A novel torque control algorithm, which adopts a two-phase excitation, is proposed to improve the performance of the Switched Reluctance Motor (SRM) drive. By exciting two adjacent phases instead of single phase, the changing rate and the magnitude of the phase currents are much reduced. Therefore the existing problems caused by the single-phase excitation such as large torque ripple during commutation, increased audible noise and fatigue of the rotor shaft are mitigated. The electromagnetic torque is efficiently distributed to each phase by the proposed Torque Distribution Function (TDF) that also compensates the effects of mutual coupling. To describe the effects of mutual coupling between phases, a set of voltage and torque equations is newly derived for the two-phase excitation. Parameters of the SRM are obtained by Finite Element Analysis (FEA) and verified by measurements. It is shown that the mutual inductance of two adjacent phases partly contributes to generate the electromagnetic torque and introduces coupling between two adjacent phases in the current or flux linkage control loop, which has been neglected in the single-phase excitation. The dynamics of the current or flux linkage loop are coupled and nonlinear due to the mutual inductance between two adjacent phases and the time varying nature of inductance. Each phase current or flux linkage needs to be controlled precisely to achieve the required performance. A feedback linearizing current controller is proposed to linearize and decouple current control loop along with a gain scheduling scheme to maintain performance of the current control loop regardless of rotor position as well as a feedback linearizing flux linkage controller. Finally, to reduce current or flux linkage ripple, a unipolar switching strategy is proposed. The unipolar switching strategy effectively doubles the switching frequency without increasing the actual switching frequency of the switches. This contributes to the mitigation of current or flux linkage ripple and hence to the reduction of the torque ripple. / Ph. D.

Understanding how genetic changes ultimately affect morphology and physiology is essential for understanding and predicting how organisms will adapt to environmental changes. Although most traits are complex and involve the interplay of many different genetic loci, some exceptions exist. These include the convergent evolution of tetrodotoxin resistance in snakes, which has a simple genetic basis and can be used as a model system to investigate the genetic basis of adaptive evolution. Tetrodotoxin is a potent neurotoxin used as a chemical defense by various animals, including toxic newts. Snakes have evolved resistance through mutations in voltage-gated sodium channels, the protein targets of tetrodotoxin, sparking an evolutionary arms race between predator and prey. In this dissertation, I describe how genomic rearrangements have led to sex-linkage of four of the voltage-gated sodium channel genes in snakes and compare allele frequencies across populations and sexes to make inferences about how sex linkage has influenced the evolution of resistance in garter snakes. By measuring gene expression in different snake tissues, I show that three of these sex-linked sodium channel genes are dosage compensated in embryos, adult muscle, and adult brain. In contrast, two channels show sexual dimorphism in their expression levels in the heart, which may indicate differences in dosage compensation among tissues. I then use comparative genomics to track the evolutionary history of tetrodotoxin resistance across all nine sodium channel genes in squamate reptiles and show how historical changes have paved the way for full-body resistance in certain snakes. Finally, I use targeted sequence capture to obtain the sodium channel sequences of salamanders and show evidence that tetrodotoxin self-resistance in toxic newts was likely accelerated through gene conversion between resistant and non-resistant sodium channel paralogs. Together, these results illustrate parallelism in evolutionary mechanisms and processes contributing to the appearance of an extreme and complex trait that arose independently in two distinct taxa separated by hundreds of millions of years. / Doctor of Philosophy / Western North America is the site of an ongoing battle between highly toxic species of salamanders (toxic newts) and their garter snake predators. In certain regions, garter snakes have countered newt defenses by evolving resistance to their toxins, and the newts have become more toxic in response. This interaction has been the focus of scientists for decades because it teaches us about the ways in which animals can respond to changes in their environment. In living organisms, DNA is used a blueprint to determine the ultimate traits that are expressed (e.g., whether an organism will have five fingers or four, or whether it will be resistant or sensitive to a toxin). By comparing DNA sequences of different life forms, we are beginning to understand the rules that determine how these blueprints are read and how they can change over time. Because life is built upon the same basic building blocks (DNA, mRNA, and proteins), information about this snake-newt system can be used to understand the way that other systems, such as humans and pathogens, might interact. In my dissertation, I compare DNA sequences from snakes and lizards to identify the history of changes leading to the extreme toxin resistance in the garter snakes. I show that toxin resistance began hundreds of millions of years ago, with all lizards having a low baseline level of resistance, and that resistance built up slowly in the lineages leading to garter snakes. I also show that because of DNA rearrangements, female snakes have fewer copies of some of the genes involved in resistance, and this may have led to differences among the sexes. Lastly, I compare DNA sequences among salamanders, revealing a similar pattern to that in snakes and lizards. Specifically, newts have evolved self-resistance to their own toxin, and this has happened gradually over hundreds of millions of years, with all salamanders having some toxin resistance. I also show that an unusual process occurred within the DNA of toxic newts, resulting in a rapid change from toxin sensitivity to toxin resistance in some genes. Taken together, this work helps advance our understanding of the processes and limitations that determine how organisms can function and change over time.

Mosquitoes belonging to the genera Anopheles transmit malaria parasites, attributing the highest mortality of any vector-borne disease worldwide. Mosquitoes belonging to the genera Aedes transmit arboviruses including dengue, which has become the most important vector-borne virus due to a drastic surge in disease incidence. The scope of the studies in this dissertation is broad, with investigations bringing together elements of classical genetics, recent advances in sequencing and genome-editing technologies, and the use of modern forward genetics approaches. Chapter 2 of this dissertation explores the use of the Oxford Nanopore Sequencing Technology for the first time in mosquitoes. This new technology provides long reads that were used to piece together the AabS3 chromosomal assembly for Anopheles albimanus. The utility of this genomic resource is demonstrated by the discovery of novel telomeric repeats at the ends of the chromosomes that could have important implications in mosquito biology and control. Chapter 3 describes a forward genetics strategy called 'Marker-Assisted Mapping' (MAM) that enables high-resolution mapping of the causal gene locus of a mutant phenotype. The principle and effectiveness of MAM is first demonstrated by mapping a known transgene insertion. MAM is then used to identify cardinal as a candidate causal gene for the spontaneous red-eye (re) mutation. Genetic crosses between the re mutant and cardinal knocking out individuals generated using CRISPR/Cas9 confirmed that cardinal indeed is the causal gene for re mutation. Chapter 4 explores three innovative strategies for mosquito sex separation by exploiting several sex-linked marker lines. We show that by linking a transgenic marker to the male-determining locus (M locus), or by linking the male-determining Nix gene to a marker, males can be precisely separated from females. We also produce a two-marker transgenic line that allows for both non-transgenic male separation and for efficient line maintenance. Finally, we discuss further applications of the resources generated and future directions stemming from these findings. Altogether, the studies described in this dissertation contribute to the overall goal of understanding mosquito biology and of controlling mosquito-borne infectious diseases. / Doctor of Philosophy / Female mosquitoes bite and transmit deadly pathogens including the malaria parasite, and viruses such as dengue, Zika, and West Nile. Control programs that attempt to limit the spread of these deadly diseases rely on the control of mosquitoes themselves. These mosquito control methods have relied heavily on indoor and outdoor insecticidal spraying. However, the efficacy of these methods has been jeopardized by the increasing prevalence of insecticide resistance. Thus, it is necessary to implement other methods for effective mosquito control. Genetic control strategies such as the Sterile Insect Technique (SIT) and Wolbachia-based Incompatible Insect Technique (IIT) are excellent solutions to overcome the limitations of current control strategies. As female mosquitoes bite and transmit disease-causing pathogens, only males are released, which necessitate the separation of the non-biting males from females before release. The aim of this work was to use recent technological advancements to better understand the genome and basic genetics of vector mosquito species, and to identify possible approaches to improve current sex separation practices. To develop a deep understanding of mosquito biology and genetics, it is crucial that a high-quality and accurate genome assembly is available. However, many mosquito genome assemblies remain fragmented. To address this limitation, we used recent advances in sequencing technologies to produce a high-quality genome assembly for the New World malaria mosquito, Anopheles albimanus. These sequencing and assembly efforts led to the discovery of novel telomere sequences at the ends of chromosomes, which could have implications for mosquito control. Forward genetics, which identifies the gene(s) responsible for a given phenotype, has been hindered by the low recombination rate in the yellow and dengue fever mosquito, Aedes aegypti. We develop a Marker-Assisted Mapping (MAM) strategy to address this problem. We first demonstrate this method by mapping the known insertion of a transgene. MAM is then used to identify cardinal as a candidate causal gene for the spontaneous red-eye (re) mutation. MAM identification of the Cardinal gene was then verified by knocking out Cardinal, which represents the first successful gene mapping in Aedes aegypti using forward genetics. The MAM strategy has broad implications as it could enable the discovery of genes involved in important traits such as insecticide resistance. To improve sex separation methods, we took advantage of several sex-linked transgenic lines to develop three novel strategies. First, we demonstrate that screening for a genetic marker that is tightly linked to the male-determining locus (M locus) is an effective approach to reduce female contamination. Second, we demonstrate that instead of linking a marker to the M locus, we can link the male-determining factor, Nix, to a genetic marker. When a Nix transgene is located adjacent to the red-eye locus with extremely tight linkage, the red-eye phenotype becomes a faithful marker for separation of males and females. Finally, we developed a two-marker genetic sexing strain that produces non-transgenic males that could be used for release, and transgenic marked males and females for efficient line maintenance.

Past research has demonstrated that emotions can accurately be communicated via touch (e.g., Hertenstein, Keltner, App, Bulleit, and Jaskolka, 2006). In stranger female dyads, physiological linkage plays a role in the mechanism whereby this successful communication occurs, as touch strengthens and lengthens linkage (Kissel, 2020). While touch has a direct impact on physiological processes, viewing touch may have similar effects. The current study explored this possibility in regard to physiological linkage. Hertenstein et al., 2006 demonstrated that participants can correctly decode emotions from observing videos of communication via touch to the forearm and hand. The current study replicated this finding with forty-seven female participants, while also determining the levels of physiological linkage between the "live" observers and the video-recorded participants from Kissel (2020) using dynamic linear time series modeling. Results showed that physiological linkage can occur between "live" and recorded participants. Participants demonstrated longer linkage times with the initial dyad they viewed, but linkage with videoed communicators whose communications were correctly perceived by their fellow videoed receiver had a larger influence on emotion word, valence, intensity, and quadrant detection accuracy. Based on these results, physiological linkage may influence empathic accuracy in virtual settings. / Doctor of Philosophy / A common American English slang expression to state that you relate to someone on a deep personal level is "I feel you." This is a verbal expression of empathy, but what if empathy goes deeper than our thoughts or memories of similar experiences? What if our bodies experience the same emotion as the person with whom we are interacting? This is possible through the phenomenon of "physiological linkage." Physiological linkage occurs when physiological signals, such as heart rate, between interaction partners start to sync up—for example, when one person's heart rate speeds up, so does the heart rate of the person with whom they are interacting. The author's thesis study demonstrated that this linkage can occur when people communicate emotions solely through touch. But what happens if you are watching these emotion communications instead of experiencing them? The current study examined if physiological linkage occurs between people watching a video and the people emoting in the video. The results showed that linkage does occur while watching emotional touch interactions and that this can help the observer understand what these emotions are (even if the observer can see no faces and hear no voices). Touch has many health benefits, so the observation that watching recorded touch interactions can have a similar bodily effect has implications for increasing health and connectedness. This is particularly important given the limited face-to-face and touch interactions, as well as the increase in video call interactions, resulting from the COVID-19 pandemic.

Soybeans are an economically important plant, with an annual crop value that consistently exceeds 20 billion dollars in the United States alone. A recent increase in demand for soybeans, stemming from its diverse applications in products such as animal feed, oil, and biofuel, has created an emphasis for soybean breeders in value added cultivars. These cultivars, have improved, or altered, agronomic or seed composition traits, allowing them to be efficiently utilized in a specific niche of the processing industry. Facilitating the development of such cultivars requires a thorough understanding of the genetic factors that affect the manifestation of value added traits. Value added traits investigated in this study include seed sucrose, raffinose, stachyose, and phytate content, seed weight, and maturity. The objective of the first part of this project was to characterize the source of low seed stachyose in soybean line PI200508. Two F2 populations, developed from PI200508 and soybean introductions which exhibited higher seed stachyose content were utilized in a QTL analysis approach that incorporated the use of the Williams82 whole genome shotgun (WGS) sequence (http://www.phytozome.org) in a candidate gene mapping approach. A predicted soybean galactosyltransferase gene was established as a candidate gene due to its observed segregation with the single low stachyose QTL observed on molecular linkage group (MLG) C2 in both populations. Sequencing of this putative gene revealed a unique 3 bp deletion in PI200508. A marker developed to exploit this deletion accounted for 88% and 94% of the phenotypic variance for seed stachyose content in the two experimental populations, highlighting its potential for use in marker assisted selection of the PI200508 source of low raffinose and stachyose. The second part of this project involved QTL analysis of seed sucrose, raffinose, stachyose, and phytate content, as well as seed weight in a linkage map for a F8 RIL population developed from the Glycine max line V71-370 and the Glycine soja introduction PI40712. Analysis across all 20 soybean MLG identified 25 QTL for these traits on MLG A1, A2, C2, D1b, D2, F, G, H, I, L, M, O. Nine of these QTL were supported across multiple environments, indicating that they, and their associated markers, could be useful to breeders working with these traits. The third part of this project used the same F8 RIL linkage map to investigate time to maturity (Reproductive stage R8). V71-370 and PI407162 differ in time to maturity when grown in Virginia, and the RILs developed from this cross displayed a wide range in maturity. Two major QTL were identified on MLG H and L. Examination of the Williams82 WGS sequence in these QTL regions revealed two predicted genes with homology to Arabidopsis thaliana light response and photoperiodism genes which were investigated as candidate soybean maturity genes. Markers developed from these predicted genes showed close association with the observed QTL, and could facilitate the further investigation of this complex trait. / Ph. D.

Exoskeletons show great promise in aiding people in a wide range of applications. One such application is medical rehabilitation and assistance of those with spinal cord injuries. Exoskeletons have the potential to offer several benefits over wheelchairs, including a reduction in the risk of upper-body injuries associated with extended wheelchair use. To fully mitigate this risk of injury, exoskeletons will need to be fully self-balancing, able to move and stand without crutches or other walking aid. To accomplish this, the Orthotic Lower-body Locomotion Exoskeleton (OLL-E) will actuate 12 Degrees of Freedom, six in each leg, using custom design linear series elastic actuators. The placement of these actuators relative to each joint axis, and the geometry of the linkage connecting them, were critical to ensuring each joint was capable of producing the required outputs for self-balancing locomotion. In pursuit of this goal, a general model was developed, relating the actuator's position and linkage geometry to the actual joint output over its range of motion. This model was then adapted for each joint in the legs and compared against the required outputs for humans and robots moving through a variety of gaits. This process allowed for the best placement of the actuator and linkages within the design constraints of the exoskeleton. The structure of the exoskeleton was then designed to maintain the desired geometry while meeting several other design requirements such as weight, adjustability, and range of motion. Adjustability was a key factor for ensuring the comfortable use of the exoskeleton and to minimize risk of injury by aligning the exoskeleton joint axes as close as possible to the wearer's joints. The legs of OLL-E can accommodate users between 1.60 m and 2.03 m in height while locating the exoskeleton joint axes within 2 mm of the user's joints. After detailed design was completed, analysis showed that the legs met all long-term goals of the exoskeleton project. / Master of Science / Exoskeletons show great promise in aiding people in a wide range of applications. One such application is medical rehabilitation and assistance of those with spinal cord injuries. Exoskeletons have the potential to offer several benefits over wheelchairs, including a reduction in the risk of upper-body injuries associated with extended wheelchair use. To best reduce this risk of injury, exoskeletons will need to be fully self-balancing, able to move and stand without crutches or relying on any other outside structure to stay upright. To accomplish this, the Orthotic Lower-body Locomotion Exoskeleton (OLL-E) will use a set of custom designed motors to apply power and control to 12 joints, six in each leg. Where these motors were placed, and how they connect to the joints they control, were critical to ensuring the exoskeleton was able to self-balance, walk, and climb stairs. To find the correct position, a set of equations was developed to determine how different positions changed each joints’ speed, strength, and range of motion. These equations were then put into a piece of custom software that could quickly evaluate different joint layouts and compare the capabilities against measurements from people and robots walking, climbing stairs, and standing up out of a chair. This process allowed for the best placement of the motors and joints while still keeping the exoskeleton relatively compact. The rest of the exoskeleton was then designed to connect these joints together, while meeting several other design requirements such as weight, adjustability, and range of motion. Adjustability was very important for ensuring the comfortable use of the exoskeleton and to minimize risk of injury by ensuring that the exoskeleton legs closely matched the movements of the person inside. The legs of OLL-E can accommodate users between 1.60 m and 2.03 m in increments of 7 mm. After detailed design was completed, additional analyses were performed to check the strength of the structure and ensure it met other long-term goals of the project.

In designing devices to produce straight-line motion, the designer has a fundamental choice between selecting sliding devices or selecting pinned linkages. Although they are more complex to design and implement, linkages will often prove a less expensive, more efficient, and generally more satisfactory option than simple sliders. The objective of this thesis is to provide a tool to the designer that serves as an aid in making intelligent decisions in the selection of four-bar linkage type straight-line-mechanisms. This thesis provides research into the selection, evaluation, and implementation of existing straight-line mechanism designs. Twenty-two straight-line mechanisms are compared for both compactness and fidelity of the straight-line path. Also, figures showing position, velocity, and acceleration of each a included. The functional product of to this work is a software program called Straight-line. Straight-line gives the designer a graphical environment from which a wide variety of straight-line mechanisms can be quickly analyzed and evaluated. The software also provides a new type-synthesis technique that allows the designer to generate a straight-line-mechanism by graphically inputting a desired path. / Master of Science

The data from genome-wide association studies (GWAS) in humans are still predominantly analyzed using single marker association methods. As an alternative to Single Marker Analysis (SMA), all or subsets of markers can be tested simultaneously. This approach requires a form of Penalized Regression (PR) as the number of SNPs is much larger than the sample size. Here we review PR methods in the context of GWAS, extend them to perform penalty parameter and SNP selection by False Discovery Rate (FDR) control, and assess their performance (including penalties incorporating linkage disequilibrium) in comparison with SMA. PR methods were compared with SMA on realistically simulated GWAS data consisting of genotype data from single and multiple chromosomes and a continuous phenotype and on real data. Based on our comparisons our analytic FDR criterion may currently be the best approach to SNP selection using PR for GWAS. We found that PR with FDR control provides substantially more power than SMA with genome-wide type-I error control but somewhat less power than SMA with Benjamini-Hochberg FDR control. PR controlled the FDR conservatively while SMA-BH may not achieve FDR control in all situations. Differences among PR methods seem quite small when the focus is on variable selection with FDR control. Incorporating LD into PR by adapting penalties developed for covariates measured on graphs can improve power but also generate morel false positives or wider regions for follow-up. We recommend using the Elastic Net with a mixing weight for the Lasso penalty near 0.5 as the best method. / Ph. D.

Plant cell wall polysaccharides are abundant natural polymers making them potential sources for sustainable and biodegradable materials. Interfacial behavior, including adsorption and enzymatic degradation, of several plant cell wall polysaccharides and their derivatives were studied with a quartz crystal microbalance with dissipation monitoring (QCM-D), surface plasmon resonance (SPR) and atomic force microscopy (AFM). Xyloglucan adsorption isotherms were obtained to probe how cellulose-hemicellulose interactions were affected by the type of cellulose substrate and molar mass of xyloglucan. Xyloglucan as small as a heptasaccharide still adsorbed irreversibly onto cellulose. Carboxymethyl cellulose (CMC) adsorption onto cellulose and viscoelastic properties and water contents of the adsorbed CMC layers were obtained from a combination of QCM-D and SPR data. The CMC samples formed hydrated and viscoelastic layers compared to the relatively rigid xyloglucan layer. Pectin model surfaces were prepared by pectin adsorption from citric phosphate buffer onto gold substrates. These pectin model surfaces were used for subsequent interaction studies with xyloglucan and enzymatic degradation behavior. There is a strong correlation between the degree of esterification (DE) and film resistance to degradation with the high DE being the most susceptible to degradation. The adsorption of two mixed linkage glucans (MLG), barley and lichen MLG, onto regenerated cellulose (RC) surfaces in the absence and presence of other matrix polysaccharides was studied. Viscoelastic properties of the resulting layer were compared as a function of the proprotion of '-(1''3) linkages with lichen MLG forming softer gel-like layers on RC. The lichen MLG layers were further used for enzymatic degradation studies with respect to enzyme concentration, temperature, pH and ionic strength. These studies show that polymer adsorption is a promising strategy to modify material surfaces and provides fundamental understanding of interactions and biodegradation of cell wall polysaccharides at solid/liquid interfaces. / Ph. D.

Pathogens colonize their hosts by releasing molecules that can enter host cells. A biotrophic oomycete plant pathogen, Phytophthora sojae harbors a superfamily of effector genes whose protein products enter the cells of the host, soybean. Many of the effectors contain an RXLR-dEER motif in their N-terminus. More than 400 members belonging to this family have been previously identified using a Hidden Markov Model. Amino acids flanking the RXLR motif have been utilized to identify effector proteins from the P. sojae secretome, despite the high level of sequence divergence among the members of this protein family. I present here machine learning methods to identify protein candidates that belong to a particular class, such as the effector superfamily. Converting the flanking amino acid sequences of RXLR motifs (or other candidate motifs) into numeric values that reflect their physical properties enabled the protein sequences to be analyzed through these methods. The methods evaluated include Support Vector Machines and a related spherical classification method that I have developed. I also approached the effector prediction problem by building functional linkage networks and have produced lists of predicted P. sojae effector proteins. I tested the best candidate through gene gun bombardment assays using the beta-glucuronidase reporter system, which revealed that there is a high likelihood that the candidate can enter the soybean cells. / Ph. D.