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Hittingtime And Pagerank, Shanthi Kannan

Master's Theses

In this thesis, we study convergence of finite state, discrete, and time homogeneous Markov chains to a stationary distribution. Expressing the probability of transitioning between states as a matrix allows us to look at the conditions that make the matrix primitive. Using the Perron-Frobenius theorem we find the stationary distribution of a Markov chain to be the left Perron vector of the probability transition matrix.

We study a special type of Markov chain &mdash random walks on connected graphs. Using the concept of fundamental matrix and the method of spectral decomposition, we derive a formula

that calculates expected hitting times …

The Excavation And Analysis Of Prehistoric Caribbean Remains: A Bioarchaeological Case Study Of A Prehistoric Female From Nevis, West Indies, Chris Keith

Master's Theses

ABSTRACT:

The Excavation and Analysis of Prehistoric Caribbean Remains: A Bioarchaeological Case Study of a Prehistoric Female from Nevis, West Indies

By Chris Keith

In the summer of 2011, the remains of a 1000 year old indigenous Caribbean woman were discovered buried on a beach near White Bay, Nevis, West Indies. The following summer, a team of excavators and osteologists, including the author, returned to Nevis to excavate and analyze the remains with the intention to learn as much as possible about the remains and, through proxy, the people to whom they belonged. We felt that through our investigations of …

Coast Redwood Community Structure And Composition Following Selective-Harvest: A Case Study Of Byrne-Milliron Forest, Amy K. Petersen

Master's Theses

The effects of selective-harvest on forest composition and structure in the southern range of the coast redwood (Sequoia sempervirens) forest have not been well documented. This case study was focused on the Byrne-Milliron Forest located in Santa Cruz County, where selective-harvest is currently the primary method of timber extraction. The purpose of this research was to determine how forest structure and composition changed in relation to time since the last harvest re-entry, the percentage cut per hectare and number of harvest re-entries. The study design consisted of 100 plots located within the Byrne-Milliron Forest, spanning over five harvest …

Using Vegetation To Reduce Nitrogen Runoff In California Caneberries, Rebecca Riesenfeld

Master's Theses

With a 700% rise in global fertilizer use in the last 50 years, agricultural lands are a significant source of nitrogen and phosphorus pollution in aquatic ecosystems worldwide. Record high levels of nitrate-contaminated runoff from agricultural sources in California's Central Coast are affecting drinking water supplies in the Pajaro Valley and increasingly threatening the ecological health of the Monterey Bay. Bands of vegetation strategically planted to control runoff and soil erosion, or vegetative filter strips (VFS), are used in urban landscapes and at some farm peripheries. On-farm vegetative diversity has been promoted for its contribution to biodiversity and pest control. …

A Promiscuous Wallflower: The Rare Zayante Sandhills Endemic Erysimum Teretifolium (Brassicaceae) Benefits From Outcrossing, Miranda Kathleen Melen

Master's Theses

The Zayante sandhills ecosystem of Santa Cruz County, California, contains a rich mosaic of plants and animals adapted to unusual soils and microclimates. In this environment, local adaptation of populations is expected to lead to greater endemism and outbreeding depression. Anthropogenic fragmentation has further isolated populations, however, which paradoxically could result in inbreeding depression. One of these plants, Erysimum teretifolium (Ben Lomond wallflower) is an endangered endemic herb in the Brassicaceae family. This study assessed genetic mixing across remnant patches of E. teretifolium in order to estimate the effects of fragmentation and the reliance on pollinators. A captive breeding colony …

Non-Additive Toxicity Of Bi-Metal Mixtures To Fathead Minnows, Natalie Rae Lynch

Master's Theses

Much research has been conducted to assess the toxicity of metals to aquatic organisms. Most of the research has focused on the toxicity of individual metals. Recently, attention has been paid to metal mixture toxicity because metals are usually present as mixtures in contaminated environments. The literature review indicates that metal mixtures may be additive, synergistic, or antagonistic to freshwater species. However, the data is not consistent and is dependent on the metal and organisms. The goal of this research is to use a systematic experimental design to characterize the toxicity of Cu, Zn, Cd and Ni mixtures to Pimephales …

The Effects Of "Stress Inoculation" On Anxiety-Related Behaviors In A Rodent Model, Rebecca Ruth Clouse

Master's Theses

Problem. Humans may face psychological stressors in their everyday life due to their ability to contemplate future events. While long-term stress exposure may be detrimental to health, this study examines the possibility that exposure to unpredictable/controllable, moderate stress may cause resilience against future stressors. This is referred to as the "stress inoculation hypothesis." The effects of unpredictable/controllable stress can be illustrated as a rightward shift in an inverted U-shaped curve, where optimal performance (the top of the curve) can be maintained at higher stress levels. -- Method. Thirty-three male Sprague-Dawley rats were tested on the elevated-plus maze (EPM) for trait …

Identification Of Clinical Markers That Predict The Outcomes Of Methicillin-Resistant Staphylococcus Aureus Infections And Identification Of Synergistic Antibiotic Combinations For The Treatment Of These Infections, Virginia Long

Master's Theses

Methicillin-resistant Staphylococcus aureus(MRSA) is a prominent nosocomial infection. Vancomycin is the mainstay of treatment, but it has a high rate of failure. Combination therapies can be used, but synergy is often not tested in clinical laboratories. Physicians are at a disadvantage because they cannot predict MRSA outcomes. The first aim of the study was to identify clinical and demographic markers that could predict infection recurrence or prolonged bacteremia. This was accomplished using retrospective chart review and statistical analysis. The second aim of the study was to identify which combinations, of those commonly used for MRSA treatment at Loyola, demonstrate the …

Functional Characterization Of A Novel Thioredoxin Domain-Containing Protein Of The Malaria Parasite Plasmodium, Rachel Kooistra

Master's Theses

A novel thioredoxin domain-containing protein of the malaria parasite Plasmodium was identified and found to be conserved among eukaryotes. This protein belongs to the phosducin-like family of proteins (PhLPs), and was therefore assigned the name PhLP1, since it is the first phosducin-like protein to be identified in Plasmodium. PhLPs have been found to have various roles in G-protein signaling, cell cycle progression, and protein folding. However, the biochemical mechanism by which PhLPs perform their function is unknown. Here is described the cloning and biochemical characterization of both PhLP1 and its human homolog TXNDC9. Both purified PhLP1 and TXNDC9 showed enzymatic …

Elucidating The Transcriptional Regulation Of Col2a1a In Zebrafish, Sonja Dabizljevic

Master's Theses

Cartilage is an important tissue in vertebrates beginning in the early embryo where it lays down the scaffolding for the skeleton, and continuing through adulthood where it makes up joints and intervertebral disks. The major component of cartilage is a filamentous protein known as Collagen type II, alpha 1 (Col2a1). Mutations in col2a1 in humans can lead to multiple congenital disorders and the early onset of joint and retinal deterioration. Our laboratory is interested in understanding the conserved transcriptional regulation of this critical structural gene utilizing the zebrafish, Danio rerio. Previously, we identified a 310 bp regulatory region (R2) 1.7 …

Environmental Drivers Of Leaf Breakdown Rate In An Urban Watershed, Ashley Rachelle Cook

Master's Theses

Leaf litter breakdown is a critical ecosystem process in urban streams, but environmental conditions in urban streams may generate confounding effects on breakdown rates. Reduced abundance of macroinvertebrate shredders may slow breakdown, but rates may increase if high nutrient concentrations stimulate microbial decomposers and if flooding enhances leaf fragmentation. We used the litter bag technique to measure the relative importance of multiple environmental drivers on breakdown of eastern cottonwood (Populus deltoides) leaves at 5 sites throughout the North Branch of the Chicago River watershed. Sites spanned a gradient of urbanization, but no specialized macroinvertebrate shredders were present at any sites. …

Role Of The Intestinal Microbiota In Gut Barrier Dysfunction Following Burn Injury, Zachary Earley

Master's Theses

Burn injury represents a major medical problem with half a million cases requiring medical attention and 4,000 deaths reported annually. Sepsis and multiple organ failure remain the leading causes of death following injury, and may be brought on by bacterial infections or toxins. The gastrointestinal tract contains approx. 100 trillion microbes; therefore, the indigenous commensal microbiota may play a role in leading to these complications or infections in burn patients. The overall objective of this project is to identify a potential mechanism whereby changes in gut bacteria may lead to intestinal inflammation or bacterial translocation--key factors which may lead to …

Life Histories, Diets, And Secondary Production Of Odonata Along A Temperature Gradient On The Copper River Delta, Alaska, Nicole Emilie Furlan

Master's Theses

Dragonflies (Odonata: Epiprocta) and damselflies (Odonata: Zygoptera) are a conspicuous aspect of the biota in ponds on southcentral Alaska's Copper River Delta (CRD). Odonate densities, secondary production, and diets were assessed in sixteen ponds classified by delta region (east vs. west) and landscape type (outwash plain (OP) vs uplifted marsh (UM)).

Enallagma boreale (Coenagrionidae) comprised 48.5% of collected odonates. Leucorrhinia hudsonica (Libellulidae) and Aeshna juncea (Aeshnidae) comprised 36.6% and 10.4% of collected odonates, respectively. L. hudsonica densities and secondary production were significantly higher (p<0.001) in west UM ponds than in other pond types. Ostracods (Ostracoda) and water boatmen (Corixidae) dominated west OP A. juncea diets. Midge larvae (Chironomidae) dominated A. juncea diets in remaining pond types, occurring in 68% of foreguts. 27% of A. juncea foreguts demonstrated intraguild predation, and 6% of foreguts demonstrated cannibalism. Foreguts containing threespine stickleback (Gasterosteus aculeatus) revealed A. juncea's apex predator role in CRD ponds.

Identifying Oncogenic Drivers In Nsclc Cells Harboring Egfr Kinase Domain Mutation With Resistance To Egfr Tki And Mesenchymal Phenotype, Yandi Gao

Master's Theses

EGFR kinase domain mutant NSCLC cells are exquisitely dependent on mutant EGFR for cell survival and proliferation. Patients with mutant EGFR respond well to the EGFR inhibitors. However, acquired drug resistance greatly limits the efficacy of the treatment. About 15% of the resistant tumors present an evidence of epithelial to mesenchymal transition (EMT). We hypothesize that the induction of mesenchymal promotes aberrant upregulation of other oncogenic drivers to replace the oncogenic mutant EGFR.

We observed overexpression of CXCR7 in NSCLC models of acquired resistance to EGFR TKI with mesenchymal phenotype. Additionally, our studies demonstrate that ectopically overexpressing CXCR7 in EGFR …

Reconsidering The Model Of Trim5Α Assembly: The Role Of The Linker2 (L2) Region In Trim5Α Assembly, Laura Johnsen

Master's Theses

The TRIM5α protein from rhesus macaques (TRIM5αrh) exhibits a remarkable ability to potently inhibit infection by Human Immunodeficiency Virus Type-1 (HIV-1). Extensive studies have shown that TRIM5α is capable of self-associating at many levels, eventually leading to the formation of a hexameric assembly that can superimpose on the hexameric lattice of the HIV-1 capsid. The mechanism underlying the self-association of TRIM5α and the molecular determinants of self-association remain to be completely understood. In this study, we show that the Linker 2 (L2) region of TRIM5rh is important for dimerization and higher order self-association, both of which are independent processes. Additionally, …

Characterizing The Mechanisms By Which Community Associated Methicillin-Resistant Staphylococcus Aureus Influences Keratinocyte Innate Immune Responses During Recurrent Infection, Ashley Lynn Larm

Master's Theses

Community associated–methicillin resistant Staphylococcus aureus (CA–MRSA) infection has become a major health concern. In human epidermal keratinocytes, S. aureus is mainly recognized through toll–like receptor 2 (TLR2) and its co–receptor, CD14. We hypothesize that CA–MRSA isolates cause recurrent infections by interrupting TLR2–mediated inflammation in keratinocytes. Recurrent CA–MRSA bacterial culture supernatant exposure to keratinocytes in vitro resulted in significant decreases in pro and anti–inflammatory cytokine and HMGB1 secretion from keratinocytes as assessed by ELISAs. Recurrent CA–MRSA live infection did not result in significant changes in cytokine or HMGB1 secretion, surface receptor expression, or NFκB activation post infection as assessed by ELISA …

History Of Freshwater Invasions In Illinois: Learning From The Past To Inform The Future, Abigail Jacobs

Master's Theses

Rates of introduction and spread of non-native species continue to increase worldwide, with freshwater ecosystems highly impacted. Many non-native species crossed between the Great Lakes and Mississippi watersheds by traveling through waterways in Illinois. I assembled a comprehensive database of occurrences of aquatic non-native species (n=99) in Illinois inland waters. The arrival of non-native species accelerated since 1873. The Great Lakes Basin was the main source of established species into Illinois. From 1990-2012 the dominant vector was unintentional release of established species non-native to North America. Sixty of the 99 introduced species established. Eighteen established species had high or very …

Denitrification In Urban Coastal Environments: A Functional Gene Study, Samantha Denise Lindemann

Master's Theses

Eutrophication is a major anthropogenic stressor on aquatic ecosystems worldwide. Jamaica Bay is located in the southeastern portion of New York City, NY (NYC). Like many other estuaries, Jamaica Bay is impacted by anthropogenic N inputs from various sources. Despite eutrophic conditions, improvements in water quality over the last few decades have prompted government agencies to promote oyster restoration to help reduce anthropogenic N in NYC waters. The effect of eastern oysters on sediment bacterial communities responsible for denitrification in Jamaica Bay was previously unknown. Those samples exposed to oysters were predicted to have high denitrification gene abundances, and thus …

Effects Of Instruction And Parent-Child Conversation On Children's Stem Learning And Transfer, Maria Marcus

Master's Theses

This study examined the effects of direct instruction and parent-child conversation on children's STEM learning, transfer abilities, and remembering. A total of forty mothers and their 5- to 6-year-old children (M = 5.87) participated in this study. Mother-child dyads were randomly assigned to one of two conditions that differed in the amount of engineering information they received prior to engaging in a building activity in a museum exhibit. The provision of engineering information fostered dyads building activities and their long-term recall of the museum visit. Implications for museum research and practice are discussed.

Characterization Of The Female Urinary Microbiota And Their Association With The Female Bladder Uroepithelium, Evann Elizabeth Hilt

Master's Theses

The current clinical dogma assumes that urine is sterile in the absence of clinically relevant infection. However, recent evidence has demonstrated the existence of a female urinary microbiota in women with and without lower urinary tract symptoms. With the knowledge that the lower urinary tract possesses its own unique microbiota, I hypothesize that certain bacterial species of the female microbiota may be the cause or play a role in lower urinary tract syndromes such as overactive bladder syndrome (OAB). About 40-50% of OAB patients do not respond to conventional anti-muscarinic and beta-3 adrenergic agonist drug treatment. One possible explanation for …

An Investigation Of The Role Of Vibrio Vulnificus Rbda And Vibrio Parahaemolyticus Sypa In Biofilm Formation, Cecilia Thompson

Master's Theses

Vibrio vulnificus and Vibrio parahaemolyticus are both bacteria that cause human infection. V. vulnificus has a polysaccharide locus, rbd, responsible for bacterial aggregation, a form of biofilm. This locus is conserved in V. parahaemolyticus and in the non-pathogen V. fischeri.

In V. fischeri, the polysaccharide locus, syp, has been extensively characterized and shown to be important for biofilm formation. In V. fischeri, the first gene, sypA, is critical for biofilm formation. V. fischeri biofilm-proficient strains form wrinkled colonies. In contrast, sypA mutants form smooth colonies, indicating a lack of biofilm formation.

To understand the function of RbdA and SypAVP, proteins …

Posttraumatic Stress, Family Functioning, And Adjustment In Urban African American Youth Exposed To Violence: A Moderated Mediation Model, Kyle Deane

Master's Theses

Exposure to community violence is a pressing public health issue that disproportionately impacts poor, urban, and ethnic minority youth. It has been associated with a multitude of negative externalizing and internalizing symptoms, most frequently with posttraumatic stress. This study investigates the role that posttraumatic stress has in mediating the relation between exposure to community violence and other adjustment difficulties. Moreover, because not all adolescents experience these difficulties in the face of significant violence exposure, the study examines the moderating role of family cohesion and support in buffering the effect of violence and posttraumatic stress on later adjustment. A sample of …

Sexual Behavior Problems In Child Welfare: Predictors Of Reliable Change, Anne Kathleen Fuller

Master's Theses

This study examined predictors of changes in children's sexual behaviors across two time points within a sample of youth in the child welfare system. Hypothesized predictors of increases or decreases in children's sexual behaviors included child attributes, positive parenting, exposure to sexuality and violence, maltreatment history and child welfare placement history, and treatment variables. Participants included 145 children with reported sexual behavior problems and their primary caregivers and mental healthcare providers. Children's sexual behaviors were classified as improved, worsened, or unchanged. Optimal Data Analysis (ODA) and multivariate classification tree analysis (CTA) via ODA were used to identify predictors of children's …

A Study Of Functional Recovery And Axonal Plasticity Following Tbi And Anti-Nogo-A Immunotherapy, Jennifer Crystal Biesiadecki

Master's Theses

Traumatic brain injury (TBI) is a leading cause of morbidity and mortality globally and often results in long term disability. Unfortunately, the success of rehabilitation techniques as therapy for TBI is limited, which may be due to the growth restrictive environment of the adult central nervous system (CNS). This environment is thought to result from glial scars, lack of neurotrophic factors, and the presence of an array of growth-inhibitory molecules. One such growth-inhibitory molecule is the protein Nogo-A. Our laboratory has shown that neutralization of Nogo-A with anti-Nogo-A immunotherapy after ischemic stroke results in improvement in functional recovery in the …

Learning To Tell Coherent Personal Narratives: Linkages To Mother-Child Reminiscing Over Time, Philip C. Hoffman

Master's Theses

Longitudinal and concurrent predictors of children's narrative coherence are identified and used to model pathways to coherence. Narrative coherence in children's independent narratives was measured at 72-months using a multidimensional (context, chronology, and theme) coding system. Fifty-three potential predictors of children's narrative coherence were considered, including children's vocabulary scores, metamemory knowledge, and measures derived from observations of mothers' and children's talk during reminiscing conversations recorded when the children were 54 and 72 months old. Optimal Data Analysis was used to generate three classification tree models to identify variables associated with whether children were low or high on three dimensions of …

Examining The Moderating Role Of Specific Coping Strategies On The Relationship Between Body Image And Eating Disorders In College-Age Women, Alexandra Calvert Kirsch

Master's Theses

A sample of college age women assessed at three time points (Time 1: Baseline, assessed before college, Time 2: End of first semester, Time 3: End of first year of college) completed measures of disordered eating, coping, and body image. Results indicated that neither adaptive (problem-focused coping or social support seeking) nor maladaptive coping styles (active emotional coping or avoidant coping) as measured at Time 1 or Time 2 moderated the significant predictive relationship between body dissatisfaction at Time 1 and disordered eating attitudes at Time 3, when adjusting for disordered eating attitudes and BMI at Time 1. However, significant …

Constructive Feedback In L2 Writing With Chinese High School Students In Taiwan, Chiawei Diane Yang

Master's Theses

The purpose of this study was to investigate the lack of motivation in L2 writing of Chinese high school students in Taiwan. The subject of this study was to examine how age, culture, and the education system in Taiwan influenced students’ motivation in learning English writing. It provided insight about how academic environments influence students’ motivation in learning English, how teachers’ feedback shapes students’ learning attitudes, and effective ways to increase students’ motivation and self-esteem. The study utilized Krashen’s (1981) affective filter hypothesis and Dornyei’s (1994) three levels of motivation theory. Ten Taiwanese students participated in this study. All of …

Teaching Reading As An Integrated Skill: An Evaluation Of Two Popular Esl Textbooks, Ingrid Mcvanner

Master's Theses

As the population of non-native English speakers rises in the United States, so too does the need for effective English language instruction, and with that, effective instructional materials. With a growing population of adult English language learners with below basic prose literacy, the need for effective adult English language literacy instruction is also evident. Because people do not use one skill at a time, this project evaluates the reading materials in two adult English language integrated skills textbooks from major publishers of ESL materials in order to provide insight into the preparation of effective integrated skills textbooks designed for adult …

Turn Of Events: How Environmental Temperatures And Artificial Nest Habitats Influence Incubation Behaviors Of Cassin's Auklets (Ptychoramphus Aleuticus), Emma Kelsey

Master's Theses

Nest attendance behaviors are critical to hatching success for most bird species. Yet, details of avian incubation behaviors are still not well understood, especially for species that nest in burrows and crevices. Cassin's auklet (Ptychoramphus aleuticus) is a burrow-nesting seabird found throughout the northeastern Pacific Ocean, including Southeast Farallon Island, California (SEFI). Artificial nest boxes have been used to monitor Cassin's auklets (hereafter auklet) breeding on SEFI. Temperatures in un-shaded nest boxes can increase significantly during extreme heat events. The effects of these elevated temperatures on auklet incubation behaviors and egg viability are not clear. In this study, egg data …

Perspiration And Motivation: An Examination Of Body Image And Exercise, Melissa Luu

Master's Theses

The purpose of this study was to examine the relationship between body image and exercise. The study examined reasons for exercise and level of exercise as potential moderators of the relationship between body appreciation and exercise. Three hypotheses were tested: there will be sex differences in level of body appreciation, there will be a positive relationship between body appreciation and level of exercise, and the relationship will be moderated by reason for exercise - either health or appearance reason and exercise level. Two-hundred-eighty-nine participants selected from an introductory psychology course pool responded to four questionnaires: the Body Appreciation Scale (BAS), …