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Spinal Plasticity: Using Spinal Learning to Inform Maladaptive and Adaptive Effects of Nociceptive Input After Spinal Cord Injury
No full textThe traditional dogma of the spinal cord as a rigid conduit of information has been challenged in recent years. Evidence demonstrates that circuitry within the spinal cord can undergo adaptive and maladaptive plasticity particularly after spinal cord injury. Our work has focused on instrumental learning in the spinal cord along with the impact of nociceptive input after spinal cord injury. In this dissertation I explored how spinal cord injury affects plasticity. This work places particular emphasis on the impact of nociceptive input and factors that allow peripheral input to drive adaptive rather than maladaptive plasticity.
This dissertation explored spinal plasticity after injury in a complete thoracic (T2) transection in order to clarify the properties of the spinal cord itself. The first series of experiments show that the consequences of training vary with duration. These experiments also revealed two unexpected findings that motivated the following two chapters.
The second series identified a previously unknown effect of exposure to controllable
stimulation. An extended exposure to controllable stimulation altered how later stimulation is
interpreted, causing it to be read as adaptive (controllable) regardless of how it was presented.
This series also identified the anatomical locus of this shift and began to clarify its mechanistic
underpinnings.
The next series of experiments clarified the impact of proprioceptive signaling on the effects of uncontrollable noxious input. These experiments found that limb position modulates how nociceptive stimulation affects spinal cord plasticity. This series revealed that noxious stimulation only impairs plastic potential when applied while the hind limbs are extended.
The final set of experiments explored the role of ionic plasticity in spinal plasticity after injury. These experiments focused on the importance of the release of the GABAergic break on adaptive plasticity. They also identified pharmacological manipulations that can be used to manipulate ionic plasticity and, as a result, spinal plasticity. This suggests the potential of harnessing ionic plasticity to drive adaptive over maladaptive change.
Collectively, these experiments highlight the potential of harnessing plasticity after spinal cord injury for good. The studies show how the consequences of nociceptive stimulation vary with duration, order of presentation, limb position, and changes in GABA-dependent inhibition
The Role of the Science Teacher: Examination of Science Education Research and Science Teacher Education
No full textScience education has repeatedly identified the teacher as the greatest classroom level factor on student learning. Given the known variance in instructor ability and quality, a failure to consider how an instructor effect may be impacting study results draws into question the validity of study analyses and conclusions that fail to adequately conduct meaningful comparisons. The first investigation of this dissertation examined 79 studies from three leading science education journals to determine the frequency and quality of attention towards instructor differences in sampling efforts. Our findings indicate that instructor difference is rarely considered to a sufficient level within science education research, even in studies with exceedingly small sample sizes. These results are concerning for research practitioners who may be neglecting a key factor in research outcomes.
Though literature surrounding science teacher preparation programs is limited, current evidence suggests that methods courses frequently foreground instructional strategies and activities rather than a more comprehensive framework for science teaching. Potential consequences for this emphasis for preservice educators include a rejection of research-based instructional strategies, weakened instructional effectiveness, and an inability to conduct effective classroom decision-making. Study two in this dissertation analyzed 30 science methods syllabi from varying institutions and education programs to provide preliminary insight into science methods emphases. Our findings support prior claims that science methods courses are highlighting instructional strategies while neglecting the crucial role of the science teacher and teacher behaviors.
The science teacher must clearly understand their role in scaffolding student thinking away from misconceptions and towards accurate understanding of scientific ideas. The final study of this dissertation sought to triangulate findings from study two by interviewing methods instructors to understand their conceptualizations of effective science teaching, the instructional role of the science teacher, and the function of teacher behaviors within that role. Our findings suggest that methods instructors often employ vague metaphorical language when describing the instructional role of the science teacher and rarely address teacher behaviors. Syllabi were found to effectively reflect methods instructors��� conceptualizations of effective science teaching and the function of teacher behaviors but were less effective in representing methods instructors��� conceptualizations of the role of the science teacher
Analytic and Semi-Analytic Calculations for Color Glass in the Weak Field Limit
No full textThe classical field approximation for color glass condensate can be solved using numerical methods and recursive analytic series solutions. The recursive analytic solution is known to have a resummation in Fourier space in the so called weak field limit. Based in this limit, the proper spacetime dependence of quantities related to the gluon two point function are derived. Namely, the gluon energy momentum tensor and corresponding angular momentum tensor, the initial motion of the nuclei after the collision, and the isotropic momentum broadening coefficient are computed.
The McLerran-Venugopalan model is one realization of color glass condensate to which our calculations can be applied. In many cases it can be used to obtain closed analytic expressions, however they are susceptible to UV and IR divergences. An alternative model which maintains UV regularity and softens the IR divergence is thus proposed. The UV region in this new model is regulated by accounting for local charge correlations in the transverse plane. The leading IR divergence is cured by enforcing global color neutrality. Analytic expressions are obtainable in this new model in the form of infinite series.
Novel insights from this work include an analytic understanding of the full time evolution of important physical quantities like energy density, pressure, and momentum broadening, including their late-time behavior; a scheme to systematically include non-constant color charge densities needed to compute realistic nuclei; a numerical understanding of the deceleration of nuclei in collisions, and (for the first time) a calculation of the transverse motion of nuclei
Uncertainty-Aware Data-Driven Approaches for Modelling Sparse Agricultural Datasets to Sustain a Society
No full textThe objective of my dissertation is to tackle the issue of sparse datasets in case of agricultural domain to design data-driven approaches that can be used to make Decision Support Systems (DSS) for optimal growth of plants, thereby reducing the cost of labor as well as improving the overall food security and environmental sustainability. In order to achieve this, my research is structured into three primary components. Firstly, it focuses on utilizing Machine Learning (ML) models and data-driven approaches to optimize nutrients in hydroponic and aquaponic environments, enhancing the growth of fish and plants within a unified system using two distinct methodologies. This addresses the inherent sparsity in agricultural datasets. Secondly, the thesis delves into the development of forecasting models for in-season prediction of canopy features in cotton crops. This predictive capability enables timely management decisions to maximize crop yield. The third objective involves the creation of data-driven approaches to model growth stages and nutrient uptake of soybeans cultivated in hydroponic environments, spanning from seeding to maturation
Computational Biomechanics for a Standing Human Body: Modal Analysis and Simulation
No full textWe develop computational mechanical modeling and methods for the analysis and simulation of the motions of a human body. This type of work is crucial in many aspects of human life, ranging from comfort in riding, the motion of aged persons, sports performance and injuries, and many ergonomic issues.
A prevailing approach for human motion studies is through lumped parameter models containing discrete masses for the parts of the human body with empirically determined spring, mass, damping coefficients. Such models have been effective to some extent; however, a much higher-fidelity modeling method is to model the human body as it is, namely, as a continuum.
We present this approach, and for comparison, we choose two digital CAD models of mannequins for a standing human body, one from the versatile software package LS-DYNA and another from open resources with some of our own adaptations. Our basic view in this paper is to regard human motion as a perturbation and vibration from an equilibrium position which is upright standing. A linear elastodynamic model is chosen for modal analysis, but a full nonlinear viscoelastoplastic extension is possible for full-body simulation.
The motion and vibration of these two mannequin models is analyzed by modal analysis, where the normal modes of motion are determined. LS-DYNA is used as the supercomputing and simulation platform. Four sets of low-frequency modes are tabulated, discussed, visualized, and compared. Higher frequency modes are also selectively displayed. We have found that these modes of motion and vibration form intrinsic basic modes of biomechanical motion of the human body. This view is supported by our finding of the upright walking motion as a low-frequency mode in modal analysis. Dynamic motions of CAD mannequins are also simulated by drop tests for comparisons and the validity of the models is discussed through Fourier frequency analysis. In the low-frequency range, our numerical results have provided a satisfactory self-consistent match as validation. All computed modes of motion are collected in several sets of video animations for ease of visualization. Samples of LSDYNA computer codes are also included for possible use by other researchers
Dry Cell Radiation Field Characterization at the Texas A&M University Nuclear Engineering and Science Center
No full textThe Nuclear Engineering and Science Center at the Texas A&M Engineering Experiment Station routinely conducts experiments involving neutron and gamma irradiations with a 1-MW TRIGA research reactor. The Center is equipped with a dry irradiation cell, which can be used for experiments requiring a mixed neutron/gamma field. However, in recent years the dry irradiation cell has not been utilized and there exists no surviving information on the radiation environment inside the cell during operation. To resolve this, a full characterization of the neutron and gamma radiation environment inside the cell has been completed.
To fully characterize the neutron flux environment inside the dry irradiation cell, neutron activation analysis has been performed on two different configurations: one with shielding and one without shielding. The program STAYSL PNNL was employed to unfold the full neutron spectrum using the experimental results of the neutron activation analysis. Furthermore, thermoluminescent dosimetry has been utilized to calculate the absorbed gamma dose rates of silicon and tissue inside the cell for each configuration. Each technique has been utilized according to industry standard practices.
The results of this work have shown that adding shielding material to the dry irradiation cell window will have a significant impact on the quantity and energy of radiation which enters the cell. With no shielding present in the window, 50-kW reactor operation produces a neutron flux of 2.59E+09 and a gamma dose rate 50.84 krad/hr in silicon. When 8 inches of high-density polyethylene shielding and 0.8 inches of lead shielding are installed in the window, the neutron flux drops to 4.81E+07 while the gamma dose rate falls to 13.45 krad/hr in silicon
Structure-Guided Strategies to Combat Antibiotic Resistance
No full textThe PhD research focuses on structure-guided strategies to combat antibiotic resistance. It includes three sub-projects: 1). SEQ-9 overcomes Mtb ribosome methylation and inhibits ribosomal activities. Antibiotics are implemented to cue tuberculosis caused by Mycobacterium to inhibit Mtb ribosomes and prevent downstream cellular activities. However, Mtb cells evolve to escape antibiotic pressure. One strategy Mtb implemented is methylation in certain adenosines, which helps Mtb with antibiotic resistance. Our studies found that a naturally derived molecule, SEQ-9, effectively inhibits the methylated Mtb ribosome. By determining the structures of SEQ-9-bound ribosomes, we concluded that SEQ-9 would undergo conformational changes to accommodate the methylation and still be able to inhibit the ribosome. Our results were part of research supported by multiple labs and a pharmaceutical company, Sanofi R&D, and are published in Cell. 2). An antibody derived from AP205 against Acinetobacter genomospecies 16 cells. This research aims to study the organizational pattern of AP205 and the phage-host relationship. Using Cryo-EM, we obtained high-resolution structures of AP205, the host acceptor, and the AP205-host receptor complex. We designed an antibody-like protein based on the structures, and the protein successfully targeted the host receptor. A collaborator is working on the antibody to illustrate its effects against the host. 3). An ongoing project studying Mtb ClpXP protease complex. Mtb ClpXP protease complex plays an essential role in cellular proteohomeostasis. The complex recognizes unfolded/misfolded proteins and degrades them to prevent abnormal activities. Dysregulation of ClpXP functions can cause detrimental effects on cells. To understand the function of the ClpXP complex, we performed structural analysis on the ClpXP complex and yielded a high-resolution structure. We also observed a structure that has yet to be discovered
Soil-Structure Interaction: From Bearing Capacity to Tolerable Movement
No full textThe increasing number of construction projects is anticipated to play a significant role in driving economic growth, emphasizing the importance of sustainable and cost-efficient built-environment and infrastructure projects. Substructure works constitute a substantial portion of the overall construction cost, averaging around 30 to 50%. This range of values rises notably with taller structures. Shallow foundations continue to be the most economical option compared to deep foundations. However, design challenges linked to shallow foundations persist, particularly in calculating the bearing capacity of shallow foundations on clays (ULS) and determining tolerable movement in building structures (SLS).
This study aims to provide valuable guidelines for designing economical and safe shallow foundation systems that meet LRFD performance criteria, with potential to influence the development of codes and standards. One specific goal is to determine the critical ultimate bearing capacity of shallow foundations on fine-grained soil. Empirical analyses, comparing results of case histories of shallow foundation load tests compiled in the TAMU-SHAL-CLAY-Load Test database to predicted bearing capacities using established theories, along with the comparison of predicted drained and undrained bearing capacities using the information from the database supplemented with data from Houston, Texas soils, revealed that the long-term/drained bearing capacity is more critical for clays with undrained strength greater than 120 kPa, while short-term/undrained bearing capacity is critical for clays with undrained strength less than 120 kPa.
By utilizing information from the database and conducting reliability analysis, geotechnical resistance factors corresponding to a specific probability of failure were proposed for the Ultimate Limit State design of shallow foundations on clays in the LRFD framework. The average of the proposed geotechnical resistance factors yielded a back-calculated FS consistent with those currently adopted in design practice.
Another goal is to determine the tolerable movement of tall building structures for designing foundations, considering the Serviceability Limit State in the LRFD Framework. Numerical simulations, explicitly accounting for soil-structure interaction, were conducted to determine limiting angular distortions to prevent structural damage to buildings on spread footings foundations and mat foundations. The results of these simulations were used to develop plots of normalized differential settlement and normalized stiffness, enabling the prediction of anticipated differential settlement between column locations or obtaining the allowable settlement for buildings on spread footings foundations and mat foundations. Reliability and the probability of exceeding limiting angular distortions were assessed using the Response Surface Method to estimate the implicit performance function, and the surrogate function was analyzed with the First Order Reliability Method. Fragility curves, providing an estimate of the probability of exceedance for a specific limiting angular distortion, were developed using the results of reliability analyses. Finally, a simple method to hand-calculate the maximum settlement of a cluster of spread footings foundation was developed by comparing the deformation behavior of a cluster of spread footings foundation and an equivalent mat foundation through numerical simulations
Using X-Ray Computed Tomography to Quantify Pore Characteristics in a Shrink-Swell Clay
No full textShrink-swell soils are those which shrink when drying and swell when wetting. This creates cracks that may measure >10 cm in width and >1 m in depth when the soil is dry. These soils have low permeability when wet but allow rapid water movement through cracks when dry. Because of their dynamic nature, these soils can cause infrastructure damage, crush crop roots, and lead to unpredictable rates and concentrations of contaminant transport. Current numerical models are not able to accurately represent the dynamic pore characteristics, and often soil shrink-swell processes are not taken into consideration at all. To better model the potential impacts of dynamic pore networks in a shrink-swell soil, it is necessary to quantify changes in pore characteristics���size distribution, connectivity, and tortuosity���that accompany changes in soil water content. X-ray computed tomography (CT) scanning is a technology used to visualize the internal structure of an object and can be used to observe and quantify porosity in a soil sample. The goal of this project is to improve our understanding of dynamic porosity in shrink-swell soil, using X-ray CT scanning to quantify crack patterns and sizes in shrink-swell soils at multiple water contents. Three intact soil cores were saturated, scanned using Xray CT, then dried and scanned again. Dragonfly, ImageJ, and MATLAB software were used for image processing and analysis of structural and porosity changes within the cores. Our results show a higher number of pores with volumes >1 mm^3 and pores with lengths >5 mm in the dried cores compared to the saturated. A higher connectivity of these pores was observed in the dried cores compared to the saturated. The knowledge gained through this study regarding changes in porosity between saturated and dried cores will improve our understanding of shrink-swell soils, contributing to improvements in shrink-swell soil���s role in regulating hydrological processes
Ira Greenbaum field notebook: GK1501-GK2000.pdf
No full textBound book, each page corresponds to a karyotype slide data.Data pages for GK1501-GK2000 corresponding to unique identifiers of specimens/samples examined for biological research. Specimens are primarily housed at Texas A&M University; Biodiverstiy Research and Teaching Collection