Approximate string matching is commonly used to align genetic sequences (DNA
or RNA) to determine their shared characteristics. In contrast with the standard
dynamic programming methods which use local edit distance models, the Walking
Tree heuristic method was created to handle non-local changes, e.g., translocations,
inversions, and duplications, altogether and...
In the United States, the utilization of digital media has assumed an omnipresent status and has altered the manner in which we communicate, conduct business, and create art and music. However, it has been demonstrated that art therapy lags behind the current culture of prolific use of digital media. To...
Fungi in the genus Tolypocladium are diverse in their host associations, but the predominant ecologies include parasites of the ectomycorrhizal genus Elaphomyces and pathogens of insects. The aim of this dissertation research is to examine the evolution of these fungi and their host associations. To accomplish this several lines of...
Sensor system plays an important role in connecting everything including human body to the electrical information systems that we have built and that we are going to build, to make the world more intelligent and efficient. One of the key propulsive forces behind these emerging techniques is CMOS scaling that...
Obstetric fistula is estimated to affect 1–2 million women worldwide, predominantly in low-resource countries in sub-Saharan Africa and southeast Asia. The primary intervention for obstetric fistula is surgery, which is described as a relatively simple surgical procedure with an extremely high psychosocial and economic benefit relative to cost. Research addressing...
A method based on fatty acid (FA) analysis is used to profile microbial community structure (MCS). Various extraction protocols are available, which alter the types of FAs extracted from soils. The more time consuming but widely used protocol extracts only FAs from phospholipids (PLFA). This technique is desirable because PLFAs...
Microalgae has been under careful consideration as a sustainable feedstock for renewable fuel recently due to its year round production with high energy yields per unit area, reduced need for arable land, water treatment benefits with nutrient cycling, and minimal competition with the food industry. Despite of all these advantages,...
Multiagent approaches are well suited to designing autonomous solutions for systems that feature complex interactions between many individuals such as in autonomous traffic systems and multi-robot exploration systems. However, creating autonomous agents that function effectively in these systems is a challenging task. In these complex environments, agents need informative reward...
The chlamydiae are a family of obligate intracellular bacteria that have a unique bi-phasic developmental cycle, unique cellular properties, and a unique set of challenges to studying its biology. While genetic manipulation is becoming routine in Chlamydia, there are significant challenges to working with this intracellular parasite. The body of...
Transcriptomics and gene expression profiling enables the elucidation of the genetic response of an organism to various environmental cues. Transcriptomics enables the deciphering of differences between two closely related organisms to the same environment and in contrast, enables the elucidation of genetic responses of the same organism to different environmental...
Over the last two decades, satisfiability and satisfiability-modulo theory (SAT/SMT) solvers have grown powerful enough to be general purpose reasoning engines throughout software engineering and computer science. However, most practical use cases of SAT/SMT solvers require not just solving a single SAT/SMT problem, but solving sets of related SAT/SMT problems....
Converting energy from ocean waves is a challenging area for control theory application because of the nonlinear dynamics in various time scales. Generally, wave energy converter (WEC) control is applied in order to maximize power absorption, in the most common wave conditions, and subject to the devices’ physical constraints. Commonly,...
Wastewater epidemiology is an emerging discipline that requires collaborative research involving analytical chemists, drug epidemiologists, and wastewater engineers. Wastewater epidemiology involves the sampling and quantitative analysis of raw wastewaters from communities for illicit drugs and their metabolites. Mass loads (mass per day) and per capita (mg per day per person)...
We study joint nonlinear state estimation with multi-period measurement vectors that are potentially corrupted by sparse gross errors. The identifiability-aware approach is proposed to leverage common characteristics of fundamentally identifiable gross errors to enhance error correction performance. First, we derive a necessary rank condition that the sparsity pattern of any...
Symbioses between microbes and multicellular eukaryotes are found in all biomes, and encompass a spectrum of symbiotic lifestyles that includes parasitism and disease, commensalism, and mutually beneficial interdependent host-microbe relationships. Regardless of outcome, these symbiotic lifestyles are governed by a complex molecular "courtship" between microbe and potential host. This courtship...
A fully-saturated poroelastic medium is confined by the sides of a cylinder, and the regions below and above the medium are filled with fluid at respective constant pressures. The filtration flow of fluid through the poroelastic medium and the small deformations of the medium are described by a quasi-static Biot...
This paper addresses the high model complexity and overconfident frame labeling of state-of-the-art (SOTA) action segmenters. Their complexity is typically justified by the need to sequentially refine action segmentation through multiple stages of a deep architecture. However, this multistage refinement does not take into account uncertainty of frame labeling predicted...
This dissertation incorporates coalition formation and probabilistic planning towards a domain-independent automated planning solution scalable to multiple heterogeneous robots in complex domains. The first research direction investigates the effectiveness of Task Fusion and introduces heuristics that improve task allocation and result in better quality plans, while requiring lower computational cost...
This dissertation addresses the problem of semantic labeling of image pixels. In the course of our work, we considered different types of semantic labels, including object classes (e.g., car, person), 3D depth values (in the range 0 to 80 meters), and affordance classes (e.g., walkable, sittable). Semantic pixel labeling is...
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne’s disease, a chronic granulomatous enteritis that plagues domestic and wild ruminants globally. During the silent stages of Johne’s disease, infected animals intermittently shed bacteria for years prior to clinical diagnosis during advanced disease stages. This strategy allows MAP to...
There are nearly two million limb amputees living in the United States of America. Loss of limbs results in profound changes in one's life. However, the underlying neural circuitry and much of the ability to sense and control movements of their missing limb is retained even after limb loss. This...
Ocean wave energy converter technology continues to advance and new developers continue to emerge, leading to the need for a general design, modeling, and testing methodology. This work presents a development of the process of taking a wave energy converter from a concept to the prototype stage. A two body...
The patterns of cell proliferation in the choroid plexuses of
embryonic and post-natal hamsters were studied by means of auto-radiography
(H³-thymidine). In addition, the PAS technique was
used to determine the times of first appearance, relative amounts,
location, and times of disappearance of glycogen free the plexuses.
Many mitotic figures...
End-user programmers often struggle to create programs that run quickly and effectively, which can be a major deterrent in completing their tasks as desired. Current research has primarily focused on catching user mistakes, such as errors or misused formulas. However, end users deal with issues other than just correctness. In...
Methods for obtaining accurate, spatially explicit estimates of biomass density in tropical forests are required to reduce uncertainties in the global carbon cycle, and to support international climate agreements and emerging carbon markets. Three-dimensional (3-D) remote sensing techniques sensitive to the vertical structure of vegetation provide a unique opportunity for...
This thesis describes a project to produce controlled release ketoprofen beads for capsules, both at Oregon State University and in an industrial scale-up operation, that are bioequivalent to the commercial product Oruvail. A bead formulation was produced by layering drug and binders in water onto nonpareil sugar seeds in a...
This study attempted to analyze the educational problems of
Tamil women, one of the communal groups in Ceylon, to trace in
broad outline the development of their education from the earliest
times to the present day, and to ascertain particularly the quality
and importance of Home Economics Education in the...
In the wake of the ``third wave'' of democratization, scholars and practitioners were optimistic regarding the ease with which countries could adopt democratic norms and institutions. However, after four decades of democracy, many competitive regimes have not improved government probity or developed strong forms of accountability. Levels of economic and...
Multi-robot teams offer promising solutions for many long term deployments in remote and dangerous domains, such as extraterrestrial or underseas exploration. However, long term deployments present many problems preventing robot teams from operating effectively. Learning over long time scales is makes it difficult to assign credit to robots' actions, as...
This dissertation proposes the use of advanced time-varying approaches for modeling the dynamics of the multipath channel in wireless communication networks. These advanced time-varying approaches include linear Kalman innovation models in observable block companion form, and neural network-based models. The e˙ectiveness of these type of models is evaluated through three...
Mycobacterium vaccae JOB5 and Graphium sp. were studied to evaluate their ability to cometabolize methyl tert-butyl ether (MTBE) and its metabolites after growth on two different alkanes, propane and iso-pentane. Both cultures were capable of cometabolizing MTBE and the metabolites, tert-butyl formate (TBF) and tert-butyl alcohol (TBA). MTBE, TBF, and...
In weak supervision learning, label information can be provided at different levels of granularity. For example, in multi-instance multi-label learning, samples are organized into bags and labels for each class are provided at the bag level. For small datasets, this approach offers means of reducing the labeling efforts. However, in...
Deep learning is becoming the latest trend in sensitive applications, such as healthcare, criminal justice, and finance. As these new applications emerge, adversaries are circumventing them.
Further, there have been concerns about the possibility of bias and discrimination in predictive applications.
In order to address these issues, we propose an...
The objective of this dissertation is to enhance the monitoring of forest ecosystems through the utilization of remotely sensed data to address the exigencies posed by the Anthropocene. On a global scale, rising temperatures and fluctuating precipitation patterns have strained forests and produced shifts in natural disturbance regimes. Additionally, the...
The performance of deep learning frameworks could be significantly improved through considering the particular underlying structures for each dataset. In this thesis, I summarize our three work about boosting the performance of deep learning models through leveraging structures of the data. In the first work, we theoretically justify that, for...
Gall-associated phytopathogens have unique evolutionary histories that haveshaped both their modes of infection and genomic structures. Pathogenicity of the gall-associated plant pathogens of the Rhodococcus, Agrobacterium, and Rathayibactergenera is mediated by horizontally acquired virulence loci. The relative ease of gainand loss of the virulence loci has confounded accurate characterization of...
In the first set of studies, 2 experiments evaluated the influence of supplement composition on ruminal forage disappearance, performance, and physiological responses of Angus × Hereford cattle consuming a low-quality, cool-season forage (8.7 % CP and 57 % TDN). In Exp. 1, 6 rumen-fistulated steers housed in individual pens were...
In recent years, the methyl erythritol phosphate (MEP) pathway to isoprenoids has been the subject of intensive research. The interest is because isoprenoids have important roles in many cellular processes essential for the survival of several pathogenic organisms, making the inhibition of this pathway an attractive target for the drug...
Environmental toxicologists and public health officials are responsible for assisting in the identification, management, and mitigation of public health hazards. As a result, there is a continued need for robust analytical tools that can aid in the rapid quantification and characterization of chemical exposure. In the first research phase, we...
Enabled by a rich ecosystem of Machine Learning (ML) libraries, programming using learned models, i.e., Software-2.0, has gained substantial adoption. However, we do not know what challenges developers encounter when they use ML libraries. With this knowledge gap, researchers miss opportunities to contribute to new research directions, tool builders do...
Oomycetes are some of the most devastating pathogens, causing upwards of billions of dollars of damage each year to plants. They also diminish ecological diversity and health through the destruction of trees and shrubs. The genome sequence of Pseudoperonospora cubensis, an obligate plant pathogen and causative agent of downy mildew...
In networked control systems (NCS) information or packets usually flow from a
sensor or a set of sensors to a remotely located controller. Then the controller
processes the received information and sends a series of control commands to the
actuators through a communication network which could be either wireless or...
While digital inclusivity researchers and software practitioners have been trying to address exclusion biases in Windows, Icons, Menus, and Pointers (WIMP) user interfaces (UIs) for a long time, little has been done to investigate if and how inclusive software design and its methods that have been devised for WIMP UIs...
Floods are the most frequent and damaging of all types of natural disasters and annually affect the lives of millions all over the globe. However, researchers seem to have overlooked the fact that floods do not recognize national boundaries. Therefore, the phenomena of shared, or transboundary floods occurring in international...
Symbiosis is the close and protracted interaction between organisms. The molecular interactions that occur during symbiosis are complex with multiple barriers that must be overcome. Many Gram-negative, host-associated bacteria use a type III secretion system to mediate associations with their eukaryotic hosts. This secretion system is a specialized apparatus for...
Mutation analysis is the gold standard for evaluating test-suite adequacy. It involves exhaustive seeding of all small faults in a program and evaluating the effectiveness of test suites in detecting these faults. Mutation analysis subsumes numerous structural coverage criteria, approximates fault detection capability of test suites, and the faults produced...
In this work, we study network coding technique, its relation to random matrices, and their applications to communication systems. The dissertation consists of three main contributions. First, we propose efficient algorithms for data synchronization via a broadcast channel using random network coding. Second, we study the resiliency of network coding...
Magnetically Assisted Fluidized Bed (MAFB) is a novel technology where an external magnetic field with constant gradient interacts with magnetically susceptible particles. The linear magnetic field creates two type of forces: external and interparticle magnetic forces. A theoretical mathematical model based on the interaction of ideal dipoles is proposed to...
Microbial ecology has been transformed by metagenomics, the study of the genetic in-formation in entire communities of organisms. In the following we develop metagenomic tools arising from the classic Wasserstein metric as applied to questions regarding the diversity between microbial communities. We provide a novel proof of the characteriza-tion of...
Programming is integrated across the workflow of multiple domains where end-user programmers, those who need to program as a means to an end, regularly need to code. In the modern setting of collaborative development, end-user programmers have to interpret the intentions behind existing code to contribute and build solutions to...