Markov chains have long been used to sample from probability distributions and simulate dynamical systems. In both cases we would like to know how long it takes for the chain's distribution to converge to within varepsilon of the stationary distribution in total variation distance; the answer to this is, called...
The method of gas-phase electron diffraction is a very useful tool for determining
the geometry of a molecule in the gas-phase to a high degree of accuracy. In this thesis,
the structures of tropone and tropolone, which are similar molecules that are both based
on a 7-carbon ring, were investigated...
Blue-striped Brodiaea or Leach's Brodiaea (Triteleia hendersonii Greene var. leachiae [Peck] Hoover, or Brodiaea hendersonii Wats. var. leachiae ) Lily Family (Liliaceae) is found in the foothills of the Siskiyou Mountains of Curry, Coos and Josephine Counties of southwestern Oregon. It is occurs in a variety of habitats including meadow...
The data is a JSON format file containing the position, velocity, and fish identifier data for 300 golden shiners in a shallow (depth of 4.5 to 5 cm) rectangular water tank (2.1 by 1.2 meters). There are 5000 individual frames (samples of position and velocity) corresponding to video taken at...
In Islam, paying and receiving interest is prohibited based on the belief that money should not be a commodity that is “rented” out; instead, Islamic lending structures arrange loans on an equity basis. This work examines the historical origins of interest prohibition and explains how different Islamic financial products provide...
One of the distinctive features of mitochondria is that they have their own DNA. When compared to nuclear DNA, it is known that mitochondrial DNA (mtDNA) not only has a much higher rate of spontaneous mutation, but also arises from metabolically distinct precursor pools. Others from our laboratory have demonstrated...
Shallow landslides are destructive natural hazards that result in widespread losses, both of infrastructure and lives, throughout the world. To help mitigate the impact of landslide hazards, they are commonly characterized across a regional scale by (1) their location and likelihood using susceptibility maps, (2) their magnitude and frequency using...
For more than 35 years we have known that the accuracy of DNA replication is controlled in
large part by the relative concentrations of the four canonical deoxyribonucleoside 5'-triphosphates (dNTPs) at the replisome. Since this field was last reviewed, about eight years ago,
there has been increased understanding of the...
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...
We investigate several aspects of the numerical solution of the radiative transfer
equation in the context of coal combustion: the parallel efficiency of two commonly used
opacity models, the sensitivity of turbulent radiation interaction (TRI) effects
to the presence of coal particulate, and an improvement of the order of temporal...
Cancer was recognized as a genetic disease at least four decades ago, with the realization that the spontaneous mutation rate must increase early in tumorigenesis, to account for the many mutations in tumor cells as compared with their progenitor normal cells. The genetic basis for cancer was established also from...
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(2001).
21. Fairman, J. W., et al. Structural basis for allosteric regulation of human
Vineyards in Oregon’s Willamette Valley are predominately planted to perennial grass cover in the alleyways of vineyards. This grass cover is grown to increase worker and equipment traction, as well as reduce erosion and manage vine vegetative vigor. However, with increasing frequencies of drought and warming temperatures, the use of...
The electrical conductivity of the pyromagmas from the Northeast
Crater of Mount Etna, Sicily was measured over the temperature
range 1032°C to 1071°C and over the frequency range 1 kHz to
400 kHz. Measurements were made using a four-terminal Wenner
array in conjunction with a Wavetek Model 110B portable signal...
This study was an ethnographic case study of a
Vietnamese unaccompanied minor in a post secondary setting.
There were two guiding questions for the study: (1) How
does the subject perceive language as it relates to
educational experience? (2) What kinds of observable
personality, cognitive, or affective factors have
contributed...
Ornithology is an exciting field with novel research emerging everyday. Researchers in bioacoustics often spend hours within the wilderness recording bird calls to analyze later in their lab. The burden of sifting through hours of audio recordings from the field continues to remain a time-consuming and manual task, despite the...
Background: The use of high-Z nanoparticles as radiation dose enhancers has been researched thoroughly over the past decade. High-Z nanoparticles introduced to a medium increase the probability of photoelectric absorption. This leads to an increase in the production of short range characteristic and Auger electrons and, thus, local radiation dose....
The intent of this work is to extend Implicit Monte Carlo Diffusion (IMD)[Gen.
2001] to account for frequency dependence and to incorporate the difference formulation[Szo. 2005] as a source manipulation variance reduction technique. This
work shows the derivation of the probabilities and the associated proofs which
govern the frequency dependent...
Nearest-neighbor resampling is a common procedure used by cartographers to
reproject raster data sets. This type of resampling is useful because it retains the data
from the original raster data set. However, during nearest-neighbor resampling some of
the original data will be lost as it is reprojected, while other data...
The purpose of this study was to determine the attitudes of
three Oregon State Penitentiary minority inmate groups -
Blacks, Hispanics, and Native Americans - towards the Activities
Programs as a rehabilitative tool. Two other purposes
were to (1) determine significant differences among group
attitudes, and (2) determine the degree...
Approximately one quarter of America's students
leave school prior to graduation. Teaching practices
need to be examined if schools are to effectively deal
with the student population. at highest risk of dropping
out. The purpose of this study was to investigate the
attending behaviors high school teachers directed to
students...
Baculoviruses comprise a diverse group of pathogens
infectious for members of the insect orders Lepidoptera, Hymenoptera
and Diptera. Of the three subgroups, two (subgroup A, nuclear
polyhedrosis virus (NPV) and subgroup B, granulosis virus (GV) are
occluded in a crystalline protein structure while the remaining
subgroup (subgroup C, non-occluded virus)...
This study examines the effects of corporate social responsibility (CSR) on merger and
acquisitions (M&A). Using data from Kinder, Lyndeberg, and Domini (KLD) Research
Analytics and Thomson’s Securities Data Corporation’s (SDC) Platinum Database, we
empirically test if CSR scores effect a firm’s propensity to pursue M&A activity.
Specifically, I examine...
Motivation: Many robots such as legged robots and prosthetic hands/arms are designed to interact with uncertain and time-varying environments to accomplish their tasks.
Observations on humans and animals during their daily tasks suggest that they adapt their leg compliance while traversing with different velocities on different grounds and adjust their...
The enzymes of dNTP synthesis in T4 infection associate to form a multienzyme complex, the T4 dNTP synthetase complex, facilitating the flow of metabolites en route to dNTPs, and their subsequent flow into DNA. Study of protein-protein interactions helps one to understand how the enzymes in the complex are organized...
Deoxyribonucleoside triphosphate (dNTP) concentrations measured in cells are not symmetric. dGTP almost always represents only 5-10% of the total dNTP pools in cells. In an in vitro replication system involving semiconservative replication from an SV 40 origin, the mutation frequency of an M13 phagemid replicated by human cell extracts in...
It is well known that the mitochondrial genome has a much higher spontaneous mutation rate than the nuclear genome. mtDNA mutations have been identified in association with many diseases and aging. mtDNA replication continues throughout the cell cycle, even in post-mitotic cells. Therefore, a constant supply of nucleotides is required...
With respect to a multienzyme complex of deoxyribonucleoside triphosphate (dNTP) synthesis somehow juxtaposed with DNA replication sites, our laboratory has demonstrated the existence of a multienzyme complex in T4-infected E. coli, named the T4 dNTP synthetase complex, but the idea of direct linkage of dNTP synthesis to DNA replication and...
Ribonucleotide reductase is a remarkable enzyme that catalyzes the rate-limiting
step in the synthesis of the 2'-deoxynucleoside triphosphates. The intent of this project
was to characterize the ribonucleotide reductase encoded by the orthopoxvirus,
vaccinia. The first objective was to study the structural and functional features of the
viral small subunit...
Structural health monitoring (SHM) systems perform automated non-destructive damage detection and characterization for a variety of large structures including civil structures such as bridges and aerospace structures such as aircrafts and space vehicles. The goals of SHM include preventing catastrophic structural failures, increasing reliability, reducing maintenance costs, and increasing the...
This dissertation describes an investigation of DNA precursor supply for mitochondrial and nuclear DNA synthesis in HeLa cells and Mouse L-cells. HeLa cells were used for the quantitation of cellular and mitochondrial deoxyribonucleoside triphosphate (dNTP) and ribonucleoside triphosphate (rNTP) pools and of changes in pools in response to treatment with...
Ribonucleoside diphosphate reductase (RR) from vaccinia virus was recently cloned and overexpressed rn Escherichia coli. The amino acid sequence identities of the small and large subunits between the mouse and the vaccinia virus reductase are approximately 80 and 72 percent, respectively. In addition, vaccinia virus RR displays similar complex allosteric...
Vaccinia virus-infected animal cells have been used to
study the interactions between the replication of
deoxyribonucleic acid (DNA) and the biosynthesis of its
nucleotide precursors. Some antimetabolites that inhibit
DNA replication have as their targets enzymes of nucleotide
biosynthesis. Furthermore, the disruption of nucleotide
metabolism can alter the fidelity of...
Ribonucleotide reductase is an important enzyme in the control of
DNA replication within the cell. Ribonucleotide reductase exerts its
control through enzymatic reduction of nucleoside diphosphates. The
bacteriophage T4 enzyme is an example of the class of iron-requiring
reductases which also includes E. coli and mammalian ribonucleotide
reductases. The two...
Electroencephalogram (EEG) signals have recently gained attention to classify associated hand movement. This is particularly useful for amputees with prostatic hands or people who are unable to move their hands voluntarily. Among the decoding algorithms used to classify hand movements are support vector machines and multilayer perceptron networks. In this...
The dihydrofolate reductase gene of bacteriophate T4
has been investigated at the structural level to elucide the
unusual regulation of expression of this gene and possible
evolutionary relationships between the ohage and drug resistance
factors-encoded dihydrofolate reductases (DHFR).
A 1.1-kilobase-pair restriction fragment of the T4
multiple mutant dec8 containing frd,...
Bacteriophage T4 gene 42 encodes dCMP hydroxymethylase, an
enzyme unique to the deoxyribonucleotide metabolism of T-even
bacteriophages. To study biochemical and biophysical properties of
the enzyme, as well as the interaction of dCMP hydroxymethylase with
other DNA precursor biosynthetic enzymes in vitro, availability of large
amounts of the enzyme is...
Vaccinia virus infected monkey kidney cells had been previously shown
to have an increased ribonucleoside diphosphate reductase (RR) activity. DNA
from mutant virus resistant to hydroxyurea were digested with restriction
endonucleases and were shown to have substoichiometric amounts of the Hind
III F fragment. Additional information from Southern blotting experiments...
The effects of oligoribonucleotides of identical or similar sequences to a
ribosomal protein binding site, specifically S8, on prokaryotic 30S ribosomal assembly
were investigated in Escherichia coli. The oligoribonucleotides were expected to bind to
the target protein S8 and block its incorporation into the 30S subunit, resulting in a nonfunctional...
The first committed step in DNA biosynthesis occurs by direct reduction of
ribonucleotides. This reduction is catalyzed by ribonucleotide reductase (RNR), an
enzyme which uses a unique radical mechanism to facilitate the transformation. All four
DNA precursors are synthesized by a single enzyme. Therefore, an intricate pattern of
regulation has...
Significance: Movement intent decoding algorithms can interpret human bioelectrical signals to control prosthetic limbs with many degrees of freedom (DOFs). This work involves decoding volitional movement intent from surface electromyogram (sEMG) signals to control prosthetic arms. To train these algorithms, patients flex their muscles to “follow” a movement prompt, and...
Movement intent decoders, which interpret volitional movement intent from human bioelectric signals, can be incorporated into modern neuroprostheses to offer people living with limb loss or paralysis the potential to regain their lost motor control. Machine learning methods have become the research standard for continuous decoders with high degrees of...
Investigators have been studying an aggregate
containing enzymes of deoxyribonucleoside triphosphate
biosynthesis in T4-phage infected bacteria. They suggest
that it behaves as an organized complex, efficiently
channeling DNA precursors to the replication apparatus.
Previous work has suggested that about 10 enzyme
activities remain associated through several fractionation
steps. This multi-enzyme...
In order to maintain genetic stability in eukaryotes, tight regulation of the relative sizes of deoxyribonucleoside triphosphate (dNTP) levels inside the cell is essential for optimal fidelity of DNA replication. Ribonucleotide reductase (RNR) is the enzyme responsible for proportional production of DNA precursors. Studies on regulation of this enzyme, the...
Loss of a limb can severely impact everyday way of life. Prosthetics provide a way to return functionality to the user and improve quality of life. However, most prosthetic systems currently available in the market lack sensory feedback making them comparatively more difficult to use resulting in prosthetic abandonment. Therefore,...