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Description
Cellular and molecular biologists often perform cellular assays to obtain a better understanding of how cells work. However, in order to obtain a measurable response by the end of an experiment, the cells must reach an ideal cell confluency. Prior to conducting the cellular assays, range-finding experiments need to be

Cellular and molecular biologists often perform cellular assays to obtain a better understanding of how cells work. However, in order to obtain a measurable response by the end of an experiment, the cells must reach an ideal cell confluency. Prior to conducting the cellular assays, range-finding experiments need to be conducted to determine an initial plating density that will result in this ideal confluency, which can be costly. To help alleviate this common issue, a mathematical model was developed that describes the dynamics of the cell population used in these experiments. To develop the model, images of cells from different three-day experiments were analyzed in Photoshop®, giving a measure of cell count and confluency (the percentage of surface area covered by cells). The cell count data were then fitted into an exponential growth model and were correlated to the cell confluency to obtain a relationship between the two. The resulting mathematical model was then evaluated with data from an independent experiment. Overall, the exponential growth model provided a reasonable and robust prediction of the cell confluency, though improvements to the model can be made with a larger dataset. The approach used to develop this model can be adapted to generate similar models of different cell-lines, which will reduce the number of preliminary range-finding experiments. Reducing the number of these preliminary experiments can save valuable time and experimental resources needed to conduct studies using cellular assays.
ContributorsGuerrero, Victor Dominick (Co-author) / Guerrero, Victor (Co-author) / Watanabe, Karen (Thesis director) / Jurutka, Peter (Committee member) / School of Mathematical and Natural Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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Description
Pharmacokinetics describes the movement and processing of a drug in a body, while Pharmacodynamics describes the drug's effect on a given subject. Pharmacokinetic/Pharmacodynamic(Pk/Pd) models have become a fundamental tool when predicting bacterial behavior and drug development. In November of 2009, Katsube et al. published their paper detailing their Pk/Pd model

Pharmacokinetics describes the movement and processing of a drug in a body, while Pharmacodynamics describes the drug's effect on a given subject. Pharmacokinetic/Pharmacodynamic(Pk/Pd) models have become a fundamental tool when predicting bacterial behavior and drug development. In November of 2009, Katsube et al. published their paper detailing their Pk/Pd model for the drug Doripenem and the bacteria P. aeruginosa. In their paper, they determined that there is a dependent relationship between the drug's effectiveness and the dosing strategy of the drug. Therefore, this thesis has applied optimal control in order to optimize the drug's effectiveness, while not burdening the subject with the side effects of the drug. Optimal Control is a mathematical tool used to balance two competing factors. As a result, it has become a useful tool used to make decisions involving complex behavior. By using Optimal Control, the model will maximize the drug's effect on the bacterial population of P. aeruginosa, while minimizing the drug concentration of Doripenem. In doing so, our research will enable doctors and clinicians to maximize a drug's effectiveness on the body, while minimizing side effects.
ContributorsSawkins, Bryan Thomas (Author) / Camacho, Erika (Thesis director) / Wirkus, Stephen (Committee member) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
Glioblastoma (GBM) is the most common malignant primary brain tumor in adults and is linked to poor survival in affected patients due to its invasive and aggressive nature. The potential role of sexual dimorphism in GBM outcomes has long been overlooked. Notably, males and females differ in tumor behavior across

Glioblastoma (GBM) is the most common malignant primary brain tumor in adults and is linked to poor survival in affected patients due to its invasive and aggressive nature. The potential role of sexual dimorphism in GBM outcomes has long been overlooked. Notably, males and females differ in tumor behavior across many cancers1, which may be attributable to differences in genetic makeup and physiology, and in GBM there is a difference in incidence rate between males and females. The aim of the study was to investigate sex differences in GBM patients and compare median survival outcomes (OS) and progression-free survival outcomes (PFS) between sexes based on tumor location, laterality, age, tumor volume, and extent of resection. Patients who received standard-of-care (Stupp protocol) consisting of surgical intervention, concomitant chemoradiation, and 6 cycles of adjuvant temozolomide (TMZ) were included in this study to investigate sex differences in tumor characteristics (n = 216; males: n = 129, females: n = 87). Pre-surgical MRIs, specifically T1Gd sequences, were analyzed to determine tumor laterality and location. The patient cohort was divided into two groups indicating the extent of resection (EOR) they received: Gross Total Resection (GTR) and Subtotal Resection (STR). Additionally, the patient cohort was split into three age groups (Group I: 18-29, Group II: 30-49, and Group III: >50). Analyses were done using independent t-test and Cox proportional hazard modeling to determine which variables affect patient survival. The log-rank test was utilized to compare differences in survival rate in Kaplan-Meier analysis.
Overall, our results suggest that female patients receiving standard-of-care may have a better prognosis than male patients. There was a significant difference in OS and PFS in females showing an increase in survival. Additionally, survival was significantly different between sexes following resection, with female patients receiving STR or GTR having longer OS and PFS than males. The difference in median OS between sexes is more pronounced among younger patients. Among five different brain locations, female patients who possess a frontal lobe tumor may live longer than male patients. The apparent difference in OS for patients living >1000 days in the Kaplan-Meier plot warrants further investigation in a larger cohort. Following tumor resection, female patients with a frontal lobe tumor may survive longer in comparison to male patients. Comparing brain hemispheres, patients who possessed a tumor on the left may survive longer. Investigating tumor location and tumor laterality, our results suggests that female patients with a left frontal lobe tumor show a significant survival advantage in comparison to females who possess a right frontal lobe tumor.
ContributorsLorence, Julia (Author) / Swanson, Kristin (Thesis director) / Massey, Susan Christine (Committee member) / Rubin, Joshua (Committee member) / Arizona State University. College of Nursing & Healthcare Innovation (Contributor) / School of Life Sciences (Contributor) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description

Medicolegal forensic entomology is the study of insects to aid with legal investigations (Gemmellaro, 2017). Insect evidence can be used to provide information such as the post-mortem interval (PMI). Blow flies are especially useful as these insects are primary colonizers, quickly arriving at a corpse (Malainey & Anderson, 2020). The

Medicolegal forensic entomology is the study of insects to aid with legal investigations (Gemmellaro, 2017). Insect evidence can be used to provide information such as the post-mortem interval (PMI). Blow flies are especially useful as these insects are primary colonizers, quickly arriving at a corpse (Malainey & Anderson, 2020). The age of blow flies found at a scene is used to calculate the PMI. Blow fly age can be estimated using weather data as these insects are poikilothermic (Okpara, 2018). Morphological analysis also can be used to estimate age; however, it is more difficult with pupal samples as the pupae exterior does not change significantly as development progresses (Bala & Sharma, 2016). Gene regulation analysis can estimate the age of samples. MicroRNAs are short noncoding RNA that regulate gene expression (Cannell et al., 2008). Here, we aim to catalog miRNAs expressed during the development of three forensically relevant blow fly species preserved in several storage conditions. Results demonstrated that various miRNA sequences were differentially expressed across pupation. Expression of miR92b increased during mid pupation, aga-miR-92b expression increased during early pupation, and bantam, miR957, and dana-bantam-RA expression increased during late pupation. These results suggest that microRNA can be used to estimate the age of pupal samples as miRNA expression changes throughout pupation. Future work could develop a statistical model to accurately determine age using miRNA expression patterns.

ContributorsHerrera-Quiroz, Demian David (Author) / Parrott, Jonathan (Thesis director) / Weidner, Lauren (Committee member) / School of Mathematical and Natural Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

Forensic entomology is an important field of forensic science that utilizes insect evidence in criminal investigations. Blow flies (Diptera: Calliphoridae) are among the first colonizers of remains and are therefore frequently used in determining the minimum postmortem interval (mPMI). Blow fly development, however, is influenced by a variety of factors

Forensic entomology is an important field of forensic science that utilizes insect evidence in criminal investigations. Blow flies (Diptera: Calliphoridae) are among the first colonizers of remains and are therefore frequently used in determining the minimum postmortem interval (mPMI). Blow fly development, however, is influenced by a variety of factors including temperature and feeding substrate type. Unfortunately, dietary fat content remains an understudied factor on the development process, which is problematic given the relatively high rates of obesity in the United States. To study the effects of fat content on blow fly development we investigated the survivorship, adult weight and development of Lucilia sericata (Meigen; Diptera: Calliphoridae) and Phormia regina (Meigen; Diptera: Calliphoridae) on ground beef with a 10%, 20%, or 27% fat content. As fat content increased, survivorship decreased across both species with P. regina being significantly impacted. While P. regina adults were generally larger than L. sericata across all fat levels, only L. sericata demonstrated a significant (P < 0.05) difference in weight by sex. Average total development times for P. regina are comparable to averages published in other literature. Average total development times for L. sericata, however, were nearly 50 hours higher. These findings provide insight on the effect of fat content on blow fly development, a factor that should be considered when estimating a mPMI. By understanding how fat levels affect the survivorship and development of the species studied here, we can begin improving the practice of insect evidence analysis in casework.

ContributorsNoblesse, Andrew (Author) / Weidner, Lauren (Thesis director) / Parrott, Jonathan (Committee member) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Studying the effects of viruses and toxins on honey bees is important in order to understand the danger these important pollinators are exposed to. Hives exist in various environments, and different colonies are exposed to varying environmental conditions and dangers. To properly study the changes and effects of seasonality and

Studying the effects of viruses and toxins on honey bees is important in order to understand the danger these important pollinators are exposed to. Hives exist in various environments, and different colonies are exposed to varying environmental conditions and dangers. To properly study the changes and effects of seasonality and pesticides on the population dynamics of honey bees, the presence of each of these threats must be considered. This study aims to analyze how infected colonies grapple more deeply with changing, seasonal environments, and how toxins in pesticides affect population dynamics. Thus, it addresses the following questions: How do viruses within a colony affect honey bee population dynamics when the environment is seasonal? How can the effects of pesticides be modeled to better understand the spread of toxins? This project is a continuation of my own undergraduate work in a previous class, MAT 350: Techniques and Applications of Applied Mathematics, with Dr. Yun Kang, and also utilizes previous research conducted by graduate students. Original research focused on the population dynamics of honey bee disease interactions (without considering seasonality), and a mathematical modeling approach to analyze the effects of pesticides on honey bees. In order to pursue answers to the main research questions, the model for honey bee virus interaction was adapted to account for seasonality. The adaptation of this model allowed the new model to account for the effects of seasonality on infected colony population dynamics. After adapting the model, simulations with arbitrary data were run using RStudio in order to gain insight into the specific ways in which seasonality affected the interaction between a honey bee colony and viruses. The second portion of this project examines a system of ordinary differential equations that represent the effect of pesticides on honey bee population dynamics, and explores the process of this model’s formulation. Both systems of equations used as the basis for each model’s research question are from previous research reports. This project aims to further that research, and explore the applications of applied mathematics to biological issues.

ContributorsReveles, Anika (Author) / Kang, Yun (Thesis director) / Nishimura, Joel (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Natural Sciences (Contributor) / School of Earth and Space Exploration (Contributor)
Created2023-05
Description

This outlines a mathematical model created in MATLAB for the purposes of predicting nitrous oxide emissions from wastewater treatment plants with updated an updated understanding of AOB metabolic pathway.

ContributorsOverbey, Jorja (Author) / Hart, Steven (Thesis director) / Young, Michelle (Committee member) / Wirkus, Stephen (Committee member) / Barrett, The Honors College (Contributor) / School of Music, Dance and Theatre (Contributor) / School of Mathematical and Natural Sciences (Contributor)
Created2023-05
Description

The field of forensic science has been growing and changing with improvements in DNA analysis. One field affected is forensic entomology, which is exploring many ways in which DNA can increase the application of insects in forensic science. One application being explored is the use of insects as a source

The field of forensic science has been growing and changing with improvements in DNA analysis. One field affected is forensic entomology, which is exploring many ways in which DNA can increase the application of insects in forensic science. One application being explored is the use of insects as a source of human DNA in a criminal investigation. Using flies as a source of foreign DNA can also be utilized in ecological research to conduct surveys on the various species present in different environments. This experiment intends to determine if flies can act as a viable source of alternate DNA. This will be accomplished by an ecological survey of DNA extracted from flies. DNA extractions were performed on flies gathered from parts of the greater Phoenix area. The DNA was then amplified with primers targeting different animal species and examined to observe what animals the flies had come in contact with. Several samples had contamination due to human error and were not able to be evaluated. One DNA extraction out of fifteen yielded pig DNA, indicating flies can be used as a source of DNA. Future experiments should use different animal primers and amplify sections of DNA that can determine the different species consumed by flies. Further research into flies as a DNA source can increase the amount of information available to forensic scientists as well as improve ecologist’s observation of an environment’s biodiversity.

ContributorsRiccomini, Brianna (Author) / Parrott, Jonathan (Thesis director) / Marshall, Pamela (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Natural Sciences (Contributor)
Created2023-05
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Description
Since its isolation from a rhesus monkey in the Zika forest of Uganda in 1947, Zika virus (ZIKV) has spread into many parts of the world, causing major epidemics, notably in the Americas and some parts of Europe and Asia. The flavivirus ZIKV is primarily transmitted to humans via the

Since its isolation from a rhesus monkey in the Zika forest of Uganda in 1947, Zika virus (ZIKV) has spread into many parts of the world, causing major epidemics, notably in the Americas and some parts of Europe and Asia. The flavivirus ZIKV is primarily transmitted to humans via the bite of infectious adult female Aedes mosquitoes. In the absence of effective treatment or a safe and effective vaccine against the disease, control efforts are focused on effective vector management to reduce the mosquito population and limit human exposure to mosquito bites. The work in this thesis is based on the use of a mathematical model for gaining insight into the transmission dynamics of ZIKV in a population. The model, which takes the form of a deterministic system of nonlinear differential equations, is rigorously analyzed to gain insight into its basic qualitative features. In particular, it is shown that the disease-free equilibrium of the model is locally-asymptotically stable whenever a certain epidemiological quantity (known as the reproduction number, denoted by R0) is less than unity. The epidemiological implication of this result is that a small influx of ZIKV-infected individuals or vectors into the community will not generate a large outbreak if the anti-ZIKV control strategy (or strategies) adopted by the community can reduce and maintain R0 to a value less than unity. Numerical simulations of the model, using data relevant to ZIKV transmission dynamics in Puerto Rico, shows that a control strategy that solely focuses on killing immature mosquitoes (using highly efficacious larvicides) can lead to the elimination of ZIKV if the larvicide coverage (i.e., proportion of breeding sites treated with larvicides) is high enough (over 90%). Such elimination is also feasible using a control strategy that solely focuses on the use of insect repellents (as a means of personal protection against mosquito bites) if the coverage level of the insect repellent usage in the community is high enough (at least 70%). However, it is also shown that although the use of adulticides (i.e., using insecticides to kill adult mosquitoes) can reduce the reproduction number (hence, disease burden), it fails to reduce it to a value less than unity, regardless of coverage level. Thus, unlike with the use of larvicide-only or repellent-only strategies, the population-wide implementation of an adulticide-only strategy is unable to lead to ZIKV elimination. Finally, it is shown that the combined (integrated pest management) strategy, based on using all three aforementioned strategies, is the most effective approach for combatting ZIKV in the population. In particular, it is shown that even a moderately-effective level of this strategy, which entails using only 50% coverage of both larvicides and adulticides, together with about 45% coverage for a repellent strategy, will lead to ZIKV elimination. This moderately-effective combined strategy seems attainable in Puerto Rico.
ContributorsUrcuyo, Javier (Author) / Gumel, Abba (Thesis director) / Hackney Price, Jennifer (Committee member) / School of Mathematical and Natural Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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Description
Consequences of drug abuse and addiction affect both men and women, but women tend to rapidly progress through drug addiction phases, have higher drug dependency, and have higher relapse rates. Ovarian hormones fluctuate with female reproductive cycles and are thought to cause increased sensitivity to psychostimulants. Additionally, intermittent social defeat

Consequences of drug abuse and addiction affect both men and women, but women tend to rapidly progress through drug addiction phases, have higher drug dependency, and have higher relapse rates. Ovarian hormones fluctuate with female reproductive cycles and are thought to cause increased sensitivity to psychostimulants. Additionally, intermittent social defeat stress induces social avoidance, weight loss, and long-lasting cross-sensitization to psychostimulants, which is associated with increased FosB/ΔFosB expression in the nucleus accumbens (NAc) shell. In this study, we examined the estrous cycle in female rats on social defeat stress-induced amphetamine cross-sensitization through FosB/ΔFosB expression in the NAc shell. Every third day for ten days, we induced social defeat stress in rats through short confrontations with a lactating female resident rat and her pups. In parallel, a group of rats were handled for control. Vaginal swabs were taken daily to assess estrous stage. Ten days after the last stress exposure, rats were administered a low dose of amphetamine (0.5 mg/kg, i.p.), which induced cross-sensitization in stressed rats, evidenced by enhanced locomotor activity. Approximately 3-10 days after amphetamine challenge, brain tissue was collected for immunohistochemistry analyses. Stressed female rats had lower body weight gain, higher social avoidance, and increased FosB/ΔFosB expression in the NAc shell. Differences in FosB/ΔFosB expression in the NAc shell was also observed in handled animals in different estrous stages. Furthermore, rats in proestrous/estrous stages displayed enhanced social defeat stress-induced amphetamine cross-sensitization in comparison to rats in metestrous/diestrous stages. Elucidating the effects of the female reproductive cycle on drug use may provide a novel approach to treatments or therapies in preventing women’s stress-induced vulnerability to substance abuse.
ContributorsAzuma, Alyssa (Author) / Neisewander, Janet (Thesis director) / Nikulina, Ella (Thesis director) / Hammer, Ronald (Committee member) / School of Mathematical and Natural Sciences (Contributor) / Watts College of Public Service & Community Solut (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05