RNA-Sequencing (RNA-Seq) has rapidly become the de facto technique in transcriptome studies. However, established statistical methods for analyzing experimental and observational microarray studies need to be revised or completely re-invented to accommodate RNA-Seq data's unique characteristics. In this dissertation, we focus on statistical analyses performed at two particular stages in...
RNA-Sequencing (RNA-Seq) has been widely adopted for quantifying gene expression changes in comparative transcriptome analysis. For detecting differentially expressed genes, a variety of statistical methods based on the negative binomial (NB) distribution have been proposed. These methods differ in the ways they handle the NB nuisance parameters (i.e., the dispersion...
An intersection, due to its vehicle and pedestrian conflict movements, experiences complex traffic situations that might contribute to crashes. In the city of Corvallis, OR, historically more than 80% of the total crashes have occurred within an intersection or have been designated as intersection-related. It is important to develop a...
The objective of this thesis is to design a high speed digital FIR filter. The inputs of the
system come from a Delta-Sigma modulator. This FIR filter takes 1024 inputs,
multiplies them with their coefficients and adds the results. The main design task is to
take the input data, which...
This dissertation describes the development of a mechanistic
overlay design procedure. The mechanistic analysis represents a new
trend in both new pavement and overlay design. The greatest advantage
of the mechanistic pavement analysis is that it considers the
fundamental characteristics of materials to be used, is capable of
considering changes...
Full integration of CMOS low noise amplifiers (LNA) presents a challenge for low
cost CMOS receiver systems. A critical problem faced in the design of an RF CMOS LNA
is the inaccurate high-frequency noise model of the MOSFET implemented in circuit
simulators such as SPICE. Silicon-based monolithic inductors are another...
On June 20, 2017, members of the environmental engineering and science (EES) community convened at the Association of Environmental Engineering and Science Professors (AEESP) Biennial Conference for a workshop on antimicrobial resistance. With over 80 registered participants, discussion groups focused on the following topics: risk assessment, monitoring, wastewater treatment, agricultural...
We investigated DNA methylomes of pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles. Epigenetic alteration of B-ALLs occurred in two tracks: de novo methylation of small functional compartments and demethylation of large intercompartmental backbones. The deviations were exaggerated in lamina-associated...
Drosophila suzukii (Spotted Wing Drosophila) has recently become a serious invasive pest of fruit crops in the USA, Canada, and Europe, leading to substantial economic losses. D. suzukii is a direct pest, ovipositing directly into ripe or ripening fruits; in contrast, other Drosophilids utilize decaying or blemished fruits and are...
Drosophila suzukii (Spotted Wing Drosophila) has recently become a serious invasive pest of fruit crops in the USA, Canada, and Europe, leading to substantial economic losses. D. suzukii is a direct pest, ovipositing directly into ripe or ripening fruits; in contrast, other Drosophilids utilize decaying or blemished fruits and are...
Importance
Randomized trials of anti-hypertensive treatment demonstrating reduced risk of cardiovascular events in older adults included participants with less comorbidity than clinical populations. Whether these results generalize to all older adults, most of whom have multiple chronic conditions, is uncertain.
Objective
To determine the association between anti-hypertensive medications and CV...
The study of natural products (NPs) and their application has shaped humanity. Starting with the idea of using plants as medicine, it has now grown into the science of purifying and identifying organic molecules from nature to study their inherent biological activities. Understanding the molecular structures of NPs is the...
Relieving phosphorus loading is a key management tool for controlling Lake Erie eutrophication. During the
1960s and 1970s, increased phosphorus inputs degraded water quality and reduced central basin hypolimnetic
oxygen levels which, in turn, eliminated thermal habitat vital to cold-water organisms and contributed to the
extirpation of important benthic macroinvertebrate...
Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins ( HST), which are recognized by their host in a genotype-specific...
The purpose of this review is to stimulate new ideas regarding low-dose environmental mixtures and carcinogens and their potential to promote invasion and metastasis. Whereas a number of chapters in this review are devoted to the role of lowdose environmental mixtures and carcinogens in the promotion of invasion and metastasis...
The emerging field of regenerative medicine is mainly approached by two different aspects. First is the use of stem cell based models to generate a suite of differentiated cells for therapeutic applications and the alternative approach is to utilize the non-mammalian models that have the inherent capacity to regenerate their...
Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that...
Vitamin E (VitE) is necessary for vertebrate embryonic development. VitE prevents lipid peroxidation (LPO), which requires detoxification by cellular antioxidant systems subsequently involving reducing power derived from energy metabolism. Thus, VitE protects metabolic networks in the developing embryo and the integrated gene expression networks compensating for and impaired by LPO-induced...
We present a measurement of the correlation between the spins of t and t quarks produced in proton–
antiproton collisions at the Tevatron Collider at a center-of-mass energy of 1.96 TeV. We apply a matrix
element technique to dilepton and single-lepton+jets final states in data accumulated with the D0 detector...
This study considers trade-offs between timber harvest and carbon
sequestration on National Forest and other public lands by contemporaneously linking
a model of public harvest and inventory to a carbon accounting system. The public
harvest model treats three harvest scenarios. The first minimizes the cost of meeting
harvest requests that...
Grassland recovery from degradation is increasingly occurring worldwide. Diverse managements have been considered as effective ways to restore degraded grassland, but it remains unclear how semi-arid grasslands respond to long-term grazing exclusion and fenced mowing. Here, a study was conducted under open grazing, grazing exclusion and fenced mowing in a...
In light of broadening racial/ethnic educational attainment gaps, growing diversity within young populations, and the increasingly critical relationship between higher education and outcomes in adulthood, understanding the factors that shape educational attainment is an especially important task for research. With this goal in mind, the current study examined how national...
Aqueous, two-phase systems (ATPSs) may form upon mixing two solutions of independently water-soluble compounds. Many separation, purification, and extraction processes rely on ATPSs. Predicting the miscibility of solutions can accelerate and reduce the cost of the discovery of new ATPSs for these applications. Whereas previous machine learning approaches to ATPS...
Long-term functional changes after whole-body vibration (WBV) training have been attributed to adaptations in the neuromuscular system. The present study examined the effect of four weeks of WBV training on muscle function outcome variables [rate of force development (RFD), electromechanical delay (EMD)], and spinal control mechanisms (pre-synaptic inhibition). Forty young...
We examined two case studies to demonstrate the advantages of sulfite chemistry for pretreating underutilized woody biomass to produce sugars through enzymatic saccharification. In the first case study, we evaluated knot rejects from a magnesium-based sulfite mill for direct enzymatic sugar production. We found that the sulfite mill rejects are...
Considering the deadly impacts of commercial motor vehicle (CMV) crashes on road safety, many previous studies have put in efforts to find the determinants of CMV crash injury severities. However, studies examining the impact of the different number of lanes on CMV crash
injury severities are lacking. Besides, the importance...
Air-cathode fabrication is currently a key factor that hinders the scaling up of microbial fuel cell (MFC) technology. A new type of cathode material that contains porous polyethylene (PE) sheet and a blended activated carbon (AC) and highly conductive carbon back (CB) layer was developed for the first time. The...
A novel design, material, and fabrication method are presented to fabricate a passive micro-ball valve. Microvalves are critical components in microflow control devices used to control the fluid flows in microchannels. These microflow control devices can be integrated with microsensors to form micro analysis systems. Glass/silicon-based fabrication is complicated and...
A higher level of efficiency in the production of doubled-haploids must be achieved if
this procedure is to be beneficial in plant improvement. Of equal importance is the
development of protocols, which are not genotypic specific and result in progeny that represent
a random sample of gametes from the parental...
Evacuation strategies have been established for most user groups in tsunami inundation zones; however, surprisingly little information is available for a growing visitor group - surfers. For near-shore tsunami events, Oregon surfers, who recreate in the nearshore region, must make life or death choices when deciding what to do in...
Here, liquid water path (LWP), cloud fraction, cloud top height, and cloud base height retrieved by a suite of A-train satellite instruments (the CPR aboard CloudSat, CALIOP aboard CALIPSO, and MODIS aboard Aqua) are compared to ship observations from research cruises made in 2001 and 2003–2007 into the stratus/stratocumulus deck...
Antagonistic effects of Epicoccum purpurascens,
Aureobasidium pullulans, Trichoderma spp., and Botrytis
cinerea on establishment of Monilinia fructicola infections
in cherry and peach blossoms were assessed in field and mist
chamber studies. Conidia of each fungus were applied to
blossoms that were subsequently inoculated with conidia of
M fructicola. Mist chamber...
In multi-instance multi-label (MIML) learning, datasets are given in the form of bags, each of which contains multiple instances and is associated with multiple labels. This paper considers a novel instance clustering problem in MIML learning, where the bag labels are used as background knowledge to help group instances into...
New graphite intercalation compounds (GICs) containing N,N-n-alkyl substituted pyrrolidinium cation intercalates (Py[subscript n.m], n, m = alkyl chain lengths) are obtained via cationic exchange from stage-1 donor-type GIC [Na(ethylenediamine)₁.₀]C₁₅. Powder X-ray diffraction and thermogravimetric analyses are used to determine the GIC structures and compositions. [Py₄.₈]C₄₇·0.71DMSO and [Py₈.₈]C₄₈ with intercalate monolayers...
The use of duplex stainless steels (DSS) in nuclear power generation systems is limited by thermal instability that leads to embrittlement in the temperature range of 204°C to 538°C. New lean-grade alloys, such as 2101, offer the potential to mitigate these effects. Thermal embrittlement was quantified through impact toughness and...
Vibrio cholerae is autochthonous to various aquatic niches and is the etiological agent of the life-threatening diarrheal disease
cholera. The persistence of V. cholerae in natural habitats is a crucial factor in the epidemiology of cholera. In contrast to the
well-studied V. cholerae-chitin connection, scarce information is available about the...
In multi-instance multi-label (MIML) instance annotation, the goal is to learn an instance classifier while training on a MIML dataset, which consists of bags of instances paired with label sets; instance labels are not provided in the training data. The MIML formulation can be applied in many domains. For example,...
We report malt quality QTLs relevant to breeding with greater precision than previous mapping studies. The distribution of favorable alleles suggests strategies for marker-assisted breeding and germplasm exchange.
This study leverages the breeding data of 1,862 barley breeding lines evaluated in 97 field trials for genome-wide association study of malting...
Chloroplast genomes of conifers are unusual in a
number of respects, including the possession of much
repetitive DNA. By studying the distribution and sequences
of dispersed repetitive DNA, I hoped to gain insight into
the mechanisms of chloroplast genome evolution.
I used restriction mapping and DNA sequencing to
characterize dispersed...
On November 6, 1988, two strong earthquakes (Mw: 7.0 and 6.8) separated
by about 13 minutes occurred in Yunnan Province, China. The aftershocks located
by Kunming Telemetered Seismic Network form a lineament approximately 120 km
long and 20 km wide with the long dimension oriented approximately N30°W. The
epicenter of...
Thiamin is an essential nutrient in the human diet. Severe thiamin deficiency leads to beriberi, a lethal disease which is common in developing countries. Thiamin biofortification of staple food crops is a possible strategy to alleviate thiamin deficiency-related diseases. In plants, thiamin plays a role in the response to abiotic...
There is little, if any, direct fossil evidence of the cardiovascular, respiratory, reproductive or digestive biology of dinosaurs. However, a variety of data can be used to draw reasonable inferences about the physiology of the carnivorous theropod dinosaurs (Archosauria: Theropoda). Extant archosaurs, birds and crocodilians, possess regionally differentiated, vascularized and...
In budding yeast, many of the genes that encode enzymes required for DNA precursor synthesis (MCB genes) are expressed under cell cycle control in late G1/S. The relationship between MCB gene expression, dNTP synthesis and DNA synthesis was investigated by using α factor-synchronized Saccharomyces cerevisiae. The levels of all four...
Genome defense likely evolved to curtail the spread of transposable elements and invading viruses. A combination of effective defense mechanisms has been shown to limit colonization of the Neurospora crassa genome by transposable elements. A novel DNA transposon named Sly1-1 was discovered in the genome of the most widely used...
Premise of research. A new, morphologically distinct, anatomically preserved conifer assignable to the basal Cupressaceae, which was subject to arthropod infestation during life, has been discovered within a marine carbonate concretion from the Coniacian (Late Cretaceous) Eden Main locality of Vancouver Island, British Columbia. Methods. Specimens were studied from anatomical...
Euphausiid krill play a critical role in coastal and oceanic food webs, linking primary producers to upper trophic levels. In addition, some species support commercial fisheries worldwide. Despite their ecological importance, the genetics of these important species remain poorly described. To improve our understanding of the genetics of these ecological...
Microbial electrochemical systems (MESs) have attracted much research attention in recent years due to their promising applications in renewable energy generation, bioremediation, and wastewater treatment. In a MES, microorganisms interact with electrodes via electrons, catalyzing oxidation and reduction reactions at the anode and the cathode.
The bacterial community of a...
In this report, we present climate projections for Union County that are relevant to specified natural hazards for the 2020s (2010–2039) and 2050s (2040–2069) relative to the 1971–2000 historical baseline. The projections are based on multiple global climate models for both a lower greenhouse gas emissions scenario (RCP 4.5) and...
In this report, we present climate projections for Morrow County that are relevant to specified natural hazards for the 2020s (2010–2039) and 2050s (2040–2069) relative to the 1971–2000 historical baseline. The projections are based on multiple global climate models for both a lower greenhouse gas emissions scenario (RCP 4.5) and...