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Description
The fundamental photophysics of fluorescent probes must be understood when the probes are used in biological applications. The photophysics of BODIPY dyes inside polymeric micelles and rhodamine dyes covalently linked to proteins were studied. Hydrophobic boron-dipyrromethene (BODIPY) dyes were noncovalently encapsulated inside polymeric micelles. Absorbance and fluorescence measurements were employed to study the photophysics of these BODIPY dyes in the micellar environments. Amphiphilic polymers with a hydrophobic character and low Critical Micelle Concentration (CMC) protected BODIPYS from the aqueous environment. Moderate dye loading conditions did not result in ground-state dimerization, and only fluorescence lifetimes and brightnesses were affected. However, amphiphilic polymers with a hydrophilic character and high CMC did not protect the BODIPYS from the aqueous environment with concomitant ground-state dimerization and quenching of the fluorescence intensity, lifetime, and brightnesses even at low dye loading conditions. At the doubly-labeled interfaces of Escherichia coli (E. coli) DNA processivity β clamps, the interchromophric interactions of four rhodamine dyes were studied: tetramethylrhodamine (TMR), TMR C6, Alexa Fluor 488, and Alexa Fluor 546. Absorbance and fluorescence measurements were performed on doubly-labeled β clamps with singly-labeled β clamps and free dyes as controls. The absorbance measurements revealed that both TMR and TMR C6 readily formed H-dimers (static quenching) at the doubly-labeled interfaces of the β clamps. However, the TMR with a longer linker (TMR C6) also displayed a degree of dynamic quenching. For Alexa Fluor 546 and Alexa Fluor 488, there were no clear signs of dimerization in the absorbance scans. However, the fluorescence properties (fluorescence intensity, lifetime, and anisotropy) of the Alexa Fluor dyes significantly changed when three methodologies were employed to disrupt the doubly-labeled interfaces: 1) the addition of sodium dodecyl sulfate (SDS) detergent to denature the proteins, 2) the addition of clamp loader (γ complex) to open one of the two interfaces, and 3) the use of subunit exchange to decrease the number of dyes per interface. These fluorescence measurements indicated that for the Alexa Fluor dyes, other interchromophoric interactions were present such as dynamic quenching and homo-Förster Resonance Energy Transfer (homo-FRET).
ContributorsDonaphon, Bryan Matthew (Author) / Levitus, Marcia (Thesis advisor) / Van Horn, Wade (Committee member) / Woodbury, Neal (Committee member) / Arizona State University (Publisher)
Created2018
Description
Exposure of blood plasma/serum (P/S) to thawed conditions, greater than -30°C, can produce biomolecular changes that misleadingly impact measurements of clinical markers within archived samples. Reported here is a low sample-volume, dilute-and-shoot, intact protein mass spectrometric assay of albumin proteoforms called “ΔS-Cys-Albumin” that quantifies cumulative exposure of archived P/S samples to thawed conditions. The assay uses the fact that S-cysteinylation (oxidation) of albumin in P/S increases to a maximum value when exposed to temperatures greater than -30°C. The multi-reaction rate law that governs this albumin S-cysteinylation formation in P/S was determined and was shown to predict the rate of formation of S-cysteinylated albumin in P/S samples—a step that enables back-calculation of the time at which unknown P/S specimens have been exposed to room temperature. To emphasize the capability of this assay, a blind challenge demonstrated the ability of ΔS-Cys-Albumin to detect exposure of individual and grouped P/S samples to unfavorable storage conditions. The assay was also capable of detecting an anomaly in a case study of nominally pristine serum samples collected under NIH-sponsorship, demonstrating that empirical evidence is required to guarantee accurate knowledge of archived P/S biospecimen storage history.
The ex vivo glycation of human serum albumin was also investigated showing that P/S samples stored above their freezing point leads to significant increases in glycated albumin. These increases were found to occur within hours at room temperature, and within days at -20 °C. These increases continued over a period of 1-2 weeks at room temperature and over 200 days at -20 °C, ultimately resulting in a doubling of glycated albumin in both healthy and diabetic patients. It was also shown that samples stored at lower surface area-to-volume ratios or incubated under a nitrogen atmosphere experienced less rapid glucose adduction of albumin—suggesting a role for oxidative glycation in the ex vivo glycation of albumin.
The ex vivo glycation of human serum albumin was also investigated showing that P/S samples stored above their freezing point leads to significant increases in glycated albumin. These increases were found to occur within hours at room temperature, and within days at -20 °C. These increases continued over a period of 1-2 weeks at room temperature and over 200 days at -20 °C, ultimately resulting in a doubling of glycated albumin in both healthy and diabetic patients. It was also shown that samples stored at lower surface area-to-volume ratios or incubated under a nitrogen atmosphere experienced less rapid glucose adduction of albumin—suggesting a role for oxidative glycation in the ex vivo glycation of albumin.
ContributorsJeffs, Joshua W (Author) / Borges, Chad R (Thesis advisor) / Van Horn, Wade (Committee member) / Williams, Peter (Committee member) / Arizona State University (Publisher)
Created2018
Description
The current trend of interconnected devices, or the internet of things (IOT) has led to the popularization of single board computers (SBC). This is primarily due to their form-factor and low price. This has led to unique networks of devices that can have unstable network connections and minimal processing power. Many parallel program- ming libraries are intended for use in high performance computing (HPC) clusters. Unlike the IOT environment described, HPC clusters will in general look to obtain very consistent network speeds and topologies. There are a significant number of software choices that make up what is referred to as the HPC stack or parallel processing stack. My thesis focused on building an HPC stack that would run on the SCB computer name the Raspberry Pi. The intention in making this Raspberry Pi cluster is to research performance of MPI implementations in an IOT environment, which had an impact on the design choices of the cluster. This thesis is a compilation of my research efforts in creating this cluster as well as an evaluation of the software that was chosen to create the parallel processing stack.
ContributorsO'Meara, Braedon Richard (Author) / Meuth, Ryan (Thesis director) / Dasgupta, Partha (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Aside from uplifting and tearing down the mood of a young LGBTQ+ kid, journalistic media has the potential to alter the way audiences understand and react to individuals of the LGBTQ+ community. Looking at the rhetorical approaches, frameworks, and expanded narratives of news sources, this project engages with the concepts of same-sex marriage, lifestyles, bans, and children in education in order to attain an understanding of what media messages are being shared, how they are being communicated, and what the implications of such rhetoric are. Summary of the findings:
• Same-sex marriage as the win that cannot be repeated.
Infamously known as the central legal battle for the LGBTQ+ community, same-sex marriage finds itself in many political speeches, campaigns, and social commentaries. Interestingly, after being legalized through a Supreme Court decision in the United States, Same-Sex Marriage finds itself framed as the social inevitability that should not be repeated in politics or any legal shift. In other words, “the gays have won this battle, but not the war.”
• There are risks around the “LGBTQ+ lifestyle” and its careful catering to an elite minority and the mediation through bans.
The risks of the LGBTQ+ “lifestyle” date back far, with many connotations being attached to being LGBTQ+ (AIDS epidemics, etc.). In modern journalism, many media outlets portray LGBTQ+ individuals to be a tiny minority (.001% according to some) that demands the whole society to adhere to their requests. This framework portrays the LGBTQ+ community as oppressors and obsessed advocates that can never “seem to get enough” (ex: more than just marriage). The bans are framed as the neutralizing factor to the catering.
• LGBTQ+ children and topics in academic and social spaces are the extreme degree.
When it comes to LGBTQ+ issues and conversations as they revolve around children, media outlets have some of the most passionate opinions about them. Often portrayed as “the line that shouldn’t be crossed,” LGBTQ+ issues, as they find themselves in schools and other spaces, are thus portrayed as bearable to a certain degree, never completely. Claims of indoctrination are also presented prominently even when institutional efforts are to protect LGBTQ+ kids.
• Same-sex marriage as the win that cannot be repeated.
Infamously known as the central legal battle for the LGBTQ+ community, same-sex marriage finds itself in many political speeches, campaigns, and social commentaries. Interestingly, after being legalized through a Supreme Court decision in the United States, Same-Sex Marriage finds itself framed as the social inevitability that should not be repeated in politics or any legal shift. In other words, “the gays have won this battle, but not the war.”
• There are risks around the “LGBTQ+ lifestyle” and its careful catering to an elite minority and the mediation through bans.
The risks of the LGBTQ+ “lifestyle” date back far, with many connotations being attached to being LGBTQ+ (AIDS epidemics, etc.). In modern journalism, many media outlets portray LGBTQ+ individuals to be a tiny minority (.001% according to some) that demands the whole society to adhere to their requests. This framework portrays the LGBTQ+ community as oppressors and obsessed advocates that can never “seem to get enough” (ex: more than just marriage). The bans are framed as the neutralizing factor to the catering.
• LGBTQ+ children and topics in academic and social spaces are the extreme degree.
When it comes to LGBTQ+ issues and conversations as they revolve around children, media outlets have some of the most passionate opinions about them. Often portrayed as “the line that shouldn’t be crossed,” LGBTQ+ issues, as they find themselves in schools and other spaces, are thus portrayed as bearable to a certain degree, never completely. Claims of indoctrination are also presented prominently even when institutional efforts are to protect LGBTQ+ kids.
ContributorsNieto Calderon, Ramon Antonio (Author) / Himberg, Julia (Thesis director) / Sturges, Robert (Committee member) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Waltz, is a collection of poems written to play along the boundaries between sound, language, and meaning. As a vehicle for exploration, the poems in Waltz, commandeer themes of nostalgia, love, loss, and abstraction, all of which build up and break each other down to create something of a nonlinear narrative, and concomitant sketch of the poet.
ContributorsAieta, Joseph (Author) / Ball, Sally (Thesis director) / Liston, Chelsea (Committee member) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The primary purpose of this thesis is two-fold: (1) to understand the resources presently available for Native American college student leaders at Predominantly White institutions (PWIs), and; (2) to consider ways to develop their leadership abilities and knowledge of how experience with college leadership contributes to becoming successful leaders with/in their Indigenous communities. The secondary purpose of this thesis is to propose additional resources for PWIs that can inform Native American leadership practices across academic disciplines and fields through the creation of the Indigenous & Innovative Leadership course syllabus and conference. This Honor's Thesis Project begins by exploring leadership development opportunities for Native American undergraduate students at Arizona State University, a predominantly White institution. Also explored are conceptions of Indigenous leadership as it applies to engagement in or with on-campus student organizations, tribal governments, and within surrounding Indigenous communities. This project has implications for thinking about American Indian student success beyond graduation and the role leadership and organization development has for the success of tribal communities.
ContributorsTom, Megan Joyce (Author) / Brayboy, Bryan (Thesis director) / Solyom, Jessica (Committee member) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This thesis discusses three recent optimization problems that seek to reduce disease spread on arbitrary graphs by deleting edges, and it discusses three approximation algorithms developed for these problems. Important definitions are presented including the Linear Threshold and Triggering Set models and the set function properties of submodularity and monotonicity. Also, important results regarding the Linear Threshold model and computation of the influence function are presented along with proof sketches. The three main problems are formally presented, and NP-hardness results along with proof sketches are presented where applicable. The first problem seeks to reduce spread of infection over the Linear Threshold process by making use of an efficient tree data structure. The second problem seeks to reduce the spread of infection over the Linear Threshold process while preserving the PageRank distribution of the input graph. The third problem seeks to minimize the spectral radius of the input graph. The algorithms designed for these problems are described in writing and with pseudocode, and their approximation bounds are stated along with time complexities. Discussion of these algorithms considers how these algorithms could see real-world use. Challenges and the ways in which these algorithms do or do not overcome them are noted. Two related works, one which presents an edge-deletion disease spread reduction problem over a deterministic threshold process and the other which considers a graph modification problem aimed at minimizing worst-case disease spread, are compared with the three main works to provide interesting perspectives. Furthermore, a new problem is proposed that could avoid some issues faced by the three main problems described, and directions for future work are suggested.
ContributorsStanton, Andrew Warren (Author) / Richa, Andrea (Thesis director) / Czygrinow, Andrzej (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Genocide studies have traditionally focused on the perpetrator’s intent to eradicate a particular identity-based group, using the Holocaust as their model and point of comparison. Although some aspects of the Holocaust were undoubtedly unique, recent scholars have sought to challenge the notion that it was a singular phenomenon. Instead, they draw attention to a recurring pattern of genocidal events throughout history by shifting the focus from intent to structure. One particular branch of scholars seeks to connect the ideology and tactics of imperialism with certain genocidal events. These anti-imperialist genocide scholars concede that their model cannot account for all genocides, but still claim that it creates meaningful connections between genocides committed by Western colonialist powers and those that have occurred in a neoimperialist world order shaped according to Western interests. The latter includes genocides in postcolonial states, which these scholars believe were shaped by the scars of their colonial past, as well as genocides in which imperial hegemons assisted local perpetrators. Imperialist and former colonial powers have contributed meaningfully to all of these kinds of genocides, yet their contributions have largely been ignored due to their own influence on the creation of the current international order. Incorporating the anti-imperialist perspective into the core doctrine of genocide studies may lead to breakthroughs in areas of related policy and practice, such as prevention and accountability.
ContributorsParker, Ashleigh Mae (Author) / Thies, Cameron (Thesis director) / Sivak, Henry (Committee member) / School of Politics and Global Studies (Contributor) / School of Social Transformation (Contributor) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
In the last few years, billion-dollar companies like Yahoo and Equifax have had data breaches causing millions of people’s personal information to be leaked online. Other billion-dollar companies like Google and Facebook have gotten in trouble for abusing people’s personal information for financial gain as well. In this new age of technology where everything is being digitalized and stored online, people all over the world are concerned about what is happening to their personal information and how they can trust it is being kept safe. This paper describes, first, the importance of protecting user data, second, one easy tool that companies and developers can use to help ensure that their user’s information (credit card information specifically) is kept safe, how to implement that tool, and finally, future work and research that needs to be done. The solution I propose is a software tool that will keep credit card data secured. It is only a small step towards achieving a completely secure data anonymized system, but when implemented correctly, it can reduce the risk of credit card data from being exposed to the public. The software tool is a script that can scan every viable file in any given system, server, or other file-structured Linux system and detect if there any visible credit card numbers that should be hidden.
ContributorsPappas, Alexander (Author) / Zhao, Ming (Thesis director) / Kuznetsov, Eugene (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Political polarization is the coalescence of political parties -- and the individuals of which parties are composed -- around opposing ends of the ideological spectrum. Political parties in the United States have always been divided, however, in recent years this division has only intensified. Recently, polarization has also wound its way to the Supreme Court and the nomination processes of justices to the Court. This paper examines how prevalent polarization in the Supreme Court nomination process has become by looking specifically at the failed nomination of Judge Merrick Garland and the confirmations of now-Justices Neil Gorsuch and Brett Kavanaugh. This is accomplished by comparing the ideologies and qualifications of the three most recent nominees to those of previous nominees, as well as analysing the ideological composition of the Senate at the times of the individual nominations.
ContributorsJoss, Jacob (Author) / Hoekstra, Valerie (Thesis director) / Critchlow, Donald (Committee member) / Computer Science and Engineering Program (Contributor) / School of Politics and Global Studies (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05