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Description
The pathogenesis of type 1 diabetes (T1D) is still not fully understood in the scientific community. Evidence has shown that viral infections are one of the important environmental factors associated with the disease development. Seven of the top T1D related viruses were selected to study the prevalence of viral humoral

The pathogenesis of type 1 diabetes (T1D) is still not fully understood in the scientific community. Evidence has shown that viral infections are one of the important environmental factors associated with the disease development. Seven of the top T1D related viruses were selected to study the prevalence of viral humoral response in T1D patients using our innovative protein array platform called Nucleic Acid Programmable Protein Array (NAPPA). In this study, each viral gene was individually captured using various PCR based techniques, cloned into a protein expression vector, and assembled as the first version of T1D viral protein array. Humoral responses of IgG, IgA, and IgM were examined. Although each class of immunoglobulin generated a wide-range of reactivity, responses to various viral proteins from different proteins were observed. In summary, we captured most of the T1D related viral genes, established viral protein expression on the protein array, and displayed the serum response on the viral protein array. The successful progress will help to fulfill the long term goal of testing the viral infection hypothesis in T1D development.
ContributorsDavis, Amy Darlene (Author) / LaBaer, Joshua (Thesis director) / Qiu, Ji (Committee member) / Desi, Paul (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2013-05
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Description
As robots become more prevalent, the need is growing for efficient yet stable control systems for applications with humans in the loop. As such, it is a challenge for scientists and engineers to develop robust and agile systems that are capable of detecting instability in teleoperated systems. Despite how much

As robots become more prevalent, the need is growing for efficient yet stable control systems for applications with humans in the loop. As such, it is a challenge for scientists and engineers to develop robust and agile systems that are capable of detecting instability in teleoperated systems. Despite how much research has been done to characterize the spatiotemporal parameters of human arm motions for reaching and gasping, not much has been done to characterize the behavior of human arm motion in response to control errors in a system. The scope of this investigation is to investigate human corrective actions in response to error in an anthropomorphic teleoperated robot limb. Characterizing human corrective actions contributes to the development of control strategies that are capable of mitigating potential instabilities inherent in human-machine control interfaces. Characterization of human corrective actions requires the simulation of a teleoperated anthropomorphic armature and the comparison of a human subject's arm kinematics, in response to error, against the human arm kinematics without error. This was achieved using OpenGL software to simulate a teleoperated robot arm and an NDI motion tracking system to acquire the subject's arm position and orientation. Error was intermittently and programmatically introduced to the virtual robot's joints as the subject attempted to reach for several targets located around the arm. The comparison of error free human arm kinematics to error prone human arm kinematics revealed an addition of a bell shaped velocity peak into the human subject's tangential velocity profile. The size, extent, and location of the additional velocity peak depended on target location and join angle error. Some joint angle and target location combinations do not produce an additional peak but simply maintain the end effector velocity at a low value until the target is reached. Additional joint angle error parameters and degrees of freedom are needed to continue this investigation.
ContributorsBevilacqua, Vincent Frank (Author) / Artemiadis, Panagiotis (Thesis director) / Santello, Marco (Committee member) / Trimble, Steven (Committee member) / Barrett, The Honors College (Contributor) / Mechanical and Aerospace Engineering Program (Contributor)
Created2013-05
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Description
I worked on the human-machine interface to improve human physical capability. This work was done in the Human Oriented Robotics and Control Lab (HORC) towards the creation of an advanced, EMG-controlled exoskeleton. The project was new, and any work on the human- machine interface needs the physical interface itself. So

I worked on the human-machine interface to improve human physical capability. This work was done in the Human Oriented Robotics and Control Lab (HORC) towards the creation of an advanced, EMG-controlled exoskeleton. The project was new, and any work on the human- machine interface needs the physical interface itself. So I designed and fabricated a human-robot coupling device with a novel safety feature. The validation testing of this coupling proved very successful, and the device was granted a provisional patent as well as published to facilitate its spread to other human-machine interface applications, where it could be of major benefit. I then employed this coupling in experimentation towards understanding impedance, with the end goal being the creation of an EMG-based impedance exoskeleton control system. I modified a previously established robot-to-human perturbation method for use in my novel, three- dimensional (3D) impedance measurement experiment. Upon execution of this experiment, I was able to successfully characterize passive, static human arm stiffness in 3D, and in doing so validated the aforementioned method. This establishes an important foundation for promising future work on understanding impedance and the creation of the proposed control scheme, thereby furthering the field of human-robot interaction.
ContributorsO'Neill, Gerald D. (Author) / Artemiadis, Panagiotis (Thesis director) / Santello, Marco (Committee member) / Santos, Veronica (Committee member) / Barrett, The Honors College (Contributor) / Mechanical and Aerospace Engineering Program (Contributor)
Created2013-05
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Description
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

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
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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

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
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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

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
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Description

Despite the fact that seizures are commonly associated with autism spectrum disorder (ASD), the effectiveness of treatments for seizures has not been well studied in individuals with ASD. This manuscript reviews both traditional and novel treatments for seizures associated with ASD. Studies were selected by systematically searching major electronic databases

Despite the fact that seizures are commonly associated with autism spectrum disorder (ASD), the effectiveness of treatments for seizures has not been well studied in individuals with ASD. This manuscript reviews both traditional and novel treatments for seizures associated with ASD. Studies were selected by systematically searching major electronic databases and by a panel of experts that treat ASD individuals. Only a few anti-epileptic drugs (AEDs) have undergone carefully controlled trials in ASD, but these trials examined outcomes other than seizures. Several lines of evidence point to valproate, lamotrigine, and levetiracetam as the most effective and tolerable AEDs for individuals with ASD. Limited evidence supports the use of traditional non-AED treatments, such as the ketogenic and modified Atkins diet, multiple subpial transections, immunomodulation, and neurofeedback treatments. Although specific treatments may be more appropriate for specific genetic and metabolic syndromes associated with ASD and seizures, there are few studies which have documented the effectiveness of treatments for seizures for specific syndromes. Limited evidence supports l-carnitine, multivitamins, and N-acetyl-l-cysteine in mitochondrial disease and dysfunction, folinic acid in cerebral folate abnormalities and early treatment with vigabatrin in tuberous sclerosis complex. Finally, there is limited evidence for a number of novel treatments, particularly magnesium with pyridoxine, omega-3 fatty acids, the gluten-free casein-free diet, and low-frequency repetitive transcranial magnetic simulation. Zinc and l-carnosine are potential novel treatments supported by basic research but not clinical studies. This review demonstrates the wide variety of treatments used to treat seizures in individuals with ASD as well as the striking lack of clinical trials performed to support the use of these treatments. Additional studies concerning these treatments for controlling seizures in individuals with ASD are warranted.

ContributorsFrye, Richard E. (Author) / Rossignol, Daniel (Author) / Casanova, Manuel F. (Author) / Brown, Gregory L. (Author) / Martin, Victoria (Author) / Edelson, Stephen (Author) / Coben, Robert (Author) / Lewine, Jeffrey (Author) / Slattery, John C. (Author) / Lau, Chrystal (Author) / Hardy, Paul (Author) / Fatemi, S. Hossein (Author) / Folsom, Timothy D. (Author) / MacFabe, Derrick (Author) / Adams, James (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2013-09-13
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Description

There is a growing body of scientific evidence that the health of the microbiome (the trillions of microbes that inhabit the human host) plays an important role in maintaining the health of the host and that disruptions in the microbiome may play a role in certain disease processes. An increasing

There is a growing body of scientific evidence that the health of the microbiome (the trillions of microbes that inhabit the human host) plays an important role in maintaining the health of the host and that disruptions in the microbiome may play a role in certain disease processes. An increasing number of research studies have provided evidence that the composition of the gut (enteric) microbiome (GM) in at least a subset of individuals with autism spectrum disorder (ASD) deviates from what is usually observed in typically developing individuals. There are several lines of research that suggest that specific changes in the GM could be causative or highly associated with driving core and associated ASD symptoms, pathology, and comorbidities which include gastrointestinal symptoms, although it is also a possibility that these changes, in whole or in part, could be a consequence of underlying pathophysiological features associated with ASD. However, if the GM truly plays a causative role in ASD, then the manipulation of the GM could potentially be leveraged as a therapeutic approach to improve ASD symptoms and/or comorbidities, including gastrointestinal symptoms.

One approach to investigating this possibility in greater detail includes a highly controlled clinical trial in which the GM is systematically manipulated to determine its significance in individuals with ASD. To outline the important issues that would be required to design such a study, a group of clinicians, research scientists, and parents of children with ASD participated in an interdisciplinary daylong workshop as an extension of the 1st International Symposium on the Microbiome in Health and Disease with a Special Focus on Autism (www.microbiome-autism.com). The group considered several aspects of designing clinical studies, including clinical trial design, treatments that could potentially be used in a clinical trial, appropriate ASD participants for the clinical trial, behavioral and cognitive assessments, important biomarkers, safety concerns, and ethical considerations. Overall, the group not only felt that this was a promising area of research for the ASD population and a promising avenue for potential treatment but also felt that further basic and translational research was needed to clarify the clinical utility of such treatments and to elucidate possible mechanisms responsible for a clinical response, so that new treatments and approaches may be discovered and/or fostered in the future.

ContributorsFrye, Richard E. (Author) / Slattery, John (Author) / MacFabe, Derrick F. (Author) / Allen-Vercoe, Emma (Author) / Parker, William (Author) / Rodakis, John (Author) / Adams, James (Author) / Krajmalnik-Brown, Rosa (Author) / Bolte, Ellen (Author) / Kahler, Stephen (Author) / Jennings, Jana (Author) / James, Jill (Author) / Cerniglia, Carl E. (Author) / Midtvedt, Tore (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2015-05-07
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Description

Background: Despite the high prevalence of seizure, epilepsy and abnormal electroencephalograms in individuals with autism spectrum disorder (ASD), there is little information regarding the relative effectiveness of treatments for seizures in the ASD population. In order to determine the effectiveness of traditional and non-traditional treatments for improving seizures and influencing other

Background: Despite the high prevalence of seizure, epilepsy and abnormal electroencephalograms in individuals with autism spectrum disorder (ASD), there is little information regarding the relative effectiveness of treatments for seizures in the ASD population. In order to determine the effectiveness of traditional and non-traditional treatments for improving seizures and influencing other clinical factor relevant to ASD, we developed a comprehensive on-line seizure survey.

Methods: Announcements (by email and websites) by ASD support groups asked parents of children with ASD to complete the on-line surveys. Survey responders choose one of two surveys to complete: a survey about treatments for individuals with ASD and clinical or subclinical seizures or abnormal electroencephalograms, or a control survey for individuals with ASD without clinical or subclinical seizures or abnormal electroencephalograms. Survey responders rated the perceived effect of traditional antiepileptic drug (AED), non-AED seizure treatments and non-traditional ASD treatments on seizures and other clinical factors (sleep, communication, behavior, attention and mood), and listed up to three treatment side effects.

Results: Responses were obtained concerning 733 children with seizures and 290 controls. In general, AEDs were perceived to improve seizures but worsened other clinical factors for children with clinical seizure. Valproic acid, lamotrigine, levetiracetam and ethosuximide were perceived to improve seizures the most and worsen other clinical factors the least out of all AEDs in children with clinical seizures. Traditional non-AED seizure and non-traditional treatments, as a group, were perceived to improve other clinical factors and seizures but the perceived improvement in seizures was significantly less than that reported for AEDs. Certain traditional non-AED treatments, particularly the ketogenic diet, were perceived to improve both seizures and other clinical factors. For ASD individuals with reported subclinical seizures, other clinical factors were reported to be worsened by AEDs and improved by non-AED traditional seizure and non-traditional treatments. The rate of side effects was reportedly higher for AEDs compared to traditional non-AED treatments.

Conclusion: Although this survey-based method only provides information regarding parental perceptions of effectiveness, this information may be helpful for selecting seizure treatments in individuals with ASD.

ContributorsFrye, Richard E. (Author) / Sreenivasula, Swapna (Author) / Adams, James (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2011-05-18
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Description
Background
Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the

Background
Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment on the pace of biological discovery. It is thus imperative to design an automated system for efficient image annotation and comparison.
Results
We present a computational framework to perform anatomical keywords annotation for Drosophila gene expression images. The spatial sparse coding approach is used to represent local patches of images in comparison with the well-known bag-of-words (BoW) method. Three pooling functions including max pooling, average pooling and Sqrt (square root of mean squared statistics) pooling are employed to transform the sparse codes to image features. Based on the constructed features, we develop both an image-level scheme and a group-level scheme to tackle the key challenges in annotating Drosophila gene expression pattern images automatically. To deal with the imbalanced data distribution inherent in image annotation tasks, the undersampling method is applied together with majority vote. Results on Drosophila embryonic expression pattern images verify the efficacy of our approach.
Conclusion
In our experiment, the three pooling functions perform comparably well in feature dimension reduction. The undersampling with majority vote is shown to be effective in tackling the problem of imbalanced data. Moreover, combining sparse coding and image-level scheme leads to consistent performance improvement in keywords annotation.
ContributorsSun, Qian (Author) / Muckatira, Sherin (Author) / Yuan, Lei (Author) / Ji, Shuiwang (Author) / Newfeld, Stuart (Author) / Kumar, Sudhir (Author) / Ye, Jieping (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Ira A. Fulton Schools of Engineering (Contributor)
Created2013-12-03