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This thesis focused on grasping tasks with the goal of investigating, analyzing, and quantifying human catching trends by way of a mathematical model. The aim of this project was to study human trends in a dynamic grasping task (catching a rolling ball), relate those discovered trends to kinematic characteristics of the object, and use this relation to control a robot hand in real time. As an ultimate goal, it was hoped that this research will aide in furthering the bio-inspiration in robot control methods. To achieve the above goal, firstly a tactile sensing glove was developed. This instrument allowed for in depth study of human reactionary grasping movements when worn by subjects during experimentation. This sensing glove system recorded force data from the palm and motion data from four fingers. From these data sets, temporal trends were established relating to when subjects initiated grasping during each trial. Moreover, optical tracking was implemented to study the kinematics of the moving object during human experiments and also to close the loop during the control of the robot hand. Ultimately, a mathematical bio-inspired model was created. This was embodied in a two-term decreasing power function which related the temporal trend of wait time to the ball initial acceleration. The wait time is defined as the time between when the experimental conductor releases the ball and when the subject begins to initiate grasping by closing their fingers, over a distance of four feet. The initial acceleration is the first acceleration value of the object due to the force provided when the conductor throws the object. The distance over which the ball was thrown was incorporated into the model. This is discussed in depth within the thesis. Overall, the results presented here show promise for bio-inspired control schemes in the successful application of robotic devices. This control methodology will ideally be developed to move robotic prosthesis past discrete tasks and into more complicated activities.
ContributorsCard, Dillon (Co-author) / Mincieli, Jennifer (Co-author) / Artemiadis, Panagiotis (Thesis director) / Santos, Veronica (Committee member) / Middleton, James (Committee member) / Barrett, The Honors College (Contributor) / School of Sustainability (Contributor) / Mechanical and Aerospace Engineering Program (Contributor) / W. P. Carey School of Business (Contributor)
Created2014-05
Description
Electromyography (EMG) and Electroencephalography (EEG) are techniques used to detect electrical activity produced by the human body. EMG detects electrical activity in the skeletal muscles, while EEG detects electrical activity from the scalp. The purpose of this study is to capture different types of EMG and EEG signals and to determine if the signals can be distinguished between each other and processed into output signals to trigger events in prosthetics. Results from the study suggest that the PSD estimates can be used to compare signals that have significant differences such as the wrist, scalp, and fingers, but it cannot fully distinguish between signals that are closely related, such as two different fingers. The signals that were identified were able to be translated into the physical output simulated on the Arduino circuit.
ContributorsJanis, William Edward (Author) / LaBelle, Jeffrey (Thesis director) / Santello, Marco (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2013-12
Description
AMPylation is a post-translation modification that has an important role in the survival of many bacterial pathogens by affecting the host cell's molecular signaling. In the course of studying this intercellular manipulation, there has only been modest progression in the identification of the enzymes with AMPylation capabilities (AMPylators) and their respective targets. The reason for these minimal developments is the inability to analyze a large subset of these proteins. Therefore, to increase the efficiency of the identification and characterization of the proteins, Yu et al developed a high-throughput non-radioactive discovery platform using Human Nucleic Acid Programmable Protein Arrays (NAPPA) and a validation platform using bead-based assays. The large-scale unbiased screening of potential substrates for two bacterial AMPylators containing Fic domain, VopS and IbpAFic2, had been performed and dozens of novel substrates were identified and confirmed. With the efficiency of this method, the platform was extended to the identification of novel substrates for a Legionella virulence factor, SidM, containing a different adenylyl transferase domain. The screening was performed using NAPPA arrays comprising of 10,000 human proteins, the active AMPylator SidM, and its inactive D110/112A mutant as a negative control. Many potential substrates of SidM were found, including Rab GTPases and non-GTPase proteins. Several of which have been confirmed with the bead-based AMPylation assays.
ContributorsGraves, Morgan C. (Author) / LaBaer, Joshua (Thesis director) / Qiu, Ji (Committee member) / Yu, Xiaobo (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2013-05
Description
This thesis focused on understanding how humans visually perceive swarm behavior through the use of swarm simulations and gaze tracking. The goal of this project was to determine visual patterns subjects display while observing and supervising a swarm as well as determine what swarm characteristics affect these patterns. As an ultimate goal, it was hoped that this research will contribute to optimizing human-swarm interaction for the design of human supervisory controllers for swarms. To achieve the stated goals, two investigations were conducted. First, subjects gaze was tracked while observing a simulated swarm as it moved across the screen. This swarm changed in size, disturbance level in the position of the agents, speed, and path curvature. Second, subjects were asked to play a supervisory role as they watched a swarm move across the screen toward targets. The subjects determined whether a collision would occur and with which target while their responses as well as their gaze was tracked. In the case of an observatory role, a model of human gaze was created. This was embodied in a second order model similar to that of a spring-mass-damper system. This model was similar across subjects and stable. In the case of a supervisory role, inherent weaknesses in human perception were found, such as the inability to predict future position of curved paths. These findings are discussed in depth within the thesis. Overall, the results presented suggest that understanding human perception of swarms offers a new approach to the problem of swarm control. The ability to adapt controls to the strengths and weaknesses could lead to great strides in the reduction of operators in the control of one UAV, resulting in a move towards one man operation of a swarm.
ContributorsWhitton, Elena Michelle (Author) / Artemiadis, Panagiotis (Thesis director) / Berman, Spring (Committee member) / Barrett, The Honors College (Contributor) / Mechanical and Aerospace Engineering Program (Contributor)
Created2015-05
Description
The purpose of this project was to identify proteins associated with the migration and invasion of non-transformed MCF10A mammary epithelial cells with ectopically expressed missense mutations in p53. Because of the prevalence of TP53 missense mutations in basal-like and triple-negative breast cancer tumors, understanding the effect of TP53 mutations on the phenotypic expression of human mammary epithelial cells may offer new therapeutic targets for those currently lacking in treatment options. As such, MCF10A mammary epithelial cells ectopically overexpressing structural mutations (G245S, H179R, R175H, Y163C, Y220C, and Y234C) and DNA-binding mutations (R248Q, R248W, R273C, and R273H) in the DNA-binding domain were selected for use in this project. Overexpression of p53 in the mutant cell lines was confirmed by western blot and q-PCR analysis targeting the V5 epitope tag present in the pLenti4 vector used to transduce TP53 into the mutant cell lines. Characterization of the invasion and migration phenotypes resulting from the overexpression of p53 in the mutant cell lines was achieved using transwell invasion and migration assays with Boyden chambers. Statistical analysis showed that three cell lines—DNA-contact mutants R248W and R273C and structural mutant Y220C—were consistently more migratory and invasive and demonstrated a relationship between the migration and invasion properties of the mutant cell lines. Two families of proteins were then explored: those involved in the Epithelial-Mesenchymal Transition (EMT) and matrix metalloproteinases (MMPs). Results of q-PCR and immunofluorescence analysis of epithelial marker E-cadherin and mesenchymal proteins Slug and Vimentin did not show a clear relationship between mRNA and protein expression levels with the migration and invasiveness phenotypes observed in the transwell studies. Results of western blotting, q-PCR, and zymography of MMP-2 and MMP-9 also did not show any consistent results indicating a definite relationship between MMPs and the overall invasiveness of the cells. Finally, two drugs were tested as possible treatments inhibiting invasiveness: ebselen and SBI-183. These drugs were tested on only the most invasive of the MCF10A p53 mutant cell lines (R248W, R273C, and Y220C). Results of invasion assay following 30 μM treatment with ebselen and SBI-183 showed that ebselen does not inhibit invasiveness; SBI-183, however, did inhibit invasiveness in all three cell lines tested. As such, SBI-183 will be an important compound to study in the future as a treatment that could potentially serve to benefit triple-negative or basal-like breast cancer patients who currently lack therapeutic treatment options.
ContributorsZhang, Kathie Q (Author) / LaBaer, Joshua (Thesis director) / Anderson, Karen (Committee member) / Gonzalez, Laura (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2015-05
Description
Five immunocompetent C57BL/6-cBrd/cBrd/Cr (albino C57BL/6) mice were injected with GL261-luc2 cells, a cell line sharing characteristics of human glioblastoma multiforme (GBM). The mice were imaged using magnetic resonance (MR) at five separate time points to characterize growth and development of the tumor. After 25 days, the final tumor volumes of the mice varied from 12 mm3 to 62 mm3, even though mice were inoculated from the same tumor cell line under carefully controlled conditions. We generated hypotheses to explore large variances in final tumor size and tested them with our simple reaction-diffusion model in both a 3-dimensional (3D) finite difference method and a 2-dimensional (2D) level set method. The parameters obtained from a best-fit procedure, designed to yield simulated tumors as close as possible to the observed ones, vary by an order of magnitude between the three mice analyzed in detail. These differences may reflect morphological and biological variability in tumor growth, as well as errors in the mathematical model, perhaps from an oversimplification of the tumor dynamics or nonidentifiability of parameters. Our results generate parameters that match other experimental in vitro and in vivo measurements. Additionally, we calculate wave speed, which matches with other rat and human measurements.
ContributorsRutter, Erica (Author) / Stepien, Tracy (Author) / Anderies, Barrett (Author) / Plasencia, Jonathan (Author) / Woolf, Eric C. (Author) / Scheck, Adrienne C. (Author) / Turner, Gregory H. (Author) / Liu, Qingwei (Author) / Frakes, David (Author) / Kodibagkar, Vikram (Author) / Kuang, Yang (Author) / Preul, Mark C. (Author) / Kostelich, Eric (Author) / College of Liberal Arts and Sciences (Contributor)
Created2017-05-31
Description
Tactile and proprioceptive sensory feedback are the two sensory modalities that make up haptic sensation. The degree which these two sensory modalities are integrated together is not very well known. To investigate this issue a set of experiments were set into motion separating these sensory modalities and testing what happens when a person’s proprioceptive system is perturbed. A virtual reality system with haptic feedback along with a weighted object were utilized in a reach, grasp, and lift task. The subjects would lift two objects sequentially and try to judge which one was heavier. This project was split into three different experiments to measure the subject’s perception in different situations. The first experiment utilized the virtual reality system to measure the perception when the subject only has proprioceptive inputs. The second experiment would include the virtual reality system and the weighted object to act as a comparison to the first experiment with the additional tactile input. The third experiment would then add perturbations to the proprioceptive inputs through the virtual reality system to investigate how perception will change. Results from experiment 1 and 2 showed that subjects are almost just as accurate with weight discrimination even if they only have proprioceptive inputs however, subjects are much more consistent in their weight discrimination with both sensory modalities. Results from experiment 3 showed that subjective perception does change when the proprioception is perturbed but the magnitude of that change in perception depends on the perturbation performed.
ContributorsPerrine, Jacob (Author) / Santello, Marco (Thesis director) / Toma, Simone (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
Description
The membrane proximal region (MPR, residues 649–683) and transmembrane domain (TMD, residues 684–705) of the gp41 subunit of HIV-1’s envelope protein are highly conserved and are important in viral mucosal transmission, virus attachment and membrane fusion with target cells. Several structures of the trimeric membrane proximal external region (residues 662–683) of MPR have been reported at the atomic level; however, the atomic structure of the TMD still remains unknown. To elucidate the structure of both MPR and TMD, we expressed the region spanning both domains, MPR-TM (residues 649–705), in Escherichia coli as a fusion protein with maltose binding protein (MBP). MPR-TM was initially fused to the C-terminus of MBP via a 42 aa-long linker containing a TEV protease recognition site (MBP-linker-MPR-TM).
Biophysical characterization indicated that the purified MBP-linker-MPR-TM protein was a monodisperse and stable candidate for crystallization. However, crystals of the MBP-linker-MPR-TM protein could not be obtained in extensive crystallization screens. It is possible that the 42 residue-long linker between MBP and MPR-TM was interfering with crystal formation. To test this hypothesis, the 42 residue-long linker was replaced with three alanine residues. The fusion protein, MBP-AAA-MPR-TM, was similarly purified and characterized. Significantly, both the MBP-linker-MPR-TM and MBP-AAA-MPR-TM proteins strongly interacted with broadly neutralizing monoclonal antibodies 2F5 and 4E10. With epitopes accessible to the broadly neutralizing antibodies, these MBP/MPR-TM recombinant proteins may be in immunologically relevant conformations that mimic a pre-hairpin intermediate of gp41.
ContributorsGong, Zhen (Author) / Martin Garcia, Jose Manuel (Author) / Daskalova, Sasha (Author) / Craciunescu, Felicia (Author) / Song, Lusheng (Author) / Dorner, Katerina (Author) / Hansen, Debra (Author) / Yang, Jay-How (Author) / LaBaer, Joshua (Author) / Hogue, Brenda (Author) / Mor, Tsafrir (Author) / Fromme, Petra (Author) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Infectious Diseases and Vaccinology (Contributor) / Innovations in Medicine (Contributor) / Personalized Diagnostics (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2015-08-21
Description
The focus of this project investigates high mobility robotics by developing a fully integrated framework for a ball-balancing robot. Using Lagrangian mechanics, a model for the robot was derived and used to conduct trade studies on significant system parameters. With a broad understanding of system dynamics, controllers were designed using LQR methodology. A prototype was then built and tested to exhibit desired reference command following and disturbance attenuation.
ContributorsKapron, Mark Andrew (Author) / Rodriguez, Armando (Thesis director) / Artemiadis, Panagiotis (Committee member) / Industrial, Systems & Operations Engineering Prgm (Contributor) / Electrical Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Cleavage and polyadenylation is a step in mRNA processing in which the 3’UTR is cleaved and a polyA tail is added to create a final mature transcript. This process relies on RNA sequence elements that guide a large multimeric protein complex named the Cleavage and Polyadenylation Complex to dock on the 3’UTR and execute the cleavage reaction. Interactions of the complex with the RNA and specific dynamics of complex recruitment and formation still remain largely uncharacterized. In our lab we have identified an Adenosine residue as the nucleotide most often present at the cleavage site, although it is unclear whether this specific element is a required instructor of cleavage and polyadenylation. To address whether the Adenosine residue is necessary and sufficient for the cleavage and polyadenylation reaction, we mutated this nucleotide at the cleavage site in three C. elegans protein coding genes, forcing the expression of these wt and mutant 3’UTRs, and studied how the cleavage and polyadenylation machinery process these genes in vivo. We found that interrupting the wt sequence elements found at the cleavage site interferes with the cleavage and polyadenylation reaction, suggesting that the sequence close to the end of the transcript plays a role in modulating the site of the RNA cleavage. This activity is also gene-specific. Genes such as ges-1 showed little disruption in the cleavage of the transcript, with similar location occurring in both the wt and mutant 3’UTRs. On the other hand, mutation of the cleavage site in genes such as Y106G6H.9 caused the activation of new cryptic cleavage sites within the transcript. Taken together, my experiments suggest that the sequence elements at the cleavage site somehow participate in the reaction to guide the cleavage reaction to occur at an exact site. This work will help to better understand the mechanisms of transcription termination in vivo and will push forward research aimed to study post-transcriptional gene regulation in eukaryotes.
ContributorsSteber, Hannah Suzanne (Author) / Mangone, Marco (Thesis director) / Harris, Robin (Committee member) / LaBaer, Joshua (Committee member) / School of Life Sciences (Contributor, Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05