we sequenced transcriptomes from clutch-mates of a highly susceptible amphibian, Atelopus zeteki, with different infection histories. We found significant changes in expression of numerous genes involved in innate and inflammatory responses in infected frogs despite high susceptibility to chytridiomycosis.

We show evidence of acquired immune responses generated against Bd, including increased expression of immunoglobulins and major histocompatibility complex genes. In addition, fungal-killing genes had significantly greater expression in frogs previously exposed to Bd compared with Bd-naïve frogs, including chitinase and serine-type proteases. However, our results appear to confirm recent in vitro evidence of immune suppression by Bd, demonstrated by decreased expression of lymphocyte genes in the spleen of infected compared with control frogs. We propose susceptibility to chytridiomycosis is not due to lack of Bd-specific immune responses but instead is caused by failure of those responses to be effective. Ineffective immune pathway activation and timing of antibody production are discussed as potential mechanisms. However, in light of our findings, suppression of key immune responses by Bd is likely an important factor in the lethality of this fungus.

An interesting occurrence of a Rossby wave breaking event observed during the VORCORE experiment is presented and explained. Twenty-seven balloons were launched inside the Antarctic polar vortex. Almost all of these balloons evolved in the stratosphere around 500K within the vortex, except the one launched on 28 October 2005. In this case, the balloon was caught within a tongue of high potential vorticity (PV), and was ejected from the polar vortex. The evolution of this event is studied for the period between 19 and 25 November 2005. It is found that at the beginning of this period, the polar vortex experienced distortions due to the presence of Rossby waves. Then, these waves break and a tongue of high PV develops. On 25 November, the tongue became separated from the vortex and the balloon was ejected into the surf zone. Lagrangian simulations demonstrate that the air masses surrounding the balloon after its ejection were originating from the vortex edge. The wave breaking and the development of the tongue are confined within a region where a planetary Quasi-Stationary Wave 1 (QSW1) induces wind speeds with weaker values. The QSW1 causes asymmetry in the wind speed and the horizontal PV gradient along the edge of the polar vortex, resulting in a localized jet. Rossby waves with smaller scales propagating on top of this jet amplify as they enter the jet exit region and then break. The role of the QSW1 on the formation of the weak flow conditions that caused the non-linear wave breaking observed near the vortex edge is confirmed by three-dimensional numerical simulations using forcing with and without the contribution of the QSW1.

Physical mechanisms of incongruency between observations and Weather Research and Forecasting (WRF) Model predictions are examined. Limitations of evaluation are constrained by (i) parameterizations of model physics, (ii) parameterizations of input data, (iii) model resolution, and (iv) flux observation resolution. Observations from a new 22.1-m flux tower situated within a residential neighborhood in Phoenix, Arizona, are utilized to evaluate the ability of the urbanized WRF to resolve finescale surface energy balance (SEB) when using the urban classes derived from the 30-m-resolution National Land Cover Database. Modeled SEB response to a large seasonal variation of net radiation forcing was tested during synoptically quiescent periods of high pressure in winter 2011 and premonsoon summer 2012. Results are presented from simulations employing five nested domains down to 333-m horizontal resolution. A comparative analysis of model cases testing parameterization of physical processes was done using four configurations of urban parameterization for the bulk urban scheme versus three representations with the Urban Canopy Model (UCM) scheme, and also for two types of planetary boundary layer parameterization: the local Mellor–Yamada–Janjić scheme and the nonlocal Yonsei University scheme. Diurnal variation in SEB constituent fluxes is examined in relation to surface-layer stability and modeled diagnostic variables. Improvement is found when adapting UCM for Phoenix with reduced errors in the SEB components. Finer model resolution is seen to have insignificant (<1 standard deviation) influence on mean absolute percent difference of 30-min diurnal mean SEB terms.

Forecasts of noise pollution from a highway line segment noise source are obtained from a sound propagation model utilizing effective sound speed profiles derived from a Numerical Weather Prediction (NWP) limited area forecast with 1 km horizontal resolution and near-ground vertical resolution finer than 20 m. Methods for temporal along with horizontal and vertical spatial nesting are demonstrated within the NWP model for maintaining forecast feasibility. It is shown that vertical nesting can improve the prediction of finer structures in near-ground temperature and velocity profiles, such as morning temperature inversions and low level jet-like features. Accurate representation of these features is shown to be important for modeling sound refraction phenomena and for enabling accurate noise assessment. Comparisons are made using the parabolic equation model for predictions with profiles derived from NWP simulations and from field experiment observations during mornings on November 7 and 8, 2006 in Phoenix, Arizona. The challenges faced in simulating accurate meteorological profiles at high resolution for sound propagation applications are highlighted and areas for possible improvement are discussed.

Explicit solutions of the inhomogeneous paraxial wave equation in a linear and quadratic approximation are applied to wave fields with invariant features, such as oscillating laser beams in a parabolic waveguide and spiral light beams in varying media. A similar effect of superfocusing of particle beams in a thin monocrystal film, harmonic oscillations of cold trapped atoms, and motion in magnetic field are also mentioned.

In this paper, we study oscillating solutions of the 1D-quintic nonlinear Schrödinger equation with the help of Wigner's quasiprobability distribution in quantum phase space. An "absolute squeezing property," namely a periodic in time total localization of wave packets at some finite spatial points without violation of the Heisenberg uncertainty principle, is analyzed in this nonlinear model.

Amphibians vary in their response to infection by the amphibian-killing chytrid fungus, Batrachochytrium dendrobatidis (Bd). Highly susceptible species are the first to decline and/or disappear once Bd arrives at a site. These competent hosts likely facilitate Bd proliferation because of ineffective innate and/or acquired immune defenses. We show that Atelopus zeteki, a highly susceptible species that has undergone substantial population declines throughout its range, rapidly and exponentially increases skin Bd infection intensity, achieving intensities that are several orders of magnitude greater than most other species reported. We experimentally infected individuals that were never exposed to Bd (n = 5) or previously exposed to an attenuated Bd strain (JEL427-P39; n = 3). Within seven days post-inoculation, the average Bd infection intensity was 18,213 zoospores (SE: 9,010; range: 0 to 66,928).

Both average Bd infection intensity and zoospore output (i.e., the number of zoospores released per minute by an infected individual) increased exponentially until time of death (t₅₀ = 7.018, p<0.001, t₄₆ = 3.164, p = 0.001, respectively). Mean Bd infection intensity and zoospore output at death were 4,334,422 zoospores (SE: 1,236,431) and 23.55 zoospores per minute (SE: 22.78), respectively, with as many as 9,584,158 zoospores on a single individual. The daily percent increases in Bd infection intensity and zoospore output were 35.4% (SE: 0.05) and 13.1% (SE: 0.04), respectively. We also found that Bd infection intensity and zoospore output were positively correlated (t₄₃ = 3.926, p<0.001). All animals died between 22 and 33 days post-inoculation (mean: 28.88; SE: 1.58). Prior Bd infection had no effect on survival, Bd infection intensity, or zoospore output. We conclude that A. zeteki, a highly susceptible amphibian species, may be an acute supershedder. Our results can inform epidemiological models to estimate Bd outbreak probability, especially as they relate to reintroduction programs.

Laboratory investigations into the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), have accelerated recently, given the pathogen’s role in causing the global decline and extinction of amphibians. Studies in which host animals were exposed to Bd have largely assumed that lab-maintained pathogen cultures retained the infective and pathogenic properties of wild isolates. Attenuated pathogenicity is common in artificially maintained cultures of other pathogenic fungi, but to date, it is unknown whether, and to what degree, Bd might change in culture. We compared zoospore production over time in two samples of a single Bd isolate having different passage histories: one maintained in artificial media for more than six years (JEL427-P39), and one recently thawed from cryopreserved stock (JEL427-P9). In a common garden experiment, we then exposed two different amphibian species, Eleutherodactylus coqui and Atelopus zeteki, to both cultures to test whether Bd attenuates in pathogenicity with in vitro passages. The culture with the shorter passage history, JEL427-P9, had significantly greater zoospore densities over time compared to JEL427-P39. This difference in zoospore production was associated with a difference in pathogenicity for a susceptible amphibian species, indicating that fecundity may be an important virulence factor for Bd. In the 130-day experiment, Atelopus zeteki frogs exposed to the JEL427-P9 culture experienced higher average infection intensity and 100% mortality, compared with 60% mortality for frogs exposed to JEL427-P39. This effect was not observed with Eleutherodactylus coqui, which was able to clear infection. We hypothesize that the differences in phenotypic performance observed with Atelopus zeteki are rooted in changes of the Bd genome. Future investigations enabled by this study will focus on the underlying mechanisms of Bd pathogenicity.