Shale Characterization and Size-effect study using Scanning Electron Microscopy and X-Ray Diffraction

Ground failure is a major contributor of the total fatalities in underground mines in the US. Underground coal mines in the Northern Appalachian region have weak roof rock mainly composed of shale and sandstone. Characterization of shale is indispensable for developing an effective ground control plan. However, this has not been done extensively. This thesis attempts to address this issue. It investigates the variation in mechanical properties of shale with variation in size. In addition, an attempt has been made to relate the strength of shale with its petrographic parameters. X-ray diffraction technique was used to estimate the compositional parameters like quartz content, calcite content and clay content. Similarly, scanning electron microscopy was used to image the rock sample at microscale and estimate grain properties such as grain size, grain shape and grain orientation. Statistical analysis was performed to identify the extent of correlation between these parameters and strength and size of sample. From the analysis, it was observed that there was a significant difference in the strength of the sample with variation in size. In addition, samples with high quartz and calcite content showed higher average strength. Grain parameters also played a major role in influencing the strength of the sample with samples having higher average grain size inclining to have lower strength. Grain shape when defined by aspect ratio correlated with the strength of shale with higher aspect ratio contributing to higher strength. Grain orientation did not have any impact on strength. Finally, this research will help in understanding the size effect phenomenon in mines by looking into shale rock at microscopic scale and analyzing its petrographic parameters

Scaling of intrinsic noise in an autocratic reaction network

Biochemical reactions in living cells often produce stochastic trajectories due to the fluctuations of the finite number of the macromolecular species present inside the cell. A significant number of computational and theoretical studies have previously investigated stochasticity in small regulatory networks to understand its origin and regulation. At the systems level regulatory networks have been determined to be hierarchical resembling social networks. In order to determine the stochasticity in networks with hierarchical architecture, here we computationally investigated intrinsic noise in an autocratic reaction network in which only the upstream regulators regulate the downstream regulators. We studied the effects of the qualitative and quantitative nature of regulatory interactions on the stochasticity in the network. We established an unconventional scaling of noise with average abundance in which the noise passes through a minimum indicating that the network can be noisy both in the low and high abundance regimes. We determined that the bursty kinetics of the trajectories are responsible for such scaling. The scaling of noise remains intact for a mixed network that includes democratic subnetworks within the autocratic network

Qualitative and quantitative nature of mutual interactions dictate chemical noise in a democratic reaction network

The functions of a living cell rely on a complex network of biochemical reactions that allow it to respond against various internal and external cues. The outcomes of these chemical reactions are often stochastic due to intrinsic and extrinsic noise leading to population heterogeneity. The majority of calculations of stochasticity in reaction networks have focused on small regulatory networks addressing the role of timescales, feedback regulations, and network topology in propagation of noise. Here we computationally investigated chemical noise in a network with democratic architecture where each node is regulated by all other nodes in the network. We studied the effects of the qualitative and quantitative nature of mutual interactions on the propagation of both intrinsic and extrinsic noise in the network. We show that an increased number of inhibitory signals lead to ultrasensitive switching of average and that leads to sharp transition of intrinsic noise. The intrinsic noise exhibits a biphasic power-law scaling with the average, and the scaling coefficients strongly correlate with the strength of inhibitory signal. The noise strength critically depends on the strength of the interactions, where negative interactions attenuate both intrinsic and extrinsic noise

Investigation of chemical noise in multisite phosphorylation chain using linear noise approximation

Quantitative and qualitative nature of chemical noise propagation in biochemical reaction networks depend crucially on the topology of the networks. Multisite reversible phosphorylation-dephosphorylation of target proteins is one such recurrently found topology that regulates host of key functions in living cells. Here we analytically calculated the stochasticity in multistep reversible chemical reactions by determining variance of phosphorylated species at the steady state using linear noise approximation to investigate the effect of mass action and Michaelis-Menten kinetics on the noise of phosphorylated species. We probed the dependence of noise on the number of phosphorylation sites and the equilibrium constants of the reaction equilibria to investigate the chemical noise propagation in the multisite phosphorylation chain

Pulsatile signaling of bistable switches reveal the distinct nature of pulse processing by mutual activation and mutual inhibition loop

Cells often encounter various external and internal signals in a non-sustained pulsatile manner with varying amplitude, duration and residual value. However, the effect of signal pulse on the regulatory networks is poorly understood. In order gain a quantitative understating of pulse processing by bistable switches, we investigated pulse induced population inversion kinetics in bistable switches generated either by mutual activation or by mutual inhibition motifs. We show that a transient intense pulse or a prolonged weak pulse both can induce population inversion, however by distinct mechanisms. An intense pulse facilitates the population inversion by reducing the inversion time, while a weak prolonged pulse allows more late responders to flip their steady state causing increased average transition time. Although the inversion is controlled by the pulse amplitude and duration, however the fate of the inverted state is dictated by the residual signal that determines the mean residence at the flipped state. Therefore, population inversion and its maintenance require a proper tuning of all three signal parameters. Bistable system of mutual activation motif is more prone to make a transient response to the pulse however it is less susceptible to flip its steady state. While the bistability of mutual inhibition motif does not make a transient response yet it is more prone to switch its steady state. By comparing the pulse parameters and statistical properties of associated times scales, we conclude that a bistable switch originating from mutual activation loop is less susceptible to spurious signals as compared to the mutual inhibition loop

Acute Oxalate Nephropathy Due to Bilimbi Poisoning: A Case Report

Background: The concentrated juice made from Averrhoa bilimbi is rich in oxalic acid. It can cause acute oxalate nephropathy by blocking the tubules with calcium oxalate crystals. Case: An elderly woman was admitted to the hospital with a history of swelling of the legs, facial puffiness, and abdominal distention. Her biochemical study revealed features of acute renal failure. She gave history of taking half liter of bilimbi juice. Renal biopsy confirmed it was a case of acute oxalic nephropathy, which made it the second case of acute oxalic nephropathy due to ingestion of bilimbi juice ever reported from Bangladesh.Conclusion: It is not safe to consume high oxalate-containing fruits in large quantities