The abilities of plant biologists to characterize the genetic basis of physiological traits are limited by their abilities to obtain quantitative data representing precise details of trait variation and mainly to collect this data on a high-throughput scale at low cost. Deep learning-based methods have demonstrated unprecedented potential to automate...
With growing interest in mass timber, especially mass timber panels (MTP), there has been a need to better understand their structural properties. One of the most versatile uses for MTP are as floor systems. Under new code provisions, these floors can be utilized in new and taller building types, but...
Gamma Ray Bursts (GRBs) are the most energetic explosions in the Universe, producing up to $\sim10^{53}$ ergs of energy in the first few seconds of their emission -- the so-called prompt phase that is dominated by high energy X-ray and $\gamma$-ray photons. The very large luminosities released in these events...
Grid-scale energy storage systems are urgently needed to increase the flexibility and rigidity of the grid for modern society and take full advantage of the renewable green energy resources such as solar energy and wind energy. Na-ion batteries (NIBs) and K-ion batteries (KIBs) have been emerged as one of the...
This dissertation addresses object recognition in challenging settings, where distinct object classes are visually very similar (e.g., species of birds and insects) and/or access to training examples of object classes is limited (e.g., due to the associated high costs of data annotation). In this dissertation, we present a variety of...
The shallow aquifer in Southern Willamette Valley (SWV) has high levels of nitrate, and we are exploring the time trends in nitrate, and the hydrologic and land management factors that contribute to this problem. Nitrogen (N) inputs to farmland from fertilizer is thought to be the primary source of nitrogen...
Electrochemical capacitors and batteries are two major electrochemical energy storage technologies, which have been investigated extensively to meet the rapidly-growing demand for higher energy, higher power, lower cost and enhanced safety in the past few decades. With the charge storage mechanism of electrostatic charge adsorption desorption via electrical double layers,...
This thesis focuses on the problem of object tracking. Given a video, the general objective of tracking is to track the location over time of one or more targets in the image sequence. This is a very challenging task as algorithms need to deal with problems such as appearance variations,...
We explore the application of deep learning to the disparate fields of natural language processing and computational biology. Both the sentences uttered by humans as well as the RNA and protein sequences found within the cells of their bodies can be considered formal languages in computer science, as sets of...
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...
Hindcast and 21st century winds, simulated by General Circulation Models (GCMs), were used to drive global- and regional-scale spectral wind-wave generation models in the Pacific Ocean Basin to assess future wave conditions along the margins of the North American west coast and Hawaiian Islands. Three-hourly winds simulated by four separate...
High data rate transmission has become an important challenge in today digital communication systems. One of the most difficult problems faced by engineers is to transmit data at sufficiently high rates through fading channels. This is the main motivation for the research presented herein. In this thesis, we investigate a...
Paper-based microfluidic assays, like the common pregnancy test, allow for rapid screening at the point- of-care at low cost and with no instrumentation. Fabric has many similar properties to paper, but is more flexible and durable, making it a promising option for use in a variety of diagnostic and screening...
Humanities have been craving more freedom and conveniences in whatever form. Carriages evolved to cars and ultimately to aircraft so that one can reach any place in the globe within a day. The mobile phone has enabled people to make a phone call without a need to find a phone...
Hop (Humulus lupulus L. var. lupulus) is a diploid, dioecious plant with an extensive history of cultivation and use in brewing, as a textile, and for its therapeutic properties. Hop is prized for its ability to produce a variety of aromatic and flavor compounds, as well as compounds with anti-microbial...
Cryopreservation of adherent cells may be advantageous for cell types that are difficult to
preserve in suspension or when it is necessary to preserve characteristics of the adherent cultured cells. Vitrification is a promising procedure for the preservation of adherent cells that prevents ice crystal formation and the resulting dissociation...
As the aging population continues to grow worldwide, age-related complications are becoming more apparent within the aging population. One of the first age-related complications to become apparent is age-associated memory impairment and it can make the elderly more dependent on caregivers early on. The N-methyl-D-aspartate (NMDA) receptor is important to...
Building Information Modeling (BIM) offers a variety of tools to help a wide range of stakeholders in the construction industry. There has been substantial research on the advantages and challenges of implementing BIM for large and medium-sized construction companies; however, there is a dearth of research on the benefits and...
The Plant Ontology (PO;http://www.plantontology.org/" is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and...
Ocean Wave Energy Converters (WECs) operating on the water surface are subject to storms and other extreme events. In particular, high and steep waves, especially breaking waves, are likely the most dangerous to WECs. A method for quantifying the breaking severity of waves is presented and applied to wave data...
The scarcity of wireless spectrum resources and the overwhelming demand for wireless broadband resources have prompted industry, government agencies and academia within the wireless communities to develop and come up with effective solutions that can make additional spectrum available for broadband data. As part of these ongoing efforts, cognitive radio...
Within the past several years the technology of high-throughput sequencing has transformed the study of biology by offering unprecedented access to life's fundamental building block, DNA. With this transformation's potential a host of brand-new challenges have emerged, many of which lend themselves to being solved through computational methods. From de...
This thesis studies the problem of structured prediction (SP), where the agent needs to predict a structured output for a given structured input (e.g., Part-of-Speech tagging sequence for an input sentence). Many important applications including machine translation in natural language processing (NLP) and image interpretation in computer vision can be...
Optimization programming techniques were applied to
develop the least cost formulations for Pacific whiting
surimi-based seafood (PWSBS). To develop the quality
constraint functions, texture and color of whiting surimi
gels were determined by torsion test and colorimeter,
respectively. Whiting surimi gels were produced by heating
at 90°C for 15 min....
Methods were developed for the co-encapsulation of slow release compounds (SRC) with viable microbial cells in alginate and gellan gum hydrogel beads, for the in-situ aerobic cometabolic treatment of groundwater contaminated with mixtures of 1,4-dioxane and chlorinated aliphatic hydrocarbons, which will be referred to as contaminants of concern (CoC). The...
Limnology is undergoing a transition to high-throughput -omic analysis of freshwater
bacterial communities. An important first step in making the transition is to
characterize several genomes that can be used as references to guide metagenome
assembly and analysis. Here I characterize four new freshwater cyanobacterial
genomes, a pair of lake...
The environmental health science community recognizes polycyclic aromatic hydrocarbons (PAHs) as a re-emerging class of environmental pollutants due to their persistence and prominence in mixtures of concern. Due to their widespread distribution in the environment, exposure to PAHs often occur as complex chemical mixtures. Exposures are linked to numerous adverse...
Water is an absolute necessity for life as we know it. It provides a useful medium in which chemical reactions take place that allowed for the development of single cellular organisms. When combined with the evolutionary accident that was pho- tosynthesis, water became not only a useful medium chemical reactions,...
We consider the problem of computing the cannonical polyadic decomposition (CPD) for large-scale dense tensors. This work is a combination of alternating least squares and fiber sampling. Data sparsity can be leveraged to handle large tensor CPD, but this route is not feasible for dense data. Inspired by stochastic optimization's...
Headwater streams are an integral part of the ecological health of the greater stream network as they provide valuable biological habitat, provide upwards to 95% of total in channel flow, while providing downstream reaches with important constituents such as sediment and woody debris. Small headwater streams are particularly susceptible to...
This dissertation addresses few-shot object segmentation in images. The goal of segmentation is to label every image pixel with a class of the object occupying that pixel, where the class may represent a semantic object category or instance. In few-shot segmentation, training and test datasets have different classes. Every new...
Oxidative stress is recognized as an important underlying factor in the
pathogenesis of many degenerative diseases as well as normal senescence. The
free radicals, reactive oxygen species (ROS) and electrophiles produced during
oxidative stress are capable of modifying nucleic acids, lipids and proteins. There
are a variety of oxidative modifications...
Cervical cancer is the fourth most common cancer in women worldwide with human papillomavirus (HPV) being the main cause of the disease. Currently available treatment methods are limited and emphasize the need for discovery of new therapies that improve patient outcome. Chromosomal amplifications have been identified as a source of...
Rhizopus microsporus is a globally ubiquitous opportunistic human and plant pathogen that is known to harbor endosymbiotic bacteria. Differences between populations of clinical and environmental R. microsporus isolates have yet to be assessed on a global scale. Whole-genome sequence data were used to explore fungal biology and to assess potential...
Most tasks in natural language processing (NLP) try to map structured input (e.g., sentence or word sequence) to some form of structured output (tag sequence, parse tree, semantic graph, translated/paraphrased/compressed sentence), a problem known as “structured prediction”. While various learning algorithms such as the perceptron, maximum entropy, and expectation-maximization have...
Short-range wireless communications continually attract interest from both industry and academia, and it is changing our life in every aspect in the last decade. The design of wireless transceivers is the bottleneck for variety applications, due to RF modeling inaccuracy, stringent FCC regulations over the transmitted power spectrum, interference, multi-path...
During catalysis the flavoprotein domain of neuronal nitric-oxide synthase (nNOS) shuttles NADPH-derived reducing equivalents from FAD to FMN and then to the P450-heme enabling heme-based oxygen activation and subsequent NO-synthesis. The binding of Ca²⁺-activated calmodulin (Ca²⁺-CaM) to nNOS alleviates inhibition of flavin mediated electron transfer within the diflavin domain, which...
The various solution-based processes, spin coating, inkjet printing, microreactor assisted nanoparticle deposition (MANDTM) and spin-successive ionic layer absorption and reaction (Spin-SILAR) were used to demonstrate thin film electronics and anti-reflective coatings. Several aspects of thin film transistors (TFTs) were tested including a range of temperatures, annealing atmosphere, and deposition methods....
This dissertation describes two different projects. The first is the development of an oral DNA vaccine delivery system for fish. A novel oral DNA vaccine delivery system was developed for Rainbow Trout by combining non-viral vectors (polycationic liposomes or polycationic polymer) to facilitate the DNA vaccine's uptake by cell membranes...
This thesis presents accurate and time-optimal smooth reference trajectory generation techniques for manufacturing equipment such as high-speed machine tools (MT) and industrial robots (IR). Typical machining tool-paths for MTs and IRs are defined as a series of discrete linear moves. Although Point-to-Point (P2P) feed motion can be generated by interpolating...
The concept of construction industrialization, first raised in the 1960s, refers to the transfer of on-site construction work to an off-site factory to improve quality and reduce cost, time, and safety issues. In some countries, industrialization of construction projects is highly recommended and promoted by governments and local construction institutions...
The demand from consumers for more sustainable products, and the need to comply with government regulations motivates manufacturers to evaluate their operations for opportunities to reduce environmental impact and improve economic competitiveness. Manufacturers have actively improved the sustainability performance of their products through the use of sustainability assessment methods and...
Over the last decades, CMOS-integrated sensors have made impressive progress in performance, form-factor, and energy-efficiency for various applications such as imaging, physical/chemical sensing, bio/health monitoring. In the era of the artificial intelligence (AI) and the internet-of-things (IoT), such CMOS-integrated sensors are essential for massive and comprehensive data acquisition, where sensing...
The objective of the present research was to determine, by use of the progesterone receptor antagonist RU-486, whether progesterone by autocrine/paracrine action suppresses phosphatidylinositol hydrolysis, and thus, the production of prostaglandin F2a during the midluteal phase of the estrous cycle in ewes. Two experiments were performed. Experiment 1 consisted of...
Two methanotrophs, M. trichosporium OB3b and M. buryatense 5GB1, were encapsulated using two methods to investigate the potential of methane conversion for biofuel production. Ca-alginate and low melt agarose were used to immobilize the methanotrophs for batch and continuous flow column testing. Varying protein concentrations, residence times, and immobilization methods...
A significantly untapped renewable energy source exists in the world's oceans. It is estimated that if 0.2% of the ocean's untapped energy could be harnessed, it could provide power sufficient for the entire world. Ocean energy extraction is an old concept, and it is currently seeing the benefit of advancing...
The focus of this study is to develop a general and low-cost solution-based
process to fabricate micro- and nano-structured semiconductors that are suitable
for electronics. This process uses simple metal halide precursors dissolved in a
solvent (organic or aqueous) and is capable of forming uniform and continuous
thin films via...
Harvesting energy from ambient sources can provide power autonomy to energy efficient electronics and sensors. The last decade has seen a multitude of ways to scavenge energy from various sources like solar, thermal, electromagnetic, electrostatic, piezo-electric and many more. Thermal energy from human body heat is ubiquitous and can be...