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EMG-based Finger Movement Classification for Prosthetic Hand Control
No full textMillions of people around the world are suffering from the consequences of amputation.
In particular, advanced prosthetic hands could retrieve some functionality and improve
quality of life of those who lost it. The most challenging part in the prosthetic hands
is their finger control. Ideally, when the brain sends the signal for moving a finger, the
corresponding finger is detected in a very short time. Therefore, not only the accuracy
but time to reach that accuracy should be considered. EMG signal is found as a promising
mechanism to control prosthetics. Unfortunately, EMG signal is easily contaminated with
noise and various artifacts factors that deteriorates the accuracy of classification.
In this research, we addressed key challenges in EMG classification. First, we proposed 5
new features to enhance the accuracy. Second, we advocated EVM as a powerful classifier
and compared its performance with other EMG classifiers in the literature. Third, for
online classification, we employed various recurrent neural network (RNN) structures, and
showed that bidirectional-RNNs with sequential inputs could achieve higher accuracies
in a shorter time. Fourth, to make the system robust against noise, we proposed a
convolutional neural network feature learning (CNNFL) structure combined with EVM.
Fifth, to address the drawback of the Bayesian fusion method, we proposed a novel
postprocessing technique. Overall, in this research, we have customized machine learning
techniques for EMG analysis that can produce accurate classification in realtime and real
world noisy condition
Single Cell RNA Sequencing Data Analysis and Applications in Caenorhabditis Elegans Embryo Development
No full textSingle cell RNA sequencing (hereinafter “scRNA-seq”) has become a routine assay in molecular
biological research, allowing in-depth assessments of individual cell transcriptome. Here, we
used scRNA-seq datasets to study the global cellular communications in the Caenorhabditis
elegans (hereinafter “C. elegans”) embryo. As a key genetic model organism, especially for
embryo development, this nematode has an invariant cell lineage which was fully mapped,
making it the ideal model in which gene expression patterns of individual cells could be used to
construct the transcriptomic dynamic during cell differentiation and development. Even though
many aspects of C. elegans embryo have been well-characterized, many questions remain. In this
work, we highlighted the utility of scRNA-seq in inferring cell-cell interactions (hereinafter
“CCI”) in the entire embryo to characterize the coordination between cell populations and the
dynamic of signaling pathways throughout embryo development. This study is the first to
holistically study the CCI landscape throughout embryo development in C. elegans using
scRNA-seq data and should lay the framework for identifying how these different interaction
patterns control morphogenesis at the cellular and molecular levels
Accounting Information Provision and Competitive Bidding: the Case of Procurement Contract Negotiations
No full textThis paper studies how private accounting information disclosure requirements affect the
award and execution of supply contracts using a quasi-experimental setting related to government procurement. Buyer-supplier relationships are frequently marked by asymmetric
information held by suppliers about their prices. To alleviate this, buyers often require a
minimum number of competing bids be received, or else they require suppliers to privately
disclose information supporting their proposed prices. The effect of such a buyer policy
on competition is unclear. Such a policy may drive buyers to promote competition, but
information requirements can also dissuade potential suppliers from competing due to data
gathering and proprietary costs. I empirically examine the net effects of such a policy in
the context of a federal regulation that mandates contractors provide accounting data supporting their proposed pricing unless there is a sufficient number of competing bidders, for
contracts above a certain price threshold. I find that above-threshold contracts experience
greater competition than below-threshold contracts. Further, I find improvements in contract completeness (i.e., decreased reliance on cost-plus contracts) and performance (i.e., less
frequent re-negotiations and cost overruns), suggesting that these data requirements cause
scarce buyer attention to become more directed towards above-threshold contracts. My results differ among subsamples in a manner that is consistent with the documented effects
being driven by this data policy
Selective Chemical Bath Deposition of Copper Sulfides and Tin Sulfides on Functionalized Self-assembled Monolayers
No full textThe deposition of select chemical phases of semiconducting materials is an industrially complex
problem. Moreover, the currently practiced deposition methods that employ harsh conditions,
such as high temperature (>100oC), limit the ability to deposit onto polymer or organic
substrates. The development of low temperature methods is necessary for the future of flexible
electronic applications. In this work chemical bath deposition (CBD), is employed towards
selective compositional deposition of copper sulfide and tin sulfide phases on alkanethiolate self-
assembled monolayers (SAMs) substrates. SAMs are model organic systems with tunable
surface chemistry.
This work shows selective compositional deposition of copper sulfide, Cu2S or CuS, on -COOH,
-OH, and -CH3 terminated SAMs when using thiourea as a sulfur precursor deposited at pH 9 and
CuS deposited at pH 12. The selectivity of the deposit is dependent on the bath pH and surface
chemistry. Area selective deposition of CuS is also observed when using thioacetamide as a
sulfur precursor for copper sulfide CBD. Tin sulfides are also shown to be compositionally
dependent on bath pH and substrate chemistry and deposit as either SnS, SnS2, or Sn2S3
Investigation of Sweat Biomarkers for Real-time Reporting of Infection and Inflammation Using Wearable Sweat Sensor
No full textInflammatory biomarkers are modulated due to an infection or inflammatory trigger. Cytokines
are inflammatory biomarkers that orchestrate the manifestation and progression of an
infection/inflammatory event. Hence, non-invasive, real-time monitoring of cytokines can be
pivotal in assessing the progression of infection/inflammatory event. However, real-time
monitoring of biomarkers is not feasible with the current technology as most of them rely on
blood-based detection. Continuous monitoring of host immune markers in sweat can aid in realtime monitoring of the immune status. This dissertation demonstrates a wearable
SWEATSENSER device that can track the levels of immune cytokine markers in real-time from
passively expressed sweat. The developed device is of a watch form-factor that can be worn on
the arm to reliably track the biomarker response from low volumes of sweat (~1 μL) and the
biomarker levels can be monitored in real-time. The developed SWEATSENSER device was
validated for reliably reporting the levels of several cytokines and chemokines. Additionally, this
work presents a thorough validation on the presence of certain critical infection and
inflammatory markers such as interferon-inducible protein (IP-10) and tumor necrosis factor-
related apoptosis-inducing ligand (TRAIL), C-reactive protein that make it feasible for using
sweat as a biofluid for actively monitoring the health status. Additionally, human subject clinical
studies demonstrate the feasibility of non-invasively tracking infections such as influenza from
sweat. Such a wearable device can offer significant strides in improving prognosis and provide
personalized therapeutic treatment for several inflammatory/infectious diseases
Reading Plato's Republic As A Literary Text
No full textLeo Strauss has noted that in order to read Plato’s Republic, one has to postpone the philosophical question and become engrossed in the literary question. My dissertation addresses the question of what a literary analysis of Plato’s Republic might produce. My research in the philosophical tradition not only involves the modern and contemporary periods but also that of the Renaissance and earlier times and I discovered that traditional philosophers and commentators have a way of reading the Republic which is distanced from its literary content. I performed my analysis of Plato’s Republic using literary glossaries to identify literary devices, narrative tools, and conventions of writing, in the text, and to explain how Plato uses them. I discovered that Plato made a significant number of choices about how to write the text – choices which have implications not only for how the text should be read but also about how we should think of his philosophy. These findings are significant because they stand in contradiction to traditional commentaries in the philosophical tradition which never manage to produce the literary spirit inherent in the text
Microwave Plasma Pyrolysis of Biomass: Process and Applications
No full textIn order to meet the growing demands of an increasing global population without irreversibly
depleting the planet’s resources in the face of a rapidly changing climate a sustainable circular
economy will need to be adopted, one based on renewable biologically derived materials. The
Microwave Plasma Pyrolysis (MPP) process detailed in this dissertation is intended to help
enable this transition by establishing a standard methodology for the conversion of renewable
biological material feedstocks like hemp and fungi into high-value end products capable of
replacing non-renewable or petroleum-based products in a scalable and efficient manner.
To this end a custom MPP system is designed and built around a common kitchen microwave
oven and tested with commercially available hemp-based canvas fabrics as well as fungal
samples collected from the Dallas ecosystem. It is found that the MPP process converts biomass
into a matrix of carbon phases including graphite and a form of diamond called
Ultrananocrystalline Diamond (UNCD) while retaining the original sample’s superstructure.
The pyrolyzed biomass is investigated via a variety of complementary physical and chemical
characterization techniques and is shown to possess hierarchical porosity at the macro, micro,
and nanoscales. Being that this is the first time it has been reported that diamond can be
produced from a biological source in such a rapid and efficient manner, a mechanism is
discussed to explain this unique transformation, with comparisons to conventional methods of
diamond growth and production.
The application demonstrated in this dissertation as an air filtration membrane is influenced by
the global COVID-19 viral pandemic, which exposed serious failure modes in conventional
facemask systems based on non-woven electro-spun or melt-blown polypropylene fibers. Since a
fully sized facemask derived from pyrolyzed fungal mycelium or hemp canvas was not feasible
during this dissertation research, a unique methodology derived from TEM grid particle
sampling research was developed utilizing additive manufacturing and tested in collaboration
with an industry standard FDA aerosol mask testing setup using electrostatically neutral salt
particles.
Further functionalization and enhancement of the plasma pyrolyzed biomass is demonstrated
through Microwave Plasma Chemical Vapor Deposition (MPCVD), used to deposit additional
layers of diamond and other nanocarbons including graphite and graphene. Prior work in the
literature investigating applications of conventionally pyrolyzed biomass have included energy
storage in the form of high surface area nanocarbons for battery electrodes and as performance
enhancing additives in composites
Divergent Voices: the Historical Language of Baptist Religious Artifacts in the American South, 1865-1914
No full textThe postbellum American South witnessed the rise of Southern Baptists as the strongest Protestant evangelical social force in number and influence. The autonomous nature of the denomination attracted large numbers of Southerners regardless of race, class, or gender. An inverted authority structure empowered people in the pew to act decisively within their own congregation and denomination which transformed into a significant socio-political presence in the region.
Baptists were known for their dependence upon the Bible as the source or religious authority and their minimalist approach to religious artifacts and icons, but their physical material became critical to the preservation of their religious traditions. As Baptists rose to prominence, their religious things became a source of validation of their accomplishments. This project drew upon material culture ideas of Roland Barthes, Ferdinand de Saussure, Zacharias Zerubavel, Martin Heidegger, and Emile Durkheim to explore the juxtaposition of Baptist material culture and their belief in the divinity of Baptist ideology. Heidegger’s presentation of the thingness of the jug for distributing liquid and Zerubavel’s theory that common background objects have foreground
importance proved instrumental in the final analysis. Although not typically considered material culture, Baptist use of the Bible, communion cups, pulpits, pews, hymnals, buildings, and religious publications demonstrated a voice that spoke into Baptist culture thus open to analytical interrogation.
Baptist materiology, the study of Baptist things, required a multifactorial approach that included Baptist ideology, historical context, material culture, and social distinctions. The project attempted to listen to the historical objects in context of their ideological purpose, historical setting, and social influence. The logical argument flowed from the most intimate moment with the divine to the institutional experience and the hierarchical structures quite distant from the Baptist individual. The narrative followed a pattern from the autonomy of the individual to the command of the institution in sequential order beginning with the initial conversion from biblical presentation from the pulpit to immersive baptism, to the communion, to the presence in the pew, to the congregational unity of the hymnal, to the public space of the church buildings, to the corporate nature of education materials, and concluding with the religious imperialism of global missions. Baptists connected to the socio-political structures as issues of race class and gender intertwined into the narrative positioning Baptist ideology into the greater historical narrative. In the end, the trend toward institutionalism threatened the precious individualism of Baptist ideology and diverted the focus of the denomination to resort to protective means to preserve the newly acquired social prominence
Towards Understanding the Roles of Organic Bath Additives in Copper Electroless Deposition on Self-assembled Monolayers
No full textOrganic bath additives are commonly used in solution-based deposition techniques to improve the
properties of the desired material. However, despite their wide application, studies on
understanding the roles of these additives are limited. In this dissertation, we employed multiple
surface characterization techniques including X-ray photoelectron spectroscopy (XPS), time-of-
flight secondary ion mass spectrometry (TOF SIMS), Raman spectroscopy, scanning electron
microscopy with energy dispersive spectroscopy (SEM-EDS), atomic force microscopy (AFM),
and optical microscopy to investigate the effect monoethanolamine, diethanolamine,
triethanolamine, urea, guanidine, and thiourea as bath additives in the electroless deposition of
copper on self-assembled monolayers (SAMs).
Using XPS and TOF SIMS, we observed that electrolessly deposited copper is more adherent on
the –CH3 terminated SAMs. TOF SIMS spectra also showed that the mono- and triethanolamine
interact with the –CH3 terminated SAM via the amine functional group while diethanolamine
adsorbs flat on the SAM surface. These interactions allowed the deposition of copper wires via
electroless nanowire deposition on micropatterned substrates (ENDOM). Fragment ions in the
TOF SIMS spectra showed various interactions of the hydroxyl group of ethanolamines with the
–OH terminated SAMs. This indicates that polar ethanolamines interact strongly with the
hydroxyl-terminated SAM surface.
We also demonstrated a switch from copper electroless deposition at low concentrations of
thiourea to copper sulfide deposition at high concentrations of thiourea. We synthesized copper
wires using thiourea as bath additive in ENDOM. A method of depositing Cu/CuxS layer via a
two-step solution-based technique is also presented.
The electron-donating property of the heteroatom in bath additives (urea, guanidine, and thiourea)
influences its stabilizing ability. Thiourea inhibited the electroless deposition process which
allowed the deposition of small particles resulting in smooth copper film. Also, regardless of the
bath additive heteroatom, smoother films were deposited at pH 9. At pH 12, we observed two
layers of deposit: (a) ion-by-ion growth of the underlayer and (b) cluster-by-cluster growth of the
overlayer. Copper wires deposited using guanidine as bath additive at pH 9 are more uniform.
Lastly, we proposed methods to optimize the crossbar wire synthesis using multiple ENDOM
processes
Systematic Approaches for Improving Fuzzing Evaluation and Fuzzing Program Configurations
No full textIn this dissertation, we explore three approaches that improve the fuzzing evaluations and
fuzz program configurations. Fuzz testing is an automated technique that detects bugs and
potential vulnerabilities in software by executing programs with randomly and iteratively
generated inputs. This method has gained widespread adoption in practice and made sig-
nificant contributions to the detection of security bugs in real-world software. The success
of fuzz testing has motivated numerous works aiming at further improving its performance.
Such rapid development presents two significant challenges. First, the performance of fuzzers
is often evaluated empirically, involving comparisons of proposed improvements with existing
methods. The choice of performance metrics significantly influences the evaluation results.
For example, the widely-used metric of code coverage can lead to misleading conclusions
regarding which fuzzer is more effective at detecting real-world bugs. Moreover, the em-
pirical comparisons tend to solely rely on the holistic metrics, such as code coverage and
number of bugs identified at the end of fuzzing, to evaluate the overall performance. Such
holistic metrics provide limited insights on how one fuzzer A outperforms another fuzzer B,
while understanding the distinctions is crucial for practitioners to comprehend the fuzzers’
effectiveness and to facilitate further improvements. Second, the application of fuzzers is
often limited in exploring program configurations. For example, the popular fuzzer AFL
takes a fixed configuration of command-line options as input and maintains this configuration throughout the entire fuzzing process. Most of its successors inherit this setup and only
fuzz one configuration in a fuzzing run. This scenario misses the opportunity to explore bugs
that are only enabled with alternative configurations, thereby limiting the effectiveness of
fuzzing.
The first approach of this dissertation focuses on building robust performance metrics by
automatically generating fuzzing benchmarks with realistic bugs. The key idea of this approach is to match realistic bugfix patterns in real-world programs, and revert the matched
patterns to inject realistic bugs. We first manually study real-world bugfixes and summarize
bugfix patterns. We then implement a framework that takes as input the bugfix patterns and
automatically detects any code site that matches the patterns. The syntax of the pattern
is undone on the detected code sites to (re)introduce likely bugs. Using our framework, we
build a fuzzing benchmark with 10 programs and nearly 8,000 injected bugs. We evaluate 5
different fuzzers using our benchmark and demonstrate that the injected bugs are realistic,
triggerable and challenging for fuzzers.
The second approach proposes evaluating internal fuzzing mechanisms based on internal
metrics. We first develop a hierarchical formalization that represents evaluations of grey-
box fuzzing. Using this formalization, we perform a review of 44 recent fuzzing papers to
understand common practices in fuzzing evaluation. We find that papers overwhelmingly
rely on holistic metrics (e.g., number of bugs found) to evaluate a fuzzer’s performance.
While some papers do directly evaluate internal metrics, there is no widespread agreement
on the best practices. Motivated by this finding, we demonstrate the power of evaluating
internal mechanisms of fuzz testing by developing a methodology for evaluating fuzzing
hypotheses based on internal metrics. We instantiate this approach on four popular fuzzers,
and show how we can draw insights of the internal operations of fuzzers that complement
the evaluations using holistic metrics.
The third approach aims at enabling fuzzers to efficiently explore various configurations during fuzzing. We first conduct an empirical study to understand how program configurations
affect fuzzing performance. We find that limiting a fuzzing campaign to a single configuration can result in the failure to cover a significant amount of code. We also observe that
different program configurations contribute to different amounts of code coverage, challenging the idea that each one can be efficiently fuzzed individually. Motivated by these two
findings, we design and implement ConfigFuzz that transforms the target program to encode
its program options within part of the fuzzable input, so existing fuzzers’ mutation strategy
can be reused to fuzz program configurations. We evaluate ConfigFuzz on 6 target programs
and analyze the options fuzzed by ConfigFuzz and how they affect the performance