Browsing by Subject "biological"
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Item An investigation into the contamination of WSR-88D VAD wind profile output by migrating birds(Texas A&M University, 2004-09-30) Schulze, Karl WernerThe VAD Wind Profile (VWP), a time-height display of winds computed by the National Weather Service's WSR-88D radar, is known on occasion to have errors at night during the fall and spring seasons. Several studies, such Haro and Gauthreaux (1998), confirm that migrating birds often contaminate the VWP output. By means of telescopic observations of a full moon, birds were observed flying on two nights when VWP contamination was suspected. The nature of the VWP errors is consistent with migrating birds due to the seasonality, nocturnal nature, and the magnitude of the errors found (greater than 10 knots). With careful selection of data, two clusters of points on the Velocity-Azimuth Display (VAD) are found to exist at certain altitudes when birds begin migrating. One cluster of points is due to radar sample volumes containing birds, and the other cluster is from radar sample volumes without birds. Being able to determine which cluster represents the wind could allow the wind to be calculated by the VWP. Present limitations with the Radar Product Generator's processor and memory prohibit a very advanced detection algorithm. Two simple objective techniques to determine the existence of the two clusters, and determine the wind, were tested. While they show some promise, these methods require further operational testing to determine their usefulness for real-time warning of bird contamination and the reporting of the true wind.Item The effect of nutrient limitations on the production of extracellular polymeric substances by drinking-water bacteria(2013-05) Evans, Ashley Nichole; Kirisits, Mary JoBiological filtration (biofiltration) of drinking-water is gaining popularity due the potential for biodegradation of an array of contaminants not removed by traditional drinking-water processes. However, previous research has suggested that biomass growth on biofilter media may lead to increased headloss, and thus, greater energy and water requirements for backwashing. Research has suggested that the main cause of headloss might be due to extracellular polymeric substances (EPS) rather than the bacterial cells themselves. As EPS production has been shown to increase under nitrogen- and phosphorus-limited or -depleted conditions, the goal of this research was to add to the body of knowledge regarding biofiltration by studying the relationship between EPS production and nutrient limitations in drinking-water. Batch experiments with a synthetic groundwater were run with a mixed community of drinking-water bacteria under nutrient-balanced (a molar carbon to nitrogen to phosphorus ratio [C:N:P] of 100:10:1), nutrient-limited (e.g., C:N:P of 100:10:0.1), and nutrient-depleted conditions (C:N:P of 100:0:1 or 100:10:0). After 5 days, growth was measured as the optical density at 600 nanometers (OD600), and the concentrations of free and bound carbohydrates and proteins, the main components of EPS, were measured. In batch experiments with 2.0 and 0.2 g/L as carbon (mixture of acetic acid, mannitol and sucrose) increases in EPS production per OD600 and decreases in growth were noted under nutrient-depleted conditions. When the same experiments were conducted with a pure culture of Bacillus cereus, bound polysaccharides normalized to OD600 increased under nitrogen- and phosphorus-depleted conditions. Since previous research suggested that Bradyrhizobium would be an important player in EPS production in drinking-water biofilters, similar batch experiments were conducted with Bradyrhizobium. However, due to experimental challenges with Bradyrhizobium japonicum USDA 110, differences in EPS production under nutrient limitations could not be reliably assessed. Additional work is required with Bradyrhizobium. Recommendations for future work include the replication of these batch conditions in steady-state chemostats containing biofilm attachment media and in bench-scale columns. Additionally, future work should include experiments at carbon concentrations as low as 2 mg/L to match typical carbon concentrations in drinking-water biofilters.Item Simulation and Design of Biological and Biologically-Motivated Computing Systems(2014-04-17) Zhang, YongIn life science, there is a great need in understandings of biological systems for therapeutics, synthetic biology, and biomedical applications. However, complex behaviors and dynamics of biological systems are hard to understand and design. In the mean time, the design of traditional computer architectures faces challenges from power consumption, device reliability, and process variations. In recent years, the convergence of computer science, computer engineering and life science has enabled new applications targeting the challenges from both engineering and biological fields. On one hand, computer modeling and simulation provides quantitative analysis and predictions of functions and behaviors of biological systems, and further facilitates the design of synthetic biological systems. On the other hand, bio-inspired devices and systems are designed for real world applications by mimicking biological functions and behaviors. This dissertation develops techniques for modeling and analyzing dynamic behaviors of biologically realistic genetic circuits and brain models and design of brain-inspired computing systems. The stability of genetic memory circuits is studied to understand its functions for its potential applications in synthetic biology. Based on the electrical-equivalent models of biochemical reactions, simulation techniques widely used for electronic systems are applied to provide quantitative analysis capabilities. In particular, system-theoretical techniques are used to study the dynamic behaviors of genetic memory circuits, where the notion of stability boundary is employed to characterize the bistability of such circuits. To facilitate the simulation-based studies of physiological and pathological behaviors in brain disorders, we construct large-scale brain models with detailed cellular mechanisms. By developing dedicated numerical techniques for brain simulation, the simulation speed is greatly improved such that dynamic simulation of large thalamocortical models with more than one million multi-compartment neurons and hundreds of synapses on commodity computer servers becomes feasible. Simulation of such large model produces biologically meaningful results demonstrating the emergence of sigma and delta waves in the early and deep stages of sleep, and suggesting the underlying cellular mechanisms that may be responsible for generation of absence seizure. Brain-inspired computing paradigms may offer promising solutions to many challenges facing the main stream Von Neumann computer architecture. To this end, we develop a biologically inspired learning system amenable to VLSI implementation. The proposed solution consists of a digitized liquid state machine (LSM) and a spike-based learning rule, providing a fully biologically inspired learning paradigm. The key design parameters of this liquid state machine are optimized to maximize the learning performance while considering hardware implementation cost. When applied to speech recognition of isolated word using TI46 speech corpus, the performance of the proposed LSM rivals several existing state-of-art techniques including the Hidden Markov Model based recognizer Sphinx-4.Item Spatio-temporal patterns of biophysical parameters in a microtidal, bar-built, subtropical estuary of the Gulf of Mexico(2009-05-15) Gable, George M., IVPlankton communities are influenced, in part, by water exchange with adjacent estuarine and oceanic ecosystems. Reduced advective transport through tidal passes or with adjacent bay systems can affect chemical processes and biological interactions, such as nutrient cycling, phytoplankton abundance and productivity, community respiration, and zooplankton biovolume. The most threatened estuarine ecosystems are shallow, bar-built, microtidal estuaries with small water volumes and restricted connections through tidal passes and other water exchange points. This research explored spatio-temporal trends in plankton communities and the physicochemical environment in Mesquite Bay, Texas a microtidal, bar-built, subtropical estuary in the Gulf of Mexico. This research couples sampling at fixedstations for multiple physical and biological parameters with high-resolution spatial mapping of physicochemical parameters. Spatial trends were less in magnitude and affected fewer parameters in fixed station and spatial data. Two dimensional ordination plots indicated spatial heterogeneity with a more pronounced temporal trend affecting parameters including temperature, salinity as a function of inflow timing, and seasonal wind direction affecting primary production and zooplankton biovolume. Temperature was positively correlated with gross production and respiration rates during spring and late summer with sporadic positive and negative correlations with phytoplankton biomass. The timing and magnitude of freshwater inflow affected various physicochemical and biological parameters. Higher than 71-year inflow rates resulted in low salinity system wide, with spatial heterogeneity increasing over the course of the study, which was confirmed by spatial maps. Additionally, high inflow rates led to two periods of increased inorganic nutrients and dissolved organic matter. Low salinity periods coincided with persistence of higher turbidity, likely because of decreased sediment flocculation. Gross production was low at this time, and likely from light limitation. Additionally, wind magnitude and direction created spatial heterogeneity in turbidity levels and phytoplankton biomass. Zooplankton biovolume was highest during spring and late summer with high species diversity in total rotifers. Copepod biovolume and phytoplankton biomass were positively correlated. Other zooplankton taxonomic groups exhibited variable correlations with phytoplankton biomass and other taxonomic groups. Further long-term studies are needed to determine interactions of various components of trophic food-webs and account for interannual variability in all system parameters.