For a certain class of Z²-actions, we provide a proof of a conjecture that the ratio of the Perron eigenvalues of the transfer matrices of the free boundary restrictions converge to the entropy of that action. Also, a novel method for computing the entropy of Z²-actions is conjectured.
The asymmetric nature of bit errors in several practical applications provides grounds for efficient error control techniques. The Z-channel model and special classes of codes like asymmetric error detection codes and t-asymmetric error correcting/d-asymmetric error detecting codes can be successfully used in ARQ protocols for feedback error control enhancement. This...
Metacarcinus magister, the Dungeness crab, is a commercially important species on the Pacific Northwest coast as the most profitable fishery in Oregon and an important ecological player as both predator and prey. Understanding the spatial distribution of Dungeness throughout different life history stages is beneficial both ecologically and economically. Zostera...
Successful cryopreservation of bone marrow in situ within vertebral bodies offers an opportunity for quick and convenient storage of a significant quantity of bone marrow stem cells, including hematopoietic- and mesenchymal-type stem cells. However, cryopreservation of more complex large tissues and organs, such as the vertebral body (VB), remains problematic....
Computational simulations of disks are becoming an important tool to predict the the evolution of protostars and disks to better understand the formation of planets. Past research has shown that the evolution of disks and their protostar can be altered through the interaction between gravity and hydrodynamic instabilities. We perform...
Bayesian Optimization (BO) methods are often used to optimize an unknown function f(•) that is costly to evaluate. They typically work in an iterative manner. In each iteration, given a set of observation points, BO algorithms select k ≥ 1 points to be evaluated. The results of those points are...
In bioacoustics, automatic animal voice detection and recognition from audio recordings is an emerging topic for animal preservation. Our research focuses on bird bioacoustics, where the goal is to segment bird syllables from the recording and predict the bird species for the syllables. Traditional methods for this task addresses the...
Information about named entities (real-world objects) is usually harvested from different sources and organized as a multiple relational directed graph in Knowledge Bases (KBs). KBs play essential roles in many NLP modules including question answering, fact-checking, search engines, etc. KBs are big but still incomplete: relational information among entities is...
Natural Language Comprehension is a challenging domain of Natural Language Processing. To improve a model’s language comprehension/understanding, one approach would be to enrich the structure of the model to enhance its capability in learning the latent rules of the language.
In this dissertation, we will first introduce several deep models...
Spray drying has been widely used in food science for long-term storage of products such as powdered milk, and it has recently been used for preservation of more temperature sensitive products such as human blood plasma and single-cell organisms. However, there are no previous reports of successful spray drying of...
Despite the many advances in biotechnology and biomedical engineering, the need for long term organ and tissue storage remains among the unsolved problems in the field. Researchers are investigating several possible solutions to the issue that aim to maintain the function and integrity of the biological tissues during storage and...
A comprehensive tribal-level classification for the world's subfamilies of Hesperiidae, the skipper butterflies, is proposed for the first time. Phylogenetic relationships between tribes and subfamilies are inferred using DNA sequence data from three gene regions: 943 bp of cytochrome oxidase subunit I (COI) (in the mitochondrial genome), 739 bp of...
Automatic event extraction from natural text is an important and challenging task for natural language understanding. Traditional event detection methods heavily rely on manually engineered rich features. Recent deep learning approaches alleviate this problem by automatic feature engineering. But such efforts, like tradition methods, have so far only focused on...
Bioacoustics analysis can be used to conduct environmental monitoring by detecting the presence of birds species. This analysis usually involves identifying the species from their calls. In most frameworks, bird song syllables are extracted from audio recordings and individual syllables are input to a classifier to identify the species. Extraction...
Recent work in machine learning concerns the detection and identification of bird species from audio recordings of their vocalizations. Such analysis can yield valuable ecological information concerning the activity and distribution of species in the wild. Current species-identification methods require individual syllables of bird audio as input, but field-collected audio...
Even with advanced medical technology, there is still an unmet need for organs to reduce the transplant waiting list and to advance organ-related research. Cryopreservation through vitrification is one possible solution to increase organ availability. A major challenge with cryopreservation of organs is the toxicity of the cryoprotectants (CPAs) that...
There is a significant need for technological advancement in blood processing. New technologies in rapid processing of frozen blood products could significantly improve management of the blood supply chain in the United States by enabling on-demand use of frozen blood products that can be stored for 10 years instead of...
Cryoprotectants (CPAs) such as glycerol and dimethyl sulfoxide (DMSO) are commonly used during cryopreservation of cell based therapeutics. Although these additives are beneficial during freezing, it is often desirable to remove them before infusion into a patient. Currently, the most common method for CPA removal is by centrifugation. This method...
Easy-first, a search-based structured prediction approach, has been applied to many NLP tasks including dependency parsing and coreference resolution. This approach employs a learned greedy policy (action scoring function) to make easy decisions first, which constrains the remaining decisions and makes them easier. This thesis studies the problem of learning...
Semi-supervised clustering aims to improve clustering performance by considering user supervision in the form of pairwise constraints. In this paper, we study the active learning problem of selecting pairwise must-link and cannot-link constraints for semisupervised clustering. We consider active learning in an iterative manner where in each iteration queries are...
The advent of deep learning models leads to a substantial improvement in a wide range of NLP tasks, achieving state-of-art performances without any hand-crafted features. However, training deep models requires a massive amount of labeled data. Labeling new data as a new task or domain emerges consumes time and efforts...
Freeze-drying, or lyophilization, has shown great promise in addressing many of the logistical challenges of storing and preserving red blood cells (RBCs). A crucial part of any future RBC lyophilization protocol is the primary drying temperature, which affects the sample drying rate and the dried cake’s ability to form a...
This study lays the groundwork on potential techniques that could be employed to improve the post-thaw wash processing of cryopreserved human red blood cells. Transfusion of red blood cells is one of the most commonly practiced procedures in clinical medicine. Millions of red blood cell units are transfused to patients...
Successful cryopreservation of all biological specimens would have an untold positive impact on medicine and scientific research. However, cryopreservation of the most complex biological specimens, such as tissues and organs, remains elusive. Vitrification, or ice-free cryopreservation, is promising for cryopreservation of complex specimens. The biggest challenge, though, is the toxicity...
Granulocytes are a class of white blood cells essential to immune function. Granulocyte transfusions hold promise to treat many conditions, but the short-shelf life of granulocytes makes transfusions infeasible without a cell preservation method. The purpose of this study was to investigate the potential for cryopreservation of granulocytes using 30%...
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...
In open set recognition, a classifier must label instances of known classes while detecting instances of unknown classes not encountered during training. To detect unknown classes while still generalizing to new instances of existing classes, this thesis introduces a dataset augmentation technique called counterfactual image generation. This approach, based on...
Freshwater systems cycle carbon along a spatial and temporal biogeochemical continuum, across which ecosystem processes contribute to transformations of organic matter (OM). Various ecological constraints impact rates OM transformation and production and consumption of the energetic end of respiration, methane. Microbiological processing and complete reduction of carbon substrates to methane...
The agricultural sector is one of the largest contributors to global climate change but is also one of the most vulnerable to its impacts. Farmers are at increasing risk of livelihood loss, which produces risks for their physical and emotional wellbeing on a global scale. Swift and effective adaptation is...
Hatcheries are used to produce salmon to augment the number of fish available for harvest, and to supplement wild populations that may be threatened with extinction. Although traditional hatchery rearing methods can produce many fish, they can pose risk to wild populations because they tend to produce salmon with lower...
At the intersection of basic science research and clinical relevance, cancer metastasis and cell invasion is a multifaceted problem that has been investigated for the past several decades. Importantly, cancer cell plasticity, the ability of a single cell to change its phenotype without genetic mutations in response to environmental cues,...
Bacterial canker, caused by Pseudomonas syringae pv. syringae is
recognized as one of the greatest limiting factors in cherry production
in Oregon. Disease incidence may be decreased when susceptible
cultivars are high-grafted onto tolerant/resistant rootstocks. This
research was begun to develop a rapid screening method which could be
used to...
Modern wind energy is the technology of choice with a short payback period for increasing renewable energy portfolios. Bonneville Power Administration (BPA), a United States power authority in the Pacific Northwest expects to increase their wind energy capacity from 2,000 megawatts to 6,000 megawatts within the next five years. Currently...
Cnidarians, such as corals and sea anemones serve as hosts to a variety of organisms including symbiotic dinoflagellates, bacteria, virus, and apicomplexans. As corals are vital to the health and productivity of the reef ecosystem it is important to understand how these organisms interact with each component of the holobiont....
Nitrogen (N) fertilizer application can promote nitrate leaching below the rooting zone and into groundwater drinking water sources in many agricultural settings. The proper management of N application can minimize non-point source nitrate pollution to groundwater. This study examines the potential for enhanced efficiency fertilizers, specifically urea treated with a...
On a global scale, illicit economies have dramatic impacts on the physical environment. Cocaine trafficking has been recognized as a major driver of deforestation inside Central American protected areas. A key problem in studying and managing the environmental impacts of illicit economic activity is the difficulty in obtaining reliable data....
Back end of line (BEOL) metal-insulator-metal capacitors (MIMCAPs) have become a core passive component in modern integrated circuits. International Technology Roadmap for Semiconductors (ITRS) projections for scaling of analog/mixed-signal MIMCAP applications require simultaneously increasing capacitance density while maintaining low leakage current density and low voltage nonlinearity (characterized by the quadratic...
The purpose of this research was to examine the
effects of fishing on life history parameters of the spiny
lobster, Panulirus homarus. The study areas selected had
different levels of fishing pressure but relatively similar
habitats. The lowest fishing effort was found in Hadbin
while the highest fishing effort was...
This study examined two neighborhoods in San Francisco with similar earthquake-induced ground failure history -- the Marina District and the South of Market Area (SoMa) -- in the aftermath of the 1989 Loma Prieta earthquake. The earthquake struck shortly after 5 pm on October 17th, 1989 and registered 6.9 in...
The ongoing climate change has impacted the lives and livelihoods of people. A climate-related disaster acts as an exogenous shock to the economy that can have lingering effects over a larger region even if all the locations are not directly affected. Climate-related disasters do not follow the administrative boundaries. So,...
While the contemporary movement against sexual and domestic violence has roots in radical, feminist theory and anti-state, community-based modes of resistance, over the past several decades, advocates and activists have increasingly turned to corporations and the state for support through the non-profit, prison, and medical industrial complexes. This acceptance of...
Hatcheries are used to produce salmon to augment the number of fish available for harvest, and to supplement wild populations that may be threatened with extinction. Although traditional hatchery rearing methods can produce many fish, they can pose risk to wild populations because they tend to produce salmon with lower...
The Grimms’ Brothers left their mark on history when they published their first edition of the Kinder- und Hausmärchen gesammelt durch die Brüder Grimm (Nursery and Household tales Collected by the Brothers Grimm) in 1812. Among these newly published tales was that of Snow White. Within the paradigm of the...
The purpose of this study is aimed at developing a simple bioeconomic model of the Namibian rock lobster fishery, with the main objective being to incorporate economics into fisheries management in order to estimate the potential economic benefits that could accrue to the fishery given efficient management. The complex nature...
Many Hymenoptera, with their painful stings and noxious chemical defenses, exhibit bright aposematic warning color patterns and are the most frequently mimicked group of organisms. Such aposematic color patterns are found in parasitic wasps of the Neotropical Compsobracon group (Braconidae). Many members of this group exhibit color patterns similar to...