Title: Intrinsic Local Balancing of Hydrophobic and Hydrophilic Residues in Folded Protein Sequences
Author: Borukhovich, Ian
Abstract: Protein sequences may evolve to avoid highly hydrophobic local regions of sequence, in part because such sequences promote nonnative aggregation. Hydrophobic local sequences are avoided in proteins even in buried regions, where native structure requirements tend to favor them. In this dissertation, I describe three explorations of this hydrophobic suppression. In Chapter 2, I examine the occurrence of hydrophobic and polar residues in completely buried β-strand elements, and find evidence for hydrophobic suppression that decreases as a β-strand becomes more exposed. In Chapter 3, I present a generalized study of the tendency of local sequences to deviate from the hydropathy (hydrophobicity) expected based on their solvent exposure. First, I examined the hydropathy of local and nonlocal sequence groups over a large range of solvent exposures, within folded protein domains in the ASTRAL Compendium database; second, I calculated the tendency of residues within 10 positions of a nonpolar or polar reference residue to deviate from the hydropathy expected based on their structural environment. Both analyses suggested that protein sequences exhibit 'local hydropathic balance' across a range of 6-7 residues, meaning that polar and nonpolar residues are more dispersed in the sequence than expected based on solvent exposure patterns. This balance occurs in all major fold classes, domain sizes and protein functions. An unexpected finding was that it partly arises from a tendency of buried or exposed residues to be flanked by polar or nonpolar residues, respectively. This relationship may result from evolutionary selection for folding efficiency, which might be enhanced by reduced local competition for buried or exposed sites during folding. Finally, in Chapter 4, I present several exploratory analyses, including a decision-tree approach, to visualize the influence of a large number of sequence-structure properties on residue hydrophobicity. Overall, the work in this dissertation confirms that hydrophobic suppression and local hydropathic balance in general are intrinsic properties of folded proteins. I speculate that local hydropathic balance results from selection for reduced aggregation propensity, increased folding efficiency and increased native state specificity. The concept of local hydropathic balance might be used to improve the properties of designed and engineered proteins.
Intrinsic Local Balancing of Hydrophobic and Hydrophilic Residues in Folded Protein Sequences
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Air Conditioning System Fundamentals for Architecture Students
Title: Air Conditioning System Fundamentals for Architecture Students
Author: Chung, Chenwu
Abstract: This report is not only submitted in partial fulfillment of requirements for a Master of Architecture but also is designed to be used as guide to help architectural professionals and students in the selection and analysis of HVAC systems. This report divided into four sections. Part I is an introduction of basic concepts and terminologies, such as how energy is transfered, sun -earth relations, thermal resistance, and what is entropy. Part II is a review of basic HVAC systems and principles, such as heating and cooling loads, variable volume system, and Constant Volume system. In Part III, duct design will be introduced, for example, low- velocity duct design. Part IV will be applications of above principles and methods.
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"Luvina" A Short Ballet for Chamber Orchestra
Title: "Luvina" A Short Ballet for Chamber Orchestra
Author: Romo, Alfonso Molina
Abstract: Luvina is a short ballet for chamber orchestra based on well-known Mexican writer Juan Rulfo's short story Luvina, from his book El Llano en Llamas. This three-movement ballet evokes the dark world of Luvina. Each movement depicts three images from the story resulting in nine images. Musically the text is represented by the use of diverse textures and compositional techniques, including tone rows, cryptograms and the use of timbre, color, and contour. The wind - as stated in the text - is used as a leit motif serving as a transition vehicle to move the story along. Unlike other ballets that contain an inherently Mexican quality to them, this twentieth first century ballet fits under the category of a modern work that makes use of uncommon instrumentation, extended techniques and contains an atmospheric quality to it.
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Refugee Odysseys: An Ethnography of Refugee Resettlement in the U.S. After 9-11
Title: Refugee Odysseys: An Ethnography of Refugee Resettlement in the U.S. After 9-11
Author: Brogden, Mette
Abstract: By now scholars, practitioners, government officials and others in the global community have witnessed a number of countries and their populations going through extreme destruction and trying to rebuild in the aftermath. Country case studies are invaluable for their in-depth, continuous look at how a nation-state collective and the individuals who make up that collective recover, regroup, develop, but also remain very harmed for a long time. They must live among and beside their former enemies. Studies of the resettlement of refugees in a third country offer a different view: there are varied populations arriving with different socio-cultural and economic histories and experiences, and different definitions of a normalcy to which they aspire. They are in a setting that is much different than what characterized their pre-war experiences, and they do not have to rebuild out of ashes in the place that they were born. Refugees from various countries resettling in a third country have so much in common with each other from the experience of extreme violence and having to resettle in a foreign land that one key informant suggested that we think about a "refugee ethnicity." Though they would not have wished for them, they have gained numerous new identification possibilities not available to those in the country of origin: U.S. citizen, hybrid, diaspora, cosmopolitan global citizen; refugee/former refugee survivors. But the "fit" of these identities vary, because the receiving society may perceive individuals and families along a continuum of belonging vs. "othering." In the post-9-11 era in the U.S., the "belonging" as a citizen and member of the imagined community of the nation that a refugee or former refugee is able to achieve may be precarious. Will refugees resettling turn out to be vectors of socio-political disease, infecting the new host? Or will they be vectors of development and agents of host revitalization as they realize adversity-activated development in a new environment? The U.S. "host environment" has changed considerably since the modern era of resettlement began in the 1970s and then passed through the dramatic incidents of 9-11. The "hosts" have now also undergone an experience of extreme political violence. U.S. institutions are responding to the events and subsequent wars, and have themselves been changed as they adjust practices and policies in response to the trauma experienced by the people they are meant to serve. Much is in play. The times beg for a better understanding of refugees' social experiences of resettlement in a new country, the forms of suffering and marginalization they face, and the healing processes in which they engage. We need a far better understanding of what it takes to assist refugees as they work to re-constitute social networks, recover economically, find opportunity and meaning, pursue goals, and - with receiving communities--express solidarity across social dividing lines. This dissertation calls out this problematic; and analyzes it at the multi-stakeholder site of refugee resettlement.
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PVMirror – A High-Efficiency Solar Module
Title: PVMirror – A High-Efficiency Solar Module
Author: Hyatt, Justin; Mrkonich, Jeffrey; Reinhart, Lennon; Taylor, Wyatt
Abstract: To make photovoltaics (PV) and concentrated solar thermal power (CSP) more practical forms of alternative energy, creative innovations to current solar energy methods must be employed. The PVMirror – a new technology – is our solution to that problem. The PVMirror combines PV and CSP technologies by splitting the spectrum of sunlight using a dichroic mirror film. Light that is not transmitted to the solar cell is to instead be reflected to a focus, by way of a curved mirror. This hybrid of technologies is competitive, as it is both efficient and affordable compared to many other innovations in renewable energy. The PVMirror is designed to be an easy and cost-effective replacement to the reflectors used in existing CSP plants. Ultimately, we hope to demonstrate this PVMirror technology on a large scale and market it. As validated from interviewing with industry professionals, this technology has the potential to impact the world of solar energy because many industrial companies and utility-scale CSP project developers are interested in pairing CSP and PV to increase efficiency. Currently, using an outdoor sun tracker, we are testing an 18 inch by 18 inch prototype with four solar cells.
Description: Poster exhibited at GPSC Student Showcase, February 24th, 2016, University of Arizona.
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Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival
Title: Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival
Author: Schissler, Grant A.; Li, Qike; Gardeux, Vincent; Achour, Ikbel; Li, Haiquan; Piegorsch, Walter W.; Lussier, Yves A.
Abstract: Motivation: The conventional approach to personalized medicine relies on molecular data analytics across multiple patients. The path to precision medicine lies with molecular data analytics that can discover interpretable single-subject signals (N-of-1). We developed a global framework, N-of-1-pathways, for a mechanistic-anchored approach to single-subject gene expression data analysis. We previously employed a metric that could prioritize the statistical significance of a deregulated pathway in single subjects, however, it lacked in quantitative interpretability (e.g. the equivalent to a gene expression fold-change). Results: In this study, we extend our previous approach with the application of statistical Mahalanobis distance (MD) to quantify personal pathway-level deregulation. We demonstrate that this approach, N-of-1-pathways Paired Samples MD (N-OF-1-PATHWAYS-MD), detects deregulated pathways (empirical simulations), while not inflating false-positive rate using a study with biological replicates. Finally, we establish that N-OF-1-PATHWAYS-MD scores are, biologically significant, clinically relevant and are predictive of breast cancer survival (P
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Morphological examination of the relationship between astrocyte-like glia and neuronal synapses in Drosophila
Title: Morphological examination of the relationship between astrocyte-like glia and neuronal synapses in Drosophila
Author: Liu, Kendra; MacNamee, Sarah; Gerhard, Stephen; Fetter, Richard; Cardona, Albert; Tolbert, Leslie; Oland, Lynne
Abstract: The nervous system is composed of two types of cells: neurons and glia. In neuronal circuits, neurons communicate through synapses and glia play a crucial modulatory role. To modulate chemical reuptake, glia send processes close to synapses and many glia directly appose or ensheathe a synapse. This structural motif is one of the elements often included in describing a vertebrate tripartite synapse, which includes a bidirectional functional neuron-glia relationship. The exact nature of this neuron-glia communication is not well understood.
In the invertebrate fruit fly, we have also found that particular neurons and glia also have a bidirectional functional relationship. This allows us to ask new questions about glial morphology. Throughout multiple images, I identified particular neuronal synapses and surrounding glia. After creating a 3D reconstruction, I measured the distance between a particular neuronal synapse and its closest glial process. Interestingly, the neuronal synapses were not directly apposed or ensheathed by glia, and the distance to the closest glial process varied one-hundred-fold. With variable distance, functional communication is consistently present. These findings provide important insight into invertebrate neuron-glia communication, and offer new avenues to investigate the structural neuron-glia relationships that are required for reciprocal signaling between the two cell classes.
Description: Poster exhibited at GPSC Student Showcase, February 24th, 2016, University of Arizona. Recipient of the 2016 Katheryne B. Willock Library Research Award.
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Notch house Design Build Collaboration Project: House VII
Title: Notch house Design Build Collaboration Project: House VII
Author: Durrett, Tasanee
Abstract: Architecture has the power to create an inclusive society where everyone feels as if they have a voice and responsibility to a sustainable future. With collaboration and dedication, architectural design can have a huge impact on the living conditions of underrepresented communities. Working through the Drachman Design Build Coalition, the scope of the project involves designing and constructing an affordable dwelling for a low-income family in the city of Tucson, Arizona. The overall mission of building affordable housing is to provide under-served families with housing opportunities that would not be otherwise. The house will be designed as a 2-3 bedroom dwelling with 2 bathrooms, and indoor living space, outdoor living area, and a carport. Through research and physical observation, potential sites were explored, sustainable strategies were learned, and affordable housing techniques were studied. Many iterations of housing models were developed based on information gained from local books and journals written on traditional southwestern housing designs. The Notch House starts to develop as a sustainable affordable housing project designed in response to underrepresented families in Tucson.
Description: Poster exhibited at GPSC Student Showcase, February 24th, 2016, University of Arizona. 2nd Place Winner of the Creativity Undergraduate Award.
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Housing for the Hopi Community: Designing Sustainable, Affordable and Energy Efficient Housing in the Hopi Community, Linking to Cultural Patterns of Sustainability
Title: Housing for the Hopi Community: Designing Sustainable, Affordable and Energy Efficient Housing in the Hopi Community, Linking to Cultural Patterns of Sustainability
Author: LaMantia, Rachel
Description: Poster exhibited at GPSC Student Showcase, February 24th, 2016, University of Arizona.
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Applying Learning Theory to the Acquisition of Academic Vocabulary
Title: Applying Learning Theory to the Acquisition of Academic Vocabulary
Author: Bourgoyne, Ashley; Alt, Mary
Abstract: This study was designed to determine if high variability visual input would facilitate the development of conceptual representations of academic vocabulary for college-aged students. Students were trained on vocabulary in high- and low variability conditions. Their learning was assessed via a posttest which required them to identify both trained and novel images. Participants also rated accurate and inaccurate images on a scale of 1 to 9 (“accurate” –“inaccurate”) in order to assess their conceptual representations of the new vocabulary. Typical and learning-language disabled learners were studied in order to assess the effects of variability of input on different types of learners.
Description: Poster exhibited at GPSC Student Showcase, February 24th, 2016, University of Arizona.
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Pollen Foraging Bees Don't Learn Unsaturated Floral Color
Title: Pollen Foraging Bees Don't Learn Unsaturated Floral Color
Author: Newman, China Rae; Papaj, Dan; Russell, Avery
Abstract: We investigated whether bees have an innate preference for flowers with saturated pigments and whether experience altered any preference. Preference could be a result of reward quality varying by color morph and/or responses to the petals, anthers, or their combination. Consequently, we gave bees experience on one of four floral configurations created from two color morphs of Solanum tridynanum. We subsequently tested learned preference using an array of all four configurations. Changes in preference as a result of experience were not mediated by anthers, only by petals. Bees that first experienced configurations with purple petals subsequently preferred configurations with purple petals, relative to naïve bees. However, bees that first experienced white petals showed no subsequent change in preference relative to naïve bees. Surprisingly, naïve bees showed no preference for any particular floral configuration. Rather than an innate preference for flowers with more saturated colors, bees are less able to develop a preference for unsaturated types. Because individuals are more able to develop a preference for saturated flowers, these flowers experience greater visitation, and thus greater pollination success, over unsaturated types.
Description: Poster exhibited at GPSC Student Showcase, February 24th, 2016, University of Arizona.
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Using YouTube to Enhance L2 Listening Skills: Animated Cartoons in the Italian Classroom
Title: Using YouTube to Enhance L2 Listening Skills: Animated Cartoons in the Italian Classroom
Author: Maranzana, Stefano
Abstract: Today’s language teachers find increasing resources online that allow greater variety of authentic material. With the opportunities offered by digital video, the traditional listening comprehension activity has reached new potential for incidental learning and learner’s autonomy (Robin, 2011). While conscious attention is on the message delivered by the audiovisual, learners assimilate new words from context without intending to do so, stimulating incidental vocabulary learning (Carlisle, 2007). Video’s inherent multimodality makes sensory information available in various semiotic codes, allowing to the comprehension of information via separate channels (Guichon & McLornan, 2008).
This case study involves three students of advanced Italian at a large American University. It will argue in favor of video cartoons as a valuable tool to foster a constructive environment for the acquisition of the L2 (Bahrani, 2014). Specifically, we will look at British award-winning preschool cartoon Peppa Pig in its Italian version. The rationale for choosing this particular cartoon includes: 5 minutes of episode length, authentic interpersonal language and descriptive prose, slow pace of speech, familiar every-day and humorous stories, free online access and the possibility to activate captions. Furthermore, this cartoon may be used for listening comprehension for the 30 other languages in which it has been translated.
Feedback from university-level students confirms the potential of this particular cartoon and will be presented in this poster. Students reported strong motivation due to the low affective filter environment (Rule & Ague, 2005) as well as improvement in areas like vocabulary, pragmatics and idiomatic expressions from contextual clues.
Description: Poster exhibited at GPSC Student Showcase, November 7th, 2014, University of Arizona.
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The Influence of the Built Environment on the Use of Greenspace and Wellbeing
Title: The Influence of the Built Environment on the Use of Greenspace and Wellbeing
Author: Zuniga Teran, Adriana
Description: Poster exhibited at GPSC Student Showcase, November 7th, 2014, University of Arizona. Winner of the Arid Land Resource Science Award.
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Utilizing Variable Transplant Methods on the Endangered Pima Pineapple Cactus (Coryphantha scheeri var. robustispina)
Title: Utilizing Variable Transplant Methods on the Endangered Pima Pineapple Cactus (Coryphantha scheeri var. robustispina)
Author: Berthelette, Gerald; Fehmi, Jeffrey
Abstract: There has been little research carried out which assesses the ability or inability of the Pima pineapple cactus (Coryphantha scheeri var. robustispina) to be transplanted successfully, and what a successful transplant entails. From what little research has been done, experiments have demonstrated low-levels of survival, and determinate variables remain largely unknown. As a result, the U.S. Fish and Wildlife Service (USFWS) does not consider transplanting as a viable conservation measure. This study monitors [a population] of individual Pima pineapple cactus (PPC) transplanted in 2014 and distributed along the natural gas pipeline put in place by Kinder Morgan Inc. southwest of Tucson, Arizona, as well as other data sets from past transplant experiments. This post-transplant monitoring, in addition to a thorough analysis of varying transplant methodology and abiotic variables associated with each site, will be used to develop a framework for analyzing transplant successes for the PPC. Variables assessed during this study will include the influence of supplemental watering, using soil vs. bare root methods, and the number of times an individual is transplanted.
With the information gathered from the PPC along the pipeline right-of-way, along with information gathered from historical PPC transplant locations, I will present a predictive model for transplanting success of PPC using a chi-square test with the statistical software package, STATA. Success will show a clear correlation between plant vigor after transplanting and the methodology with which each cactus was moved.
Description: Poster exhibited at GPSC Student Showcase, February 24th, 2016, University of Arizona.
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Different Faces, Different Voices: A Film Analysis of Power Imbalance in Gender-Dominated Societies
Title: Different Faces, Different Voices: A Film Analysis of Power Imbalance in Gender-Dominated Societies
Author: Diaz, Kassandra
Abstract: No amount research need be referenced to justify the consensus that a power differential exists among women and men. The outcome that this power differential has created, however, varies from one society to another. The role of women in male-dominated societies is deconstructed through two films, each situated in the drug trafficking industry—one set in Latin America and the other in the United States-Mexico border. While substantial literature explores the gender power differential in the United States and developing countries, little attention is given to the impact of gender participation in the developing world. Each of these countries has diverse expectations with gender politics; that is, some countries have women as leaders in suffrage reforms and corporations, while women in other countries are not even granted the right to divorce. This paper examines the relationship between gender participation of women and their defiance of the power differential as depicted in the Brazilian film City of God and the American film Traffic. While no evidence is independently presented that economic development provides a basis for equal participation, the most important factors such as gender violence and civil liberties provide a means of understanding the gender gap from a sociopolitical perspective.
Description: Poster exhibited at GPSC Student Showcase, November 7th, 2014, University of Arizona. This research has been presented at the 2014 Annual Student Showcase, where first prize recognition in the College of Humanities was received. An earlier version was presented at the 24th Annual Graduate and Professional Symposium on Hispanic and Luso-Brazilian Literature, Language and Culture. Recognition as the first undergraduate poster presented at the graduate symposium was received, as well as an award for Best Paper. Special recognition is due primarily to Dr. Katia Bezerra, head of the Department of Spanish & Portugese, for extending an offer for me to present, to Edgard Ore-Giron for private mentorship of my work, and to Akeem Flavors in the Department of Art History for willingly assisting me practice my presentation skills.
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Navigating Love and Money: Lessons from Ukraine
Title: Navigating Love and Money: Lessons from Ukraine
Author: Anderson, Nadina
Description: Poster exhibited at GPSC Student Showcase, February 24th, 2016, University of Arizona.
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A novel strategy to attenuate the inhibitory effects of nitrite on the anaerobic ammonium oxidation (anammox) process
Title: A novel strategy to attenuate the inhibitory effects of nitrite on the anaerobic ammonium oxidation (anammox) process
Author: Li, Guangbin; Vilcherrez, David; Carvajal-Arroyo, Jose Maria; Puyol, D.; Sierra-Alvarez, Reyes; Field, Jim A.
Description: Poster exhibited at GPSC Student Showcase, November 7th, 2014, University of Arizona.
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High-risk HPV: From Infection to Cervical Cancer Progression
Title: High-risk HPV: From Infection to Cervical Cancer Progression
Author: Tseng, Roger Sean
Abstract: Human papillomaviruses (HPV) are small non-enveloped viruses that infect basal cells. Most HPV infections are mild and develop warts at the site of infection. However, some high-risk serotypes of HPV are able to promote cancer formation. Serotypes 16 and 18 are responsible for the majority of cervical cancer cases [1]. Its early proteins E6 and E7 promote oncogenesis by facilitating the acquisition of 7 hallmark traits necessary for cancer: constant signaling for proliferation, insensitivity to growth suppressors, evasion of apoptosis, limitless replicative potential, angiogenesis, immune evasion, and metastasis [1, 65, 68, 72, 76, 78, 79, 81, 82, 83, 84]. In addition to E6 and E7, specific conditions of an HPV infection seem to increase cancer incidence. Among these conditions are infection at the cervix's transformation zone, HPV genome integration with host chromosomes, inflammation and the presence of estrogen [1, 60, 61, 62, 63, 64, 69, 70, 71]. Estrogen's role in cervical cancer is not well understood. It is possible that it plays a role in the transcription of oncogenes by activating ERα and subsequently activating Sp1 [65]. Specifically, the Sp1 binding site is conserved and necessary for VEGF and hTERT expression [65, 79].
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Individual Differences in Degraded Speech Perception
Title: Individual Differences in Degraded Speech Perception
Author: Carbonell, Kathy M.
Abstract: One of the lasting concerns in audiology is the unexplained individual differences in speech perception performance even for individuals with similar audiograms. One proposal is that there are cognitive/perceptual individual differences underlying this vulnerability and that these differences are present in normal hearing (NH) individuals but do not reveal themselves in studies that use clear speech produced in quiet (because of a ceiling effect). However, previous studies have failed to uncover cognitive/perceptual variables that explain much of the variance in NH performance on more challenging degraded speech tasks. This lack of strong correlations may be due to either examining the wrong measures (e.g., working memory capacity) or to there being no reliable differences in degraded speech performance in NH listeners (i.e., variability in performance is due to measurement noise). The proposed project has 3 aims; the first, is to establish whether there are reliable individual differences in degraded speech performance for NH listeners that are sustained both across degradation types (speech in noise, compressed speech, noise-vocoded speech) and across multiple testing sessions. The second aim is to establish whether there are reliable differences in NH listeners' ability to adapt their phonetic categories based on short-term statistics both across tasks and across sessions; and finally, to determine whether performance on degraded speech perception tasks are correlated with performance on phonetic adaptability tasks, thus establishing a possible explanatory variable for individual differences in speech perception for NH and hearing impaired listeners.
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Optimizing Classroom Acoustic Performance to Promote Children's Education and Wellbeing
Title: Optimizing Classroom Acoustic Performance to Promote Children's Education and Wellbeing
Author: Elwekil, Engy Moustafa
Abstract: America was the leader in quantity and quality of high school diplomas. Today, it is ranked thirty six in the world. Some of the main factors that affect education in America are witnessing us on a daily basis. These factors affect our visual, thermal and auditory comfort levels. As environmentalists we strive to find solutions to these problems. Unfortunately, some designers aim their designs to merely aesthetics. Leaving out the environmental factor of thermal comfort to be dictated by mechanically engineers and not paying attention to how occupants interact with sound within the built environment. Today I will discuss how to design for the ears, and how sound has a major role in education promoting Children's health and wellbeing. Education reach its way to our minds through listening in adequate environment. Optimum design appreciates and is tailored to experiencing all five senses. Goal of this research: Design proper noise levels for classrooms to provide students with an optimal learning environment is imperative. Reverberation times need to be carefully sized and calculated, particularly in the primary grades when the young student's ears are not fully developed. Conduct background noise and reverberation time measurements in classrooms to assess the problem and recommend solutions. Acoustic performance design is vital. Good Sound = Happy Sound.
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