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- Creators: Barrett, The Honors College
Description
Memory CD8+ T-cells can persist in the absence of antigen, primed for immediate activation and proliferation if later exposed to the same antigen. These cytotoxic lymphocytes provide long-term immunity following an acute infection. Studies have observed that intermediate levels of general T cell transfer prior to infection may cause an inappropriate response resulting in increased pathology rather than prevention. Therefore, our study focused on a memory CD8 T-cell therapy using lymphocytic choriomeningitis virus (LCMV) specific splenocytes, which activate and proliferate at an accelerated pace compared to that of naive T-cells. LCMV is a natural murine pathogen which also poses a zoonotic infection threat to humans, and the effect of immune cell vaccination therapies for LCMV is not fully understood. We observed the effect of multiple memory CD8 T cell dosage levels on overall disease and memory CD8 T-cell response to the virus. Infection by exposure to a carrier was shown to have a reduced impact on mice receiving higher doses of memory T cells prior to infection compared to mice receiving less or no memory cells. Higher presence of activated memory cells were shown to correlate with less disease-related weight loss and accelerated recovery times. Survival rate after exposure to carriers was not shown to be affected by dosage level, warranting further research regarding the prevalence of the immunopathology observed in other studies in natural murine transmission models.
ContributorsMiller, Charles (Author) / Blattman, Joseph (Thesis director) / Holechek, Susan (Committee member) / Carmen, Joshua (Committee member) / W. P. Carey School of Business (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Tools that accurately assess physical activity and sedentary behaviors have broad implications relative to understanding the association of adverse health outcomes and these behaviors. Given the ease of distribution and inexpensive nature of self-report tools, they are the most widely used means to assess human behavior in large-scale populations. The purpose of this study was to validate the ACT24 online self-report recall for measures of sedentary and active behavior against criterion measure. Participants of a larger study were asked to complete the ACT24 recall on a random day in three different weeks during which they were wearing the criterion device. A total of 16 recalls were completed that were used to assess ACT24 measures of sedentary, active, and MVPA behavior. Four different comparisons afforded this analysis: criterion sitting time to ACT24 sedentary time, criterion standing time to ACT24 active behavior, criterion stepping time to ACT24 active behavior, and criterion stepping of 3.0+METs to ACT24 MVPA. Results for the comparisons made between ACT24 sedentary time versus criterion sitting time and ACT24 active time to criterion active time showed little systematic differences at the group level, but the limits of agreement were relatively wide. The comparisons made between ACT24 active time to criterion stepping time and ACT24 MVPA to criterion stepping time at 3.0+ METs both showed a positive systematic difference. Increased incidence of physical activity was correlated with more difference between the measures, likely due to an underestimation of criterion active time measurement. These results are important in the preliminary validity analysis of ACT24 measures of active and sedentary time. Future directions include implementing validation protocols in larger and more diverse samples.
ContributorsBrinkman, Joseph Connor (Author) / Buman, Matthew P. (Thesis director) / Hekler, Eric (Committee member) / Matthews, Charles E. (Committee member) / Barrett, The Honors College (Contributor) / W. P. Carey School of Business (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Background: While research has quantified the mortality burden of the 1957 H2N2 influenza pandemic in the United States, little is known about how the virus spread locally in Arizona, an area where the dry climate was promoted as reducing respiratory illness transmission yet tuberculosis prevalence was high.
Methods: Using archival death certificates from 1954 to 1961, this study quantified the age-specific seasonal patterns, excess-mortality rates, and transmissibility patterns of the 1957 pandemic in Maricopa County, Arizona. By applying cyclical Serfling linear regression models to weekly mortality rates, the excess-mortality rates due to respiratory and all-causes were estimated for each age group during the pandemic period. The reproduction number was quantified from weekly data using a simple growth rate method and generation intervals of 3 and 4 days. Local newspaper articles from The Arizona Republic were analyzed from 1957-1958.
Results: Excess-mortality rates varied between waves, age groups, and causes of death, but overall remained low. From October 1959-June 1960, the most severe wave of the pandemic, the absolute excess-mortality rate based on respiratory deaths per 10,000 population was 17.85 in the elderly (≥65 years). All other age groups had extremely low excess-mortality and the typical U-shaped age-pattern was absent. However, relative risk was greatest (3.61) among children and young adolescents (5-14 years) from October 1957-March 1958, based on incidence rates of respiratory deaths. Transmissibility was greatest during the same 1957-1958 period, when the mean reproduction number was 1.08-1.11, assuming 3 or 4 day generation intervals and exponential or fixed distributions.
Conclusions: Maricopa County largely avoided pandemic influenza from 1957-1961. Understanding this historical pandemic and the absence of high excess-mortality rates and transmissibility in Maricopa County may help public health officials prepare for and mitigate future outbreaks of influenza.
Methods: Using archival death certificates from 1954 to 1961, this study quantified the age-specific seasonal patterns, excess-mortality rates, and transmissibility patterns of the 1957 pandemic in Maricopa County, Arizona. By applying cyclical Serfling linear regression models to weekly mortality rates, the excess-mortality rates due to respiratory and all-causes were estimated for each age group during the pandemic period. The reproduction number was quantified from weekly data using a simple growth rate method and generation intervals of 3 and 4 days. Local newspaper articles from The Arizona Republic were analyzed from 1957-1958.
Results: Excess-mortality rates varied between waves, age groups, and causes of death, but overall remained low. From October 1959-June 1960, the most severe wave of the pandemic, the absolute excess-mortality rate based on respiratory deaths per 10,000 population was 17.85 in the elderly (≥65 years). All other age groups had extremely low excess-mortality and the typical U-shaped age-pattern was absent. However, relative risk was greatest (3.61) among children and young adolescents (5-14 years) from October 1957-March 1958, based on incidence rates of respiratory deaths. Transmissibility was greatest during the same 1957-1958 period, when the mean reproduction number was 1.08-1.11, assuming 3 or 4 day generation intervals and exponential or fixed distributions.
Conclusions: Maricopa County largely avoided pandemic influenza from 1957-1961. Understanding this historical pandemic and the absence of high excess-mortality rates and transmissibility in Maricopa County may help public health officials prepare for and mitigate future outbreaks of influenza.
ContributorsCobos, April J (Author) / Jehn, Megan (Thesis director) / Chowell-Puente, Gerardo (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
The purpose of this study is to discover the exposure and network patterns during the 2013-2015 Ebola Virus Disease epidemic. The author accomplished this by taking an opportunistic sample of news and academic articles, some of which may also capture cases untreated and therefore unrecorded by hospitals and treatment units. Most of the 315 cases came from the Washington Post, New York Times, and World Health Organization, and they consistently captured between 1-2% of WHO case numbers. The results show that of cases with known exposures, 53.6% became infected through contact with sick family members. Hospital and funeral transmission accounted for the second and third most frequent exposure scenarios at 24.6% and 12.9% respectively. The exposures over time imply that hospital and funeral transmission prevention efforts have been successful, but family transmission has remained common throughout the outbreak. Prevention initiatives should focus on families earlier in epidemics to help control EVD's spread.
ContributorsCleaton, Julie Marie (Author) / Chowell, Gerardo (Thesis director) / Hurtado, Ana Magdalena (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Among wild rodent populations, vertical transmission is believed to constitute the primary route of infection for Lymphocytic Choriomeningitis Virus (LCMV), a non-lytic arenavirus with both acute and chronic forms. When carrier mice infected at birth with the acute Armstrong strain reproduce, they generate congenital carrier offspring containing a quasispecies of LCMV that includes Armstrong as well as its chronic Clone-13 variant. This study examined the genetic trends in the vertical transmission of LCMV from mothers infected perinatally with Clone-13. Viral isolates obtained from the serum of congenital carrier offspring were partially sequenced to reveal residue 260 in the glycoprotein-encoding region of their S segment, the site of a major amino acid change differentiating the chronic and acute strains. It was found that the phenylalanine-to-leucine mutation associated with Clone-13 was present in 100% of the isolates, strongly indicating that the offspring of Clone-13 carriers contain exclusively the chronic variant. This research has broad implications for the epidemiology of the virus, and, given the predominance of Armstrong in the wild, suggests that there must be a biological cost associated with Clone-13 infection in non-carriers.
ContributorsFrear, Cody Christian (Author) / Blattman, Joseph (Thesis director) / Hogue, Brenda (Committee member) / Holechek, Susan (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
With the development of technology, there has been a dramatic increase in the number of machine learning programs. These complex programs make conclusions and can predict or perform actions based off of models from previous runs or input information. However, such programs require the storing of a very large amount of data. Queries allow users to extract only the information that helps for their investigation. The purpose of this thesis was to create a system with two important components, querying and visualization. Metadata was stored in Sedna as XML and time series data was stored in OpenTSDB as JSON. In order to connect the two databases, the time series ID was stored as a metric in the XML metadata. Queries should be simple, flexible, and return all data that fits the query parameters. The query language used was an extension of XQuery FLWOR that added time series parameters. Visualization should be easily understood and be organized in a way to easily find important information and details. Because of the possibility of a large amount of data being returned from a query, a multivariate heat map was used to visualize the time series results. The two programs that the system performed queries on was Energy Plus and Epidemic Simulation Data Management System. By creating such a system, it would be easier for people of the project's fields to find the relationship between metadata that leads to the desired results over time. Over the time of the thesis project, the overall software was completed, however the software must be optimized in order to take the enormous amount of data expected from the system.
ContributorsTse, Adam Yusof (Author) / Candan, Selcuk (Thesis director) / Chen, Xilun (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor) / Computer Science and Engineering Program (Contributor)
Created2015-05
Description
Mortality of 1918 influenza virus was high, partly due to bacteria coinfections. We characterize pandemic mortality in Arizona, which had high prevalence of tuberculosis. We applied regressions to over 35,000 data points to estimate the basic reproduction number and excess mortality. Age-specific mortality curves show elevated mortality for all age groups, especially the young, and senior sparing effects. The low value for reproduction number indicates that transmissibility was moderately low.
ContributorsJenner, Melinda Eva (Author) / Chowell-Puente, Gerardo (Thesis director) / Kostelich, Eric (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
This paper will chronicle my personal experience in trying to design and initiate a retrospective patient data study to determine the prevalence of Primary Sclerosing Cholangitis (“PSC”) in certain races/ethnic groups in Arizona. This experience will also be the basis for my proposed roadmap for a more successful future study.
My nearly 10 month thesis project of trying to complete a study yielded considerable ‘learning opportunities’ in large part due to my inexperience. I made numerous errors in sequencing tasks, grossly under-scoping elapsed time and hours for other tasks, completely overlooking other critical tasks, and being insensitive to how irrelevant I and my project were to the many professionals whose help I needed to complete the study. Based upon the knowledge I gained through this process, I will describe the design of a future study of retrospective patient data that will assess whether PSC patients in Phoenix, Arizona follow racial/ethnic trends. I chose Phoenix as an ideal location to perform this proposed study because of the diverse racial/ethnic population in the greater Phoenix area. The goal will be to obtain and review 20 years of retrospective patient data from three large hospital groups in Phoenix, identify the races/ethnicities of PSC patients, and quantify the prevalence and incidence of PSC in such races/ethnicities. The lack of IRB uniformity among the subject hospitals/clinics will pose a challenge, but a detailed outline of how to approach the IRB approval process and obtain PSC patient data from each institution is provided.
My nearly 10 month thesis project of trying to complete a study yielded considerable ‘learning opportunities’ in large part due to my inexperience. I made numerous errors in sequencing tasks, grossly under-scoping elapsed time and hours for other tasks, completely overlooking other critical tasks, and being insensitive to how irrelevant I and my project were to the many professionals whose help I needed to complete the study. Based upon the knowledge I gained through this process, I will describe the design of a future study of retrospective patient data that will assess whether PSC patients in Phoenix, Arizona follow racial/ethnic trends. I chose Phoenix as an ideal location to perform this proposed study because of the diverse racial/ethnic population in the greater Phoenix area. The goal will be to obtain and review 20 years of retrospective patient data from three large hospital groups in Phoenix, identify the races/ethnicities of PSC patients, and quantify the prevalence and incidence of PSC in such races/ethnicities. The lack of IRB uniformity among the subject hospitals/clinics will pose a challenge, but a detailed outline of how to approach the IRB approval process and obtain PSC patient data from each institution is provided.
ContributorsBuness, James Gage (Author) / Lindor, Keith (Thesis director) / Ali, Ahmad (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
This work examines one dimension of the effect that complex human transport systems have on the spread of Chikungunya Virus (CHIKV) in the Caribbean from 2013 to 2015. CHIKV is transmitted by mosquitos and its novel spread through the Caribbean islands provided a chance to examine disease transmission through complex human transportation systems. Previous work by Cauchemez et al. had shown a simple distance-based model successfully predict CHIKV spread in the Caribbean using Markov chain Monte Carlo (MCMC) statistical methods. A MCMC simulation is used to evaluate different transportation methods (air travel, cruise ships, and local maritime traffic) for the primary transmission patterns through linear regression. Other metrics including population density to account for island size variation and dengue fever incidence rates as a proxy for vector control and health spending were included. Air travel and cruise travel were gathered from monthly passenger arrivals by island. Local maritime traffic is approximated with a gravity model proxy incorporating GDP-per-capita and distance and historic dengue rates were used for determine existing vector control measures for the islands. The Caribbean represents the largest cruise passenger market in the world, cruise ship arrivals were expected to show the strongest signal; however, the gravity model representing local traffic was the best predictor of infection routes. The early infected islands (<30 days) showed a heavy trend towards an alternate primary transmission but our consensus model able to predict the time until initial infection reporting with 94.5% accuracy for islands 30 days post initial reporting. This result can assist public health entities in enacting measures to mitigate future epidemics and provide a modelling basis for determining transmission modes in future CHIKV outbreaks.
ContributorsFries, Brendan F (Author) / Perrings, Charles (Thesis director) / Wilson Sayres, Melissa (Committee member) / Morin, Ben (Committee member) / School of Life Sciences (Contributor) / Department of Military Science (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
Description
The purpose of this research is to exploit the neglect of specific populations and diseases in Latin America through an epidemiological literature review. As a small part of a larger publication, the foci of this research was the infectious disease, helminthiasis. Using manually indexed abstracts from the National Library of Medicine database in PubMed, 4,594 papers were synthesized and then processed for further review. Of those papers, 29 provided information about helminths in indigenous populations. These papers were reviewed and used in prevalence data extraction and variable analysis. The main conclusion was to reveal the fact that from an entire health database less than 30 papers provided information about the persistence of helminths in indigenous communities of Latin America. Not only that but the few papers that could be analyzed had consistently high prevalence ratios.
ContributorsGregory, Cassandre June (Author) / Hurtado, Ana Magdalena (Thesis director) / Estevez, Dulce (Committee member) / School of Life Sciences (Contributor) / School of Human Evolution & Social Change (Contributor, Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05