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.

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.

Strategies are needed to improve repopulation of decellularized lung scaffolds with stromal and functional epithelial cells. We demonstrate that decellularized mouse lungs recellularized in a dynamic low fluid shear suspension bioreactor, termed the rotating wall vessel (RWV), contained more cells with decreased apoptosis, increased proliferation and enhanced levels of total RNA compared to static recellularization conditions. These results were observed with two relevant mouse cell types: bone marrow-derived mesenchymal stromal (stem) cells (MSCs) and alveolar type II cells (C10). In addition, MSCs cultured in decellularized lungs under static but not bioreactor conditions formed multilayered aggregates. Gene expression and immunohistochemical analyses suggested differentiation of MSCs into collagen I-producing fibroblast-like cells in the bioreactor, indicating enhanced potential for remodeling of the decellularized scaffold matrix. In conclusion, dynamic suspension culture is promising for enhancing repopulation of decellularized lungs, and could contribute to remodeling the extracellular matrix of the scaffolds with subsequent effects on differentiation and functionality of inoculated cells.

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.

Investigation into the causes underlying the rapid, global amphibian decline provides critical insight into the effects of changing ecosystems. Hypothesized and confirmed links between amphibian declines, disease, and environmental changes are increasingly represented in published literature. However, there are few long-term amphibian studies that include data on population size, abnormality/injury rates, disease, and habitat variables to adequately assess changes through time. We cultured and identified microorganisms isolated from abnormal/injured and repressed tissue regeneration sites of the endangered Ozark Hellbender, Cryptobranchus alleganiensis bishopi, to discover potential causative agents responsible for their significant decline in health and population. This organism and our study site were chosen because the population and habitat of C. a. bishopi have been intensively studied from 1969–2009, and the abnormality/injury rate and apparent lack of regeneration were established.

Although many bacterial and fungal isolates recovered were common environmental organisms, several opportunistic pathogens were identified in association with only the injured tissues of C.a. bishopi. Bacterial isolates included Aeromonas hydrophila, a known amphibian pathogen, Granulicetella adiacens, Gordonai terrae, Stenotrophomonas maltophilia, Aerococcus viridans, Streptococcus pneumoniae and a variety of Pseudomonads, including Pseudomonas aeruginosa, P. stutzeri, and P. alcaligenes. Fungal isolates included species in the genera Penicillium, Acremonium, Cladosporium, Curvularia, Fusarium, Streptomycetes, and the Class Hyphomycetes. Many of the opportunistic pathogens identified are known to form biofilms. Lack of isolation of the same organism from all wounds suggests that the etiological agent responsible for the damage to C. a. bishopi may not be a single organism. To our knowledge, this is the first study to profile the external microbial consortia cultured from a Cryptobranchid salamander. The incidence of abnormalities/injury and retarded regeneration in C. a. bishopi may have many contributing factors including disease and habitat degradation. Results from this study may provide insight into other amphibian population declines.

A distinct pathovar of Salmonella enterica serovar Typhimurium, ST313, has emerged in sub-Saharan Africa as a major cause of fatal bacteremia in young children and HIV-infected adults. D23580, a multidrug resistant clinical isolate of ST313, was previously shown to have undergone genome reduction in a manner that resembles that of the more human-restricted pathogen, Salmonella enterica serovar Typhi. It has since been shown through tissue distribution studies that D23580 is able to establish an invasive infection in chickens. However, it remains unclear whether ST313 can cause lethal disease in a non-human host following a natural course of infection. Herein we report that D23580 causes lethal and invasive disease in a murine model of infection following peroral challenge. The LD⁵⁰ of D23580 in female BALB/c mice was 4.7 x 10⁵ CFU. Tissue distribution studies performed 3 and 5 days post-infection confirmed that D23580 was able to more rapidly colonize the spleen, mesenteric lymph nodes and gall bladder in mice when compared to the well-characterized S. Typhimurium strain SL1344. D23580 exhibited enhanced resistance to acid stress relative to SL1344, which may lend towards increased capability to survive passage through the gastrointestinal tract as well as during its intracellular lifecycle. Interestingly, D23580 also displayed higher swimming motility relative to SL1344, S. Typhi strain Ty2, and the ST313 strain A130. Biochemical tests revealed that D23580 shares many similar metabolic features with SL1344, with several notable differences in the Voges-Proskauer and catalase tests, as well alterations in melibiose, and inositol utilization. These results represent the first full duration infection study using an ST313 strain following the entire natural course of disease progression, and serve as a benchmark for ongoing and future studies into the pathogenesis of D23580.