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Structured 3��� UTRs Destabilize mRNAs in Plants
No full textRNA secondary structure (RSS) represents an intricate code that goes beyond the conventional genetic information, exerting regulatory roles in various biological processes, such as transcription, RNA processing, protein synthesis, and miRNA biogenesis. The 3��� untranslated regions (3��� UTRs) of mRNA emerge as critical orchestrators in gene regulation. Nevertheless, the specific roles of RSS within 3��� UTRs on gene expression remain a subject of inconsistency across diverse organisms and/or contexts.
In our study, a serendipitous discovery came to light: the primary substrate of miR159a (pri-miR159a), when inserted into a 3��� UTR, could promote mRNA accumulation remarkably. This enhanced expression was attributed to the premature polyadenylation of the transcript within the hybrid pri-miR159a-3��� UTR, resulting in a poorly structured 3��� UTR. Notably, RNA decay assays provided insights into the regulatory role of RSS within 3��� UTR. Poorly structured 3��� UTRs could promote mRNA stability, while highly structured 3��� UTRs led to mRNA destabilization both in vitro and in vivo. Furthermore, our exploration extended beyond reporter lines, as genome-wide DMS-MaPseq revealed a consistent inverse relationship between 3��� UTRs��� RSS and transcript accumulation across the entire transcriptome of not only Arabidopsis but also rice and human.
Mechanistically, transcripts with highly structured 3��� UTRs were found to be preferentially degraded by 3������5��� exoribonuclease SUPPRESSOR OF VARICOSE (SOV) and 5������3��� EXORIBONUCLEASE 4 (XRN4), resulting in decreased expression in Arabidopsis. Finally, our findings were underscored by the engineered different structured 3��� UTRs in an endogenous FLOWERING LOCUS T (FT) gene, yielding a demonstrable earlier flowering phenotype in Arabidopsis.
In summary, our study elucidates that highly structured 3��� UTRs tend to contribute to the reduced accumulation of harbored transcripts in Arabidopsis, a phenomenon that may extend to other organisms, including rice and mammals. Beyond its fundamental insights, our research introduces a pioneering strategy involving the engineering of 3��� UTRs��� RSS for the purpose of modulating plant traits in agricultural production and enhancing mRNA stability in biotechnology applications
Integrated Fracture Propagation, Fluid Flow and Geomechanics Modeling for Sealed Wellbore Pressure Analysis
No full textOffset well pressure monitoring is a useful fracture diagnostic tool for detecting pressure changes due to far-field fracture propagation. Recently, sealed wellbore pressure analysis has emerged as a low-cost diagnostic tool for fracture hit detection in unconventional development. The surface pressure gauge is installed in the offset monitor well to monitor pressure changes as hydraulic fractures propagate and intersect the wellbore. A monitor well, in this context, refers to a strategically located observation well situated near the hydraulic fracturing treatment well. It is sealed to ensure a closed system, meaning there are no perforations connected to the formation, thereby preventing fluid flow into or out of the wellbore. Inside the wellbore it is filled with a low compressibility fluid. To extend the understanding of sealed casing response, a methodology of using integrated numerical model to simulate sealed wellbore pressure is established. The objective is to investigate the strain/pressure response along the sealed wellbore under different circumstances of fracture intersection.
In this study, a workflow was presented to model fracture propagation, and estimate resulting far-field strain and pressure changes in the sealed wellbore. The integrated numerical model consists of a commercially available fracture propagation model, a three-dimensional geomechanics model, and a transient fluid flow model. Fracture propagation model is used to simulate fracture geometry and fracture net pressure. The finite element-based fluid flow model and geomechanics model of fractured rock and sealed casing were established for pressure, stress/strain modeling and solve the linear elastic stress-strain-displacement behavior within the simulation domain. Adopting this integrated approach, the internal volume change of the wellbore, and the corresponding surface pressure change can be evaluated to aid in understanding sealed wellbore pressure behavior and far-field fracture interaction.
This study includes various applications of the developed methodology. A field-scale case study and numerical investigation were conducted to interpret field-measured pressure responses during hydraulic fracturing. The model was also applied to simulate strain responses observed in a laboratory fracture experiment with embedded fiber optic cables. The comparison between simulated and measured strains validated the accuracy of the model. Finally, completion parameters were evaluated by analyzing offset wellbore pressure data. This evaluation included comparing the estimated injected volume when the fracture first intersects the offset wellbore and the magnitude of pressure response with various completion parameters such as number of clusters, cluster spacing, injection rate, and injected fluid loading. This evaluation shows the importance of optimizing completion design to enhance fracture stimulation performance
The Design of a Mobile E-Beam Treatment Station for Contaminated Soils
No full textThe presence of perfluorooctanoic substances (PFAS), a manufactured chemical used in various applications, has raised concerns due to its widespread impact on the environment and hazardous effects on human health. Energetic destructive methods such as thermal, supercritical oxidation, and the electron beam (eBeam) are currently being investigated as possible methods to mitigate this issue. These technologies are more efficient at separating contamination from its media and do not produce a contaminated byproduct. However, these technologies have yet to be proven at a scale at which it can be used to combat this contamination effectively.
This thesis investigates two different design configurations as a scaled pilot for mobile e-beam soil treatment systems by addressing structural and spatial concerns. Structural concerns were addressed by analysis completed in SolidWorks finite element analysis features. The two designs are then compared by considering factors such as radiation shielding, manufacturability, size and throughput, mobility, cost, and ease of setup. PUFFIn+ is used to simulate various electron beam soil interaction parameters such as beam energy, soil thickness and beam utilization efficiency.
These considerations and comparisons result in a final mobile electron beam facility recommendation of the following; the design should be able to be transported using only one trailer, the trailer chassis will require three or more axles and will be an oversize load, the power of the beam should be 3 MeV 50 kW, the optimal thickness of media at this beam energy is 0.5cm, the thickness of shielding if stainless steel is used should be approximately 6 inches around the treatment room, a clamshell shielding should be put around the accelerator, and all conveyors regarding media processing should be metal alloys to avoid contamination. More specific design recommendations are discussed in further detail in the text
The Addition of Cyanoacrylate Adhesive to Knots of Various Suture Loops: A Study on Tensile Strength and Suture Loop Integrity
No full textCyanoacrylate adhesive is used by some practitioners in conjunction with sutures to secure free gingival grafts to a surgical bed, in conjunction with sutures to function as a dressing for palatal harvest sites or biopsy sites, or to help maintain primary closure with bone grafting procedures. There is limited research regarding the effects of cyanoacrylate adhesive on the mechanical properties of sutures in an oral environment. Therefore, the aim of this study is to determine whether or not the addition of cyanoacrylate adhesive to suture loops impacts suture maximum tensile strength or cause of suture failure under tension.
60 samples of each suture were tied around 5 PEX pipes using a three-throw surgeon���s knot. Cyanoacrylate adhesive was applied to half of the suture knots as per the manufacturer���s instructions. The rods containing the sutures were then immersed in an artificial saliva solution and the pH and temperature were monitored. 5 suture samples of each suture type from the cyanoacrylate group, and 5 sutures of each suture type from the non-cyanoacrylate group were tested for maximum tension at the following time points: prior to submersion, 24 hours post-submersion, 3 days post-submersion, 7 days post-submersion, 10 days post-submersions, and 14 days post-submersion. Maximum tensile strength, reason for suture failure, and location of suture failure were recorded.
PGA-PCL sutures showed a 37% incidence of knot slippage when cyanoacrylate was not added to the knot. The addition of cyanoacrylate resulted in a 0% incidence of knot slippage (p=0.0048). The cause of suture failure for PTFE was always knot slippage, regardless of the addition of cyanoacrylate. On the other hand, silk, polypropylene, chromic gut, and PGA loops always failed due to suture loop breakage, regardless of the addition of cyanoacrylate. The addition of cyanoacrylate resulted in a statistically significant difference in maximum tensile strength of monofilament sutures (p=0.00041), synthetic sutures (p=0.00018), and absorbable sutures (p=0.0000031). The adhesive also improved maximum tensile strength of suture loops for silk (p=0.00088), PTFE (p=0.0091), PGA (p=0.029), and PGA-PCL sutures (p=4.4E10������), but not for polypropylene (p=0.45) or chromic gut sutures (p=0.87). The effect of the addition of cyanoacrylate to PGA-PCL was statistically significantly different at all days, except for day 14 and the retentive effect of cyanoacrylate appeared to decrease with time.
The addition of cyanoacrylate adhesive eliminates knot slippage in PGA-PCL sutures and increases the maximum tensile strength of silk, PTFE, PGA, and PGA-PCL sutures. These findings suggest that the addition of cyanoacrylate adhesive to suture knots may enhance suture loop integrity in an oral environment
A Test for Stationarity Using a Local Average of the Autocovariance of the Discrete Fourier Transform
No full textThe discrete Fourier transform of a second-order stationary process has been found to be asymptotically uncorrelated, a property which can be leveraged to create a test statistic for stationary. Building off this, we propose a version of the test where the test statistic is created by taking the local average over several partitions of the canonical frequencies, standardized using the heteroskedicity-consistent standard errors. Under the null hypothesis of stationarity this test statistic will be distributed as the sum-of-F distributions, while under the alternative hypothesis of local stationarity it will be distributed as the sum of non-central F distributions. Simulation studies show that locally averaging the DFT can result in a significant increase of power compared to globally averaging the DFT, and performs similarly to the Wavelet Packet Test, another contemporary test for stationarity
Effects of Prenatal Transportation Stress on Liver Gene Expression in Brahman Calves
No full textThe liver plays an important role in physiological processes necessary for growth and development. Stress can have negative effects on the liver, which may lead to differences in phenotype and gene expression. The objectives of this study were to evaluate phenotypic traits and liver tissue gene expression in Brahman heifer and bull calves from prenatal transportation stress (PNS) and control treatment groups. One group of pregnant Brahman cows were transported for a 2-h period every 20 d (�� 5 d) from 60 to 140 d of gestation. Another group of pregnant Brahman cows were preserved as a control. A total of 32 calves, 8 heifer and 8 bull calves from the PNS and control groups, were utilized. Calves were weighed at approximately 25 d (�� 4 d) of age. The following day, calves were euthanized and liver tissues were harvested.
Phenotypic traits evaluated include birth weight, harvest weight, liver weight, pen score, and liver weight/harvest weight. Interaction of sex and treatment was not significant for any trait (P > 0.28). Sex influenced calf birth weight, harvest weight, and liver weight (P 0.41).
Controlling the false discovery rate at 0.15, there were 4, 0, 5, 42, 15, and 3 differentially expressed genes for 1) male PNS relative to control, 2) female PNS relative to control, 3) PNS male relative to female, 4) control male relative to female, 5) male relative to female, and 6) PNS relative to control comparisons, respectively. A single stress-related gene was differentially expressed across comparisons in the study: heat shock protein family A (Hsp70) member 6 (HSPA6)
EMF Shielding of Stepper Motors as a Means of Improving the Security of CNC Operations
No full textThis paper is a documentation on a study conducted exploring possible shield samples that can be used on standardized stepper motors. The cause for this study is the existence of a security vulnerability in computer numerical control (CNC) operations in which the stepper motors that are used in this operation emit a distinctive electromagnetic field (EMF). This distinctive EMF can be captured by an EMF reader and recorded by an outside party to reproduce the operation. For private CNC operators, this is a source for an unwanted leak of data and needs to be addressed. As a preventative measure, it was proposed to explore ways to passively shield the motors in operations. Therefore, twenty-seven different shields of varying degrees of freedom were used as candidates to test the effectiveness of these degrees of freedom. The degrees of freedom include the material, infill geometry, and overall thickness. Additionally, measurements were made at two different distances from the motor to observe the shielding effects in both close range and long range. Aside from the degrees of freedom, the experiment was thoroughly controlled for accuracy. Measurements from the experiments were then collected and compiled for visual and statistical analysis. During statistical analysis, it was discovered that the data collected failed to meet the requirements of a parametric analysis leading to the use of a nonparametric means instead. The statistical analysis concluded the degrees of freedom that were specifically explored were statistically not significant. The results in this study lead to other possible factors that may prove to be more effective in shielding EMF. These other possible factors may lead to further work to be conducted outside of the scope of this thesis
Machine Learning for Design Space Exploration
No full textDesign space exploration is a crucial, yet time-intensive aspect of the silicon design lifecycle. With the increasing focus on domain-specific architectures, companies are engaged in evaluating, developing, and verifying a growing number of designs [1]. Performance architects face the challenge of identifying the optimal design within an ever-expanding design space, compounded by the complexity of modern microarchitecture designs. Architects perform design space exploration (DSE) after the microarchitecture has been finalized. DSE typically entails utilizing a scatter approach, where architects explore different configurations of parameters believed to return optimal performance numbers. This is guided by their intuition, borne out of extensive experience in the field from having designed numerous processors. Alternatively, they may perform parameter sweeps, fixing certain values, while experimenting with a subset of parameters to observe the outcomes. Architects must optimize for a wide suite of workloads, including SPEC [2], where each benchmark exhibits a unique program structure and flow, leading to an exponential design space. Additionally, cycle accurate simulators such as ChampSim [3], although faster than EDA flows and RTL models, can still take hours to run a configuration over many benchmarks. Another key issue of any simulation is the serial nature of how processors work, with running simulations, either a RTL or a C/C++ model, requires a serial processing of the instructions to simulate on the hardware. The combination of time consuming simulations with a large number of workloads makes design space exploration a costly and time consuming process.
Design space exploration in microprocessor design is an ideal candidate for the application of machine learning, considering the lengthy simulation times and the complexity of the optimization problem at hand. The rise of machine learning presents an opportunity to apply these optimization and techniques towards design space exploration. These techniques aim to teach models to find correlations through training on large amounts of data. This not only assists less experienced individuals in finding optimal solutions but also complements the expertise of seasoned architects. The proposed work aims to explore the use of machine learning for simulation predictions to shorten the total simulation time. The results can then be used to train optimization algorithms to find an optimal configuration within a design space exploration
Comprehensive Validation of Semi-Submersible Floater Dynamics: A Coupled CFD-FEM Approach with Iterative Wave Adjustment
No full textThis dissertation presents the development and application of a numerical wave tank based on an in-house Computational Fluid Dynamics (CFD) program, Fintie-Analytic Navier-Stokes (FANS). The CFD solver, featuring overset (Chimera) grid capability and dynamic memory allocation, enables efficient computation of multiple structured grid blocks with a large capacity for data interpolation between overset grids.
An analytic Directional Wave Simulation (DWS) program is coupled with the Navier-Stokes solver at the wave maker location. Numerical wave parameters, including wave elevation and velocity are transmitted from the DWS block to the CFD domain via overlapping grids. To achieve a calibrated numerical wave spectrum at target location, an iterative wave adjustment method is developed, utilizing a 4-wave decomposition scheme based on harmonics separation theory.
The free surface in the CFD domain is captured with the level set method. 5th-order Weighted Essentially Non-Oscillatory (WENO) and 2nd-order Alternative Direction Implicit (ADI) schemes are employed for spatial and time discretization of level set governing equations. To mitigate wave reflection at domain boundaries, a forcing zone method using damping source terms in the governing equations is introduced.
A nonlinear Finite Element Method (FEM) mooring model named MOORING3D is developed to investigate hydrodynamic responses of mooring systems. Coupled with the FANS program, this model explores the global performance of moored floating structures under various environmental conditions. A six-degrees-of-freedom (6-DOF) motion solver is integrated into the FANS program to update the motion of the floater.
A robust verification procedure based on the least-squares Richardson extrapolation method is introduced to estimate the discretization uncertainties of the numerical simulations. The convergence study in this research focuses on spatial and temporal discretization uncertainties.
Data from a comparative study at 2020 ISOPE conference is utilized to assess the wave generation and iterative wave adjustment method. Model tests from this comparative study investigate the nonlinear interactions of steep focused waves with a fixed cylinder. Wave elevations at target locations and wave slamming loads on the cylinder are compared with the experimental measurement and other numerical solutions for validation. The results highlight the positive effect of the iterative adjustment method on highly nonlinear numerical wave generation.
Verification and Validation (V&V) studies are conducted on the coupled CFD-FEM program using a Floating Offshore Wind Turbine (FOWT) platform model. Convergence studies include pitch free decay and regular wave tests, which are parts of the OC5 project (Offshore Code Comparison Collaboration, Continued, with Correlation project). The numerical wave profile and 3-DOF responses of the platform are validated against model test measurement and other numerical solutions. The agreement between the coupled numerical solution and the experiment validates the method.
The coupled numerical solution is employed to investigate hydrodynamic responses of the plat-form under highly nonlinear irregular wave conditions, addressing the importance of calibrating the wave to the target spectrum. Short-duration extreme wave cases and a long-duration 3-hour irregular wave case are conducted to comprehensively evaluate the integrated solver���s performanc
Crowding: An Exploration of the Effects of Methods and Sound
No full textVisitation rates continue to rise in the United States��� protected areas like national parks and national forests. This has raised management concerns for both impacts on the environment and visitor experiences. The Satisfaction Model postulates that as use levels and encounters rise in parks and protected areas, there is a threshold where the visitor experience is negatively impacted by the additional visitors. Nevertheless, decades of research indicate this relationship is complicated and multifaceted. As a result, the Satisfaction Model has evolved to include norms, use patterns and research measurement techniques as concepts that impact responses to encountering other individuals. Therefore, the purpose of this dissertation was to explore how people respond to research techniques and environment conditions, specifically the soundscape, when visiting protected areas.
Study one focused on starting point bias; a research bias where participant responses are systematically inflated or deflated due to research techniques. Research on crowding responses has frequently relied on visual methods where participants are shown a series of images with varying numbers of people visiting a protected area. The order in which the images are shown holds the potential to inflate or deflate results because the exposure to one treatment may impact responses to a subsequent treatment. This study���s findings revealed a starting point bias, but only on crowding ratings when moving from low setting density to high setting density.
Furthermore, the soundscape has become a fruitful topic for research on visitor experiences. However, little is understood about how sound impacts crowding norms. Study two explored how anthropogenic sound types impact crowding and acceptability ratings of a setting density. Direct human sounds like voices and children playing were expected to be rated more favorably than mechanical sounds. However, the rank of crowding and acceptability ratings were mixed with direct human sounds generally being rated more harshly than mechanical sounds.
Study three explored how sound loudness impacted crowding and acceptability ratings of the setting. Results indicated that loudness was only rated more harshly at the highest loudness levels. The studies are discussed in terms of their results and their impacts on theory and practice