ASU Scholarship Showcase

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.

The probiotic effects of Lactobacillus reuteri have been speculated to partly depend on its capacity to produce the antimicrobial substance reuterin during the reduction of glycerol in the gut. In this study, the potential of this process to protect human intestinal epithelial cells against infection with Salmonella enterica serovar Typhimurium was investigated. We used a three-dimensional (3-D) organotypic model of human colonic epithelium that was previously validated and applied to study interactions between S. Typhimurium and the intestinal epithelium that lead to enteric salmonellosis. Using this model system, we show that L. reuteri protects the intestinal cells against the early stages of Salmonella infection and that this effect is significantly increased when L. reuteri is stimulated to produce reuterin from glycerol. More specifically, the reuterin-containing ferment of L. reuteri caused a reduction in Salmonella adherence and invasion (1 log unit), and intracellular survival (2 log units). In contrast, the L. reuteri ferment without reuterin stimulated growth of the intracellular Salmonella population with 1 log unit. The short-term exposure to reuterin or the reuterin-containing ferment had no observed negative impact on intestinal epithelial cell health. However, long-term exposure (24 h) induced a complete loss of cell-cell contact within the epithelial aggregates and compromised cell viability. Collectively, these results shed light on a potential role for reuterin in inhibiting Salmonella-induced intestinal infections and may support the combined application of glycerol and L. reuteri. While future in vitro and in vivo studies of reuterin on intestinal health should fine-tune our understanding of the mechanistic effects, in particular in the presence of a complex gut microbiota, this the first report of a reuterin effect on the enteric infection process in any mammalian cell type.

Extra-intestinal pathogenic E. coli (ExPEC), including avian pathogenic E. coli (APEC), pose a considerable threat to both human and animal health, with illness causing substantial economic loss. APEC strain χ7122 (O78∶K80∶H9), containing three large plasmids [pChi7122-1 (IncFIB/FIIA-FIC), pChi7122-2 (IncFII), and pChi7122-3 (IncI₂)]; and a small plasmid pChi7122-4 (ColE2-like), has been used for many years as a model strain to study the molecular mechanisms of ExPEC pathogenicity and zoonotic potential. We previously sequenced and characterized the plasmid pChi7122-1 and determined its importance in systemic APEC infection; however the roles of the other pChi7122 plasmids were still ambiguous. Herein we present the sequence of the remaining pChi7122 plasmids, confirming that pChi7122-2 and pChi7122-3 encode an ABC iron transport system (eitABCD) and a putative type IV fimbriae respectively, whereas pChi7122-4 is a cryptic plasmid. New features were also identified, including a gene cluster on pChi7122-2 that is not present in other E. coli strains but is found in Salmonella serovars and is predicted to encode the sugars catabolic pathways. In vitro evaluation of the APEC χ7122 derivative strains with the three large plasmids, either individually or in combinations, provided new insights into the role of plasmids in biofilm formation, bile and acid tolerance, and the interaction of E. coli strains with 3-D cultures of intestinal epithelial cells. In this study, we show that the nature and combinations of plasmids, as well as the background of the host strains, have an effect on these phenomena. Our data reveal new insights into the role of extra-chromosomal sequences in fitness and diversity of ExPEC in their phenotypes.

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.