Matching Items (57)
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The representation of a patient’s characteristics as the parameters of a model is a key component in many studies of personalized medicine, where the underlying mathematical models are used to describe, explain, and forecast the course of treatment. In this context, clinical observations form the bridge between the mathematical frameworks

The representation of a patient’s characteristics as the parameters of a model is a key component in many studies of personalized medicine, where the underlying mathematical models are used to describe, explain, and forecast the course of treatment. In this context, clinical observations form the bridge between the mathematical frameworks and applications. However, the formulation and theoretical studies of the models and the clinical studies are often not completely compatible, which is one of the main obstacles in the application of mathematical models in practice. The goal of my study is to extend a mathematical framework to model prostate cancer based mainly on the concept of cell-quota within an evolutionary framework and to study the relevant aspects for the model to gain useful insights in practice. Specifically, the first aim is to construct a mathematical model that can explain and predict the observed clinical data under various treatment combinations. The second aim is to find a fundamental model structure that can capture the dynamics of cancer progression within a realistic set of data. Finally, relevant clinical aspects such as how the patient's parameters change over the course of treatment and how to incorporate treatment optimization within a framework of uncertainty quantification, will be examined to construct a useful framework in practice.
ContributorsPhan, Tin (Author) / Kuang, Yang (Thesis advisor) / Kostelich, Eric J (Committee member) / Crook, Sharon (Committee member) / Maley, Carlo (Committee member) / Bryce, Alan (Committee member) / Arizona State University (Publisher)
Created2021
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Public education and involvement with evolutionary theory has long been limited by both the complexity of the subject and societal pushback. Furthermore, effective and engaging evolution education has become an elusive feat that often fails to reflect the types of questions that evolution research attempts to address. Here, we explore

Public education and involvement with evolutionary theory has long been limited by both the complexity of the subject and societal pushback. Furthermore, effective and engaging evolution education has become an elusive feat that often fails to reflect the types of questions that evolution research attempts to address. Here, we explore the best methods to present scientific research using interactive educational models to facilitate the learning experience of the audience most effectively. By creating artistic and game-play oriented models, it becomes possible to simplify the multifaceted aspects of evolution research such that it enables a larger, more inclusive, audience to better comprehend these complexities. In allowing the public to engage with highly interactive education materials, the full spectrum of the scientific process, from hypothesis construction to experimental testing, can be experienced and understood. Providing information about current cancer evolution research in a way that is easy to access and understand and accompanying it with an interactive model that reflects this information and reinforces learning shows that research platforms can be translated into interactive teaching tools that make understanding evolutionary theory more accessible.

ContributorsSilva, Yasmin (Author) / Maley, Carlo (Thesis director) / Compton, Zachary (Committee member) / Baciu, Cristina (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / School of Life Sciences (Contributor)
Created2022-05
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This paper will serve as a review of relevant scleractinian coral biology and genetics, discuss the ecological and biological impacts of growth anomalies in scleractinians, discuss the importance of studying this phenomena in terms of conservation, outline and discuss the processes undertaken to elucidate possible genetic markers of the growth

This paper will serve as a review of relevant scleractinian coral biology and genetics, discuss the ecological and biological impacts of growth anomalies in scleractinians, discuss the importance of studying this phenomena in terms of conservation, outline and discuss the processes undertaken to elucidate possible genetic markers of the growth anomalies, as well as discuss growth anomalies within the context of other coral disease and the anthropocene to add clarity no the subject to the oncological discussion taking place around such anomalies.

ContributorsLittle, Patrick (Author) / Maley, Carlo (Thesis director) / Metzger, Michael (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2022-05
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This dissertation describes a series of four studies on cognitive aging, working memory, and cognitive flexibility in dogs (Canis lupus familiaris) and their wild relatives. In Chapters 2 and 3, I designed assessments for age-related cognitive deficits in pet dogs which can be deployed rapidly using inexpensive and accessible materials.

This dissertation describes a series of four studies on cognitive aging, working memory, and cognitive flexibility in dogs (Canis lupus familiaris) and their wild relatives. In Chapters 2 and 3, I designed assessments for age-related cognitive deficits in pet dogs which can be deployed rapidly using inexpensive and accessible materials. These novel tests can be easily implemented by owners, veterinarians, and clinicians and therefore, may improve care for elderly dogs by aiding in the diagnosis of dementia. In addition, these widely deployable tests may facilitate the use of dementia in pet dogs as a naturally occurring model of Alzheimer’s Disease in humans.In Chapters 4 and 5, I modified one of these tests to demonstrate for the first time that coyotes (Canis latrans) and wolves (Canis lupus lupus) develop age-related deficits in cognitive flexibility. This was an important first step towards differentiating between the genetic and environmental components of dementia in dogs and in turn, humans. Unexpectedly, I also detected cognitive deficits in young, adult dogs and wolves but not coyotes. These finding add to a recent shift in understanding cognitive development in dogs which may improve cognitive aging tests as well as training, care, and use of working and pet dogs. These findings also suggest that the ecology of coyotes may select for flexibility earlier in development. In Chapter 5, I piloted the use of the same cognitive flexibility test for red and gray foxes so that future studies may test for lifespan changes in the cognition of small-bodied captive canids. More broadly, this paradigm may accommodate physical and behavioral differences between diverse pet and captive animals. In Chapters 4 and 5, I examined which ecological traits drive the evolution of behavioral flexibility and in turn, species resilience. I found that wolves displayed less flexibility than dogs and coyotes suggesting that species which do not rely heavily on unstable resources may be ill-equipped to cope with human habitat modification. Ultimately, this comparative work may help conservation practitioners to identify and protect species that cannot cope with rapid and unnatural environmental change.
ContributorsVan Bourg, Joshua (Author) / Wynne, Clive D (Thesis advisor) / Aktipis, C. Athena (Committee member) / Gilby, Ian C (Committee member) / Young, Julie K (Committee member) / Arizona State University (Publisher)
Created2022
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Cancers of the reproductive tissues make up a significant portion of the cancer burden and mortality experienced by humans. Humans experience several proximal causative carcinogens that explain a portion of cancer risk, but an evolutionary viewpoint can provide a unique lens into the ultimate causes of reproductive cancer vulnerabilities. A

Cancers of the reproductive tissues make up a significant portion of the cancer burden and mortality experienced by humans. Humans experience several proximal causative carcinogens that explain a portion of cancer risk, but an evolutionary viewpoint can provide a unique lens into the ultimate causes of reproductive cancer vulnerabilities. A life history framework allows us to make predictions on cancer prevalence based on a species’ tempo of reproduction. Moreover, certain variations in the susceptibility and prevalence of cancer may emerge due to evolutionary trade-offs between reproduction and somatic maintenance. For example, such trade-offs could involve the demand for rapid proliferation of cells in reproductive tissues that arises with reproductive events. In this study, I compiled reproductive cancer prevalence for 158 mammalian species and modeled the predictive power of 13 life history traits on the patterns of cancer prevalence we observed, such as Peto’s Paradox or slow-fast life history strategies. We predicted that fast-life history strategists will exhibit higher neoplasia prevalence risk due to reproductive trade-offs. Furthering this analytical framework can aid in predicting cancer rates and stratifying cancer risk across the tree of life.

ContributorsDarapu, Harshini (Author) / Maley, Carlo (Thesis director) / Boddy, Amy (Committee member) / Compton, Zachary (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2022-05
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Age is the most significant risk factor for cancer development in humans. The somatic mutation theory postulates that the accumulation of genomic mutations over time results in cellular function degradation which plays an important role in understanding aging and cancer development. Specifically, degradation of the mechanisms that underlie somatic maintenance

Age is the most significant risk factor for cancer development in humans. The somatic mutation theory postulates that the accumulation of genomic mutations over time results in cellular function degradation which plays an important role in understanding aging and cancer development. Specifically, degradation of the mechanisms that underlie somatic maintenance can occur due to decreased immune cell function and genomic responses to DNA damage. Research has shown that this degradation can lead to the accumulation of mutations that can cause cancer in humans. Despite recent advances in our understanding of cancer in non-human species, how this risk factor translates across species is poorly characterized. Here, we analyze a veterinarian cancer dataset of 4,178 animals to investigate if age related cancer prevalence is similar in non-human animals. We intend for this work to be used as a primary step towards understanding the potential overlap and/or uniqueness between human and non-human cancer risk factors. This study can be used to better understand cancer development and how evolutionary processes have shaped somatic maintenance across species.

ContributorsAksoy, Selin (Author) / Maley, Carlo (Thesis director) / Boddy, Amy (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of Psychology (Contributor)
Created2022-05
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Cancer is a disease that takes the lives of almost 10 million people every year, and due to humans’ nature as multicellular organisms, it is both inevitable and incurable. Therefore, management of the disease is of utmost importance. Due to the complexity of cancer and its development, numerous computational models

Cancer is a disease that takes the lives of almost 10 million people every year, and due to humans’ nature as multicellular organisms, it is both inevitable and incurable. Therefore, management of the disease is of utmost importance. Due to the complexity of cancer and its development, numerous computational models have been developed that allow for precise diagnostic and management input. This experiment uses one of these said models, CancerSim, to evaluate the effect of proliferation rates on the order in which the hallmarks of cancer evolve in the simulations. To do this, the simulation is run with initial telomere length increased to simulate the effects of more living cells proliferating at every time step. The results of this experiment show no significant effect of initial telomere length on the order that hallmarks evolved, but all simulations ended with cancers that were dominant with cells that contained limitless replication and evade apoptosis hallmarks. These results may have been affected by limitations in the CancerSim model such as the inability to model metastasis and the lack of a robust angiogenesis solution. This study reveals how individual cell characteristics may not have a large effect on cancer evolution, but rather individual hallmarks can affect evolution significantly. Further studies with a revised version of CancerSim or another model could confirm the behavior demonstrated in this experiment
ContributorsLankalapalli, Aditya (Author) / Maley, Carlo (Thesis director) / Daymude, Joshua (Committee member) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (Contributor)
Created2022-05
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Evolution has driven organisms to develop a wide range of biological mechanisms to protect against cancer. Some organisms, including the sponge Tethya wilhelma and the Placozoa Trichoplax adhaerens have developed particularly effective mechanisms to suppress cancer and repair DNA damage. While these mechanisms are rooted in DNA damage repair and

Evolution has driven organisms to develop a wide range of biological mechanisms to protect against cancer. Some organisms, including the sponge Tethya wilhelma and the Placozoa Trichoplax adhaerens have developed particularly effective mechanisms to suppress cancer and repair DNA damage. While these mechanisms are rooted in DNA damage repair and prevention, evidence of bacteria may suggest that endosymbionts living within the organisms may plays a role as well. Likewise, other organisms, such as the flatworm Macrostomum lignano, are proven model organisms whose extensive documentation enables more in-depth analysis of biological mechanisms associated with cancer. Sponges, flatworms, and Placozoa were exposed to X-ray radiation totaling 600 Gy, 25 Gy, and up to 240 Gy, respectively. RNA sequencing and bioinformatics analyses were undergone to determine the differential gene expression of the animals at different time points. No common response to the X-ray radiation was discovered amongst all organisms. Instead, sponges showed evidence of tumor suppression and DNA repair gene upregulation including CUBN, bacterial endosymbionts showed evidence of lateral gene transfer and different DNA repair genes including FH, and flatworms showed evidence of allelic and mutational shifts in which tumorous populations became more reliant on alternate alleles and a single variant signature. This study highlights the varying mechanisms that have evolved in different organisms and the importance of studying these novel model organisms further.

ContributorsScirone, Jonathan (Author) / Fortunato, Angelo (Thesis director) / Maley, Carlo (Committee member) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (Contributor)
Created2022-05
Description
Adaptive therapy is a novel up-and-coming cancer treatment strategy to minimize chemoresistance in cells to improve patient prognosis. The standard of care cancer treatment has a fixed linear approach known as Maximum Tolerated Dose (MTD) which promotes an exponential growth of resistant cancer cell populations in the tumor. Through this

Adaptive therapy is a novel up-and-coming cancer treatment strategy to minimize chemoresistance in cells to improve patient prognosis. The standard of care cancer treatment has a fixed linear approach known as Maximum Tolerated Dose (MTD) which promotes an exponential growth of resistant cancer cell populations in the tumor. Through this treatment procedure, a population of chemoresistant cells resurges, decreasing the survival in patients, and narrowing potential treatment options (Gatenby). An assortment of chemotherapeutic drugs and dosing schedules were tested on ER+ endocrine-resistant MCF7 breast cancer cells in an immunodeficient mouse model. After the cessation of treatment, some mouse models’ tumors remained stable or began to shrink. Several immunodeficient mouse models have indicated unexpectedly high levels of neutrophils stemming from an unknown origin. We aim to understand if neutrophils' innate immunity may affect tumor size post-chemotherapy treatment and if it has therapeutic implications along with adaptive therapy. MCF7 breast cancer tumors were extracted from the mice, embedded in wax, and sliced, and immunofluorescence was performed to detect neutrophils and nuclear components. Currently, the protocol is in its third round of optimization.
ContributorsMestas, Lauren (Author) / Maley, Carlo (Thesis director) / Richker, Harley (Committee member) / Marquez Alcaraz, Gissel (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2024-05
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Life history theory offers a powerful framework to understand evolutionary selection pressures and explain how adaptive strategies use the life history trade-off and differences in cancer defenses across the tree of life. There is often some cost to the phenotype of therapeutic resistance and so sensitive cells can usually outcompete

Life history theory offers a powerful framework to understand evolutionary selection pressures and explain how adaptive strategies use the life history trade-off and differences in cancer defenses across the tree of life. There is often some cost to the phenotype of therapeutic resistance and so sensitive cells can usually outcompete resistant cells in the absence of therapy. Adaptive therapy, as an evolutionary and ecologically inspired paradigm in cancer treatment, uses the competitive interactions between drug-sensitive, and drug-resistant subclones to help suppress the drug-resistant subclones. However, there remain several open challenges in designing adaptive therapies, particularly in extending this approach to multiple drugs. Furthermore, the immune system also plays a role in preventing and controlling cancers. Life history theory may help to explain the variation in immune cell levels across the tree of life that likely contributes to variance in cancer prevalence across vertebrates. However, this has not been previously explored. This work 1) describes resistance management for cancer, lessons cancer researchers learned from farmers since adaptive evolutionary strategies were inspired by the management of resistance in agricultural pests, 2) demonstrates how adaptive therapy protocols work with gemcitabine and capecitabine in a hormone-refractory breast cancer mouse model, 3) tests for a relationship between life history strategy and the immune system, and tests for an effect of immune cells levels on cancer prevalence across vertebrates, and 4) provides a novel approach to improve the teaching of life history theory. This work applies lessons that cancer researchers learned from pest managers, who face similar issues of pesticide resistance, to control cancers. It represents the first time that multiple drugs have been used in adaptive therapy for cancer, and the first time that adaptive therapy has been used on hormone-refractory breast cancer. I found that this evolutionary approach to cancer treatment prolongs survival in mice and also selects for the slow life history strategy. I also discovered that species with slower life histories have higher concentrations of white blood cells and a higher percentage of heterophils, monocytes and segmented neutrophils. Moreover, larger platelet size is associated with higher cancer prevalence in mammals.
ContributorsSeyedi, Seyedehsareh (Author) / Maley, Carlo (Thesis advisor) / Blattman, Joseph (Committee member) / Anderson, Karen (Committee member) / Wilson, Melissa (Committee member) / Huijben, Silvie (Committee member) / Gatenby, Robert (Committee member) / Arizona State University (Publisher)
Created2023