Doctor of Philosophy

dissertationThe MAKER genome annotation and curation software tool was developed in response to increased demand for genome annotation services, secondary to decreased genome sequencing costs. MAKER currently has over 1000 registered users throughout the world. This wide adoption of MAKER has uncovered the need for additional functionalities. Here I addressed moving MAKER into the domain of plant annotation, expanding MAKER to include new methods of gene and noncoding RNA annotation, and improving usability of MAKER through documentation and community outreach. To move MAKER into the plant annotation domain, I benchmarked MAKER on the well-annotated Arabidopsis thaliana genome. MAKER performs well on the Arabidopsis genome in de novo genome annotation and was able to improve the current TAIR10 gene models by incorporating mRNA-seq data not available during the original annotation efforts. In addition to this benchmarking, I annotated the genome of the sacred lotus Nelumbo Nucifera. I enabled noncoding RNA annotation in MAKER by adding the ability for MAKER to run and process the outputs of tRNAscan-SE and snoscan. These functionalities were tested on the Arabidopsis genome and used MAKER to annotate tRNAs and snoRNAs in Zea mays. The resulting version of MAKER was named MAKER-P. I added the functionality of a combiner by adding EVidence Modeler to the MAKER code base. iv As the number of MAKER users has grown, so have the help requests sent to the MAKER developers list. Motivated by the belief that improving the MAKER documentation would obviate the need for many of these requests, I created a media wiki that was linked to the MAKER download page, and the MAKER developers list was made searchable. Additionally I have written a unit on genome annotation using MAKER for Current Protocols in Bioinformatics. In response to these efforts I have seen a corresponding decrease in help requests, even though the number of registered MAKER users continues to increase. Taken together these products and activities have moved MAKER into the domain of plant annotation, expanded MAKER to include new methods of gene and noncoding RNA annotation, and improved the usability of MAKER through documentation and community outreach

The use of bootstrap methods for analysing health-related quality of life outcomes (particularly the SF-36)

Health-Related Quality of Life (HRQoL) measures are becoming increasingly used in clinical trials as primary outcome measures. Investigators are now asking statisticians for advice on how to analyse studies that have used HRQoL outcomes. HRQoL outcomes, like the SF-36, are usually measured on an ordinal scale. However, most investigators assume that there exists an underlying continuous latent variable that measures HRQoL, and that the actual measured outcomes (the ordered categories), reflect contiguous intervals along this continuum. The ordinal scaling of HRQoL measures means they tend to generate data that have discrete, bounded and skewed distributions. Thus, standard methods of analysis such as the t-test and linear regression that assume Normality and constant variance may not be appropriate. For this reason, conventional statistical advice would suggest that non-parametric methods be used to analyse HRQoL data. The bootstrap is one such computer intensive non-parametric method for analysing data. We used the bootstrap for hypothesis testing and the estimation of standard errors and confidence intervals for parameters, in four datasets (which illustrate the different aspects of study design). We then compared and contrasted the bootstrap with standard methods of analysing HRQoL outcomes. The standard methods included t-tests, linear regression, summary measures and General Linear Models. Overall, in the datasets we studied, using the SF-36 outcome, bootstrap methods produce results similar to conventional statistical methods. This is likely because the t-test and linear regression are robust to the violations of assumptions that HRQoL data are likely to cause (i.e. non-Normality). While particular to our datasets, these findings are likely to generalise to other HRQoL outcomes, which have discrete, bounded and skewed distributions. Future research with other HRQoL outcome measures, interventions and populations, is required to confirm this conclusion

Phenomenal well-being

Hedonism is not terribly popular as a theory of well-being. And there are good reasons to question whether hedonism even supplies the best account of happiness. Yet hedonism captures something important, and it will be the goal of this essay to articulate just what that is. I suggest that hedonism provides the best account of phenomenal wellbeing (PWB). PWB is a restricted form of well-being that relates to the quality of the experience of a life—or, in other words, the quality of one’s phenomenal life. If wellbeing is characterized as “how well one’s life goes,” then PWB is “how well one’s life goes for her, from the inside.” In rating a life’s PWB, the life is judged solely on the basis of the contents of the experience of that life rated against the experience of the individual’s other possible lives. Unlike well-being, PWB is guaranteed to track more robust experiential benefits that a person gets out of living a life. In this work, I discuss the concept of well-being, including the feature of subjectrelativity that is sometimes ascribed to it; then, after introducing the concept of a phenomenal life, I develop the concept of phenomenal well-being. I propose what I take to be the best available account of PWB, which involves the hedonistic concept of satisfaction. An epistemic model of life-comparison (inspired by Peter Railton’s full information account of well-being) on which phenomenal lives are judged on the criterion of satisfaction is presented, followed by some objections, and replies, to PWB as satisfaction. Finally, some rival accounts of PWB are discussed and critiqued—notably, an account of cognitive life-satisfaction that resembles theories of “life-satisfaction” in happiness theory. The claim is that hedonism supplies the best answer to what makes the experience of our lives go best for us. In the closing chapter, I make some suggestions concerning the significance of this fact

Analyzing Multidisciplinary Team Effectiveness in an Engineering Environment: A Case Study of the West Point Steel Bridge Design Team

The West Point Steel Bridge Design Team is a group of five undergraduate seniors working to design and build a steel bridge for the annual ASCE Steel Bridge Competition. The purpose of our group’s research is to discover how multidisciplinary teams perform in academically competitive environments. This project provides a unique opportunity in the field of multidisciplinary collaborative work because the team’s success can be objectively measured against this year’s competitors and the team’s performance in previous years. The traditional structure of the West Point team consisted of three-to-five civil engineering majors. This year’s team includes a law and legal studies major and five civil engineers, two of which recently switched from systems engineering. Past designs have relied heavily on the work of previous years, which has led to stagnant performance at competitions. Our hypothesis is that by entering different perspectives into the group at an early stage, a revolutionary approach will ensue and overall performance will increase. The team did not completely disregard the designs and methods of previous teams, but the reliance on their decision-making process was more heavily scrutinized with the current multidisciplinary team. Our research is not solely limited to competitive performance. We also analyzed the decision-making process of this year’s team in comparison to previous years. While data on decision-making is not readily available, both the faculty advisor and two current team members who served on the team last year were able to provide personal insight into how the teams compare. Ultimately, this research seeks to provide groups in similar academically competitive environments an indication of whether a multidisciplinary composition will provide benefit to their team’s performance.Cockrell School of Engineerin

Non-Invasive Imaging of Coronary Artery Disease — The Expanding Role of Coronary Computed Tomographic Angiography in the Management of Low- to Intermediate-Risk Patients and Dealing with Intermediate Stenosis

Non-invasive anatomic imaging modalities play a crucial role in the diagnosis of coronary artery disease (CAD), particularly in the case of the symptomatic patient presenting in the emergency department

A Comparative Assessment of Floating and Submerged Sensor Network Deployments for Monitoring Underwater Sediment Transport Processes

Wireless Sensor Networks (WSNs) are a pioneering technology in many environmental monitoring applications owing to their ability to be deployed for long periods of time in locations that cannot be reached manually. One such use-case is the monitoring of underwater sediment transport, a process that plays a significant role in coastal erosion. Previous examples of WSNs deployed for this purpose have been in the form of underwater sensor networks (UWSNs), which have a number of shortcomings from both a practical and technical viewpoint. As such, this paper provides a comparative assessment of UWSNs and an alternative deployment approach of floating echosounding sensor networks for the purpose of monitoring underwater sediment transport

Climate and pest interactions pose a cross-landscape management challenge to soil and water conservation

Climate change and biological invasions by plant pests (weeds), agriculture and forest insect pests (insects), and microbial pests (plant pathogens) are complex interactive components of global environmental change. The influence of pest distribution and prevalence across landscapes are challenging the conservation and sustainability of natural resources, agricultural production, native biological diversity, and the valuable ecosystem services they provide (Huenneke 1997; Vitousek 1997; Juroszek and von Tiedemann 2013; Ziska and Dukes 2014). Since 2000, numerous scientific studies indicate accelerating climate change is posing substantial risks to natural and managed systems in North America (IPPC 2022). Intensified droughts, largescale wildfires, and increased demands for limited surface and groundwater water supplies in arid regions are threatening the sustainability of irrigated agriculture and contributing to economic losses (Stewart et al. 2020), while extreme rainfall events are contributing to severe riverine and urban flooding across the United States. Climate change affects crops, rangelands, forests, and natural areas directly through the immediate effects of temperature, precipitation, and atmospheric carbon dioxide (CO2) levels and thereby impacts production and management systems. These effects are amplified by climatedriven increases in weed, insect, and plant pathogen problems that further complicate related factors such as water, nutrient, and pest management (Walthall et al. 2013). Changing climates also alter physiological, ecological, and evolutionary processes that can support increased establishment, invasiveness, local spread, and geographic range changes of weeds, insects, and plant pathogens (Chidawanyika et al. 2019; Gallego-Tevár et al. 2019; Ziska et al. 2019) that have cascading effects on soil and water quality, and human livelihoods. Joshua W. Campbell is a research ecologist studying basic insect and pollinator behavior in managed and wild ecosystems at the USDA Agricultural Research Service (ARS) Pest Management Research Unit in Sidney, Montana. Michael R. Fulcher is a research plant pathologist conducting research to identify pathogenic biocontrol agents at the USDA ARS Foreign Disease-Weed Science Research Unit in Fort Detrick, Maryland. Brenda J. Grewell is a research plant ecologist focusing on understanding the biogeography of invasive plant species and the ecology of invaded systems at the USDA ARS Invasive Species and Pollinator Health Research Unit in Davis, California. Stephen L. Young is a national program leader in weeds and invasive pests at the USDA ARS Office of National Programs in Beltsville, Maryland. Received October 25, 2022. Thus, a need exists for cross-habitat and landscape/watershed-scale perspectives to improve understanding of mechanisms underlying pest fitness and impacts within and across integrated systems

Communication Education and International Audiences: Reflections on Instructional Challenges and Pedagogical Strategy

As the movement toward international education continues, institutions must be proficient when reaching and teaching international students. Instructors should engage unique learning styles, address individual student needs, and take part in additional training to effectively teach international student learners. These instructional imperatives are especially important in communication related classes, like public speaking or composition. Throughout this reflection we briefly address the current landscape of the globalized western classroom and discuss current pedagogical challenges in communication courses from the perspective of communication instructors

SN 2007gr: a Normal Type Ic Supernova with a Mildly Relativistic Radio Jet?

A nearby type Ic supernova, SN 2007gr was observed with the EVN in two epochs 60 days apart (second observation also included the Green Bank Telescope). In both cases one of the EVN stations was the Westerbork Synthesis Radio Telescope (WSRT), which recorded the observational data not only in the VLBI mode, but also in its normal interferometric mode. Thus it provided an important reference observation. In the first epoch the fluxes measured by the VLBI network and the WSRT alone match well. However in the second epoch the peak brightness observed in the VLBI experiment is much lower than the total flux recorded by the WSRT. There could be multiple reasons for this discrepancy: a resolution effect, coherence losses in VLBI, or extended emission contaminating the WSRT measurement. With new WSRT observations we costrain the level of background emission and find that there is still a difference between the corrected total flux density and the VLBI peak brightness. If one assumes that this is dominated by resolution, this would correspond to an average apparent expansion speed of ~0.4c