The GARVEE Transportation Program started by the Idaho Transportation Department has improved parts of I-84 in Boise, Idaho. These desired improvements led to the widening of a bridge over the New York Canal (NYC) in 2009. To support the wider road, additional bridge columns were installed. The new bridge columns had a larger diameter than the existing columns and raised the number of columns from 28 to 60. Construction was completed just before the irrigation season began. During the first irrigation season it was observed that waves and oscillations were occurring within the canal immediately adjacent to the bridge structure. Throughout the irrigation season, it was observed that the intensity of the oscillations would vary. It was also observed that the wave oscillations propagated upstream and downstream from the bridge structure. Both longitudinal and transverse waves were observed. The waves appeared to originate in the section of the canal that was under the I-84 Bridge. A physical model was built in 2010 at Utah State University's (USU) Utah Water Research Laboratory (UWRL) in an attempt to simulate the oscillation phenomenon and to develop potential solutions to the problem. During the original modeling work, a thorough investigation to the causes of this phenomenon was not accomplished due to time constraints. The objective of the follow-up research presented in this thesis was to qualitatively determine the causes of the oscillations. Laboratory tests were performed using the original physical model used in the original 2010 testing.

The hippocampus is one of the most intensely studied brain structures and the oscillatory activity of the hippocampal neurons is believed to be involved in learning and memory consolidation. Therefore, studying rhythm generation and modulation in this structure is an important step in understanding its function. In this thesis, these phenomena are studied via mathematical models of networks of hippocampal interneurons. The two types of neural networks considered here are homogenous and heterogenous networks. In homogenous networks, the input current to each neuron is equal, while in heterogenous networks, this assumption is relaxed and there is a specified degree of heterogeneity in the input stimuli. A phase reduction technique is applied to the neural network model of the hippocampal interneurons and attempts are made to understand the implications of heterogeneity to the existence and stability of the synchronized oscillations. The Existence of a critical level of heterogeneity above which the synchronized rhythms are not stable is established, and linear analysis is applied to derive expressions for estimating the perturbations in the network frequency and timing of the neural spikes. The mathematical techniques developed in this thesis are general enough to be applied to models describing other types of neurons not considered here. Possible biological implications include the application of high frequency local stimulation to alleviate the synchronous neural oscillations in pathological conditions such as epilepsy and Parkinson's disease and the possible role of heterogeneity in controlling the rhythm frequency and switching between various cognitive states.

Reproduction de : Thèse de doctorat : Acoustique : Le Mans : 2006. / Titre provenant de l'écran-titre. Bibliogr. p. 93-103.

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published_or_final_version / Civil and Structural Engineering / Doctoral / Doctor of Philosophy

Iron (Fe) exerts strong control over environmental biogeochemistry. As the fourth most abundant element, Fe is present in nearly all earth environments, where it plays important roles in governing the transformation and movement of organic and inorganic constituents, and in microbial respiration. Consequently, the body of work on Fe biogeochemistry is vast. This study is specifically concerned with the dynamic changes in the oxidation state of Fe (i.e., redox cycling) and their impact on the inorganic, organic and microbial components in soil. I constructed a special apparatus to fluctuate redox potential on soil slurries while concurrently sampling a wide range of biogeochemical variables (pH, redox potential, major and trace elements, CO2 release, DNA community composition charges, etc.). Previous research has documented redox fluctuations along a climate gradient in Hawaii and a primary goal of this dissertation was to reconstruct these redox fluctuations, subjected to experimental constraints afforded by a laboratory setting, with minimal disruption to the biogeochemical processes controlling Fe redox cycling. By recasting the spatial and temporal characteristics of in situ Fe redox cycling in the laboratory, I was able to form testable hypotheses regarding the importance of Fe redox oscillations to soil mineral transformations, colloid composition/dynamics and microbial community structure. A second goal of this dissertation was to explore the utility of Fe isotopic composition for providing information on soil weathering processes along age and climate gradients at the field scale in Hawaii. This portion of the study tested emerging theories of Fe isotope fractionation during mineral dissolution using well-characterized sequences in soil weathering intensity.The principal findings of the laboratory redox fluctuation experiments are that Fe redox oscillations: (1) trigger an increase in the crystallinity of Fe-oxides; (2) mobilize colloids containing refractory elements (e.g., Zr, Nb, U, etc.); (3) reveal redox sensitive rare earth element (REE) anomalies in the aqueous phase; and (4) induce changes in the microbial community favoring microbes capable of growth under both oxic and anoxic conditions. The principal finding of the Fe isotope measurements is that isotopic composition is directly related to weathering intensity in the field, consistent with theoretical predictions.

Parkinson’s disease (PD) is a movement disorder that is of basal ganglia origin. It is characterized by a severe loss of dopaminergic input to the striatum and symptoms such as bradykinesia, rigidity and tremor. There is growing evidence that PD is associated with pathological synchronous oscillatory activity in the basal ganglia, which primarily occurs in the 11-30 Hz range, the so-called beta band. The aim of this project was to better understand the oscillatory activity recorded from the basal ganglia of PD patients and to elucidate the significance of this activity in PD. To do this, neuronal firing and local field potentials (LFPs) were recorded from the subthalamic nucleus (STN) and globus pallidus internus (GPi) of PD patients undergoing stereotactic neurosurgery for implantation of therapeutic deep brain stimulation electrodes. Beta oscillatory LFP activity in the STN and GPi was found to be coherent with, and reflect to a certain degree, rhythmic activity in a population of local neurons. I have demonstrated for the first time that the degree of beta oscillatory firing in the STN, which is maximal in the motor portion, correlates with the patients’ benefit from dopaminergic medications, but not with baseline motor deficits. My study has also established that beta oscillatory firing in the STN does not positively correlate with the patients’ tremor scores and that during periods of tremor patients tend to have less beta oscillatory firing and increased neuronal oscillatory firing at the tremor frequency. Temporal examination of the LFPs recorded during periods of intermittent resting tremor revealed that stronger tremor is associated with increased LFP power in the low gamma range (35-55 Hz) and there is a decrease in the ratio of beta to gamma coherence. Similarly, a change in balance between oscillatory activities was observed during levodopa-induced dyskinesias. Finally, when the oscillatory activity in the GPi of PD patients was compared to that in dystonia I found that in dystonia, oscillatory LFP activity is less likely to reflect the neuronal firing. These findings indicate that beta oscillatory activity in the basal ganglia might reflect the degree of dopamine deficiency in the striatum and that the relative strength of oscillatory rhythms may play an important role in mediating the pathological features in PD.

Stimulation of urine production by the Malpighian (renal) tubules in Rhodnius prolixus is regulated by at least two diuretic hormones, CRF-related peptide and serotonin, that have traditionally been believed to function through the activation of cAMP-mediated intracellular second messenger pathways. In this study I demonstrate that serotonin stimulation triggered, in addition to cAMP, intracellular Ca2+ waves in the Malpighian tubule cells of R. prolixus. Treatment with the intracellular Ca2+ chelator BAPTA-AM blocked the intracellular Ca2+ waves and reduced serotonin-stimulated fluid secretion by 75%. This suggests a role for intracellular Ca2+ signaling in the excretory system of R. prolixus. Serotonin stimulated Malpighian tubules (MTs) exposed to Ca2+-free saline plus BAPTA-AM secreted an abnormal fluid, showing: increased K+ concentration, reduced Na+ concentration and lower pH. These results along with measurement of transepithelial potential (TEP) suggest that the basolateral Na+:K+:2Cl- cotransporter (NKCC) activity is reduced in tubule cells treated with BAPTA-AM, suggesting that Ca2+ is required to modulate the activity of the basolateral NKCC. Treatment with the non-hydrolysable cell-permeable cAMP analog, 8Br-cAMP, produced fluid with the same K+ and Na+ concentration and at the same secretion rate as serotonin-stimulated tubules. In addition, 8Br-cAMP triggered intracellular Ca2+ oscillations similar to those obtained with serotonin. 8Br-cAMP-stimulated tubules treated with BAPTA-AM decreased their fluid secretion by about 40% and increased Na+ concentration, similar to the effect observed on serotonin-stimulated tubules. Therefore, I conclude that the intracellular Ca2+ waves triggered by serotonin are mediated by cAMP. The role of inositol-3-phospate (InsP3) in Ca2+ release was tested by treating the tubules with the InsP3 receptor blocker xestospongin. The treatment decreased fluid secretion rate as well as the amplitude of Ca2+ waves in serotonin-stimulated tubules. These results suggest that serotonin activates the production of InsP3 and, most likely, diacylglycerol (DAG). Thus, I decided to test whether the protein kinase C (PKC) may be involved in serotonin-stimulated secretion. The PKC inhibitors chelerythrine and bisindolylmaleimide (BIM) decreased secretion fluid rate in serotonin-stimulated tubules by 50% and 70%, respectively. Fluid secreted by tubules treated with BIM showed no differences in K+ and Na+ concentrations compared to controls, however both ion fluxes decreased. The evidence suggests that PKC is involved in serotonin stimulated secretion; the mechanism is still not understood. Taken together, the results suggest that cAMP, Ca2+ and PLC-PKC pathway are involved in serotonin stimulated secretion. However cAMP stimulation is enough for maximal secretion rate. Therefore PLC-PKC must act downstream of cAMP. Based on those results we hypothesize that serotonin binds a GPCR, increasing cAMP by activation of an adenylate cyclase (AC). Subsequently, cAMP is somehow able to activate PLC, which finally produces Ca2+ release, PKC activation and NKCC upregulation.

Parkinson’s disease (PD) is a movement disorder that is of basal ganglia origin. It is characterized by a severe loss of dopaminergic input to the striatum and symptoms such as bradykinesia, rigidity and tremor. There is growing evidence that PD is associated with pathological synchronous oscillatory activity in the basal ganglia, which primarily occurs in the 11-30 Hz range, the so-called beta band. The aim of this project was to better understand the oscillatory activity recorded from the basal ganglia of PD patients and to elucidate the significance of this activity in PD. To do this, neuronal firing and local field potentials (LFPs) were recorded from the subthalamic nucleus (STN) and globus pallidus internus (GPi) of PD patients undergoing stereotactic neurosurgery for implantation of therapeutic deep brain stimulation electrodes. Beta oscillatory LFP activity in the STN and GPi was found to be coherent with, and reflect to a certain degree, rhythmic activity in a population of local neurons. I have demonstrated for the first time that the degree of beta oscillatory firing in the STN, which is maximal in the motor portion, correlates with the patients’ benefit from dopaminergic medications, but not with baseline motor deficits. My study has also established that beta oscillatory firing in the STN does not positively correlate with the patients’ tremor scores and that during periods of tremor patients tend to have less beta oscillatory firing and increased neuronal oscillatory firing at the tremor frequency. Temporal examination of the LFPs recorded during periods of intermittent resting tremor revealed that stronger tremor is associated with increased LFP power in the low gamma range (35-55 Hz) and there is a decrease in the ratio of beta to gamma coherence. Similarly, a change in balance between oscillatory activities was observed during levodopa-induced dyskinesias. Finally, when the oscillatory activity in the GPi of PD patients was compared to that in dystonia I found that in dystonia, oscillatory LFP activity is less likely to reflect the neuronal firing. These findings indicate that beta oscillatory activity in the basal ganglia might reflect the degree of dopamine deficiency in the striatum and that the relative strength of oscillatory rhythms may play an important role in mediating the pathological features in PD.

A survey of the theory of neutrino oscillations in dense matter and neutrino backgrounds is presented. We discuss collective neutrino systems using the gyroscopic pendulum analogy and describe the motion that results from self-induced parametric resonances. The effects of dense matter on the flavour oscillations of neutrinos are also detailed. This theory is applied to the case of continuous supernova neutrino spectra and explanations of the spectral swapping behaviour seen in numerical studies are summarized. The results of numerical simulations of supernova oscillations in turbulent supernova backgrounds are presented and discussed. We study the motion of two example supernova neutrino spectra and examine the differences in the dynamics and flavour evolution that results from adding turbulent fluctuations to the supernova matter background. We also investigate the effect that fluctuations in the neutrino density can have on the oscillation behaviour. We find that in general the final neutrino spectra emerging from the inner supernova regions are quite robust to fluctuations in the backgrounds in our model, while the intermediate dynamics can be very strongly altered. Some significant changes in the final spectra are also found to occur when the neutrino background density fluctuations are large. We give a detailed review of the resonant matter effects that determine the survival probabilities of atmospheric muon neutrinos. The differences between various Earth density models are described, and these models are then used to predict the flux of muon-type neutrino events in the Deep Core extension to the IceCube detector. We use recent results from the detector collaboration and build on previous work which considered the sensitivity of the detector to the mass hierarchy, and show that uncertainties in the Earth's density can have a significant influence on the event rates.