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- Creators: Artemiadis, Panagiotis
This dissertation studies a phase based oscillator constructed with a second order dynamic system and a forcing function based on the phase angle of the system. This produces a bounded control signal that can alter the damping and stiffens properties of the dynamic system. It is shown analytically and experimentally that it is stable and robust. It can handle perturbations remarkably well. The forcing function uses the states of the system to produces stable oscillations. Also, this work shows the use of the phase based oscillator in wearable robots to assist periodic human motion focusing on assisting the hip motion. One of the main problems to assist periodic motion properly is to determine the frequency of the signal. The phase oscillator eliminates this problem because the signal always has the correct frequency. The input requires the position and velocity of the system. Additionally, the simplicity of the controller allows for simple implementation.
Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.
Data Availability: All genomic and transcriptomic sequence files are available from the NIH-NCBI BioProject database (accession numbers PRJNA352725, PRJNA352726, and PRJNA281763). All genome assembly, transcriptome assembly, predicted protein, transcript, genome annotation, repeatmasker, phylogenetic trees, .vcf and GO enrichment files are available on Harvard Dataverse (doi:10.7910/DVN/EH2S9K).