Since the social realization of barrios and ghettos in the United States, scholastic analyses of their locations have formed conclusions ranging from proximity to labor centers to social population controls (Jargowsky, 1996) (Meyer, 2000). One topic which social scientists have avoided when addressing the geographic localization of poverty, is that of the plot itself. Specifically are there undesirable qualities, either geographically or geophysically, of the land where ghettos are built that makes it less attractive to populations with higher social standing? Here we show that a majority of “high poverty” zones in three American cities are built in areas which are more susceptible to damage by earthquakes and/or landslides. These conclusions were formed, by performing geographical comparisons of poverty population maps comprised of U.S. Census data to geological hazard maps provided by United States Geological Survey. Seattle, Los Angeles; both focuses of “The Other Burgess Model,” and Hawaii were selected for comparison. In all three cases, areas with the largest concentration of families and individuals under the U.S. poverty line were more likely to be in areas of greater threat from earthquakes or landslides. My results suggest that populations living in poverty are more likely to be both physically and financially affected by these two natural forms of disaster. In the United States where safety from landslide and earthquakes are protected under the Bill of Rights, it is both illegal and unjust for populations with less access to resources to be directed towards areas of greater hazard. I anticipate this project will be a starting point for further research on the imbalance of safety concerns brought about social, economic, and ethnic inequalities.

Chronic social-stress is known to lead to a number of aberrant behaviors, including anxiety and depression. Using a mouse model of social-defeat stress, this project aims to better understand the relationship between the kappa-opioid receptor (KOR), a G-protein coupled receptor (GPCR) previously shown to be activated by multiple forms of stress, and its role in generating anxiety-like and aversion behaviors in mice. Different forms of stress lead to the release of the endogenous KOR agonist, dynorphin, which activates an intracellular signal transduction cascade resulting in anxiety-like and aversion behaviors. Prior studies have demonstrated that the long-acting KOR antagonist, norbinaltorphimine (norBNI), is able to reduce social-defeat induced social avoidance behaviors when administered prior to social defeat stress exposure. Although these studies have implicated the KOR system in social-defeat induced behaviors, pretreatment of pharmacotherapies prior to a stress event is limited in therapeutic benefit.  In this research, the ability of norBNI to reverse repeated social-defeat induced changes in social behaviors was tested by administering norBNI following exposure to the social-defeat stress. The results have so far shown that post treatment with norBNI is able to effectively counter the altered social interaction behaviors caused by a repeated social-defeat stress; moreover, the reversal of the stress-induced social interaction deficits also correlates with a reduction in anxiety-like behaviors. These data suggest that social interaction deficits are due to increased anxiety in previously benign social settings, and norBNI has the therapeutic potential to reverse these social-stress induced behavior alterations.

The carotid artery bifurcation is one of the main sites of atherosclerosis, a disease that causes plaque buildup on artery walls, which can lead to Stroke. Through examination of the flow in the carotid artery bifurcation, we expect to better understand the influence of hemodynamics on plaque formation and growth, as well as on potential treatments. In order to investigate this, we have designed a model of the carotid artery using medical imaging and computer aided design software (SolidWorks). We are investigating rapid prototyping techniques to create a physical model of the carotid artery. Utilizing the physical model of the carotid artery lumen, we cast a mold made of water soluble material. This allows us to remove the mold leaving behind a reconstruction of the carotid artery with the necessary physical properties. Currently this project is focused on finding an ideal casting process that preserves the optical clarity. The next phase of this research will be to examine flow through the mold using particle image velocimetry (PIV). The setup of the PIV involves adding tracer particles to the flow that are illuminated with a laser. Using the light scattered by the particles to record the displacement collected with a photographic camera synchronized with the laser illumination. These images will be processed using an algorithm that compares the displacement from two consecutive images. The velocity of the flow will be calculated from the displacement of the tracer particles and its profile is used to determine the shear stress acting on the walls of the artery. This measurement of the stress acting on the arterial wall, together with the transport of chemical species to and from the arterial wall, is crucial in understanding the influence of hemodynamics on the physiology of the arterial wall and the development of atherosclerosis.

Neural networks are often employed to model the brain. One such model developed by Numenta’s research group is the hierarchical temporal memory (HTM) model. A comparison of the HTM model and more conventional neural networks such as the network architectures available in the Stuttgart Neural Network Simulator (SNNS) is missing from the literature. This study aims to report on the performance on machine learning problems of HTM neural networks as compared to the performance of other common network architectures. The HTM neural network will either be built on the JAVA platform using the descriptions in Numenta’s publications or be used as provided by Numenta for public use. The SNNS network architectures will be used as provided by the University of Stuttgart. Possible learning problems considered will include: motion detection, character recognition, recognition and tracking of humanoid forms, object identification, and general pattern recognition. Possible SNNS network architectures include: backpropagation through time (for recurrent networks), quickprop through time (for recurrent networks), self-organizing maps (Kohonen maps), TDNN (time-delay networks) with backpropagation, Elman networks and extended hierarchical Elman networks. Evaluation of a network’s performance on each problem will be based on accuracy of identification, and time required for computation, while holding learning resources constant (same time exposure and same number of examples during learning stage). A qualitative comparison of the similarities of the learning problems to cortical learning algorithms and brain architectures may be attempted depending on time constraints. These results will be useful for evaluating both the usefulness of HTM neural networks and their connection to the cortical learning algorithm.

Diabetes is an escalating health issue that can lead to a multitude of health problems, including heart disease, blindness and death. In 2011, the Center for Disease Control reported that diabetes afflicts 25.8 million Americans, is the seventh leading cause of death, and that it incurs an annual cost of $174 billion. Type II Diabetes Mellitus (T2DM) accounts for 90-95% of adult diabetes, for which there is no definitive cure. Studies show that 84% of patients undergoing Roux-en-Y Gastric Bypass (RYGB) experience near immediate, weight-independent remission of T2DM, and virtually all achieve improved glycemic control. The exact mechanism of remission is a quandary, however the hypothesis is that RYGB improves glucose homeostasis and insulin sensitivity through differential expression of gastrointestinal peptides. To explore the molecular mechanisms of this, 44 Ossabaw pigs are obtained and raised on a high fat diet that promotes weight gain and insulin resistance. Pigs are randomized to undergo one of 5 operations: RYGB (n=8), RYGB with Vagotomy (n=8), Gastrojejunostomy (n=8), Gastrojejunostomy with Duodenal Exclusion (n=8), or sham (n=4). Intravenous glucose tolerance tests (IVGTT) and meal tolerance tests (MTT) are performed once before the surgery, then again at 30 and 60 days after the surgery. Gastrointestinal tissue samples are collected during surgery and at necropsy on day 60. Samples are taken from the following sites: the stomach, proximal and distal duodenum, proximal and distal jejunum, proximal and distal ileum, and the pancreas. IVGTT and MTT blood samples will be used to determine the physiologic response by analyzing glucose, insulin, GLP-1, PYY, GIP, and ghrelin levels. GI and pancreatic tissue samples will undergo histopathological and mRNA analysis to provide insight into the differential expression of peptides at various locations. The conclusions of this study will help determine the mechanism of glycemic improvement and the cause of T2DM remission.

Emotion is a human universal but interpretation of facial expressions and the prescribed meaning may differ across cultures. In Faces and Feelings we attempt to examine this cultural variation by testing East Asian and European American participants’ responses to various stories presented with photos of facial expressions. Recent research has indicated that European Americans judge faces primarily using features of the face, whereas East Asian participants judge faces inferring from the person’s social situation. Expanding on this, we predict different factors such as interdependence and dialectical thinking will influence interpretation of facial expressions cross-culturally. Participants are asked to complete a computer-based experiment consisting of essay responses, multiple choice questions and demographic information. We will then perform qualitative analyses on the data collected. We expect our results from this ongoing study to yield similar results to the earlier pilot studies which supported the hypotheses. While people in every culture express their feeling on their faces, there may be differences in what those expressions communicate and in how they reflect what a person is feeling. Knowledge of these differences may help diverse cultures understand and relate to each other in positive and more productive ways.

People always say ‘never talk about religion at a party,’ this is true even for college students. But if you’re a female in college, talking about religion is not only taboo, it’s unheard of. After being brought up by parents with two different ideologies, Christianity and Islam, I set out with this research project to better understand what role religion plays for my other female peers. Analyzing predominantly what their chosen theology means to their identity, how they advocate for their faith, how their ideology intersects with dating and what they perceive to be the biggest misconception about them for being religiously affiliated. I chose women who were students at UW from a variety of majors who identified with either Christian or Islamic based faiths, since this is where the majority of my previous research and experience has been. My primary methods were through long-form interviews, ethnographic observations and interacting with them on a daily basis as they moved their lives and their faith. Hearing about the challenges these women overcome on a daily basis just for identifying with a particular religion has solidified my hypothesis that ideology plays a pivotal role in their undergraduate career. Based on my research thus far, it has proven that it affects them in regards to their academics, involvement on campus and their interactions with their peers on campus. Further research will yield more information about the depth that these affects have taken. Overall, the outcomes have also been both surprising and inspirational to see how these women embrace, advocate and represent their faith. This work aims to open up and spark some dialogue about what religion means to college students and how societal framework does not always accurately represent these identities.

According to the World Health Organization, every year about 3.3 million babies are stillborn and more than 4 million die within 28 days of birth. Yet the death of a baby remains a very difficult subject in contemporary American society and bereavement interventions in perinatal medicine are still quite limited. This research will expand our understanding of the role photography plays in assisting parents with the process of mourning neonatal, perinatal, and infant death. By examining the perspectives of healthcare professionals, photographers, and parents in regard to the practice of bereavement photography, the research will investigate the ways in which photographs are used and transmitted, in both the private realm of bereaved families and the public domain of cyberspace. This study aims to understand how photography is used in the process of memory making and consequently, how the act of creating memories enables emotional healing. Finally, it will explore how bereavement photography exists at the junction of two shifts simultaneously occurring in cultural practices and social attitudes: the renegotiation of the boundaries between public and private, and the development of newer, characteristically modern, expressions of grief. This work has the potential to raise awareness about this developing mourning practice and increase the efficacy of bereavement interventions in neonatal and perinatal care, with the ultimate goal of providing a more widely available framework for helping parents cope with this hitherto often unspoken of, and invisible, loss.

Recent advances in genome sequencing have allowed for the study of metagenomes, genetic material recovered directly from environmental samples. This has produced an enormous number of enzyme sequences without efficient methods for characterization. Since it is unknown whether a characterized enzyme is the best catalyst for a specific reaction, uncharacterized, natural enzymes in the metagenome may be better candidates for catalyzing the specific reaction. Thus, I am developing methods to search for and computationally characterize metagenomic enzymes with the same function as enzymes of therapeutic and commercial interest. By utilizing the Rosetta Software Suite to produce highly accurate models of enzyme structures, this method will evaluate an enzyme sequence’s potential for catalysis directly from a gene sequence. In order to validate my computational techniques, I will experimentally determine catalytic rates of enzyme candidates. As the method for an efficient metagenome search is still unknown, I am working to determine proper parameters for a homology search by using visual and statistical analysis of enzyme structure models in order to produce a diverse set of genes for experimental characterization.

Gluten intolerance disorders such as Celiac sprue elicit a painful immunological response in the intestines of patients who consume gluten. Gluten is a polypeptide found in wheat, barley, and rye, and contains repeating Pro-Gln-Leu-Pro (PQLP) motifs. Currently the only treatment for gluten intolerance is elimination of gluten from the diet. Our goal is to design an enzyme therapeutic that can be taken as a drug therapeutic in pill form. The engineered enzyme will break down the immunogenic PQLP motifs before gluten reaches the small intestine and can elicit an inflammatory response. Kumamolisin-As, a protein isolated from Alicyclobacillus sendaiensis, demonstrates promising proteolysis on PQ residues, and works in the low pH of the stomach. Using the protein-engineering program “FoldIt,” we designed novel mutations to Kumamolisin to improve its activity on PQLP. Our best version of the enzyme, dubbed KumaMax, degrades gluten over 700 times faster at pH 4 than SC-PEP, an enzyme currently in clinical trials. After further protein characterization, we hope to start clinical trials on KumaMax with the future goal of creating an effective treatment for gluten intolerance.

Life is abundant on planet Earth but we have relatively few locations in which we can study environments similar to those on other celestial bodies. One possible terrestrial feature that is similar to those on some of the moons of Saturn and Jupiter is Lake Vostok, located under 4000 meters of ice in Antarctica. If we can prove that life can survive in this desolate environment that has been covered by ice for the last 35 million years, there is a heightened chance that extraterrestrial life exists within our own solar system. To study this area, we are designing a probe that will melt through the ice and take measurements from the lake to determine if bacteria or other life forms can survive in such a harsh environment. The main goals of my project were to create a mechanism that will allow the probe to move vertically in the lake via user control, determine the optimal cable and wire storage method for such a large endeavor, and eventually design a housing for the probe that can withstand immense pressure without leaking. I did this by using 3D computer aided design software and pressure and stress analysis tools. From these designs, I manufactured actual prototypes to test my concepts. Eventually, this work will lead to a functioning probe that will survey Lake Vostok and other sub-glacial lakes in an attempt to find evidence of life.

Plants respond with a sink stimulation of photosynthesis when colonized by bacterial and fungal mutualists, which compensates for costs of carbohydrate allocation to the microbes. Problems may arise when light is limited and plants cannot increase photosynthesis. We hypothesize that under such conditions the costs for maintaining the mutualism outweigh the benefits, which ultimately turns the beneficial microbes into parasites exploiting resources and reducing host fitness. We study these plant-microbe interactions under different light availabilities using lima bean plants, rhizobia (nitrogen-fixing bacteria), and mycorrhizal fungi. In our study, we apply two levels of light (full light and light intensity reduced by 50%) and four levels of microbial inoculation (sterile soil, rhizobia, mycorrhiza, and rhizobia x mycorrhiza). Fitness-relevant plant parameters are measured including plant vegetative growth as well as flower and seed production. Our study will provide first insights into potential shifts in functional interactions between plants and plant-associated microbes under light limitation.

Escherichia coli can contaminate food, such as beef and spinach, causing illnesses ranging from recurring diarrhea to death in susceptible individuals. They may produce a toxin typically associated with another harmful bacterium known as Shigella spp. This toxin is referred to as “Shiga-toxin”, and E. coli that produce this toxin are known as STECs. While E. coli O157 remains the most common STEC in the United States there are over 100 STECs that can be just as harmful. My project, conducted in collaboration with individuals at CSUEB and the USFDA, involves identifying chemical indicators that would help detect different strains of non-O157 E. coli in contaminated foods, and determining if these STECS are vulnerable to a coliphage and a Bdellovibrio sp. invasion. Specifically, nine different STECs were chosen to be screened for their ability to produce catecholate siderophores (phenolates), such as enterobactin, chelating compounds important for some pathogenic bacteria in the acquisition of iron. The same STECs were screened for the presence of acyl homoserine lactones, chemicals involved in bacterial communication, also known as quorum sensing, and expression of virulence factors. Assays were conducted to determine if a coliphage and a Bdellovibrio sp. can infect these STECs. Detection and identification of non-O157 STECS is not easy, which hinders determination of their origin and, subsequently, how to eliminate them. If new tools, such as the use of predators or chemical indicators were developed to facilitate detection of these bacteria, then determination of the source of contamination (e.g., packing plants and fields) may occur, and quicken measures that prevent or, at least, decrease further infection, disease and/or death.

The overall objective of this research project is to develop a high-yield site-specific bioconjugation method for use in developing new cancer therapy agents using the reaction of benzaldehydes with oxyamines. Bioconjugation is the term to describe the development of new pharmaceuticals. It often involves coupling one biomolecule (e.g. monoclonal antibody) with another chemical species (e.g. drug, toxin, radionuclide-binding molecule). The first aim of the project is to synthesize four water-soluble discrete-sized polyethylene glycol (dPEG)-benzaldehyde derivatives, and then determine their relative reaction rates with a water-soluble oxyamine compound. The fastest reacting compound is determined by high performance liquid chromatography (HPLC) analyses and studied further. The second aim in the research project is to conjugate the two most reactive dPEG-benzaldehydes to a monoclonal antibody. The final aim is to assess the bioconjugation reaction of a biotin-oxyamine derivative with the two benzaldehyde-modified antibodies. The biotin-oxyamine conjugation yields will be determined using an avidin-binding (HABA) assay that uses UV quantification.

Infection depends on the successful colonization of a host by a pathogen. For a virus to infect its host, it must come into contact with the host, gain entry into target cells, and replicate. There are a variety of factors that could influence the likelihood of a host becoming infected. For example, a higher concentration of virions in the environment will increase the probability that a host will come into contact with one. The relationship between viral concentration and the number of hosts infected could exhibit various forms, such as linear, logarithmic, or exponential. Viral genetic differences could also influence infectivity if certain genotypes are more effective at initiating infections. In this study we examined the relationship between dose size and the proportion of hosts infected by the fish rhabdovirus Infectious hematopoietic necrosis virus (IHNV), and whether this relationship differed between virus genotypes. We compared the minimum infectious dose of two genotypes, one with higher virulence (HV) and one with lower virulence (LV), to determine how infectivity is associated with virulence. Previous studies indicate that at 100% infection levels, HV reaches higher viral loads than LV, in addition to having a host entry advantage, but to our knowledge the minimum infectious dose of either genotype has not been investigated. We hypothesized that the more virulent genotype would have a lower minimum infectious dose. We infected groups of fish with 10¹, 10², 10³, 10⁴, and 2x10⁵ pfu/mL of one of the two genotypes. After allowing the virus three days to initiate an infection, the fish were euthanized and their viral RNA was extracted and counted with quantitative real-time PCR to determine whether each fish was infected. The information gained about infectious dose can be used to produce a more refined understanding of viral fitness, and thus, viral evolution.

 As a river feeds into the ocean, a buoyant, laterally spreading, rapidly moving layer of fluid which runs seaward over the ocean surface (i.e., a river plume) is formed. At the interface between the fluids, shear stress creates turbulence, which causes mixing and plume deceleration. Additionally, pressure differences due to density differences and the plume surface slope create a pressure imbalance. The interplay of these and other processes are poorly understood. This lack of understanding is in contrast to the importance of river plumes dynamics: plume dynamics determine the ultimate concentration of contaminants and biological debris (notably red tide) in a larger (geostrophic) scale current which forms after the plume decelerates significantly. This geostrophic current runs along the coast and can transport contaminants to coastal marine ecosystems, beaches, and coastal communities. In order to predict the potential danger in the propagation of river contaminants along coasts, it is necessary to develop a quantitative understanding of plume dynamics. To this end, a momentum balance (an application of Newton’s Second Law to fluid flow) is currently being carried out. The relevant terms in this balance are the along-flow pressure gradient, the vertical turbulent interfacial stress gradient, and the total acceleration. Each of these terms can be constructed from velocity and density profiles which have been obtained for different experiments under both channelized and spreading conditions using particle image velocimetry (PIV) and particle laser-induced fluorescence (PLIF). By comparing the relative magnitudes of terms in the balance, a quantitative understanding of the importance of different dynamical processes will be obtained, and by comparing the form of the balance in channelized and spreading cases, a hypothesized relationship between spreading (which causes the fluid to collapse and accelerate) and turbulence/mixing (the magnitude of which is determined by the speed of the plume) will be investigated.

 The social phenomenon of mass incarceration has opened the door to a full range of perplexing issues that continue to stymie researchers and policy makers. One particular and obdurate social problem is sexual offending, which seems immune to the so-called "evolving standards of decency" ideas espoused by the United States Supreme Court. Whereas society's rules of law and punishment are theoretically evolving to become more civilized and less barbaric, the practices of many of its citizens, including sex offenders, is not keeping pace with the evolution of ideas and behaviors. In fact, sex offenses are a ubiquitous fact of life - directly or indirectly - for many people in the United States. Not even a prison mandate issued by President George Bush in 2003 called the Prison Rape Elimination Act has positively affected the problem of sexual victimization in prison. This research seeks to add prisoners' voices to the ongoing conversation that exists among researchers and policy developers on the complicated and emotionally charged subject of sex offenders. This research asks a simple question: What are prisoner attitudes about sex offenders? The hypothesis maintains that inmate attitudes, when measured by the CATSO (Community Attitudes Toward Sex Offender) scale, will mirror mainstream attitudes that have been measured using the same instrument. The purpose of this study is to improve prison policies that pertain to sexual victimization by revealing a piece of the prison rape and prison violence puzzle that may be hidden within the attitudes of men and women held captive in U.S. prisons. 

The purpose of this study was to examine how students from different backgrounds and ethnic groups experience UW-River Falls. Previous studies, including the Campus Climate Survey (surveying all faculty, staff, and students in 2009), have shown that white students may experience fewer incidents of discrimination or bias as compared to students of color. While the Campus Climate survey gave us a broad understanding of differential experiences on campus, we felt it was important to dig deeper into students’ beliefs and experiences. In addition to asking about experiences of discrimination on campus more generally and with professors, we also asked about a variety of other issues: GPA and time spent studying, perceptions of their own intelligence, levels of self esteem and ethnic identification, and background experiences (among many other questions). Our survey was based on a much larger survey of UCLA students (Sidanius, Levin, van Laar, & Sears, 2008) that was modified to fit UW-River Falls. The survey was administered to over 293 students from across campus in classes, student organization meetings, and special sessions set up to collect data (General Psychology Participant Pool). Our results indicated that students of color had lower GPA’s and felt less smart than white students but they also reported studying more on average. Students of color reported lower Self Esteem but higher ethnic identification than whites and they perceived UW-River Falls as less diverse than whites. Students of color reported more experiences of discrimination on campus as well as more biased professors. Finally, among students of color it seems that ethnic identification may have a somewhat protective effect. Higher levels of ethnic identification were correlated with higher self esteem, but also with greater perceptions of campus and professor bias.

In recent years, gold nanoparticles have been utilized in biomedical applications due to their biocompatibility as well as unique optical properties. In order for the gold nanoparticles to become effective agents, they are functionalized with vectors that will target the nanoparticles to specific cells to be imaged. Conventionally, hybrid gold nanostructures have been produced by complex, multistep chemical cross-linking bioconjugation procedures usually involving biologically-unfriendly stringent conditions. To overcome difficulties related to conventional cross-linking methods, we propose a novel surface functionalization platform using biocompatible gold-binding peptide templates (AuBP). AuBPs were previously selected from combinatorial FliTrx peptide library and demonstrated nanomolar binding affinities to a gold surface under physiological conditions. We then conjugated AuBP with other binding domains engineered to bind to the constant Fc-region of an antibody (FcBP). This antibody is then recognized by receptors in the cell membrane for absorption. The bifunctional AuBP-FcBP peptides self-assemble on the surface of the gold nanoparticles, and effective gold binding is shown through a localized surface plasmon resonance, high-salinity stability assay and gel electrophoresis. A dot blotting assay is used to confirm the binding of the antibodies. These peptide-functionalized and cell-specific nanoprobes have a great potential for developing novel bioimaging tools for diagnostics and therapy.

Mesanchymal stem cells (MSC) can differentiate into a variety of cell lineages, including adipocytes, chondrocytes, and osteoblasts. This gives them great potential for use in regenerative medicine. To harness this potential, we must understand the effects of the various stimuli that can be applied to cells in in vitro culture. We produced an ECM mimetic nano-grooved cell culture substrate via capillary force lithography. An agarose diffusive microfluidic device was used to establish an SDF-1 α gradient across the nanogrooved substrate. Bone marrow derived mesanchymal stem cells (BM-MSC) were seeded on the substrate, and live cell imaging was carried out over a few days’ time. Using the time-lapse images, the differentiation, proliferation, motility, and elongation of the BM-MSC were analyzed and quantified. Understanding the synergistic effects of topography and bio molecular gradients will prove helpful in future efforts to create MSC regenerative medicines.

Neutrinos and antineutrinos are elementary particles with no electric charge and very small masses. From neutrino oscillation experiments we know their mass differences but not their absolute scale. Additionally, it is unknown whether neutrinos are their own antiparticles. These are two of several significant questions in neutrino physics and are important for furthering our fundamental understanding of the universe as we extend the Standard Model of particle physics. These questions can be probed by a search for the rare hypothetical radioactive decay known as neutrinoless double beta decay. The Majorana Demonstrator experiment will look for neutrinoless double beta decay in ⁷⁶Ge. Currently, the Majorana Demonstrator is in the development stage, and involves the collaboration of several universities and national laboratories. My research characterizes electrical crosstalk between nearby readout channels for this experiment. As neutrinoless double beta decay is hypothesized to such a rare process, a thorough understanding of the electrical crosstalk is necessary to adequately interpret the measured signals.

Measuring client adjustment throughout psychotherapy has been supported as a method to improve client outcome upon cessation of treatment. Weekly assessments inform the clinician how the client is responding to therapy and illuminate when adjustments to treatment may be necessary.  The Evidence-Based Assessment System for Clinicians (EAS-C) is a computerized outcome tracking system that allows psychotherapists to measure weekly progress and instantly view results with their clients in session. While there are excellent measures for tracking general psychological adjustment, many are too lengthy and arduous to facilitate completion on a weekly basis. Therefore, we created the seven-item Brief Adjustment Scale for EAS-C. We hypothesized a high correlation between the BASE-7 and the Outcome-Questionnaire 45.2, an established measure of psychological functioning. Furthermore, we hypothesized participants would report more willingness to complete the BASE-7 and would rate it as easier to complete than the OQ-45.2. Adult participants were recruited through the online survey website, Mechanical Turk, and completed the BASE-7, OQ-45.2, and an acceptability and utility questionnaire online. The BASE-7 correlated highly with the OQ-45.2, indicating high concurrent validity. Participants rated the BASE-7 significantly more acceptable than the OQ-45.2, suggesting participants would be more willing to complete the BASE-7 on a weekly basis. Participants’ ratings of the utility of the BASE-7 and the OQ-45.2 were not significantly different, indicating participants believed both measures would adequately communicate levels of psychological distress to a mental health provider. These findings demonstrate that the BASE-7 is a valid tool for measuring psychological distress that may be more suitable for weekly administration than lengthier measures. As a brief outcome measure, the BASE-7 is a promising new tool that may be used to inform both clinician and client of treatment progress over time.

A vast quantity of water is moving in the atmosphere under the direct influence of solar energy. Therefore, it is important to understand the energy balance to characterize the behavior of the water cycle of a particular region. Water gets back from ocean and land masses to the atmosphere through the process of evaporation and evapotranspiration (ET). Evapotranspiration is an important phenomenon in the water cycle for the estimation and evaluation of the available water resources. If we understand how ET is changing over space and time, then we can more accurately calculate the crop water requirement (CWR) at a high resolution for that region. This can help farmers in managing water resources very efficiently. Current research has difficulty in projecting how ET is going to change over different locations in the future. Therefore, through this research we are trying to understand the partition of the energy balance components and quantify them to help the water management in southern Idaho. To support this research, we will use the data from both Land Surface Hydrology Model and field observations and present the trends in surface energy balance components, including net radiation, latent (ET), sensible and ground heat fluxes. 

Marine based industries, particularly the shellfish industry, are increasingly concerned about the viability of their product due to changing ocean pH conditions. Many other organisms with calcareous shells or exoskeletons are impacted by this change in sea water acidity due to anthropogenic gases. One such organism is the Artemia salina, or brine shrimp. Acidification causes dissolution of the shells into calcium and carbonate ions that float freely in the water. It was hypothesized that three closed systems could be created to replicate the ocean conditions of the present and future, specifically in 50 years and 100 years. Brine shrimp were chosen to be test subjects due to their ease of propogation. The closed systems provided pH, Ca2+ concentration, and the vitality of the tested brine shrimp community data. The working hypothesis is that Ca2+ ion concentration will increase as the exoskeletons dissolve with the decrease of pH.

Organic matter (OM) production and decomposition is important to wetland health as it serves to cycle nutrients throughout the ecosystem. Current wetland monitoring programs in the Laurentian Great Lakes focus on structural indicators, such as fish, bird, and vegetation communities but lack the use of functional metrics such as organic matter processing. In this study we aim to create a new suite of functional indicators that focus on OM production and decomposition. Decomposition rates were measured using mesh litter bags containing dried bulrush tissue (Schoenoplectus acutus) as well as by the use of cotton strips incubated for 8 weeks at 20 coastal wetlands of Lakes Michigan and Huron. Nutrient limitation of decomposition was also measured using nutrient diffusing bags containing nitrogen, phosphorus, and a combination of nitrogen and phosphorus fertilizers. OM production rates were measured by periphyton biomass accrual on acrylic rods over an 8-week period. In addition, nutrient diffusing substrates were deployed to test the effects of nutrient limitation on algae growth. We predicted that decomposition rates would be positively associated with higher nutrient concentrations. We also predicted that algae growth rates would be greatest on substrates containing high nutrient concentrations. When developed, functional indicators could be used alongside current structural indicators to provide a better overall assessment of wetland health.

Where plankton reside in the water column is affected, among other things, by haloclines. Therefore the salinity stratification of the water can have major effects on the levels of plankton present. Our study focused on Possession Sound zooplanktons’ response to varying levels of salinity in a vertically stratified column. We questioned the preferred salinity level of various zooplankton found in a sample of Possession Sound water. We hypothesized that most zooplankton will prefer waters approximately 24 ppt since that is the average salinity of Possession Sound. We have so far looked at literature surrounding the subject and constructed the necessary apparatuses for the experiment. As part of our spring thesis research, we plan on observing the plankton’s response to the introduction to this environment.

Bioaccumulation of heavy metals due to river runoff is a pressing issue. Through the Ocean Research College Academy (ORCA), I will conduct research during the spring term analyzing the presence of heavy metals in the Puget Sound and the possible bioaccumulation in harbor seals. Sediment is collected using a Van Veen Grab from set sites around the Puget Sound once a month for the span of a year. Sediment samples will also be taken from various sites along the Snohomish River during the month of April. These samples will be sent to the Everett Environmental Laboratory to be tested for levels of mercury, arsenic, lead, zinc, cadmium, and copper. We will then attempt to obtain harbor seal excrement from the Everett Marina and send to the lab to be tested for the heavy metals listed above by the beginning of May. The data will be used to compare the amount of heavy metals found in the sediment of the Puget Sound to the amount of heavy metals found in secondary consumers (in this study harbor seals).

Pyroclastic Density Currents (PDCs) are the most dangerous hazard associated with explosive volcanic eruptions. Due to the danger associated with observing these ground-hugging currents of searing hot gas, ash, and rock in real time, their processes are poorly understood. In order to understand flow dynamics, including what controls how far PDCs travel and how they interact with topography, it is necessary to study their deposits. The May 18th, 1980 eruption of Mt. St. Helens produced multiple PDCs, burying the area north of the volcano under tens of meters of PDC deposits. The eruption is one of the best observed on record, and deep drainage erosion over the past 30 years has exposed the three-dimensional structure of the PDC deposits, making this intensive study possible. For each flow unit we measure deposit thickness, bedding style, clast size, density and sorting, and degree of pumice rounding with distance from source. The intricate vertical and lateral facies changes and complex cross-cutting relationships away from source, including rapid changes in bedding and granulometry characteristics within each unit, indicate that the currents interacted with complex topography early in their propagation. We use this observation and analysis to better understand and interpret flow dynamics. The data we collect will be used to refine and validate numerical models of PDCs, ultimately providing a more accurate hazard assessment for explosive eruptions.

Perception of natural hazards and risk among Pacific Northwest (PNW) residents is not well known. Familiarity with a given population's perception of natural hazards and the threats they present is vital for the development of effective education prior to and emergency management response after a natural event. While much work has been done in other active tectonic regions, little work has been completed in our region. The objective of this work is to assess the current perception of earthquake and volcanic hazards in the PNW, and to better understand the factors which drive the public's behavior concerning preparedness and response. We developed a survey to assess the participants' knowledge of natural hazards common to the region, perception of risk concerning these hazards, and level of preparedness should a natural hazard occur. The survey was distributed to the PNW public via a class project in 'Living with Volcanoes' (ESS 106) in March of 2011 and 2012, which returned more than 1000 responses. Here we highlight the responses from the UW student population because of their uniqueness as a large semi-transient population (typical residence of less than 5 years). Knowledge of natural hazards and proximity to hazard sources was found to be low/inaccurate, which corresponds to a low perception of risk. Understanding/awareness of evacuation/coping protocol for natural hazards was also found to be low, suggesting this large, semi-transient population lacks the understanding of proper preparation for and response to a natural hazard. Results from the survey indicate need for education of this population concerning the risks of natural hazards in this region and the steps for better preparedness. The ultimate goal of further education is to create a "culture of safety" rather than "moments of reaction" (USGS initiative).

Comic books have long been used as an educational tool to improve and protect public health in the U.S. In 2008, the Native Comic Book Project (NCBP) was launched as a youth-focused community education project of Native People for Cancer Control (NPCC); a National Cancer Institute funded Community Network Program Center, based at the University of Washington. The availability of cancer screening tests, high quality health care, encouragement for health promoting behaviors, and access to cancer clinical trials, are often not available to tribal communities. As a result, American Indians and Alaska Natives (AI/ANs) experience the worst cancer related disparities and have the poorest survival rate among all other racial/ethnic groups. The purpose of the NCBP is to reduce cancer risk by involving AI/AN youth in creating comic books on health topic such as health living, tobacco use, cancer risk, disease prevention, and physical fitness. The NCBP is modeled after Dr. Michael Bitz’s The Comic Book Project, but is adapted for AI/AN youth and incorporates Native storytelling and traditional ways of living. We are currently conducting a formal evaluation of the NCBP using pre- and post-intervention assessments to measure knowledge, habits, and decision-making regarding tobacco use, healthy eating, exercise habits, and human papilloma virus (HPV).

Many university student organizations host events for a broader population than just their member base. Yet, these organizations’ events often lack visibility among the broader student population. We examined this problem in the context of the University of Washington, a large public university in the Pacific Northwest. The goal of this project was to develop an effective solution for both students and organizations. To understand students’ needs, we deployed a survey to the general student population and received 72 responses. We also interviewed three student organization leaders and six students on event attendance habits. Based on this data, we identified key features for an information system that would be responsive to students’ needs. To refine these ideas, we developed and tested feature concepts in multiple prototypes to explore various designs. With this feedback, we then built a website that provides students with: (1) access to more events; (2) ability to personalize profiles to display only events likely of interest to them; and (3) integration with Facebook. Specifically, when students create an account on the website, they are able to select specific “tags” (i.e., social, academic development, and so forth) and specific student organizations that match their interests. The events displayed in students’ profiles match their set preferences. From the organizational perspective, our solution enables easier promotion of events. A core focus of the website is Facebook integration. Students are able to log in to our website with their Facebook accounts for their convenience. Student organizations are able to create a profile, then upload events to our website by directly importing events information from Facebook. For our solution to be successful, the website must gain wide adoption by students and organizations. Ultimately, we hope wide usage of our website will lead to increased event visibility and participation amongst the student community.

As young people between the ages of 16 and 24 become more engaged in their communities, they begin to seek out ways to contribute to volunteer activities. As this occurs, young people often need to track their service efforts, and organizations need to regularly reach out to volunteers and validate their participation. Despite advancements in web technology, paper logs that are prone to becoming unorganized or misplaced are still used by people and organizations as the primary method for keeping track of volunteering records. Such was the case for our nonprofit client, the University of Washington Foundation. To improve this situation, we first conducted a literature review on attitudes and behavior around volunteering. We then designed an online survey that was filled out by 64 qualifying respondents, and conducted 20 in-person interviews with students from local Seattle Public Schools and the University of Washington. Results suggested that young people consider (1) organization, (2) history tracking, and (3) event coordination as important qualities in helping to better manage their volunteering efforts. Building on those findings, we sought to create a web application called vTracker that allows volunteers to centralize their records in an online database for better safekeeping, verification, and retrieval. vTracker’s design and implementation process included the creation of wireframe diagrams, user interface design specifications, and a functional prototype. According to feedback from students and our client organization that tested our prototype, vTracker provides a convenient way for volunteers to set personal service goals and have their volunteer hours validated by participating organizations; similarly, organizations can share volunteer opportunities, confirm volunteer profile records, and recommend the work of their volunteers. Eventually, the Student Philanthropy Education Program of the University of Washington Foundation will adopt the web application as an active record-keeping tool because vTracker effectively streamlines their volunteer management process.

Quorum sensing is cell density-dependent communication that regulates many functions in bacteria. Signal synthases (I) produce acyl-homoserine lactones, which diffuse into the environment and activate signal receptors (R) when they reach a critical concentration. Synthases and receptors often form cognate pairs. The soil bacterium Burkholderia thailandensis encodes three I-R pairs. The I-R1 system controls cell-cell aggregation and activates many putative aggregation factors including the bce genes that likely encode an exopolysaccharide. The I-R2 system controls antibiotic production. The antibiotics are members of the bactobolin family and are effective against both Gram-positive and Gram-negative bacteria. Both aggregation and antibiotics are believed to promote competitiveness in the diverse soil communities where B. thailandensis is found. We have developed genetic screens to learn more about quorum-controlled antibiotics and aggregation in B. thailandensis. The first screen identified bactobolin-resistant isolates of the soil bacterium Bacillis subtilis, which is normally sensitive to bactobolin. We submitted these mutants for whole genome sequencing to investigate the mutations that confer resistance, and with our results we hope to gain insight into how bactobolin acts on target cells. The second screen was designed to isolate variants that overproduce aggregation factors. Quorum sensing mutants do not wrinkle but variants arise that produce aggregation factors by other means. We are isolating such variants and identifying the underlying mutations to understand how they compensate for the loss of quorum sensing regulation. This may reveal the elements involved in regulating aggregation. These variants will also be useful to learn about the advantages of aggregation in different contexts. Through our two screens we hope to better understand quorum-controlled aggregation and antibiotic phenotypes. Our findings will be useful in further studies of the importance of each of these in competition.

Helmets have been trusted to provide protection against head impacts for millennia and have become a universally promoted piece of safety equipment. Current helmet standards provided by NOCSAE, SNELL, and ASTM for football, ski, motorcycle, and other activities specify the requirements for critical impacts under varying conditions such as; temperature, impact location, and impact energy. However, most standards only minimally account for the effects of sub-critical collisions and the natural fatiguing processes experienced by a helmet during its use. Intuition suggests that these seasonal cycles and minor impacts attenuate the utility of protective headgear; however, a scientific inquiry into such effects could illuminate or invalidate this assumption. The working hypothesis of the research team under Professor Randal Ching and Irv Scher was that sub-critical impacts and seasonal cycling would diminish a helmet’s protective abilities (as measured by metrics such as peak linear acceleration and severity indices), and the goal was to illustrate that current standards and refurbishing methods need to account for these various effects of age and use. Accordingly, my research group designed a helmet drop tower to test a variety of different helmets (football, motorcycle, and ski) according to SNELL and NOCSAE standards, and used helmets were compared to their new counterparts. Direct comparisons between used and new helmets were used to evaluate the effects of age and minor impacts on helmets, the effectiveness of current standards at predicting the utility of helmets, and the expected lifetime of helmets under given conditions. As the first independent study of helmet performance in the state of Washington, this study could give vital feedback to helmet manufacturers, helmet standard foundations, and helmet users alike.

Statistically, Asian Americans have significantly lower traffic accidents than any other minority group in the United States. However, there exists a stereotype that Asian Americans are a bigger risk on the road than any other ethnicity. This study explored the perspectives of Asian Americans, specifically Korean American women living in the city of Bellevue. Despite having enough English speaking skills to live comfortably in America, they had either a difficult time understanding roadway signs and posts, or if they did, it was not intuitive at first glance or within the time span necessary to make a decision on the road. The major problem that these Asian Americans felt was that in their homeland, many traffic decisions were made based on their instincts due to minimal roadway signs, or enforcement was so minimal that conforming to these traffic laws were not a priority to them. They reported that this mentality was reinforced more so because even when traffic laws were ignored, accident rates were low. This suggests that Asian Americans, though involved in less traffic accidents, make decisions less-rapidly, are confused on the road, or less readily conforming to traffic regulations. This study helps uncover a largely untapped field of study involving traffic safety within minority groups, and will further contribute to future research in similar topics.

The Human Papillomavirus (HPV) is the most common sexually transmitted infection and some types have been linked to cervical cancer. Approximately twenty million Americans are currently infected with HPV, and an additional six million will become infected next year. In 2006 a vaccine was approved to protect against certain types of HPV. This research seeks to understand the attitudes and beliefs surrounding the decision to be vaccinated. Specifically, the research will examine how perceived risk of infection by HPV has affected the vaccination decisions in the unique cohort of women who were above the recommended vaccination age when it was first released. Through focus groups and anonymous, online questionnaires involving undergraduate women in Seattle, this research examines factors, especially sexual contact, that affect perceived risk. This investigation is repeated with a cohort of undergraduate men of the same age in Seattle in an effort to explore any possible differences in perceptions that seem to be polarized by gender. By uncovering young adult perceptions of HPV vulnerability, this project can provide insight to future public health work related to HPV vaccines and other sexually transmitted infections.

Many examples of control systems are found in modern-day industrial applications, ranging from the Segway to cruise control in an automobile. The self-stabilizing inverted pendulum serves as an archetypal problem by which the robustness of such control systems, which use feedback to control themselves, is measured. In this project, I analyze several simple control systems involving the inverted pendulum, and attempt to find their stability solution. I have also built a computer simulation in Mathematica, a computational software package, which demonstrates fundamental concepts in control theory, as well as the difficulty of manual control and the usefulness of feedback in self-stabilizing systems. This simulation provides a useful learning tool to users who otherwise have little experience with the theory of control. Finally, I investigate theoretical problems related to the so-called radius of stability, which is a number that tells us how far we may deviate from equilibrium before the control system fails. I hypothesize that as further variables are introduced into a control model, the radius of stability will decrease accordingly. Since control systems are widely used in modern day society, it is important that we understand the stability of such systems, thereby maximizing the safety and effectiveness of their applications.

What the media has termed as Mad Cow disease is a form of Transmissible Spongiform Encephalopathy (TSE). It is also known as a prion disease and occurs when the normal prion protein in the brain misfolds. This is thought to induce other prion proteins around it to misfold, leading to brain degeneration. Scrapie is a form of TSE in sheep; primarily infecting the central nervous and lymphoreticular systems. There is currently little explanation for why the process occurs, although, studies show that cytokines may be involved. Scrapie will not readily cause disease in normal mice. However, transgenic mice can be infected. These transgenic mice have a prion gene knockout with an insertion of the sheep version of the prion gene, which makes them susceptible when directly infected with scrapie prions. To further our understanding of prion diseases, we aimed to learn more about its source material, transmission, host genetic markers, and immune response with the help of a transgenic mouse model. We challenged transgenic mice with scrapie via the intracerebral route and observed them for signs of disease. Certain tissues were collected and analyzed at multiple points of infection for infectivity, potential co-localized proteins, cytokine dynamics, and growth factors. Various cytokine levels could increase, decrease, or stay the same throughout the infection period. This will enable a better characterization of immune response to prion disease and potentially provide a measure of disease progression using blood cytokine levels.

Plants sense and respond to changes in their environment. For example, elongation of the embryonic stem ensures seedlings reach light after they germinate. This critical stage in a plant’s life is highly regulated by hormones, including gibberellic acid (GA) and brassinosteroids (BRs). Using the model system Arabidopsis thaliana, we discovered GA and BRs interact to control stem elongation during early development. We found that treating seedlings with both hormones resulted in a synergistic growth response during some phases of development but not others. We are exploring the genetic basis of this response using seedlings mutant in different aspects of their GA and BR pathways. For example, DWF4ox seedlings over-express a gene that encodes a BR biosynthetic enzyme. These seedlings make more BRs and have an enhanced growth response. DELLAs (RGA and GAI) repress growth and are degraded by GA. Seedlings that have reduced DELLA (rga gai) function also have enhanced growth. We are testing the growth responses of the DWF4ox rga gai triple mutant looking at hypocotyl elongation rates. By using these and other mutants that have compromised GA and BR pathways we hope to better understand the molecular mechanism of the interaction between these two hormones.

Alcohol use continues to be a widespread and serious problem among college students. In recent years, the posting of alcohol-related content on social media such as Facebook has become an increasing concern. However, little research has evaluated the link between alcohol content on Facebook and students’ actual alcohol use. Recent findings suggest that the prevalence of alcohol-related content on an individual’s Facebook wall may be predictive of alcohol-related problems. We expected that the more students posted about alcohol, and the more their friends posted about alcohol, the more likely it was that students would report more actual drinking, more alcohol-related problems, and higher perceptions of how much others drink. A sample of 1148 undergraduate students (657 women, 403 men) completed a web-based survey that included measures of their Facebook use, their typical drinking behavior, their alcohol-related problems, and their perceptions of typical student drinking norms. Data were analyzed using generalized linear modeling. Results were consistent with hypotheses. After controlling for gender and number of Facebook friends, both participants’ postings about alcohol and their friends’ postings about alcohol were significantly associated with greater drinking, more alcohol-related problems, and higher drinking norms. Thus, the alcohol-related content that students post and that their friends post on Facebook is related to real-life drinking behavior and may be an important risk factor for predicting hazardous drinking. Future research should focus on the implications that students’ alcohol-related Facebook content may have on potential screening for treatment and research purposes, as well as on Facebook itself as a potential platform for treatment interventions.

The concept of "inclusion" is a class placement method for children who have special needs; this involves integration into a classroom with traditional student group populations. Previous research states to the extent possible, and deemed appropriate, students with special needs have been known to benefit simply by being surrounded in a learning environment with diverse peers. While the focus is usually on the particular child(ren) with special needs, research mainly analyzes cognitive development. There may be various positive impacts placed upon the other students on social and emotional levels of development. This literature review examines whether classroom inclusion enhances a typically developing student's sense of empathy, acceptance, and equity for non-traditional student (including students with special needs) population groups among the developing traditional four year old students. This research project anticipates that there will be "enriched" development and a higher sense of empathy, acceptance and equity for the general population groups. These inquiries will be addressed through a literature review to synthesize what we currently understand about the effect of inclusion on typically developing children. The review will investigate work related to empirical studies on preschoolers' experiences in inclusive classrooms. Additional investigation will include foundational perspectives as presented by leading scholars and organizations in the field of early childhood special education. Based upon future findings, the examination of further research of behavioral patterns amongst both populations will be implicated.

Paraeducators are increasingly becoming a key component in special education. As class sizes increase, schools are hiring paraeducators to work with students with disabilities.  However, qualifications and training of paraeducators are minimal in most states. In Vermont, only 30% of jobs specifically required previous experience working with children. The majority of states have no educational requirements for paraeducators beyond a high school diploma. Typically, paraeducators do not receive much training besides an orientation to school policies and special education teachers do not usually help paraeducators understand IEP (individualized education plan) goals. Unfortunately, these kinds of practices lead to turnover rates that can be as high as 50% for recent hires. High turnover rates are costly to the school district, impede cooperation between IEP team members, and negatively impact student learning. A review of recent research pertaining to paraeducator training and instructional strategies for working with students with special needs led to the development of this toolkit. The purpose of this toolkit is to support paraeducators and classroom volunteers who are working with students with a variety of special needs in many different classroom settings. This toolkit provides information about specific disabilities, instructional strategies, background information on special education, and further resources. Particular emphasis was placed on special education in Washington State. There are more paraeducators in the United States than there are special educators—under IDEA (Individuals with Disabilities Education Act), trained paraeducators are allowed to provide special education instruction. However, most paraeducators get little to no training and a great deal of responsibility for students vulnerable to academic failure or stagnation. This toolkit was designed in the hopes that, as a free resource, it could provide much needed background information to paraeducators and classroom volunteers.

A continuous measurement of wall shear stress can be achieved using shear sensitive liquid crystal coatings (SSLCC). Utilizing thin films of polymer-embedded birefringent liquid crystals as sensors, they deform elastically when subjected to shear stresses. The light passing through the SSLCC is recorded with a charge-coupled device camera and is processed by the specialized birefringence detecting Milliview. Shear magnitude and direction are determined from the results. A single coating comprises of polymers, solvents, and liquid crystals in varying proportions. When applied to a surface, solvents vaporize, leaving liquid crysals embedded inside polymer structures. By adjusting the proportions of the components, the viscosity and curing rate of the coatings can be controlled to match the method of application. A series of formulations were applied to a flat, glass substrate using methods such as airbrushing and direct deposition. Each combination was tested repeatedly at free-stream speeds ranging from 5 m/s to 36 m/s. The best coatings were determined by optical clarity, surface smoothness, signal strength, and reusability both through visual observation and testing in a small wind tunnel. Few combinations yielded both a high signal strength and reusability.

Relationships can be beneficial in many aspects of one’s life. For example, intimate relationships may provide individuals with the ability to cope in stressful circumstances. On the other hand, it may cause an individual to experience more stress during different situations. Bergman and Surrey (2009) found couples may experience as many as 3 or 4 stressful situations in a given day. According to previous research, couples faced with certain stressful situations will often look to their significant other for support (Neff, 2009). I will be looking at intimate romantic couples for this study. I will examine if couples help or hinder their partners during a stressful situation. By using math problems as a stressor, I will examine how couples cope with stress with their partner and if their significant other increases or decreases their stress during and after the process of solving a math problem. Having each one take the survey, I will be assessing the stress levels of both partners. In this study, I will use the Math Self-Concept Scale (MSCS), the Statistics Test Anxiety-Emotionality (STAE), Cooperative Problem-Solving Measure (CPSM), Subjective Units of Distress Level (SUDS), and math equations for the survey they will be taking. These measures will examine each individual’s level of stress before, during, and after the survey questions are completed.  I anticipate, during the process of solving math equations, the involvement of an individual’s partner will either increase or decrease their stress levels associated with the activity. I hypothesize that the individuals who are assisting their partners who are taking the survey will find themselves more stressed during the problem solving process and less stressed after the activity ends. This study could provide professionals and counselors with some valuable information that could perhaps teach couples more successful methods of support and communication.

Phytoliths, microscopic plant silica bodies, inform us about the types of plants that remain in the fossil record, allowing for reconstruction of past flora, climate, and ecosystems. The existing method for reconstructing vegetative structure and habitat type (open vs. closed) using phytoliths depends on the presence of presumed open-habitat grass types. This method may not be able to reliably reconstruct vegetation type when open-habitat grass phytoliths are absent, and depends on the assumption that open-habitat grasses have always been restricted to open environments. Therefore, a taxon-free, morphological approach may be more informative for inferring habitat openness using fossil phytolith assemblages. This study looks at the effects of light variation on epidermal cell shapes in modern grasses as a first step in creating a proxy for determining habitat type from the fossil record. Based on patterns observed in dicotyledonous plants, we hypothesize that epidermal grass cells will be more undulated when grown in reduced lighting condition. To test this, five species of grasses were grown in varying light treatments (20%, 60%, 100% (control), and 120% relative to the control). We took morphometric measurements of long and short cell types from epidermal peels and calculated their degree of undulation (UI). Results show three species where long cells had higher UI in deep shade (20% light) than in enhanced light (120% light), though the relationship is non-linear. With short cells only one species displayed a continuous increase in UI as light levels decreased. Thus, data from long cells show the greatest promise for use in the fossil record. To further test this method for paleoecological work, the UI of epidermal cells in soil phytolith assemblages from known modern habitat types will also need to be examined to see whether this UI and light correlation persists under natural growth conditions.

In the failed state of Somalia, piracy is increasing exponentially, impacting all nations that engage in trade or travel in the region. The economic and human cost of piracy is sure to rise as the situation devolves into maritime terrorism. Although current anti-piracy efforts are moderately successful, there is room for improvement. This report has thoroughly researched the situation to create one comprehensive source for understanding piracy in the Horn of Africa. Research methods included reviewing secondary source material, in addition to interviews with professionals working in counter-piracy efforts and with Somalis in the United States. The coordinator of the U.S. Office of Counter-Piracy and Maritime Security, Donna Hopkins, and her team provided assistance through interviews, contacts with people working in Somalia and around the world, and other valuable sources. The research was compiled into a task force report that provides recommendations for the U.S. State Department, and for other organizations involved in counter-piracy efforts. The following recommendations provide alternative courses of action to address current imperfections in the international architecture’s counter-piracy campaign. Social media should be utilized to launch an anti-piracy information campaign that engages the vast Somali Diaspora. Because piracy is a land-based problem with a maritime manifestation, a grassroots approach to address the land-based causes of poverty and political instability must be instated. National prosecutions and detentions should be supported and facilitated through new international legal frameworks. Passive defensive measures must be expanded on commercial vessels and armed guards should be utilized. The three parallel naval forces patrolling the area are insufficient protection against pirates and must be consolidated into one international force. Finally, the U.S. must expand its diplomatic engagement with regional governments in Somalia through imams and clan elders if the fight against piracy is to succeed.

The purpose of this study is to conduct an analysis of the availability of quality multicultural children’s literature in Treasure Valley elementary schools. Of particular interest are several schools from the Boise and Kuna School Districts. Four schools will participate in the study, including at least one Spanish/English dual immersion school or program. Current research suggests multicultural literature supports the psychosocial well-being of students in all classrooms. Exposure to a variety of cultures increases awareness and acceptance among students, reading multicultural literature encourages children to reaffirm the values of their own culture and come to appreciate those of others. Furthermore, multicultural literature, defined as literature that accurately portrays diverse views and cultures, has a significant impact on students’ developing identities. For these reasons this study focuses on the multicultural literature availability and content of school libraries in elementary schools. In this study I will investigate the availability, or lack thereof, of multicultural literature and the quality of the multicultural literature available in the school libraries by analyzing the library’s multicultural collection. The measure used to analyze the literature will be composed of distinguished books that have received any of the following awards: Notable Books for a Global Society Award, multicultural literature awards such as the Coretta Scott King Award and the Pura Bulpre Award from the American Library Association, and the Carter Woodson Award; within the past five years. This study will also take into account the need for multicultural literature in the particular schools by comparing the demographic population of the schools and the relationship to the library’s inclusion or lack of inclusion of multicultural literature. This study will prove useful to teachers, administrators, librarians, and parents when making decisions in regards to literature purchases and donations for school libraries. It also provides critical information that can be used to analyze student levels of engagement with library resources.

X-linked severe combined immunodeficiency (X-SCID) is caused by a mutation in the interleukin 2 receptor gamma (IL2Rγ) gene, which is required for lymphocyte development. Affected patients lack functional lymphocytes and die unless cured through bone marrow transplant or gene therapy. However, gene therapy treatment was stopped due to risk of leukemia resulting from insertional mutagenesis, and this prompted the pursuit of alternate treatments, such as gene repair. Gene repair requires the use of two essential components, a homing endonuclease and a repair template, that harness homology directed repair mechanism, which repairs double stranded DNA breaks in cells. Homing endonucleases are enzymes used to target and cut DNA near a mutation in the genome, while a repair template is the DNA sequence used to correct the mutation. My project involved performing experiments to optimize specific components of gene repair using the Sce-SCID mouse model that contained a recognition sequence for the homing endonuclease, I-SceI proximal to the IL2Rγ mutation. I used adeno-associated viral vectors (AAV) to deliver I-SceI and a repair template to hematopoietic stem cells (HSC) isolated from Sce-SCID mice. I tested the hypothesis that delivery of AAV encoding I-SceI homing endonuclease to Sce-SCID HSC would result in recognition and cutting of the Sce locus. Cutting of the Sce locus is essential to gene repair because it initiates the repair of DNA double stranded breaks through homology directed repair with the repair template. Previous experiments in the Rawlings lab demonstrated cutting of the Sce locus with stable I-SceI expression, but my experiments involved transient AAV delivery. Transient delivery is critical for the safety profile of gene repair. Once I-SceI cutting was established with transient delivery, I performed experiments that invovled both I-SceI and repair template in an attempt to correct the SCID phenotype of the Sce-SCID mouse.

Diffuse Large B-Cell Lymphoma (DLBCL) is one of the most common types of non-Hodgkin's Lymphoma with a 50.4% five-year survival rate.  Previous work has shown that some patients with aggressive DLBCL have increased expression of the transcription factor NF-kß, which can alter normal growth and function of B-lymphocytes.  Interestingly, a protein upstream of NF-kß in the B-Cell Receptor Pathway called PKCß is found to be highly activated in many DLBCL cases, suggesting that PKCß overexpression may be altering the lifecycle of those with DLBCL.  Therefore, PKCß may be a significant new target for therapy.  We designed a transgenic mouse expressing a dominant active form of PKCß expressed only in B-cells (Rosa26 DAPKCß XCD19-Cre).  With this model, we measured differences in B-cell  germinal center development and in antibody responses between WT and DA PKCß-Cre mice immunized with T-dependent antigen NP-CGG.  We hypothesized that DA PKCß-Cre mice may have an increased response compared to WT because of its dominant active form of PKCß, which leads to increased NF-kß and hyper-activation of the responding B-cells.  Thus, we used ELISA and ELISPOT assays to quantify the expressed antibodies and immunohistochemistry to analyze the architecture of the spleen.  Immunohistochemistry has shown that the immunized DA PKCß-Cre mice have slightly larger germinal centers than WT mice, although not statistically significant.  Immunized DA PKCß-Cre mice show no difference in serum antibody levels by ELISA, but have slightly increased numbers of anitbody producing cells by ELISPOT.  Overall, the data suggests that over expression of PKCß in B-cells results in a hyper-proliferative phenotype, but does not strongly alter the antibody response to the T-dependent antigen NP-CGG.  Since we saw a difference in mice immunized with Pertussis, which stimulates the Toll-like Receptor (TLR) Pathway, we will look at different responses of TLR ligands in vivo and in vitro.

This project’s goal is producing microporous scaffold for tissue growth. These scaffolds are made out of crosslinked 2-hydroxyethyl methacrylate (HEMA), a hydrogel. They are formed by polymerizing the HEMA around polymethyl methacrylate (PMMA) beads that are of a constrained and predetermined size. The PMMA is washed away and we are left with a porous scaffold of precise pore size. These scaffolds are used to encourage tissue growth and reduce inflammation and the foreign body reaction. The purpose of my research is to investigate blood vessel penetration into scaffolds by producing the largest sized scaffolds I can using novel techniques. We are currently limited to tissue scaffolds of a maximum thickness of 1 mm using our current techniques. With a larger thickness our scaffolds could be used for many more applications that are presently unavailable with a thin scaffold. Our methods are varied and include creating multiple mold designs, polymerizing techniques, and chemical washing techniques. Once I can create these larger scaffolds we will test them in vivo to evaluate the foreign body reaction as well as angiogenesis in the region. There is a large range of possible future applications for these scaffolds. They could be tuned to encourage many different types of tissue growth.

Healthy pregnancies and optimal fetal development are crucial to ensure a healthy future for not only the mother and child but for our society as a whole. In addition to personal health behaviors and genetic factors, environmental toxins can pose significant risks to the pregnant woman and her developing fetus. A recently initiated longitudinal study of children in Ramsey County, Minnesota seeks to investigate the long term health consequence of exposure to environmental pollutants including radiation and selected chemicals. Prenatal education, including avoidance of environmental contaminants, for pregnant women can help reduce these risks and complications by informing pregnant woman about the impact of environmental factors. The purpose of this research was to determine prospective mothers’ awareness and knowledge of environmental impacts upon pregnancy and fetal development. Data were collected by written survey from pregnant women attending selected prenatal education classes in both rural and urban Minnesota cities.

 A Plasma Pencil Atmospheric Mass Spectrometer (PPAMS) is a new surface analysis device which allows mass spectrometry (MS) to be conducted on samples under normal atmospheric conditions. This enables surface analysis on samples that could previously not be analyzed under the current standard vacuum-based techniques, broadening the field of surface analysis. However, characterization of this method of surface analysis needs to be done in order to maximize the benefits of the PPAMS device and to determine the extent to which the traditional vacuum-based methods can be replaced. This process of characterization involves determining the ionization rate of the plasma pencil probe, performing various experiments while changing parameters (i.e. sample concentration, thickness, and gas type), and comparing results to established methods. Our current investigation is focused on the determination of the ionization rate of the PPAMS device. Initial experiments were performed on polyurethane-based samples dissolved in dimethyl acetamide and spun-coated onto a gold-coated silicon wafer. These samples were then probed by the PPAMS over controlled time intervals. A multivariate statistical method, Principal Components Analysis (PCA), was used to evaluate whether the MS signals obtained varied as a function of exposure time. We hypothesized that the signal would resemble our bare gold background once all of the polyurethane had been ionized. Instead, the MS signal was found to stay constant over a 15 minute exposure time implying a longer exposure time is needed. Current work is focused on evaluating the effect of PPAMS exposure to polymer thickness as a secondary means of evaluating ionization. Future work will center on investigating the changes to the ionization rate under different experimental conditions. The results of our device characterization will provide valuable insight into the limits of the PPAMS device that will enable improved experimental design.

This project was conducted as part of a larger research endeavor called the Triadic Eye Gaze (TEG) project, a 5-year study funded by the National Institutes of Health. The TEG study is an ongoing investigation into the efficacy of one type of communication intervention for children 10 to 25 months of age with moderate-to-severe motor impairments and delayed expressive communication. Our project's purpose was to compare the routine interventions these children received for early signals of communication to standard clinical practices as recommended in the literature. We specifically wanted to know how much treatment the children were receiving and from which professionals, how much of that early intervention focused on communication, and how parents were involved in the treatment sessions. The population for this study was a convenience sample from the larger TEG study, comprised of 15 children with a range of disorders including cerebral palsy, several genetic syndromes, and general developmental delay. Intervention documents, including Individualized Family Service Plans, daily notes, and attendance records, were obtained for each participant from the appropriate birth-to-three center. Quantitative data reduction methods were used to determine the average number of treatment sessions per month, average minutes of treatment per month, and the proportion of total treatment time that each professional provided. Qualitative methodology was used to determine how much of the intervention focused on early communication signals and how parents were involved in this intervention. Results will be compared to clinical practices recommended in the literature. If we find inconsistencies, it will suggest that the typical treatment these children receive is not sufficient. It will be imperative to conduct further research with a larger, more in-depth study to expand upon these findings.

Decision making and risk factors such as media, peers/friends, and family, represent the two main areas that researchers have examined in an effort to understand the cause of disordered eating. Research on decision making has identified a strong tendency toward self-gratifying or disadvantageous decision making among disordered eating populations. Furthermore, persons with disordered eating demonstrate sensitivity towards risk factors as a source for self-perception which in turn plays a large role in binge eating symptomology. However, research on the interaction of these two components with regards to disordered eating is yet unexplored. This gap in understanding was the source of inquiry for my study. Binge Eating Disorder (BED) is the most prevalent of the eating disorders. Being that I did not have access to a sizable BED group, I focused on subthreshold BED (SBED). I hypothesized that (a) SBED participants will demonstrate disadvantageous decision making; (b) SBED participants will place high value on media, peers, and family as a source self-perception; (c) SBED participants’ high sensitivity to media, peers and family promotes self-gratifying DM; (d) Gender differences will be significant with regards to external risk factors, but no difference in decision making. Participants were recruited from introductory psychology classes. An online survey was administered to measure eating attitudes, decision making pattern, and influence of media, peers, and family on binge eating symptomology. I anticipate finding that SBED participants demonstrate decision making impairments and sensitivities to risk factors. Additionally, I anticipate differences in the way risk factors are perceived between genders. Understanding the interaction between decision making and risk factors could lead to possible therapies for and preventive measures against disordered eating. A more in-depth study of clinical and subthreshold disordered eating is needed to ascertain a clearer understanding of the interplay between these two key components of disordered eating.

Augmenting course material to be relevant and accessible to students is a ubiquitous challenge throughout academia. We aimed to design, develop, and evaluate the effectiveness of activities meant to promote the learning of difficult concepts in Anatomy and Physiology. More specifically, we focused on the neurophysiology chapter of an open access Anatomy and Physiology course sponsored by the Carnegie Mellon Open Learning Initiative (OLI). This course is being created for pre-nursing students attending community colleges. We used the six-level schema of Bloom’s Taxonomy, a module addressing the knowledge and development of intellectual skills, to design learning activities that encouraged students to analyze, synthesize, and evaluate concepts rather than simply recall, explain, and define them. By compelling students to work at higher cognitive levels during the learning process, we hypothesized that there would be a corresponding elevation in critical thinking skills and a deeper understanding of the material. Our curriculum design strategy was informed by cognitive science research that shows increases in learning efficacy when students are motivated to work at higher cognitive levels. Assessments were designed to align with these higher cognitive level learning activities. Our learning activities were tested by Anatomy and Physiology students using Carnegie Mellon’s OLI course. The Carnegie Mellon course uses an innovative digital dashboard platform which allowed us to track individual student’s understanding of concepts before, during, and after using our materials so that we were able to analyze their success and effectiveness. We revised our learning activities based on these results.

Cognitive theorists argue that mental states, including disorders, are generated and maintained by personal, subjective beliefs, and that events can only be appropriately labeled by the individual experiencing them. Additionally, pervasive negative thoughts are a part of both depression and anxiety. Whereas with depression a person is likely to believe they are incompetent, or that life is hopeless, with anxiety a person is likely to have negative thoughts about what might happen or about threats in the future. Additionally, high levels of self-hate are associated with bulimia and high levels of self-control are associated with anorexia. Current research indicates a connection between depression, anxiety, and self-talk (ST). However, studies have yet to examine whether ST in men suffering from depression, anxiety, or disordered eating (DE) differs from that of women. The purpose of this study is to explore potential gender differences in ST (as measured by the automatic thoughts questionnaire-revised and the anxious self-statements questionnaire) with student’s scores on the Beck Depression Inventory, the State-Trait Anxiety Inventory, and the Eating Disorders Inventory. These differences, if found, may help to explain the disparity between the prevalence of depression, anxiety, and DE between genders. Women are twice as likely as men to be diagnosed with depression or anxiety and ten times as likely to be diagnosed with an eating disorder. We hypothesize that there will be differences in ST between men and women, and that these differences in ST will mediate the relation between gender and depression, anxiety, and disordered eating.

Adolescent use of alcohol, tobacco, and illicit drugs is on the rise in the United States. According to the Centers for Disease Control's (CDC) annual National Youth Risk Behavior Survey (NYRBS), nearly fifty percent of all teens have smoked cigarettes at some point and nearly seventy-five percent have tried alcohol. Research has established several factors known to put adolescents at risk for negative behaviors, including family problems, socioeconomic status, and lack of parental supervision. However, fewer studies have examined what factors prevent at-risk adolescent populations from using alcohol, tobacco, and illicit drugs. Many potential factors have been identified as buffers for at-risk adolescent populations; some these are creativity, service learning, and community involvement. But research investigating these factors is still limited in scope. The present study examines relationships between protective factors and risky health behaviors of at-risk adolescents. First, we pilot-tested our measures on emerging adult college students and found that students who reported higher levels of family cohesion reported lower levels of cigarette use, illicit substance use, and drunk driving. However, contrary to our hypothesis, the higher the level of reported creativity, the more students reported illegal drug use. Based on our preliminary findings, we are revising our survey and plan to survey adolescents at a Boise, Idaho community center about their use of alcohol, tobacco, and illicit drugs using the NYRBS. In addition, factors thought to serve as buffers against these risky health behaviors, including the five characteristics of Positive Youth Development, competence, confidence, connection, character, and caring using the Positive Youth Development Inventory (PYDI). We hypothesize that adolescents who possess these five characteristics will be less likely to engage in risky behaviors. We will test this hypothesis using Pearson's r correlations. Using our research findings, we hope to suggest future prevention program offerings to the community center.

Post-Traumatic Stress Disorder (a.k.a., PTSD) is prevalent among military veterans. Due to the ghastly nature of war, veterans have witnessed violent and disturbing events that affect them for the rest of their lives. Upon returning from duty, these veterans often have difficulty making the transition from the battlefield to civilian life. Veterans’ experiences in the battlefield often results in years of emotional, behavioral, sexual and social issues. This lingers for a lifetime, unless these veterans are helped. To identify ways to assist veterans with PTSD, this study will focus on male veterans who served in the Afghanistan War from 2001 to 2011. During the research process, this study will focus on the following questions: 1) what is the scope of depression among this population? 2) How does depression cause barriers to civilian life? The purpose of this research is to enhance understanding of depression related to Post-Traumatic Stress Disorder (PTSD) for military veterans. Many families have veterans who go through difficulties, and this study may assist them in addressing PTSD and related depression issues. The research will be done by analyzing literature written about military veterans, and literature written by veterans themselves. Through greater understanding of the factors that contribute to stress and other mental health issues of Afghanistan War, veterans returning to civilian life, may better prevent and alleviate much of their suffering.

In the United States, there are approximately 50,000 people newly infected with HIV each year. Fear of rejection and other factors related to stigma affect how and when people communicate their HIV status. Research has shown that HIV disclosure through non-face-to-face modes, for example with e-mail and chat, afford benefits that include helping both parties control and process emotions and lessening the chance of violence. To help facilitate the process of an HIV-positive person communicating her or his HIV status in an effective, informative, and non-face-to-face manner, we designed an e-disclosure service called PositiveMagnetism. PositiveMagnetism is a web-supported animated e-card service, allowing the sender to input personalized text and video to convey a message to the recipient. The personalized message is incorporated into an educational video of evidence-based facts and preventative tips regarding HIV - all conveyed in an animated info-graphic form. PositiveMagnetism consists of three parts: a website allowing a person to upload or webcam a personalized video message; an animated e-card video incorporating HIV facts and prevention strategies with the personalized video message; and an invitational e-mail welcoming the recipient of the e-card to view the e-card video. We assembled and collaborated with an advisory board consisting of HIV/AIDS researchers, people living with HIV, and other related professionals to help us throughout the design process. In addition, we conducted two surveys targeting participants who have experienced HIV disclosure. The contributions of this work are design artifacts consisting of a service website, an animated infographic of core supportive information, and a video prototype demonstrating two users (sender and receiver) interacting and utilizing the PositiveMagnetism service. This work contributes to increasing knowledge, awareness, and education regarding HIV to help facilitate HIV disclosure between potential serodiscordant partners.

When water is placed in contact with a hydrophilic surface and light, a zone clear of all solutes measuring several micrometers long forms at the area of contact. The water in this exclusion zone (EZ) differs from bulk water in that EZ water is negatively charged, more viscous, and highly stabilized with the water molecules being further aligned and constrained. The energy required to generate this zone comes from ultraviolet, visible, and near-infrared wavelengths of light, and while the specific mechanism for their production is unknown, it is hypothesized that light increases hydrogen bonding from the hydrophilic surface into the water, producing the EZ. Metals also contain the necessary properties for generating EZs, and have the potential of producing exclusion zones on a large scale. Current results show that EZs form only when the interface between copper and water is exposed to sunlight, suggesting that exposure to light specifically at the interface might be responsible for producing a photoelectric effect involved with separating the interfacial water into EZ water. Repetitions will be needed to confirm the trend that sunlight light is responsible for producing EZs along copper. A positive result will have significant influence on developing water filtration technologies using just sunlight and copper by harvesting the pure EZ water, fit for drinking. The potential also exists to engineer solar panels using copper and sunlight, and harvesting the stored negative charge in the EZ as a source of energy.

The human body is roughly two-thirds water, much of which interacts with intracellular hydrophilic surfaces, materials that exhibit water-attracting properties. Near any hydrophilic surface such as biological tissue, a zone of water extending a few hundred micrometers from the surface called the “exclusion zone (EZ)” exhibits exclusive and stunning properties far different from those in normal, bulk water. For instance, EZ water does not exist as a solid, liquid, or gas but instead forms a unique, ordered liquid crystalline state that is solute-free, highly organized, and electrically polarized. When EZs are exposed to light, their sizes increase as they absorb and store energy. Cells could utilize this potential energy through growth or other cellular activities. However, it is hypothesized that EZs absorb not only light energy, but also other energy sources such as acoustic energy. To measure the effects of sound on EZs, sheets of hydrated Nafion, a hydrophilic polymer that generates EZs, were submerged in water and exposed to various frequencies and intensities of audible sound produced from an underwater speaker. Microspheres, small spherical particles made from synthetic material, were used to visualize the EZs. Because EZs exclude solutes, the EZs were represented by the areas void of microspheres. During and after exposure to sound, the EZ sizes were monitored over time. Recent results showed that during exposure to multiple audible frequencies (1-8 kHz), the sizes of the EZs decreased transiently. After the sound was removed, in some cases, the size recovered to its original value. These results may suggest enormous biological implications. Everyday sounds produced in our environment could have a large impact on cellular behavior.

Curiously, Black Cottonwood (Populus trichocarpa) thrives on the rocky riverbanks of Washington under nutrient-poor conditions few other species dare tolerate. Their prosperous lives could be the result of nitrogen-fixing bacteria that inhabit the tree's stems and roots. It is the hypothesis that these endophytic bacteria provide trees with organic nitrogen throughout their lives, where the river side substrate fails to provide sufficient nitrogen for the Poplar to otherwise live. Wild Black Cottonwood seeds were collected from Three Forks Park along the Snoqualmie River in Washington then grown in greenhouses. Endophytes were isolated from these trees and tested for the presence of the nitrogenase gene (nifH) using PCR. The nitrogenase proteins equip bacteria to fix atmospheric nitrogen into forms plants can readily use. Understanding the life cycles, inoculation techniques and genetic make-ups of these bacteria enable us not only to grasp a little better the diversity of life, but to think beyond Black Cottonwoods, to how these bacteria could be recruited to be used on crops and degraded fields. Nitrogen is necessary for plants and often a growth limiting factor; harnessing these nitrogen-providers may help reduce our dependency of energy-intensive industrial ammonia.

 The effect of viral evolution on the duration of latency in Human Immunodeficiency Virus Type 1 (HIV-1) infection has been studied extensively in men. The asymptomatic latency period, after HIV-1 infection and before the onset of Acquired Immune Deficiency Syndrome (AIDS), is characterized by high viral variability. In many cases, a viral phenotype that utilizes CXCR4 and/or CCR5 receptors on target host cells to advance HIV-1 infection progress also emerges during this period. Despite known sex-dependent variation in the progression of HIV-1, the effect of viral evolution and CXCR4/CCR5 utilizing virus (X4 virus) prevalence on HIV-1 latency has not yet been studied in women. I am investigating trends in viral evolution in 9 women from seroconversion until initiation of antiretroviral therapy. I will then compare my results to previously studied male viral evolutionary trends. Ultimately, a total of 72 blood plasma samples, an average of 8 samples from each woman collected progressively during the course of infection, will be used to generate 25-30 HIV-1 sequences per time point. These sequences will then be evaluated through 1) viral divergence from a founder strain 2) viral population diversity and 3) emergence and prevalence of X4 viruses. I will then analyze the relationship between viral evolutionary trends and X4 virus prevalence, and the duration of HIV-1 infection before the onset of AIDS. Ultimately, a comparison between the sexes will be made. Furthering the scientific communities’ knowledge of sex-related HIV-1 infection variation could lead to more effective sex-specific treatment and vaccine development. The important biological question of whether sex can influence HIV-1’s evolutionary path will be addressed. This project is currently in the preliminary stage of sequence generation. Trend analysis and conclusions will take place in Fall 2012.

RNA Polymerase V is a DNA-dependent RNA polymerase involved in RNA-directed DNA methylation (RdDM) (Matzke M et al 2007). RdDM is required for transcriptional silencing of intergenic regions, repetitive DNA, and transposons genome-wide. Arabidopsis polV mutants show increased developmental instability and aberrant root hairs. We hypothesize these phenotypes are the result of alterations in transcriptional silencing and we predict changes in transcriptional silencing are due to altered chromatin accessibility. To asses chromatin accessibility in polV mutant plants we will use a technique called DNaseI-seq that chops up chromatin with a restriction enzyme. This technique allows us to measure which regions of the genome are highly accessible to transcriptional machinery and which are not. Currently, I am developing transgenic plant strains as well as quality control assays to improve DNaseI-seq feasibility in polV mutant plants.  Thus the knowledge will enhance our understanding of developmental instabilities in Arabidopsis and plants in general.
 

The composition and abundance of lipids preserved in lake sediments provides information on the past environment, and changes in this geochemical signal through time may be driven by climate. To understand precipitation changes in the Pacific over the last few thousand years, sediment cores have been collected from lakes on multiple islands, including Poza de Los Diablos and Pozas Verdes on Isabela Island in the Galapagos. Lipids from these sediment cores were solvent-extracted, individual compounds were identified by gas chromatography-mass spectrometry (GC-MS), and abundances of these compounds were quantified using a gas chromatograph-flame ionization detector (GC-FID). Poza de Los Diablos data reveal elevated concentrations of both middle and long chain-length n-alkanes from approximately 1450 to 1850 AD, and indicate an enhanced contribution of material from both aquatic and terrestrial plants during this interval, which may be caused by shifting hydrologic patterns. However, these changes might also reflect a local event such as an altered flow path for surface water due to river or wave erosion. To improve our understanding of paleoenvironmental changes indicated by the Poza de los Diablos data, lipids from cores taken from nearby Pozas Verdes were also extracted and analyzed by GC-MS and GC-FID. Due to their close proximity (<1 km), any climate event that affected Posa de Los Diablo would have also affected Pozas Verdes, but with significantly different modern salinity (Diablos = 10, Verdes = 40) and ecology, each lake is likely to have responded quite differently to changing precipitation patters. By analyzing both records together we seek to improve our interpretation of the past environment.

This research focuses on the reproduction and adaptation of Khmer (Cambodian) classical dance and its role in the maintenance and transmission of culture in the Cambodian community of Long Beach, California. The term “reproduction” is used because this cultural art form has been modified and influenced by a wide range of events in Khmer history, including the period when the Khmer Rouge, a communist group, seized control of Cambodia. The genocide of the Khmer Rouge resulted in the death of nearly two million Cambodians, including 90 percent of Khmer classical dancers. The life threatening atmosphere in Cambodia, as well as the cultural suppression experienced, led to the mass displacement of Cambodians who sought refuge in Long Beach, California. Upon their arrival in Long Beach, Cambodians began to reestablish their cultural practices, including Khmer classical dance, which had been prohibited during the Khmer Rouge period. The purpose of this research is to observe Khmer classical dance and the success of its reproduction and transmission in Long Beach. This research is based on data collected from participant-observation and personal interviews at Khmer Arts Academy (a non-profit dance studio), and observations at the Cambodian Art and Culture Exhibition, held November 2011. After studying Khmer classical dance in Long Beach, I have developed conclusions with regard to the significance and need for dance in the Cambodian community. My data suggests that performing Khmer classical dance at cultural events, celebrations, and festivals allows Cambodians to ensure the transmission and maintenance of their culture, and illustrates their success in sustaining and reclaiming their cultural identity.

Increasing the efficiency of biofuel production is critical to decrease the dependence and consumption of fossil fuels. In the United States, most car fuel contains about 10% ethanol, the result of fermentation, and 90% gasoline. The process of fermenting sugars into ethanol relies on agricultural stocks, decreasing the area of arable land available for food production. Non-agricultural plant species can be used, but the lignocellulose material from the total plant contains both five and six carbon sugars. Baker’s Yeast can ferment the six carbon sugars, but a novel yeast species is necessary to ferment the five carbon sugars. The goal of my research is to isolate and identify wild yeast species growing in non-agricultural plants that ferment five carbon sugars, such as xylose, into a usable product; xylitol in this case. Xylitol can be sold as an artificial sweetener to subsidize the overall costs of biofuel production, or alternatively, may be converted to ethanol through biochemical pathways that some yeast species have. After attempting to grow yeast from nine different plant species growing in Pack Forest with xylose as their only carbon source, one yeast species from red alder, Alnus rubra, exhibited growth. The other eight species did not show significant growth compared to controls: common Baker's Yeast and PTD3, a previously isolated yeast. Further research of these yeasts was not pursued. Next, AR (for Alnus rubra), was tested for xylitol production. First, AR was grown in a medium with xylose as its sole source of sugar. By placing the growth culture in an air-tight flask, any xylitol production would be prevented from evaporating, making it measurable with a high-performance liquid chromatography machine. The yeast isolated from red alder successfully fermented xylose into xylitol, making it a potential source of efficient biofuel production.

Pain is a complicated sensory experience involving several neural circuits and structures. Previous research has examined the neural activity associated with processing and perceiving pain. One study examined the relationship between the average self-reported pain ratings and the average electrophysiological brain activity of Spinal Cord Injury Participants with chronic pain, as measured by electroencephalography (EEG). Significant relationships between pain perception and alpha wave activity around the sensory integration areas of the brain (electrode sites T3 and T4) were found. This study aims to further explore the relationship between expression and perception of pain and corresponding EEG measurements. Waveform analysis of the raw EEG data recorded just before and after the reporting of each pain rating will allow us to examine pain-related neural activity in more detail surrounding the time the participant consciously perceived and rated their pain.  Independent Component Analysis (ICA) allows us to isolate and examine the specific contribution of each frequency at each electrode.  Main effects of each wavelength and how they may interact will also be explored. Analysis software will help us graphically visualize and model the data, creating a preliminary visual representation of the neural activity measured. Further use of neuroimaging analysis software will help to better understand neural pain pathways. With further analysis, it may be possible to utilize computer programs to create a model that can imitate and test these indicated circuits. This analysis will provide us with a more dynamic understanding of the “chronic pain brain” and  will provide a baseline against which to compare brain activity after treatments.

Most adults have some degree of atherosclerosis. In a subset of these individuals, atherosclerosis progresses more rapidly. Increased activity of proteases (enzymes that digest proteins) in atherosclerotic plaques is a plausible cause both of atherosclerosis progression and of atherosclerotic plaque rupture. Plaque rupture is often a terminal event that results in blockage of arteries, heart attacks and strokes. Urokinase plasminogen activator (uPA, a protease that is present in plaques) functions by converting plasminogen (a zymogen, or enzyme precursor) into its active form, plasmin. The uPA/plasminogen pathway facilitates macrophage migration, enhances the release of inflammatory mediators, and activates other proteolytic enzymes, all of which may contribute to atherosclerosis progression and plaque rupture. We hypothesize that inhibition of uPA will decrease atherosclerosis progression and prevent plaque rupture. To begin to test our hypothesis, we use a mouse model of uPA-accelerated atherosclerosis (mice that are genetically predisposed to develop atherosclerosis and express high levels of uPA). We inject an antibody (mU1) that binds to and inhibits uPA, or a control antibody, and we measure atherosclerosis in aortic roots and pinned aortas. We anticipate finding less atherosclerosis in mice treated with mU1. We also expect to find fewer macrophages in atherosclerotic plaques of mice treated with mU1. If we find that inhibition of uPA decreases atherosclerosis progression and that it is also well tolerated by mice, we will later set up an experiment in older mice to determine whether anti-uPA treatment with mU1 will prevent plaque rupture. If uPA activity contributes to atherosclerosis progression, and if inhibiting uPA decreases atherosclerosis progression and prevents plaque rupture, drugs could be developed that inhibit uPA. These drugs could be used to treat humans who are at high risk for atherosclerosis progression and plaque rupture.

The purpose of this study is to address the question of whether graduate students, who have finished their undergraduate study at Boise State University (BSU), feel they were adequately prepared by their undergraduate education to meet writing challenges at the graduate level. Professors have also raised questions as to what level of preparedness incoming graduate students should have. With BSU set to implement a new approach to learning writing across the curriculum, this study may aid in defining at-risk areas in writing; identified by both graduate students and faculty. Surveys will be given to graduate students who have completed their undergraduate degree from Boise State University as well as to the faculty teaching graduate courses. The purpose of the survey is to get students to self-assess the level of their preparedness and identify specific areas of deficiency. The survey given to the faculty will be much the same but with an emphasis on evaluation of the writing of incoming graduate students in general. Follow-up focus group discussions will enable more in-depth exploration of issues raised by the surveys. Data from these surveys will be analyzed and correlated with the outcomes of the new Communication in the Discipline (CID) courses to see if there are areas of writing need - and if the new CID courses will fill those needs. I hypothesize that there will be areas in which each group wants improvement, and that there will be a strong correlation between the two groups. I also propose that the CID course outcomes will specifically address some of the identified areas of need. This research project has the potential to identify areas of current need, as well as provide a base from which follow-up research may evaluate the ongoing success of the Boise State CID courses.

For an animal whose brain only contains about 100,000 neurons, the fruit fly is capable of striking behavioral complexity. The goal of our work is to identify neuronal circuits that process sensory cues and transform them into changes in motor activities. Our work relies on the Gal4-UAS (Upstream Activation Sequence) system, a commonly used genetic tool that allows us to label and manipulate small subsets of neurons. The system takes advantage of different enhancer elements to drive expression of the Gal4 transcription factor in various tissues. When Gal4 flies are bred with UAS flies that contain GFP (green fluorescent protein) or RFP (red fluorescent protein), the Gal4 will bind to the UAS, and enable the production of GFP or RFP. This allows the desired cells to fluoresce, which can be tracked using a microscope. With this, we can identify Gal4 lines with interesting neuronal expression patterns and test the function of these neurons in Drosophila. Expressing the ion channel UAS-TrpA1, for example, activates neurons when the temperature is shifted from 22 °C to 27 °C. I crossed different Gal4 drivers to UAS-TrpA1. After performing a temperature shift on the progeny, I observed that various Gal4 flies became twitchy while others collapsed. These behaviors were reversible when the temperature shift ended. Fluorescing the Gal4 lines that allow for this behavior would allow insight as to the activated neurons in the brain and thoracic ganglia. The confocal images would allow us to see the neuronal expression. Through this model organism we can hope to comprehend and apply the knowledge in understanding complex systems, for example, what neurons coordinate behaviors such as navigation and locomotion.

Over the last decade, neurofeedback has become increasingly popular as a potential treatment option for various neurodevelopmental and neurological disorders. As a completely noninvasive procedure, electroencephalographic (EEG) neurofeedback uses auditory or visual methods to provide an individual with information derived from scalp-electrode recordings of his or her own brain activity. The feedback information may relate to the spatial distribution of activation across the brain or the energy distribution across specific frequency bands. To date, no studies have been undertaken to investigate the potential use of EEG neurofeedback in the clinical management of stuttering. Stuttering is a high-prevalence (1% of the population) speech disorder that often develops into a chronic, life-long problem with severe social implications. The ultimate causes are unknown, but recent studies have revealed structural and functional neural deficits that impact sensorimotor functioning. The present project therefore aims to test the feasibility of developing EEG neurofeedback procedures that may reduce the severity of stuttering in adult participants. Initial testing with 19 data channels and BCI2000 software focuses on reliably discriminating between rest and speech or nonspeech motor activity and designing conceptually relevant feedback displays that represent the spatial or energy distribution of the recorded brain signals.  If successful, this research could have important clinical implications in the treatment of stuttering.

Adductor spasmodic dysphonia (ADSD) is a rare neurological disorder characterized by the involuntary spasm of the vocal folds, which results in an effortful, strained voice quality. This altered voice quality may result in negative reactions from speakers with ADSD as well as their communication partners. One qualitative study reported that some ADSD speakers expressed feeling inadequate, as though their “capabilities” were called into question, when conversing with others. In reality, the way in which individuals perceive a person with a communication disorder may reveal inherent biases that extend beyond voice quality. For example, when researchers manipulated the rate and pitch of a normal voice sample, listeners similarly altered their assessment of that speaker’s characteristics, such as intelligence. Literature also indicates that the more severe an individual’s voice quality, the more negatively that individual’s traits will be perceived. Additional studies have examined how listeners’ perceptions of voice quality relate to a speaker’s voice handicap; neither topic has been investigated in ADSD. Therefore, the objectives of this study are: 1) to determine whether there is a relationship between listeners’ perceptions of severity of ADSD speech with perceived speaker’s confidence; and, 2) to determine whether listeners’ ratings of speaker confidence relate to speakers’ self-rated voice handicap. Twenty speakers with ADSD were previously recorded and completed validated questionnaires (Voice Handicap Index; VHI). Twenty inexperienced listeners are enrolled in this study. These participants will listen to and judge ADSD speech samples on overall vocal effort and speaker confidence using 100 mm visual analog scales. It is hypothesized that speakers with more severely effortful voices will receive lower ratings of speaker confidence. It is also expected that more negative assessments of confidence will correlate with a speaker’s higher VHI score. Results of this study have implications for understanding the role of potential biases in ADSD outcomes.

The San Juan Islands of Washington are a unique habitat for both humans and wildlife. Although geographically close to many urban cities, these islands remain relatively rural and have maintained close connections to wildlife. Marine and terrestrial wildlife are very different in their ecology and how humans perceive them. Yet, there are few distinctions between how marine and terrestrial wildlife is generally presented in educational materials for the public. The San Juan Islands are also home to a large, seasonal ecotourism industry. Consequently, there tends to be a high density of tourists in the area, particularly during the summer. I worked with Wolf Hollow Wildlife Rehabilitation Center in Friday Harbor, WA on San Juan Island to evaluate human interactions and attitudes regarding wildlife. For ten weeks I volunteered and used participant observation methods at the facility. I conducted eight semi-structured interviews ranging from 30 to 120 minutes to examine differences in human actions and attitudes towards terrestrial and marine wildlife, as well as any differences in attitude between visitors and residents of the islands. Initial results indicate that, unlike visitors, residents are more likely to view all wildlife as a nuisance. Moreover, marine animals tend to be more appreciated and less intentionally harmed by humans. Based on these findings I evaluated the current outreach materials used by Wolf Hollow and made recommendations for improvements, which included implementing new methods and materials in order to more effectively educate the public about how to live harmoniously with all types of wildlife.

With global temperature predicted to increase by 1-6 degrees C by 2100, the question of how species will adapt to such a rapidly changing environment is becoming increasingly urgent. Some of the most widely observed responses to climate change have been changes in phenology, or the timing of life-history events such as the timing of migration, flowering, or mating. These apparent adaptations may be the result of genetic evolution or plasticity, and while both can prevent a species from extirpation during rapid environmental shifts, they vary markedly in their long-term effects on population viability. The Pacific salmon, Oncorhynchus, are one group of organisms whose survival is intimately linked to climate conditions. Because salmon die after they spawn, their entire life cycle depends on the success of one spawning season, which in turn depends on their ability to migrate up rivers to spawn during months favorable to their survival. Even small increases in water temperature and flow rates can greatly increase pre-spawning mortality for these fish. Using existing knowledge of Chinook life-history and fine-scale climate projections for the Columbia River Basin, together with an eco-evolutionary model, we assess the potential for Chinook salmon to shift their migration timing to adapt to future climate change. We hypothesize that Chinook are likely to have the evolutionary potential to allow them to avoid spawning during the warmest times on a long-term scale. While this is reassuring for the survival of pacific salmon, in general the extent of adaptability will depend on the life-history of the organism of interest.

Marine Spatial Planning (MSP) has become a critical framework for the adaptive management of marine conservation. MSP incorporates the entire ecosystem into management practices in order to sustain healthy fisheries as well as a thriving environment. The MSP process includes creating an optimal monitoring strategy in order to yield the most positive results for the well-being of the ecosystem. In my capstone I explored the importance of spatial and temporal trends for making effective monitoring strategies for adaptive management within the MSP framework. The research relied upon GIS (Geographic Information Systems), which is regarded as a vital tool for creating MSP strategies. In order to examine the effect of spatial zonation on management decisions I used copper rockfish (Sebastes caurinus) data from the San Juan Islands from 1994, 1999, and 2000. This data was used to create a map illustrating the influence different spatial zones have on the information management obtains in order to form adaptive management strategies. Furthermore, in order to investigate the effect of temporal binning on MSP I used killer whale (Orcinus orca) data from the same relative location from 1996-2001. I categorized the data into different periods, or "bins" of time, and analyzed how these bins impact management decisions. In both examples a threshold was created from the given data that would in theory trigger management action in order to quantitatively prove that the spatial and temporal way in which a species is monitored does affect regulatory and marine spatial planning decisions. Hopefully, by proving this statement with specific case studies I will also identify any consistent trends from the data that may be helpful in determining monitoring strategies to enhance marine spatial planning and conservation for those particular species in this region. ArcGIS will be used in order to illustrate the results and produce further geostatistics on the data.  

The Short-tailed Albatross (Phoebastria albatrus) is listed as endangered under the US Endangered Species Act (ESA) due to small population size, and limited breeding range. The Short-tailed Albatross (STAL) breeds on Torishima and Minami-kojima Islands off Japan and migrates to Alaskan waters during the summer. The NOAA Alaska Fisheries Science Center’s Observer Program, in collaboration with the USFWS, instructs observers to carry out seabird monitoring activities in addition to their recording of bycatch during fishing operations. Using Observer Program seabird sightings and vessel-bird interaction data from 1993-2009, we examined potential vessel interaction threats to the recovery of the population, as well as the frequency and geographic expansion of Short-tailed Albatross sightings. Our data indicate that Short-tailed Albatross sightings increased more than the Short-tailed Albatross population during this time period (6.5% population growth per year), with observer days remaining relatively stable. We also found that incidences of discard feeding and/or vessel following are not increasing disproportionately to population size as the population continues to grow, thus it is unlikely that vessel interactions threaten the STAL population recovery. Lastly, we found that the sightings of Short-tailed Albatross show an eastward expansion since 1993, thus suggesting an expansion of this species within their historic range.

 Myocardial infarction, heart failure, and congenitive heart disease are leading causes of morbidity and mortality worldwide. However, current cell therapies remain inadequate in addressing this clear medical need. One of the primary obstacles limiting the success of cell therapies is that stem cell derived cardiomyocytes (SCDCM’s) tend to be functionally immature, providing only a small fraction of the force generation of their matured counterparts. Thus, the work here focuses on developing a growth platform which incorporates topographical and mechanical properties in order to rapidly and thoroughly mature SCDCM’s. The field of tissue engineering is becoming increasingly aware of the roll that the extracellular matrix (ECM) plays in driving cellular differentiation and behavior, and the importance this has on the design of biomimetic scaffolds and growth platforms. A study of the native cardiac environment has revealed that the presence of aligned nanoscale matrix fibers plays a key role in establishing organization within the myocardium. This insight has allowed us to construct polymeric scaffolds which mimic the in vivo ECM, greatly improving cardiac culture techniques. There exists an optimal feature size and configuration at which nanogrooved topography is successful in promoting anisotropic alignment and elongation of cardiomyocytes, an increased action potential conduction velocity, and the substantial expression of cell-cell coupling proteins. Our current focus rests on understanding the way in which mechanical and chemical variations to the growth substrate can affect cell morphology and contractile properties when manipulated in conjunction with nanoscale topographical stimulation. This research will provide a strong foothold towards the development of a cardiac patch, which, implanted directly onto the infarct surface of the heart, could reduce scar tissue formation, promote healing and angiogenesis, and provide crucial contractile and mechanical strength.

Approximately 1 million Americans live with a lower-limb amputation and this number is increasing. During both the postoperative recovery period (up to 18 months) and the subsequent period patients undergo substantial changes in the volume and shape of their residual limb. Therefore, both the fit and comfort of their prosthetic are compromised. Edema, gait instability and skin irritation are often severe consequences. Patients often use socks, pads and fluid-filled bladders to compensate for these changes in volume. I am currently investigating the fluctuations in the volume of the residual limb of below-the-knee (trans-tibital) amputees. The goal is to identify patterns in the volume fluctuations over the course of the day. We have created sock logs on which patients record the changes in their sock ply during the day. Our goal is to provide practitioners, patients, and industry with insight into how often and when patients change their sock ply. We hope, with this knowledge, to propose more automated solutions for patients to manage their residual limb volume. Automation is needed because many patients elect not to change sock ply even though they need to so as to maintain a proper prosthetic fit. Similarly, our research is also focused on investigating the correlation between limb volume changes and the need for a new socket. With this data, we hope to establish a relationship between the changes in sock ply and the time at which a new prosthetic socket is needed. We predict that we will be able to foresee when a patient requires a new socket based on changes in their sock ply. With this knowledge, the information will be shared with practitioners with an expectation that it will allow them to change their daily practices to recognize the need for a new socket.

In recent years, increasing numbers of single amino acid mutations in cardiac troponin C (cTnC) have been identified in patients with cardiomyopathies. The troponin protein complex regulates cardiac muscle, as Ca2+ binding to cTnC initiates contraction. Previous studies of the mutations associated with hypertrophic cardiomyopathy (HCM) patients show increased Ca2+ sensitivity and of those with dilated cardiomyopathy (DCM) patients, decreased Ca2+ sensitivity. However, it is still unclear how a change in Ca2+ signaling might precipitate the disease, and unknown why a myofilament protein variant affects the Ca2+ transient, which is regulated by calcium handling proteins. This project focuses on the I61Q cTnC variant, which previous studies have shown decreases fraction shortening (produce weaker contractions) and Ca2+ binding of myofilaments. Determining how or if abundance and activity of sarcoplasmic reticulum (SR) proteins vary will shed light on the mechanism behind the change in Ca2+ transient. All cardiomyocytes were isolated from healthy adult rats and transfected by adenoviruses containing the I61Q gene. Transduced cardiomyocytes were cultured for 48 hours. Then, Western blotting determined abundance of Ca2+ handling proteins in the SR, such as phospholamban and SERCA-2.  SDS-Page gels were used to determine protein phosphorylation. Using imaging software to analyze the bands in the gel will result in a quantitative comparison of protein abundance and phosphorylation. The difference in protein expression and regulation provide insights for understanding the mechanism behind the change in Ca2+ sensitivity, and potentially allow I61Q to be delivered through gene therapy in patients with HCM to restore normal Ca2+ sensitivity. Past contractile measurements were performed at 25°C, but since the heart normally operates at 37°C, future experiments will be performed at this temperature for transduced cardiomyocytes. Contractions will be induced by electrical stimulation so that cell lengths, rates of sarcomere contraction/relaxation, and Ca2+ transients can be measured simultaneously using IonOptix video microscopy.

Latinos are the largest and fastest-growing majority in Washington State, but over the past thirty years they have been systematically underrepresented in local office. This research focuses on city council and school board races across the ten counties which have the largest Latino populations, and the resulting report is the first to document the severe history of Latino underrepresentation in Washington. Through the same surname analysis used by the Department of Justice in its investigations of racially polarized voting, we analyzed the precinct-by-precint electoral results and found that Latino candidates are routinely defeated by non-Latino candidates. Previous studies have demonstrated that at-large elections - which are used in more than 90% of Washington's local races - tend to dilute minority votes and depress minority representation when minority candidates run against majority candidates. We found that Latinos win far less than half of their races against non-Latinos, suggesting that the extensive use of at-large elections has been combined with racially motivated voting patterns to systematically deny Latino candidates local office. Through interviews with Latino leaders and prominent members of various communities in Yakima County, we also found that Latino communites face more than just structural barriers to effective political participation and proportional representation. Our findings strongly suggest that the Revised Code of Washington ought to be amended to allow local jurisdictions to move away from at-large elections, that local jurisdictions should strive to provide more bilingual services, and that community organizations ought to prioritize the cultivation of local Latino leaders. This report was written as part of the State of the State for Washington Latinos project, which is an ongoing community-based research program at Whitman College. Our research was conducted in partnership with the National Voting Rights Advocacy Initiative.

This study focuses on how the global efforts of a politically active and increasingly visible movement of adult autistic activists are challenging the common framing of autism and shifting the contemporary autism debate. Common representations throughout the autism field contextualize the autistic experience through diagnostic categories of difference, constructed primarily by psychologists, neurologists, educators, and service providers. These characterizations are determined through observational criteria such as delayed communication, repetitive physical behaviors, and marked deficits in social skills. While the deficit mindset dominates the media and the public perception of autism, there is a lack of attention and research on how the social impact of these ‘perspectives from the outside’ influence the lived experience of autistic adults. This work counters the hegemonic deficit interpretation by investigating the multiple meanings of autism, and studying whether politicized tensions over autistic representations—and misrepresentations— influence public conversations surrounding service delivery, treatment design, and provisions of care. Drawing on qualitative cultural research methods including narrative, textual and image analysis, as well as ethnographic field notes, this study critically analyzes the lived experience of adult autistics and their efforts to re-humanize public assumptions about autism while living in a society, they suggest, that stigmatizes their experience as emotionally isolated, socially deficient, and mentally diseased. I analyze the socio-political discourse of autism and the conflicting representations put forth by medical professionals, mainstream media, institutions, scholars, and—autistics. These contradictory interpretations produce a cultural system of difference engaged in debate over autistic autonomy, self-determination, and justice. To critically engage this ‘culture war’ this inquiry considers who has the right to speak for the autistic community? Whose values are characterized as authentic by the public? Finally, this investigation asks, can autistics redefine autism and how will this definition reframe their position in political discussions about them? 

Despite a surge in research efforts over the past two decades, scientific understanding of the mechanisms underlying motor learning remains limited. Although many procedures have been designed to assess an individual’s ability to update motor commands in an altered environment, few attempts have been made to design procedures that assess, and possibly improve, an individual’s ability to learn a completely novel mapping of motor commands and sensory consequences. This is unfortunate because the latter approach has potential clinical applications: various brain disorders cause sensorimotor deficits, and learning alternative movement strategies may aid recovery. Whereas the above studies focused on hand or arm movements, our own research focus is on the speech motor system. The present project aims to design protocols to test and quantify the ability of the speech motor system to learn neural representations of a novel link between motor commands and sensory results. We make use of 3D electromagnetic motion capture technology that tracks 3 position coordinates and 2 angles for up to 9 sensors on the tongue, lips, and jaw; thus for a maximum of 45 dimensions. These 45 dimensions are mapped onto 2 dimensions of movement for a cursor displayed on a computer monitor. As subjects are instructed to move the cursor, their performance (i.e., learning of the novel mapping) is quantified. We will also test individuals from a clinical population (such as those with motor speech disorders or stuttering) and analyze their performance over time to design the most optimal techniques and procedures for quantifying the speech sensorimotor system’s ability to learn the complex relationship between a high-dimensional movement space and a 2D visual space.

Despite major advancements in our understanding of the neural systems involved in persistent developmental stuttering (PDS), the causal mechanisms underlying acquired neurogenic stuttering (ANS) remain poorly understood. ANS typically occurs after stroke, and its primary symptoms resemble those of PDS (i.e., within-word dysfluencies). However, individuals with ANS often show no adaptation effect and no fluency-enhancement with altered auditory feedback. To date, little is known about differences and similarities between ANS and PDS in terms of the loci of stuttering—that is, the locations of stuttering moments within spoken utterances. Brown’s research on PDS has shown that stuttering is more likely to occur on (1) longer words, (2) words that occur early in the sentence, (3) content words, and (4) words that start with a consonant. In this study, we therefore compared ANS and PDS with regard to the distribution of stuttering moments as quantified by Brown’s word weights (for each stuttered or fluent word, 0-4 points are assigned based on the aforementioned four factors). As expected, adults with PDS showed greater word weights for stuttered versus fluent words. Individuals with ANS showed a highly similar pattern with greater word weights for stuttered versus fluent words. Calculating word weights for each factor separately (word length, sentence position, grammatical class, initial consonant) revealed that the ANS group also did not differ from the PDS group in the relative influence of each individual factor. Thus, although there are several known differences between acquired neurogenic and developmental stuttering, the loci of stuttering appear to be influenced by similar factors in both disorders. Of those factors, word length and grammatical class had the strongest influence on the occurrence of dysfluencies in both groups. These findings can be used to generate new hypotheses regarding the neural basis of fluent and dysfluent speech production.

Previous studies have shown that neurologically healthy subjects learn to generate adaptive motor commands when either sensory feedback (e.g., visual or auditory information) or the movements themselves (e.g., arm movements for reaching or jaw movements for speech) are experimentally perturbed - a phenomenon known as sensorimotor adaptation. In parallel, a different line of research has shown that for both nonspeech and speech movements the central nervous system (CNS) differentiates between self-generated and externally-caused sensory input by comparing actual and predicted inputs - a detected mismatch causes the input to be attributed increasingly to external sources. Here, we investigate these two phenomena in combination by means of two experiments that examine whether sensorimotor adaptation in speech production is diminished, or even abolished, when an auditory feedback perturbation (shifted formant frequencies) is either delivered with increasing delays or made increasingly large. Based on our own pilot data and recent findings from other labs, we hypothesize that increasing either the delay or the extent of the formant perturbation will cause the CNS to increasingly interpret the perceived error as an external manipulation rather than a production error that requires adaptive corrections in future trials. For each experiment, acoustic analyses are used to determine adjustments in subjects’ produced formant frequencies from a baseline phase (unaltered feedback) to the perturbation phase (formant-shifted feedback) across conditions varying in delay and amount of shift in the auditory feedback signal.

English holly (Ilex aquifolium) is an increasingly prominent invader of western Washington forests, yet little data exists on its effects on western Washington native flora. A population study of holly in a 15.9 acre study area in St. Edward State Park suggests that holly reduces the abundance and diversity of native vegetation. We hypothesized that these negative effects are caused by shading and/or litter fall from holly canopy. We studied native vegetation cover in four treatments (holly shade, holly litter, holly shade + litter, neither) to determine the importance of these two factors. We also contrasted photosynthetic photon flux densities (PPFD) under holly canopy with PPFD under native tree canopy and in full sun, and compared PPFD under holly canopy with existing data on compensation points for native plant species occurring in the park. If holly reduces native vegetation through shading, we expect to see reduced native vegetation abundance in our shade treatments and to find that PPFD levels underneath holly canopy are lower than required for some or all native plant species. If holly leaf litter is suppressing growth, we expect to see reduced native vegetation abundance in our litter treatments and to find that holly leaf litter is deep enough to negatively affect seed germination. Preliminary results suggest a significantly lower total vegetation cover underneath holly canopies compared with total cover outside of holly canopies, and we have recorded leaf litter depth as much as 17 cm underneath holly canopies. This study will provide quantitative data which can aid forest managers in assessing the threat holly poses to western Washington forest biodiversity. Results and implications will be discussed.

Fungal endophytes live cooperatively within the tissue of nearly all land-plants. Symbiotic fungi can provide great benefits to their plant host, often observed as increased growth or stress tolerance. I hypothesize that fungal endophytes increase the invasive ability of agressively invasive plant species. Phragmites australis is a common wetland reed with a global distribution. Roughly 200 years ago an agressive European genotype was introduced to North America. This non-native genotype out competes native genotypes and forms dense monocultures along the edge of both salt and fresh water. These monocultures not only reduce plant diversity but manipulate the ecosystem by altering soil chemistry and changing the physical structure of the land-water interface. P. australis is a considerable problem along the Great Lakes in Michigan and in Grey's Harbor, WA. I have isolated and identified the most abudnant filamentous fungal endophytes from both WA and MI populations of invasive P. australis. The endophyte communities at each location show almost no similarity, suggesting that P. australis aqcuires endophytes from the environment rather than carrying endophytes with it. By innoculating rice and turf grass with P. australis fungal endophytes and growing them under various conditions, I aim to discover the symbiotic funciton of these fungi. Additional experiments investigate the effectiveness of various field tested fungicides on individual P. australis fungal endophytes grown in culture. The long term goal of this project is to develope a novel method for erradicating invasive plants by targeting vital mutualistic fungal endophytes. P. australis fungal endophytes in culture are sensitive to field tested fungicides and the next phase of this projet will investigate the effect of fungicides on symbiotic plant.

Paris has a long history of being one of the most beautiful cities in the world. In the immediate postwar era, despite public opposition, a towering, Manhattan-like skyscraper was built in the middle of Paris, marring the traditional skyline. It was initially backed by President Charles de Gaulle. But because of the lack of funding as well as public protest, its construction was delayed over a decade. An American real estate developer, Wylie F. L. Tuttle, was the major force behind this controversial matter. So our questions are -- How did this controversial tower come about? And who is Tuttle and how did he get involved? My professor, Meredith Clausen and I formulated the hypothesis that Tuttle must have been a well-established real estate developer in the U.S. Also, we hypothesized that somehow must have had strong and powerful connections in France and internationally. I started my research by a background search on Mr. Tuttle. An initial hurdle was that he was not cited in any electronic text database. So I had to search more specifically in the historical archives of the NYT, Wall Street Journal, and other daily newspapers. At this point, I am moving on to researching American real estate developers who began invested in Paris in the postwar era, and how Tuttle got interested in this international investment. Thus far I have found some but only limited information about Wylie Tuttle. My professor as well emailed Carol Willis, adjunct professor of Urban Studies at Columbia University and the curator of Skyscraper Museum, who replied she had never heard of him. With more research, I hope to find out how he got involved in this politically as well as urbanistically controversial American “invasion” of Paris. My goal is to supply this missing piece in real estate investment history.

The Common Core State Standards were developed in collaboration with teachers, school administrators, and experts, in order to provide a clear and consistent framework to prepare American students for college, the workforce, and successful competition in the global economy (www.corestandards.org). The Standards for English Language Arts & Literacy in History/Social Studies, Science, and Technical Subjects (henceforth, “the Standards”) were published on June 2, 2010 and have since been adopted by forty-five of the fifty states, including Washington. As schools begin the enormous effort of re-shaping their curricula to meet the Standards, students and teachers will find themselves subject to many changes. This presentation focuses on the changes that will impact the teaching of literature in the high school English Language Arts (ELA) classroom. It reveals the underlying assumptions the Standards make about literary texts: that they are not argumentative texts, that they therefore cannot be used toward the teaching of argument, and that they are therefore somewhat irrelevant to the Standards’ goals of college and career readiness. It then draws upon interviews I conducted with local ELA-teachers and relevant academic literature in order to critique these assumptions, demonstrating that literature not only can be used to teach argument, but should be. In short, it makes the case that using literature to teach argument better prepares students for college and the workforce than the use of informational text alone and, moreover, imparts the additional benefit of preparing students for responsible citizenship in a democracy.

Research on resilience (ability to overcome obstacles in life) has shown that early childhood socio-emotional competence is a strong predictor of future resilience as an adolescent and adult. Research shows that resilience is not a stable quality of individuals, but rather a changeable, dynamic pattern of functioning that is influenced by protective factors such as positive relationships, strong attachment bonds, and self-regulation skills. Early childhood intervention programs have been found to make lasting effects on the functioning of individuals into adulthood. Children who have attended preschool programs are less likely to be incarcerated, drop out of school, and placed into special education programs. (Barnett, 2002) However, research on preschool intervention has focused mostly on cognitive and adult outcomes, rather than socio-emotional competence in childhood. This study seeks to learn if preschool programs targeting disadvantaged children, is related to outcomes of protective factors and behavioral concerns, as measured the the DECA-C, an assessment tool becoming widely used to study resilient functioning in children ages 2 to 5 years. The design of this study involves two full-day, demographically-similar preschool classrooms. In addition to comparing children’s scores on the DECA instrument, teachers were audio-taped and observed for 20 hours to identify the quality of teacher-child relationships, a factor known to be very influential to child self-efficacy. It is hypothesized that children that participate in high-quality preschool intervention programs will show higher DECA scores measured over the course of one year. This research has implications for teacher-training, curriculum design, and family programs that have a stronger emphasis on socio-emotional development in low-income early childhood classrooms. This research is also specifically interested in how early childhood intervention can promote resilience to future adverse life experiences for underprivileged children.

The recent increase in international students at the University of Washington (UW) has been an extremely controversial issue. As undergraduate tutors in a writing center that serves these students, we are concerned with how this changing institutional climate affects both the students we work with and the university. This has prompted us to ask: What are these students’ needs, how can we best support them, and what institutional structures and policy must be changed or developed in response to the increasingly multilingual and multicultural demographic of the university? Through further development of a peer-led group tutoring program, Targeted Tutoring (TT), we have explored these questions and their implications for academic support models and policy relating to English Language Learners (ELLs) and international students. In particular, we have focused on researching ELL policy and support mechanisms at other universities and developing research designed to assess how student feedback about classroom and writing experiences and their perceptions of second-language writing at UW can be used to improve existing programs and policy. In practice, this has focused on efforts to design student-centered research methods and materials (reflective writing, surveys, interviews and observations), used in conjunction with TT, that can supply student feedback in order to assess our response, and the university’s response, to the increasingly diverse student body. While incomplete, this research has already shown promise. It has demonstrated the value of opening new avenues for students to communicate their needs, concerns, and views – providing the university with a clearer picture of these students’ needs and enabling a more effective response to, and support of, an increasingly diverse student body. In doing so, our research has the potential to be a valuable resource for students, administrators, and academic support programs and inform the university’s response to the changing student population at all levels.

From the late 14th through the 15th century, the German Hanse was a major player in economic, political, and military conflict –areas traditionally associated with state actors –throughout northern Europe, despite being a decentralized, non-sovereign, non-territorial entity. The Hanse was a late medieval/early modern trade organization, the driving purpose of which, from its founding and throughout its development, was to provide for the mutual protection of its member cities’ merchants in the course of their business and ensure and expand their rights and privileges in foreign ports; to protect their merchants against the predations of both pirates and kings. It is thus one of the great historical ironies that the Hanse became a source of piracy and mercantile harassment rivaling those of the sovereign states of Northern Europe. The Hanse’s relations with England throughout the late 14th and 15th century, especially in the decades surrounding the English dynastic struggle of the Wars of the Roses and concurrent Anglo-Hanseatic War, exemplify the Hanse’s role as a state-like actor in international conflict. Current scholarship on the Hanse focuses on cliometric trade analysis and linear narrative history, but I emphasize the unique nature of the Hanse and how it determined their actions on the international stage, critically reading Parliamentary records, royal appeals, and major secondary sources in light of my analysis of the Hanse’s foundational documents. I explore the motivations of the Hanse in its conflicts with England and determine that the Hanse’s use of piracy and the harassment of English merchants represented a natural continuation of their founding principles. My research addresses questions of the motivations and internal dynamics of one of the most successful and longest-lasting international trade leagues to-date as it interacted with more traditional state-entities in diplomatic and economic contexts.  

In twelfth-century northern England, the historical imagination was dominated by the region’s most powerful and most popular saint.  The bishops of Durham drew on St. Cuthbert’s renowned history and well-established authority to underline their own spiritual legitimacy. Involvement with the saint’s cult was not limited to the ecclesiastical elite or the monks of the cathedral convent. Throughout the twelfth century, lay interest in the religious life dramatically increased, and saints’ cults were a popular focus of lay religious energy. Reginald of Durham’s Libellus de admirandis beati Cuthberti virtutibus, complied in the 1160s and 70s, provides a richly detailed glimpse of this period when the saint’s miracle working powers were claimed by religious and laity alike. Much scholarly attention has already been paid to the increasing prevalence of pilgrimage to Cuthbert’s shrine in the twelfth century. Pilgrims who visited Durham generally sought miraculous cures, and as we would expect there is a higher proportion of stories about healing miracles in the Libellus than in earlier Cuthbertine hagiography. But pilgrims were not the only laity who became involved in St. Cuthbert’s cult in the twelfth century. In addition to stories of miraculous healing, Reginald’s Libellus contains accounts of the saint arbitrating the conflicts of lay inhabitants of the bishopric of Durham. My research examines these often overlooked “miracles of justice” in order to provide a fuller picture of lay interaction with St. Cuthbert in twelfth-century Durham. I analyze miracle stories involving freeing from false imprisonment, protection of lay interests, and punishment of immoral behavior in order to explore how and why members of every social strata increasingly claimed the patronage of the saint in order to mediate secular conflict. What emerges is a clearer portrait of a distinctive local political and social culture underlined by communal association with St. Cuthbert.

The Svoboda Diaries project seeks to translate and digitize a nineteeth century travel diary written in Arabic by a nineteen-year-old European named Alexander Svoboda. The Newbook project is the second phase of the Svoboda Diaries Project. The first phase of this project focused on the development, transcription, and translation of the travel journal. Alexander Svoboda kept a thorough record of his journey including a trip with his family across the desert to Damascus, from there by train and boat to Cairo, then finally to Brindisi and Paris. Phase one of the project resulted in an XML mark-up text in both Arabic and English automatically rendered in HTML for web display together with notes and supporting materials such as maps, PDF's, rare books, and a Wikipedia associated with the site, referred to as a Svobodapedia, which organizes our rare materials into a easily accessible database. Presently our group is collecting and organizing images and genealogical material, to identify family members within the diary and lead to a better understanding of the Svoboda family and others who traveled with Alexander. Many factors have been undertaken on our road to publication, including correcting and regularizing the XML tagging and formatting to result in an errorless XML mark-up language. Finally, collaborating on a Newbook website, where text, supporting material, and a print-on-demand version of the text will be available to the public. The Newbook project is a collaborative effort, including research faculty, PhD students, and undergraduate researchers, the result of this this union has led to a more comprehensive approach to creating a visually interactive publication.

How exactly is history of science related to philosophy of science? Answers range from denying there exists any substantial relation at all to asserting that the relation is one of necessity, in which philosophy of science without history of science is worse off and vice versa. In this research I give a brief survey of the relevant literature. I then suggest that thus far the various approaches taken toward resolving the general problem have not been satisfying and, hence, that a new approach is needed. I use a case-based analysis of a recent essay in philosophy of science by Kyle Stanford to demonstrate what I believe to be a novel, fruitful approach to the problem. Rather than speculating about the relation in the abstract, in this new approach I focus on how Stanford uses history of science to make his philosophical argument go through in practice. Here the problem becomes: How is history of science related to philosophy of science in Stanford’s essay? I argue that the payoff of this approach is that although the conclusion I draw is not as general in scope as those offered by previous philosophers, in its narrowness this new approach is more detailed and, hence, more illuminating of the relation between history of science and philosophy of science. Attending to how philosophers work out this problem in practice, I argue, is the approach that we should take in trying to understand the nature of this precarious relation. Finally, I compare my analysis of Stanford’s essay with some of the existing accounts delineated in the beginning of the paper, in order to determine whether any of the generalizations they offer hold in this particular case.

The American Farmland Trust estimates that we are losing more than an acre of farm and ranch land every minute. This rapid conversion of farmland to residential and commercial development presents an urgent and dangerous problem, as it severely compromises our ability to grow our own food, and raises serious issues of food security, resiliency, and environmental degradation. However, there are numerous tools that counties can employ to reverse this trend and protect local farmland. Counties are in the driver’s seat when it comes to farmland preservation, and this research looks critically at what counties can do to prevent conversion using the tools of regulation, development rights, tax incentives, and economic development, while highlighting the Puget Sound Basin as a case study for what is working and what needs improvement at the county level. I gathered most of this information in my internship with the American Farmland Trust, where I worked with a graduate student to create a scorecard using the above criteria, and used it to evaluate the farmland protection programs of the 12 counties in the Puget Sound Basin. Among our findings are that total farmland acreage in the Puget Sound is dwindling, that no county reaches the ideal in farmland protection programs, and that farmland across the Sound remains vulnerable. Fortunately, there are a number of counties that are using certain tools very effectively, and counties can draw on one another’s strengths and examples to shape better farmland protection programs across the region.

The immune response of individuals with disrupted sleep such as night-shift workers has been shown to decrease relative to individuals with regular sleep patterns. Cytokines are small molecules secreted as part of the immune response to infection. Certain cytokines have been shown to regulate sleep, and this regulation likely constitutes a critical component of the immune response. A common consequence of exposure to unusual light-dark (LD) cycles, such as those under jetlag or shift-work schedules, is the internal desynchronization of circadian rhythms. This desynchronization is associated with disruptions in the sleep-wake cycle and we hypothesize that this disruption may be linked to abnormal secretion of cytokines. Using an animal model of internal desynchronization, we exposed rats to a 22-hour LD (11L: 11D) cycle which leads to desynchronization of the sleep stages known as Rapid Eye Movement Sleep (REMS) and nonREM sleep (NREMS). In these animals, the temporal sequence of REMS and NREMS changes stably between days of alignment, in which the sequence is normal, and days of misalignment, in which this sequence is disrupted. We will analyze levels of three cytokines, interleukins 1, 6, and tumor necrosis factor (TNF) over a 24-hour period in animals either bled during days of alignment or during days of misalignment. Our hypothesis predicts lower production levels of these cytokines in misaligned rats.The implications of this study may indicate that the alignment of circadian rhythms, particularly of the sleep-wake cycle, are critical to maintaining normal cytokine levels and to sustaining normal immune response.

When a photon is absorbed by materials called semiconductor nanocrystals or quantum dots (QDs), the energy from the photon is also absorbed and can be used to excite the semiconductor nanocrystals. If the energy of the photon is at least twice the energy of the bandgap, or the energy between two specific states, at least two charge carriers can be created. Charge carriers are inherent in any material which can absorb energy and undergo a process of excitation to a higher energy state by the photon followed by relaxation to its normal energy state accompanied by a release of energy. Conversely, when the energy of the light does not exceed twice the band gap, only one excitation is observed. If a material exhibits the property of creating multiple charge carriers, often called Multiple Exciton Generation (MEG), it can be stated that this material will likely enhance a solar cell since energy from the light absorbed by the cell will result in multiple charge carriers created followed by multiple relaxations and the releasing of energy. MEG has been shown to exist in a variety of QDs. Here, we attempt to confirm the presence of MEG in germanium QDs. This was done by pumping 400 nm and 800 nm light with a pump-probe laser and collecting the absorbance spectra at different power levels. The spectra can be analyzed to demonstrate if MEG occurs by comparing the absorbance at these different power levels. The results have provided no conclusive evidence of MEG in germanium nanoparticles. This result allows for further research to be performed on what may impact MEG and what materials are ideal for MEG.

At a time in the United States when religious participation by youth has decreased (in a recent Pew Forum report, those born in 1981 or later hold the lowest church attendance) there is a rapidly growing church with roots in Washington: Mars Hill. Practicing a unique brand of evangelism, Mars Hill employs a variety of methods, some of them technological, to attract increasing numbers both in their campuses and online. In order to explore what these methods were, I began attending services and researching the current state of religious participation in American Protestants. I then approached my conception of Mars Hill through the works of various philosophers, including Paul Tillich and Emmanuel Levinas. The third aspect of my work is a journal-based account of my experience throughout this project. My project will reflect the above methods in three main sections: The Numbers, The Theory, and The Experience. I plan to present what it is about the reality of Mars Hill that is fulfilling and attractive for today’s religious population. The reality Mars Hill creates uses novel modes of delivery for its message, which has a high-production value and can be found on Facebook, Twitter, and an Iphone app, among a larger web presence. In addition, Mars Hill offers an experience of community that substantiates strict doctrine on a weekly basis and provides unique accountability for members. This doctrine argues against a conception of Christianity as a “religion”, which moves Mars Hill into a space of new orthodoxy where meaning is born from contradiction in the potentialities embedded in language. My telling of my experience there will demonstrate the difficulty I experienced regarding the dichotomy between participant and observer roles, resulting in a difficult ultimate decision. To uncover the difference in Mars Hill, I started with numbers, continued with theory, and end in experience.

 CARICOM (Carribean Community) is a community based trade agreement association within the Caribbean region which is comprised of 15 nations. Regional progression is outlined through accelerated, coordinated, and sustained economic development. Theoretically, CARICOM has been ideal in the growth and expansion of the post-colonial Caribbean market. With the rise of it’s global and local commerce, CARICOM can be criticized as a neocolonial paradigm. Although this organization has historically been instrumental in Caribbean advancement, it has begun to reinforce systems of oppression and create cultural rifts within political nationalism. Research will comprise a collection of ethnographic interviews and thorough analysis of text course reserves from the University of the West Indies in Cave hill, Barbados. It was evident throughout my fieldwork in the Caribbean, that tourism still remains a major sector of its economy. How does regional tourism negotiate power relations within Caribbean nations? I will explore possible avenues of exploitation, degradation, and discrimination within Caribbean tourism and its evocative nature of neo-colonialism.

What makes one country happier than another? For centuries mankind has searched for an answer to what brings bliss, producing a great variety of answers. Over the past two years I have been on my own search; first collecting data and readings from varying scholars and fields of education, I then presented my findings at last year’s URS. A major division between western medicine and eastern wisdom split my presentation, and left me wanting a more visceral experience. Fortunately, my advisers Dr. David Barash and Dr. Judith Lipton took on a book to tackle my primary question, and allowed me to watch their house in the Central American sunspot, Costa Rica. Additionally, Costa Rica had been named the world’s happiest country by several organizations. Both my advisers and I had some qualms on how these organizations (World Happiness Database, Yale Environmental Performance, Happy Planet Index) addressed such subjective variables, and thus my project split. For the summer, I was to explore the country, conduct informal interviews with locals, tourists, and collect field notes to form answers towards some broad questions. Are Costa Rican’s the world’s happiest? What mechanics create such joy? Finally, what can we learn from them? Presently, I am conducting further investigations on how these organizations rank happiness. Possible methodological faults are addressed by comparing mental health and social inequalities to their rankings. In my attempt to put boundaries on an abstract emotion, quantitative and qualitative in nature, I have distilled cloudy answers to what makes us happy. I view these as primal ingredients towards a universal ‘elixir’. This ‘happiness variable’ takes flexibility, openness, purpose, & awareness to create. I believe we all have the capacity to be happy and hope to present some tools discovered while researching to help construct understanding and accessibility to this enriching experience.

 In 1943 Hanford, Washington became home to the first full scale nuclear production complex and is now the most contaminated nuclear Superfund site. How have the lived experiences, local knowledge, health indicators and perceptions of risk in disparately-impacted communities shaped the complex processes of planning and decision-making of the clean-up at Hanford? Community Based Action Research can provide critical insight into the socio-cultural dimensions of the Hanford site needed to understand the complex processes that shape clean-up efforts, and how those decisions affect the lives of primary stakeholders. This methodology can also be utilized to critically examine how those decisions impact the experiences and health of the larger community. Archival research, participant observation and interviewing have been utilized to identify stakeholder groups and create accessible collaborative descriptive accounts of the Hanford site. This research will add to our collective understanding of the importance and use of cultural resources found on the Federal reservation, the contemporary economic importance of the super fund site, as well as how Hanford has and continues to affect a diverse array of stakeholders. This research has the potential to contribute to understandings of environmental justice policies as well as increase involvement of marginalized stakeholders and facilitate the implementation of collaborative, sustainable solutions to mitigate threats to population health and safety.

Poetry is a versatile tool in the Arab tongue and is the medium which the nation’s civilizations are constructed. It holds an exalted position in Iraq, qualifying it as the conversational mode for all the pulsations of public and private life. It is and has been an important outlet for the expression of people's suffering due to the harsh conditions experienced by Iraqis during the twentieth century, while Iraq was under the domination of the Ottoman Empire and later the British. Poetry is a mirror which reflects the events of this era. Poets formed salons in different cities in which poetry became one of the important links between people in Iraqi society. This study depends principally on literary research including books written in Arabic as well as some written in English. This project contains a short analysis of Iraqi history until 1940 and focuses on the events from 1900-1940 in relation to Iraqi poetry, and an analysis of the poems of al-Jawahiri and al-Baseer with a specific emphasis on concurrent Iraqi social movements, also this project addresses how their poetry interacted with the socio-historical atmosphere of the revolution of Iraq in the year 1920. Poetry in Iraq is indicative of Iraqi passions and emotions and reflects the nature of the Iraqi people’s experience, including the culture, religion, education, history, beliefs, and politics of that time. I intend to reveal how culture, knowledge, and Iraqis’ daily lives and concerns are reflected in poetry. Ultimately, this is an exploration of how poetry highlights the bonds of human relationships in this community.

While sexual co-mingling of the races in the Americas began as early as the first cases of colonization, miscegenation remained an unspoken taboo in America until roughly the mid-century, when many cases of mixed-race couples began increasing in visibility in local communities, popular culture, and the courts. These couples found themselves thrust into the spotlight as either martyrs for the cause, fuel for the propaganda against mixed unions, or examples for popular interest pieces in magazines and newspapers. The role of news outlets in bringing public awareness to the presence of interracial relationships, for good or for bad, was crucial. This project explores newspaper articles over a 20 year period (late 1950s through the early 1970s) from three American Black newspapers: New York Amsterdam News, Pittsburg Courier, and Atlanta Daily World, and analyzes them from several perspectives, considering regional differences, date of the article (before or after the Loving v. Virginia decision), and subject matter of the article. Findings revealed several themes: emphasis on the white, female opinion, shifting generational divides, and the role of celebrity and celebrity mixed unions in public interracial marriage awareness. This project displays my discoveries in how the black community felt about interracial marriages during this period, as well as how the black media sought to influence public opinion regarding the topic.

In today’s digital world, cultural transmission through popular media, such as music, occurs on a grander scale than ever before, connecting people and ideas across the globe. Dancehall music is deeply embedded in Jamaican culture as a culturally significant source of self-identification, but it has also spread globally. This is a study of the globalization of culture through popular media, including aspects of production, dissemination, consumption and appropriation of Jamaican dancehall music in the United States. Many studies of the commodification of culture describe diminished creative authenticity; however this study will attempt to situate actors in their social context as culture creators. It will address the dynamics of economic production and artistic creation as cultural products and social processes, while exploring the strategies employed to create and disseminate music. By looking at cultural transmission through music as a social process, this study is seeking to address questions of authenticity and hybridity, explore local and global identities, and reveal cultural assumptions stemming from musical interactions as key discursive elements in the limited body of research concerning dancehall music culture.

While red blood cell transfusions require basic blood type matching (A+, B-, O+, etc...), effective platelet transfusions require complex histocompatibility matching, testing to make sure specific alleles of genes are the same between donor and recipient so as to prevent rejection; this is similar to the testing required for organ transplants. Currently, platelets are transfused from random donors until a patient shows signs of rejection, at which point a blood center must attempt to find a histocompatible donor out of its registry to donate on short notice. Using a canine model, the Slichter lab has created a treatment, through a combination of filtration leukoreduction to remove antigen presenting white cells (APCs) and irradiation to inactivate residual APCs, which may prevent transfused recipients from rejecting non-histocompatible donor platelets. In my research, I will focus on canine immune responses to platelet transfusions. The lab transfuses canines with mismatched, treated platelets and measures the recovery and survival of radiolabeled donor platelets to document rejection; antibody levels are also measured, to correlate decreased donor platelet recoveries and survivals as being immune mediated. I perform an Enzyme-Linked Immunoabsorbent spot (ELI-spot) assay to test the production of gamma interferon (IFN-g). IFN-g is produced primarily by activated T-h1 and CD8 lymphocytes as well as other cells such as macrophages and mast cells. As such, the ELI-spot serves as a direct indication of the very beginning of an immune response. My research aims to expand on the current antibody data and directly correlate the recipient’s response to transfused platelets with the results of the ELI-spot assay. This research allows a direct link between cell interactions and immune responses, which can then be compared to the donor’s platelet recovery and survival data to see if a correlation exists. This will allow us to better judge the effectiveness of various platelet treatments by identifying significant correlations between in vitro data and post-transfusion platelet responses. Not only can this lead to breakthroughs in platelet delivery, but the results may also be useful in detecting early organ transplant rejection.

Minimally invasive surgical (MIS) techniques, such as laparoscopic surgery (performed through small incisions using specialized tools), are an integral part of modern medicine and the future of surgery. Technologically advanced tools such as MIS robots are promising to replace or augment existing MIS manual tools. MIS robots improve on manual surgery, as they can incorporate increasingly sophisticated features such as force feedback for surgeons, automatic identification of diseased tissues, and partial automation of surgical tasks. These features can reduce patient pain, recovery time and thus healthcare costs by eliminating unintended damage to tissue and providing surgeons with tools to perform surgery more effectively. Each of these new features either requires or would greatly benefit from an accurate mathematical description of the dynamic mechanical properties for the tissues with which surgeons interact. Dynamic tissue property quantification requires that we apply a range of forces to the tissue and measure the resulting displacements. We have designed, built, and calibrated a device capable of collecting the necessary data to obtain an equation relating applied force to tissue displacement for any tissue of interest. We will process the data obtained from this device using an advanced signal processing and system identification algorithm (unscented Kalman filtering), which will evaluate the fit to the data recursively over time. This will allow us to maintain accurate results as the tissue properties change over time. This setup allows us to collect and analyze data from tissues including (but not limited to) in vivo abdominal organs in pigs. In addition to being an important study that has not been performed in the literature, the real-time collection and analysis of this data could have profound implications in partially automating surgery.

The Paul Yager Lab in the University of Washington’s Bioengineering Department has been researching the dynamics of fluids on two dimensional paper networks of nitrocellulose. Knowledge of this science will allow for the development of distributed diagnostics, akin to pregnancy tests, that can be used in remote settings without access to electricity or medical supplies. By testing the storage and flow of various proteins and carbohydrates on nitrocellulose, we are developing lateral flow enzyme-linked immunosorbent assays (ELISAs) for the diagnosis of various diseases. My research involves the control of proteins once they are already on the nitrocellulose membrane. By printing proteins and carbohydrates in various conformations onto the nitrocellulose, we were able to test the effectiveness of our methods for delaying and mixing protein flow. We showed that you can delay protein flow by printing a wall of sugar around the protein that needs to dissolve before the protein can flow with the liquid. We tested the flow patterns of two consecutive patterns of proteins and found that we can predict the time and efficiency with which they arrive at the downstream mixing site. We also developed ways to effectively load up to 1µl of solution onto the nitrocellulose strips. This research will be useful in the eventual development of a working ELISA, when combined with other results from researchers in the lab.

A reversible tissue adhesive is a surface that is capable of sticking to tissues repeatedly without losing adhesive ability, similar to how geckos' feet can adhere to smooth and rough dry surfaces. This project seeks to combine the reversible adhesion exhibited by geckos and the bacterium E. coli, a model for receptor-ligand tissue adhesives. This technology has the potential to benefit laparoscopic forceps designs, which are required to manipulate delicate tissues easily punctured or torn during a medical procedure. FimH is an adhesive protein expressed at the end of E. coli fimbriae that binds reversibly to mannose, a sugar expressed in human endothelial tissues. A FimH receptor-ligand adhesive has worked on small length scales (μm²), but adhesion fails at larger scales (cm²), possibly due to the propagation of a single crack at the adhesive interface. My project addresses this failure by 1) fabricating the geometry of the existing adhesive in PDMS allowing an interface size without damaging force instruments and 2) combining E. coli fimbriae with polymer molds of micron-sized pillar arrays that mimic the topology of gecko footpads and arrest crack propagation on dry surfaces. Spherical PDMS slices of increasing size (40μm – 300μm radii) were coated with mannose and brought down to fimbriated cell-culture plates. Results show that PDMS measures higher adhesion (226 nN) than the existing receptor-ligand adhesive (25 nN), indicating a successful increase in adhesive interface size. The PDMS surface can be used to measure and compare the adhesive capabilities of various micropillar array geometries coated with E. coli fimbriae. In conclusion, micropillar geometries that measure higher adhesion than plates coated with fimbraie have the potential to be developed into a tissue adhesive. Future studies may show reversible adhesion is achieved when fimbriated-micropillar substrates are brought in contact with cultured and dissected tissues.

The 2007 financial crisis and subsequent recession in the United States has brought the political economy of unsustainable debt to the forefront of the minds of people everywhere in a way not seen in decades.  This paper will delve into the puzzle of why neither dominant political party has been able to institute the recommendations of the four highly regarded debt and deficit reduction commissions in light of their general consensus regarding goals that need to be met in order to avoid a currency crisis.  We ask the question: Why has the Congress of the United States failed to enact measures to reverse the trajectory of the triple deficits of the United States (fiscal, trade, unfunded liabilities) and thereby avoid this crisis?  Our hypothesis is that decades of continued entrenchment of budgetary, trade, and social policies led to gridlock.  We will investigate the coalitions that have formed around the aging baby boomer population, national health care, and national defense.  First, we will discuss the recommendations of the various commissions.  Second, we will review the literature regarding the interests and coalitions within representative bodies contending with looming fiscal imbalances. Third, we will analyze the interest groups, coalitions, and beneficiaries of inaction at this particular time and relate this to the previous literature review.  Finally we speculate as to what would be necessary for congress to act, and what are the likely scenarios if congress fails to act. Having done so, it is our hope that we can provide policy makers and constituents with a deeper understanding of the political-economic problem that the country faces.

This project explores whether steady increases in inequality; the neoliberal retreat of the State from social protection; and the Great Recession of 2008 produce new forms of cross class interaction, identity formation, and action around the themes of poverty and inequality. Specifically, we are interested in studying the production, maintenance, and renegotiation of middle class-ness in the context of rising inequality. Using a variety of qualitative methods including, but not limited to, ethnography, archival research, PAR, and critical GIS, we hope to investigate a series of questions on middle class responses to and involvements with poverty. What are the sites at which these interactions can be studied? What sorts of ideas about poverty and inequality are produced in different 'sites of governance' and 'zones of encounter'? Through this research, we'll investigate potentials for social alliance around poverty in the Seattle region, as well as spaces of increased difference and class-based tensions.

This paper examines cooperation between the United Steelworkers and the Mexican ‘Mineros’ Union, a relationship that began in the early 2000s and evolved into a close alliance after 2006. The alliance moved beyond the limitations of prior attempts at international labor solidarity that were constrained by a focus on symbolic gestures, a lack of connection with workers and domination by the Global North. I argue that confronting the corporate private sector through labor organizing is central to contesting the economic and social landscape of NAFTA-era North America. The two unions understand this potential and have proposed integration into a single body, though this brings a new set of challenges. I give a critical overview of the pitfalls of union mergers, particularly issues of member alienation, organizational identity and local autonomy. Flexibilized supply chains, the informalization of work and other corporate schemes have compounded these impediments to building strong unions. This essay contends that joint action, particularly organizing drives and corporate campaigns, effectively fights this erosion of working standards and engenders transnational solidarity as a culture within union membership, thereby facilitating integration. This strategy combines communication between leaders with the tangible mobilization of workers, forming the authentic and multi-layered relations of mutuality needed to rebuild worker power in a neoliberal age. High-profile debates over free trade and globalization sparked an explosion in academic literature in the 1990s that theoretically mapped out a ‘new labor internationalism,’ but the literature’s case studies failed to live up to its expansive proposals. Drawing on union agreements, newsletters and interviews with officials, this paper gives a deeper example of new labor internationalism in which the Steelworkers and Mineros are creatively continuing the long tradition of industrial unionism as a transformative social force that bridges multiple physical and social borders.

M dwarf stars, which are smaller, dimmer, and redder than our Sun, are the most common type of star in our galaxy. Like our Sun, these stars exhibit activity due to inherently strong magnetic fields at their surfaces. In M dwarfs, this activity is often classified by the emission line strength of the first transition of the hydrogen Balmer series (H alpha). We examine a sample of five equal-mass M dwarf wide binaries; these “twin” stars should have nearly identical stellar properties and therefore have very similar spectral features. We hypothesize that these stars should exhibit nearly identical properties in H alpha. If our hypothesis proves false, it means there are unexpected dynamics present in the binary system. In initial observations to classify these objects, we found that the M dwarfs in each binary, which were twins in every other way, showed very different levels of H alpha emission. To examine the range of H alpha line strengths we obtained a time series of optical spectra using the Astrophysical Research Consortium’s 3.5-meter telescope at Apache Point Observatory in New Mexico. In each binary, the slightly less massive star exhibits stronger mean H alpha, consistent with large survey results. Using data from 70 hours over 14 nights, we determined our stars have a characteristic variability timescale of around 2 hours; indicating our sample is active on shorter timescales than the typical rotational period.

Exoplanets are planets outside our solar system. As they do not emit light of their own, these objects have historically been much harder to find and study than stars. One detection method exploits the slight dimming of a star caused by a planet passing across its face. In astronomy, these events are termed transits, and they cause distinct u-shaped dips in the lightcurve—a plot of observed brightness versus time—of their host star. In recent years, the Kepler Space Telescope has provided lightcurve data on a fixed group of stars that is unprecedented in precision. Our research is primarily concerned with searching released Kepler data for previously undiscovered exoplanets. Due to the vast quantity of information, we have developed a pipeline of computer code to expedite the search process. The code, written in python, detrends variations in quiescent star brightness to normalize each lightcurve around a fixed, flat value. This readies the data for input to a Quasi-Periodic Automated Transit Search algorithm (QATS). Thus far, we have identified a handful of planet candidates as well as a number of undocumented binary star systems. Current and future tasks involve automating QATS output classification to further improve the efficiency of the planet finding process.

When massive stars reach the end of their lives, they erupt in enormous explosions known as supernovae, leaving behind clouds of shocked gas and dust known as supernova remnants (SNR). The primary technique to measure the mass of the progenitor star requires waiting for the star to explode and examining pre-explosion Hubble Space Telescope archival images of the site, which may or may not exist. This technique is constrained by rarity of supernovae, and as such only ~25 progenitors have any mass constraint whatsoever in the literature. We employ an alternative technique in which we examine color-magnitude diagrams of the regions surrounding known supernovae to measure their star formation history. We then use this star formation history to assign an age to the progenitor star.  By employing stellar evolution models, we convert this age to a mass. Because we do not rely on identification of the specific progenitor star in the images, we are free to apply our technique to cataloged SNR, drastically increasing the number of available targets. We apply our method to ~135 cataloged remnants in the nearby spiral galaxies M31 and M33, representing a dramatic increase in the number of currently known masses. We examine the distribution of these derived masses and comment on implications for supernova physics.

Spinocerebellar ataxia type 7 (SCA7) belongs to a family of neurodegenerative diseases characterized by degeneration of Purkinje cell neurons (PC) within the cerebellum, which leads to motor dysfunction. The disease results from a CAG tract expansion mutation of the ataxin-7 gene. This type of expansion is common within the SCA family along with other neurological disorders like Huntington’s disease. Recent research has provided evidence for a non-cell autonomous degeneration of PCs, which means that other cell types cause the PCs to degenerate. One population of cells that may be involved is the inferior olive (IO). The IO, which is known to degenerate in humans, is made up of neurons and is located within the brainstem. The axons of the IO, known as climbing fibers, extend to the cerebellum and synapse with PCs. These climbing fibers transport neurotrophic factors to the PCs. We hypothesize that loss of neurotrophic factors due to the degeneration of climbing fibers may contribute to the disease state of SCA7.
To support this belief, we seek to characterize the climbing fibers by immunohistochemistry. I have stained cerebellar sections of non-transgenic and SCA7 positive mice for VGLUT2, a marker of climbing fiber terminals. In order to understand whether a change in climbing fibers occurs before or after presentation of the disease I have also stained sections from multiple time points. To analyze the differences between the groups I have focused on measuring the amount of VGLUT2 positive puncta in regions proximal and distal to the Purkinje cell soma. Preliminary results indicate that a change in distribution of puncta occurs in mice in the late stages of disease.
 

Alzheimer's disease (AD) is the leading cause of dementia, and its precise cause is still unknown. Mutations in the two Presenilin (PS) genes, Presenilin 1 and Presenilin 2 (PS2), cause AD. Understanding how AD mutations impact PS function may help us understand AD pathogenesis. One function of PS involves calcium (Ca2+) transfer between the endoplasmic reticulum (ER) and mitochondria. Presenilin 2 (PS2) and mutant PS2 (mtPS2) in particular have been shown to increase this transfer, possibly causing mitochondrial Ca2+ overload. This could lead to metabolic dysfunction, which has been suggested as a key pathogenic mechanism in AD. Establishing a link between PS mutations and mitochondrial dysfunction would support this hypothesis. One symptom of mitochondrial dysfunction is changes in mitochondrial fragmentation and localization. "Fragmented," rather than interconnected, "branchlike" mitochondrial networks are associated with increased ER-mitochondria Ca2+-transfer and apoptosis. Furthermore, while healthy mitochondria move towards energy-demanding neuronal processes, mitochondria with reduced ATP production stay near the nucleus. To determine the effects of PS2 and mtPS2 on mitochondrial fragmentation and localization, wild-type (wt) and mtPS2 (N141I) transgenic mouse cortical neurons were infected with a lentiviral vector expressing mitochondrial targeted red fluorescent protein (DsRed). Fixed cultures were imaged using confocal microscopy and analyzed using Huygens software. Currently, we have plated, infected, and analyzed sample preparations for mitochondrial length, sphericity, and other characteristics associated with fragmentation, as well as mitochondrial volume as a function of distance from the soma. Using this paradigm, we will also challenge cultured wt and mtPS2 neurons with camptothecin and staurosporine, inducers of mitochondrial fission and fusion, respectively. If mtPS2 induces mitochondrial dysfunction, mtPS2-expressing neurons should exhibit more mitochondrial fragmentation and mitochondria localized nearer to the soma. This would provide evidence for mitochondrial dysfunction in AD, supporting further research into mitochondrial changes in AD and a better understanding of AD’s etiology.

The effects of amphetamine on learning and memory are important areas of research due to the widespread use of amphetamine among people, ranging from prescription to recreational. It has been shown in animals that repeated treatment of amphetamine will result in sensitization to the drug. Sensitization is a process through which treated subjects develop an elevated response to a drug. Long term potentiation (LTP) is a physical change strengthening the connection between synapses that is thought to underlie learning and memory. Enhancement of LTP in the striatum has been shown to occur as a result of amphetamine use. The striatum is a brain region important in mediating a large number of behaviors including motor control and learning. For this reason it is possible that sensitization to amphetamine may affect learning in mice. To investigate this possibility, wild-type mice sensitized to amphetamine were tested in behavioral paradigms designed to measure learning ability. It was found that they do not show enhanced performance in motor learning, appetitive learning, or spatial learning, but they may show an improvement over controls when they are required to alter their strategy to escape from a water-maze. In order to explore the neurological pathway through which sensitization to amphetamine may affect learning, we also tested knockout mice that lack N-methyl-D–aspartate-type glutamate receptors (NMDARs) in medium spiny neurons, the primary neuron type in the striatum. In many brain regions, NMDARs are important for various forms of learning and memory, and it has been shown that these knockout mice display impaired motor and appetitive learning and yet are still able to sensitize to amphetamine. Using the same learning paradigms as with our wild-type mice, we found that knockout mice did not show any enhancement in motor or appetitive learning as a result of amphetamine sensitization.

The process of cellular reproduction is dependent upon precise timing and coordination of regulatory events. Oscillations in cyclin-dependent kinase (Cdk) activities drive the cell cycle by regulating changes in the phosphorylation states of protein substrates. This dynamic and intricate signaling network of protein phosphorylation is a central component of the cell-cycle control system and enables the cell to modulate cellular functions and processes. Despite extraordinary advances in depth of coverage, phosphoproteomics experiments have struggled to expand in breadth, often comparing thousands of phosphorylation sites between only two moments in time. Such snapshots provide a biased view of the highly dynamic phosphoproteome and ignore important contextual information. To meet this challenge, we are developing robust and reproducible phosphoproteomic methodologies and utilizing mass spectrometry to study the changes in S. cerevisiae phosphoproteome over the course of the cell cycle. I first analyzed the reproducibility of the sample preparation techniques and data acquisition methodologies, which are key factors in the ability to distinguish true differences between different samples. Repeat analyses of 10 identical samples consisting of the entire yeast phosphoproteome were conducted, and preliminary results show that about 70% of the total identified phosphoproteins and 37% of the total identified phosphorylation sites were detected in all 10 repeat analyses with a variance in quantitation of less than 5%, indicating an accurate measurement of changes across the runs. I am now collecting global measurements of relative phosphorylation and protein changes in 5-minute intervals over the entirety of the cell cycle in a synchronously growing population to identify and quantify the proteins present at each time point of the cell cycle. This research will provide a wealth of information on the dynamics of proteome and phosphoproteome regulation throughout the cell cycle and unlock new insights into the biology of defective checkpoints in cancer.

Bacterial conjugation is a form of horizontal gene transfer that serves as an important source of genetic plasticity and diversity in both Gram positive and Gram negative bacteria. It has also been proved to be advantageous for dissemination of antibiotic resistance. Conjugation is a plasmid-mediated mechanism that allows single stranded DNA to be transferred across cell membranes from a donor to a recipient cell. In Escherichia coli, the conjugative F (fertility) plasmid encodes all necessary proteins for assembling the transfer apparatus thus allowing transfer and propagation of DNA into a recipient bacterial cell. Previous conflicting studies of bacterial conjugation in E. coli have shown DNA transfer to occur between donor and recipient pairs in intimate cell-cell contact or between distant donor and recipient pairs, connected only by the pilus, a filamentous protein extended from the donor cell. Using various fluorescent protein constructs to differentially mark donor and recipient cells and F plasmid DNA itself, we visualize conjugation in real time with single-cell resolution by fluorescent microscopy. Here we show that conjugation occurs only when donor and recipient cells are in intimate and close physical contact with each other. In addition, there appears to be no preference for cellular orientation for transfer. Furthermore, we propose a simple rate equation to model DNA transfer between bacteria and measure the rate of DNA transfer per unit time per cell contact. This quantitative model is a tool to elucidate conjugation at a single-cell scale and will provide a deeper understanding into the mechanism of bacterial conjugation.

Speciation is the process by which one species becomes two species that can no longer interbreed. A common hypothesis is that infertility between closely related species is due to the rapid evolution of DNA double-strand-break hotspots that are active in meiosis. DNA double-strand-breaks play an important role in meiosis by initiating recombination after chromosome replication and can be repaired as crossovers. However, hotspots where most of the breaks happen are preferentially lost to gene conversion during DNA repair. It is a mystery how hotspots are maintained over evolutionary time when they are constantly destroyed during meiosis. We hypothesize that hotspots rapidly appear and disappear over evolutionary time, which results in speciation. Schizosaccharomyces kambucha and Schizosaccharomyces pombe are two very closely related fission yeast species that are 99.5% identical at the DNA sequence level. Mapping out the hotspots of Schizosaccharomyces kambucha and comparing them to those of Schizosaccharomyces pombe will be a useful way to test our hypothesis. For this experiment, we have created Schizosaccharomyces kambucha mutants that can no longer repair the breaks so that we can pull out the broken DNA pieces using Chromatin Immunoprecipitation and locate where the DNA double-strand-break hotspots are in the genome. We expect to see the hotspots of Schizosaccharomyces kambucha differ from those of Schizosaccharomyces pombe, which will support the hypothesis that the difference in DNA double-strand-hotspots is indeed contributing to speciation. This research can be extended further to explain speciation in other organisms or unexplained infertility between human couples.

Human embryonic stem cells (hESCs) are pluripotent, or able to differentiate into all cell types of a developing embryo. They can be used to engineer human tissue, but are prone to immune rejection when used in medical treatment. Similar to hESCs but derived from the reprogramming of adult somatic cells, human induced pluripotent stem cells (hiPSCs) were developed that have the potential for use in regenerative therapy with less risk of rejection. However, hiPSC research faces its own challenges, such as inefficient reprogramming rates and variation in observed pluripotency. Previous research has shown that methylation patterns of hESCs can be distinguished from hiPSCs at both the DNA and histone level, suggesting less pluripotency in hiPSCs than in hESCs. While exhibiting greater overall methylation on DNA but less on histones, many of the hypermethylated DNA regions of hESCs are adjacent to these differentially methylated histones. The location of the hypermethylated regions suggests that erasing specific histone methylation marks may improve hiPSC reprogramming rates by creating a more open chromatin landscape, and may create a cascade effect that allows for additional methylation of the genome. This experiment investigates the correlation between histone methylation and hiPSC reprogramming efficiency and accuracy. We reprogrammed human fibroblast cells with lentiviruses expressing various demethylases and transcription factors in order to compare resultant hiPSC methylomes to traditional hiPSC and hESC lines. Opening of the chromatin is expected to improve reprogramming rates and allow for proper methylation of the genome, creating an hiPSC closer in phenotype to hESCs and more useful for clinical therapies.

Ubiquitin is a small post-translational signaling molecule. Its roles in repairing damaged DNA, apoptosis and protein degradation make it critical for tumor suppression. Genetic mutations affecting proteins in the ubiquitination pathway have been implicated in multiple inherited human cancers. The ubiquitination pathway attaches the protein ubiquitin (Ub) onto a substrate molecule with the help of three enzymes, ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2), and ubiquitin ligase (E3). Transfer of Ub onto the substrate requires the formation of a thioester bond between Ub and E2, denoted as E2~Ub. A catalytically active E3 ligase which can bind E2~Ub, but never directly binds Ub, is also necessary. E3’s catalytic mechanism is not fully understood. One function of E3 is to bring E2~Ub and substrate in close enough proximity to facilitate a reaction. However, E3 enhances the release of Ub from E2~Ub in the absence of substrate molecules. This suggests E3 plays a role in priming E2~Ub for transfer of Ub. Using site directed mutagenesis and protein-protein interaction assays visualized through western blotting, I have investigated what electrostatic properties of Ub are important for E3’s catalytic activity. Informative Ub mutations don’t stop formation of E2~Ub, but disrupt the catalytic activity of E3. I propose that polar/charged Ub residues in the contact region between Ub and E2 affect E2~Ub binding modes, promoting inhabitance of E2~Ub conformations favorable to Ub transfer upon binding of E3.

The glass transition temperature is a feature of polymer systems that dictates the transition between glassy and molten-like states in amorphous solids. Glassy polymers have many advantageous properties and are highly desirable for commercial and industrial uses. However, the conditions that lead to glass formation are usually well above room temperature, making implementation of most polymer glasses unfeasible. In a recent discovery, ultra-stable poly(methyl methacrylate) (PMMA) glasses were formed using a technique known as matrix assisted pulsed laser evaporation (MAPLE). These results showed a significant decrease in the polymer’s density, while maintaining chemical stability under normal conditions. The exciting experimental discoveries hold great promise for future technological developments. However, there is much to understand about the underling atomic scale features that arise from MAPLE deposited glassy polymer films. To help answer some of these questions, molecular dynamics (MD) computer simulations were used to understand the mechanisms behind the ultra-stable polymer formation. Previous studies include observing the collapse of the polymer PMMA from an extended to a globular-like state under various solvent and temperature conditions. This poster will show how we track formation of the globular state using different order parameters (e.g., radius of gyration) and also show our generalized strategy for quickly building new polymer simulations. Understanding the fundamentals behind ultra-stable glass formation can unlock discoveries in the development and implementation of new materials.

HIV has infected over 30 million people worldwide and has resulted in the loss of millions in healthcare costs. HIV vaccines have the potential to prevent infection and drastically reduce infection rates. A potential strategy for vaccine development is to elicit a mucosal immune response, since sexual transmission of the virus is the leading cause of new infections. A successful functioning vaccine would deliver an HIV antigen, such as the highly conserved regions of the HIV membrane surface protein gp41, and an adjuvant, such as the synthetic organic molecule R848, through mucosal and cellular barriers. Here, a delivery vehicle for a complex HIV vaccine is synthesized by using a single emulsion method to formulate a polymeric nanoparticle, consisting of a biodegradable polymer core surrounded by a lipid layer. Previous research has shown that a lipid shell increases serum stability and immunocompatibility in vivo. First, design parameters, such as solvent and surfactant properties, were modified to yield consistently monodisperse populations of nanoparticles with controlled size and surface chemistries. Different methods for encapsulating the adjuvant into the polymer core were also explored. The encapsulation efficiency and drug loading of the adjuvant, as measured using liquid chromatography, was less than 1%. We delivered an HIV antigen by intercalating it within the lipid layer surrounding the polymeric core. Encapsulation efficiency of the antigen was measured with a proof-of-concept peptide attached to a fluorophore. We used ELISA and cell culture studies to test for the controlled release and immunogenicity of the immunogens. Finally, a mouse model will be constructed to test the particles in vivo. This project demonstrates a design for creating nanoparticles with controlled characteristics for eliciting a comprehensive immune response against HIV.

Human immunodeficiency virus (HIV) has claimed more than 25 million lives worldwide, and a further 33.2 million are currently living with the disease. Current treatment for HIV involves highly active antiretroviral therapy (HAART), which commonly involves the oral administration of a combination of small-molecule drugs that target HIV at different stages in the viral replication cycle. Oral administration requires larger doses of drug due to loss during metabolism, which can lead to greater costs and increased toxicity for patients. To avoid these issues, a lipid-encapsulated hydrogel nanoparticle was synthesized as a mucosal drug delivery vehicle for small-molecule antiretroviral drugs. The nanoparticles, comprising a crosslinked polyacrylamide core surrounded by a phosphatidylcholine bilayer, were synthesized via photopolymerization and characterized using dynamic light scattering for size, zeta potential, and morphology. They were then synthesized encapsulating zidovudine or tenofovir, which are reverse transcriptase inhibitors, or maraviroc, an entry inhibitor, and the encapsulation efficiency and in vitro release kinetics were measured using high-pressure liquid chromatography. In vitro cellular uptake of the nanoparticles was measured using bone marrow dendritic cells (BMDCs). The nanoparticles showed a tenfold increase in the encapsulation efficiency of all three drugs and a slower release profile as compared to liposomes encapsulating the same drugs, indicating that this system allows for HAART dose reduction. The nanoparticles were also taken up preferentially by BMDCs as compared to drug-loaded liposomes and soluble drug, further indicating greater targeted delivery of drugs to infected cells and suggesting a future use for the delivery vehicle as an HIV vaccine.

With more than 5 million new infections each year, the HIV pandemic presents a growing problem to which a cure has thus far been elusive. High rates of mutation and variability across HIV strains complicate antibody production via the secondary immune response. HIV surface protein shedding (gp120 and/or gp41) via membrane-proximal external region (MPER) specific antibodies has been shown to neutralize viroid infectivity1, however the conserved MPER of gp41 remains protected by surface proteins, and denatures when removed from its lipid environment. We have developed a vaccine system using lipid bilayer-polymer core virus-like nanoparticles (VLPs) that allows for the delivery of MPER in a native conformation. These VLPs have been controlled for size, polydispersity, and surface characteristics to allow intercalation and presentation of MPER in a hydrophobic state. We plan to characterize cellular uptake and cytotoxicity characteristics of these VLPs using in vitro assays. We will evaluate secondary immune response in a mouse model, examining antibody titers post inoculation. This vaccine platform may prove to be a robust technique for the delivery of hydrophobic antigen moieties, readily uptaken and producing a strong antibody response with low cytotoxicity.

 Microencapsulation of xenogeneic recombinant cells within Alginate Poly-L-lysine Alginate (APA) matrices is an alternative approach to drug delivery. The APA encapsulation matrix protects xenogeneic cells derived from individuals or species foreign to the host immune system without the need for immunosuppressive or genetic therapy. Furthermore, matrix permeability allows for the continuous delivery of secreted cellular therapeutics at the implantation site. Although this technology is well-established, the ability of these cell-loaded APA particles to secrete antigens activating specific immunity towards HIV over long periods of time has not been studied. My research is aimed at developing implantable, cell loaded microcapsules capable of producing immunostimulatory molecules preventing the transmission of HIV in the genital mucosa. Using cellular viability and quantitative protein assays, my work will examine the long-term stability and protein production of human 293T cells expressing fluorescent HIV pseudovirions. The immunomodulatory effect of cell-loaded APA microcapsules will then be investigated using cell reporter assays. The results of this research may demonstrate the ability of cell-loaded microcapsules to deter HIV transmission over long periods of time by priming the immune system for HIV attack. We expect that this research could lead to studies of the ability of these particles to provide long term protection against HIV infection in animal models. The results of this work may also be applicable for developing vaccination strategies for other sexually transmitted infections.

Conventional belief has held that the icy regions of our solar system and planet are too cold to support life. However, new research has suggested that below the surface of some moons, like Saturn's Enceladus, lay pockets or oceans of liquid water. In addition, lakes, rivers, and whole ecosystems have been discovered beneath glaciers, areas previously thought devoid of such features. Unfortunately, accessibility remains a primary challenge to further study of these areas. One Applied Physics Laboratory experiment aims to provide a simple and practical alternative to current ice bore-hole technology by developing a heated probe that simply melts through the ice collecting data as it descends. As part of this project, I designed and developed a thermal temperature string, to be deployed behind the probe as it descends, to monitor the conditions of the glacier at depth. The result is a sensor array capable of providing data on the internal glacial temperature for prolonged periods of time. The thermal string consists of a number of sensors evenly spaced along a 100-meter bus wire and controlled by a microcontroller. This microcontroller samples the temperature of the ice at each sensor and stores the resulting data in onboard memory. Currently, the prototype setup transmits the data to a computer, which employs software I have written to interpret this data and display the sensor temperatures. In the future, the software will apply a quadratic calibration correction to achieve expected accuracies of ±0.05°C or better, compared to ±0.5°C without it. We plan to use this sensor array as part of the available instrumentation onboard the probe in places like the Greenland ice sheet or Antarctica. The design can also be modified for other types of sensors or experiments.

Gliomas are invasive, fatal brain tumors that can be detected using magnetic resonance imaging (MRI). However, MRI does not reveal the entire size of tumor. By using a mathematical model developed by Kristin R. Swanson and colleagues, glioma growth can be quantified from the diffusion rate of the tumors cells, the net proliferation rate, and the carrying capacity of the tissue. These parameters are unique to each patient and can be determined by measuring the tumor volume from different MRI modalities as they change over time. Our lab collects data from patients consented to our study and records information about what treatments a given patient receives, since this can affect how the image appears. In my role as a member of the measurement team, I examine patient images to determine the extent of tumor burden on a given date. To obtain these measurements, I use Calcmri, a MATLAB program developed by our lab. Depending on the modality, enhancement on MRI slices can indicate tumor volume as well as other fluids. Calcmri can adjust the intensity threshold at which MRI enhancement will appear, which allows me to isolate the tumor and specify a region for the program to measure. I measure a series of two-dimensional cross section images in order to calculate a combined into 3-dimensional volume. These measurements are used to model the growth of the tumor, “in silico”. Our lab uses information from these models to discover clinical applications, such as to suggest more accurate treatment dosages and to predict life expectancy, which follows an overall goal to better capture the extent and invasion of tumor burden than what appears on MRI.

There is a high need for transitional housing in areas affected by natural disasters, particularly transitional housing that is permanent, high performing, economical, and sustainable. Current solutions, predominantly large tents, do not provide a satisfactory living state for the tens of thousands of people displaced by these natural disasters. Alternate housing options have been developed and implemented, but the response of these alternatives under seismic loading has not been sufficiently studied. A promising alternative is the use of strategically stacked earthbags in combination with frictional material between the bags, strapping, and render for aesthetic purposes. The placement and configuration of these materials impacts the flexural and shear response of the entire housing system. Through modeling force versus deflection of various models, we can predict the response of the earthbag structure. Using strategic bag placements and placement of restraining components, the goal is to quantify the response of the structure. We anticipate that weaving strapping throughout the bags will provide more resistance to buckling and failure in the configurations discussed throughout this paper. By quantifying the relationship of materials and response, we can design an economical and viable transitional housing solution to respond more predictably under earthquake loading. The design of this structure can provide an economical, accessible, and easily constructible housing alternative.

Ulnar-Mammary Syndrome (UMS) is a congenital syndrome that is characterized by ulnar abnormalities and breast hypoplasia. The Bamshad Lab discovered that UMS is caused by mutations in the gene, TBX3. The goal of our project is to find novel TBX3 mutations that cause UMS, and expand the knowledge of how different mutations correlate to the severity of the disease. We collected DNA samples from three UMS families, and sequenced the exons of TBX3 via Sanger sequencing. Sequence analysis software allowed us to search the sequence for mutations and their locations within the gene. In the family K31928, previous screening showed that the proband and her sister, have a mutation called 1294_1301dup8. We screened the parents for mutations in TBX3, and we found that the father had the insertion mutation as well. The father’s clinical findings were very mild, but this screening confirmed that he passed the mutation causing UMS to his daughters. No mutations were found in members of the other two UMS families. The next step of this project is to investigate, in the families without TBX3 mutations, other candidate genes, as well as regulatory regions of TBX3, for mutations that could cause UMS.

The selective activation and functionalization of the C-H bonds of arenes and alkanes would directly yield products that are of importance to industry. Late transition metal complexes have shown great promise in the selective activation of C-H bonds. Coordinated acetate has also been shown to facilitate thermolytic C-H activation by electrophilic metal centers. The results of our studies concerning the reactivity of high valent tridentate rhodium and iridium bis-acetate complexes with unactivated arenes and alkanes will be presented. Specifically, the reactions of the complexes (NCN)Ir(OAc)₂(H₂O) (1) and (NOCON)M(OAc)₂(H₂O) (2; M= Rh, Ir) under a variety of conditions will be discussed. Novel complex 2 was synthesized in 65% yield and characterized using 1H and 13C NMR spectroscopy and X-ray crystallography.

Obesity and atherosclerosis (AS) are major contributors to poor health in the developing world. Hepatic lipase (HL), an enzyme produced in the liver that plays a central role in plasma lipid metabolism, may affect both obesity and AS. HL converts large, cholesterol rich high density lipoproteins (HDL) into cholesterol poor HDL that will circulate through the body and collect cholesterol, possibly reducing AS development. However, HL also converts intermediate density lipoproteins (IDL) into low density lipoproteins (LDL), which is a major risk for AS development. We hypothesized that lipoprotein hydrolysis by HL releases free fatty acids that may modulate satiety and therefore play a role in obesity. It was recently discovered that HL promotes weight gain and food consumption (in mice with HL) whereas the absence of HL protected against weight gain (in mice without HL), supporting our hypothesis. To apply this discovery to human disease, we created a transgenic mouse model expressing human HL. We created a catalytically inactive HL (ciHL) mouse model to study the contribution of non-hydrolytic properties of HL to obesity. Our current study utilizes these mouse models to assess the role of catalytic and non-catalytic effects of HL in promoting weight gain by assessing daily food intake and weight gain and by determining energy expenditure using indirect calorimetry. Because HL lipoprotein hydrolysis might have both pro-and anti- atherogenic effects, we are also examining the contribution of active and catalytically inactive HL to AS in mouse models that have been crossed with LDL receptor-deficient mice, a validated atherosclerosis model with high plasma cholesterol. In this model we will test the hypothesis that catalytically active HL promotes atherosclerosis. If our hypotheses that HL contributes to obesity and atherosclerosis are supported in the humanized mouse models,  a pharmaceutical agent could be developed to inhibit HL in humans.

Autosomal DNA, the non-recombining Y chromosome (NRY), and mitochondrial DNA (mtDNA) are all efficient means of predicting an individual's genetic ancestry. Commercially available autosomal DNA ancestry estimates are obtained using loci that show large frequency differences between continental groups known as ancestry informative markers (AIMs), and NRY and mtDNA ancestry estimates rely on haplogroup information to trace an individual's genetic lineage. Since autosomal DNA is bi-parentally inherited and the NRY and mtDNA are uni-parentally inherited, autosomal DNA potentially contains more information regarding an individual's genetic heritage than the NRY or mtDNA. Our goal is to determine the accuracy of NRY and mtDNA ancestry estimates for predicting autosomal DNA ancestry. Ancestry estimates have been obtained for 965 individuals from a global panel of human populatins from the Human Genome Diversity Project (HGDP-CEPH). Ancestry estimates were compared based on one's biogeographical ancestry or the geographic location of one's ancestors. Autosomal DNA ancestry was determined by the greatest proportion of ancestry based on seven biogeographic groups: African, European, Middle Eastern, Central/South Asian, East Asian, Oceanian, and American. Since each haplogroup is associated with a biogeographic group, the accuracy of NRY and mtDNA haplogroups in predicting autosomal DNA ancestry was determined based on a statistically signifcant number of individuals classified with their correct autosomally determined biogeographical ancestry. This information is useful to assess the quality of different ancestry estimations for use in population-based studies and direct-to-consumer ancestry tests. 

This research explores the function and dynamics of gold nanoparticles functionalized with azobenzene- modified DNA. When exposed to UV light, the azobenzene groups photoisomerize, melting the DNA and dissociating aggregated nanoparticles. This process is reversible with introduction to blue light, initiating the isomerization that allows the DNA to rehybridize and the particles to form aggregates once again. Our research focuses on the dynamics of this transition, determining the extent of trans-cis isomerization of the azobenzene DNA coupled to gold nanoparticles, a process which is monitored through pronounced changes in light absorption between the trans and cis conformations. This information creates a baseline for future photoswitching calculations, accounting for differences in behavior between free azobenzene DNA and such DNA in the presence of gold nanoparticles. We also use the kinetics of the light-induced dissociation and reassociation to provide information about the composition of the DNA, with respect to location of the azobenzene group embedded in the DNA strand. This information can assist with detection and location of base-pair mismatches within the coupled DNA.

          Disproportionate collapse is a phenomenon in which the localized failure of a small portion of a structure triggers the failure of adjoining members, resulting in damage disproportionate to the original cause. In Steel Gravity Framing Systems (SGFSs), connections between members are designed solely to support nominal gravity loading in shear, exemplifying a system which may be particularly vulnerable to collapse if subjected to unanticipated loading.  If unanticipated loading compromises a column’s ability to resist gravity loading in a SGFS, demands on the shear connections become significantly more complex. Under this scenario, gravity loading initially induces primarily shear and bending moment on the connections, which are resisted through friction and clamping forces and later through horizontal bearing forces at the bolt holes when the friction is overcome. As the beams rotate, the gravity loading becomes resolvable into components perpendicular and parallel to the beam axes, generating large tension forces in the connections. Thus, connections originally designed only to resist shear are subjected to a complex combination of bending moment, shear, and tension forces.  This research experimentally investigates the behavior of steel gravity framing connection subassemblages under loading consistent with a column losing its load carrying capacity in order to evaluate connection performance and system-level integrity of existing SGFSs. Furthermore, once the demands on the connections are adequately characterized, practical solutions to improve connection robustness and SGFS integrity can be developed.

Despite widespread global immunization with the current tuberculosis (TB) vaccine, BCG, TB remains a serious problem, killing almost 2 million people every year. In addition, because BCG is a live vaccine it is unsafe to give to immunocompromised individuals, especially those with AIDS. Therefore, a new and effective vaccine that is safer is urgently needed. We are testing nanoparticles blended with polymers, designed to stimulate CD4 and CD8 T cells, as a delivery system for a TB vaccine. Nanoparticles coated with M. tuberculosis epitopes recognized by both CD4 and CD8 T cells were used to immunize mice subcutaneously. T cell responses were detected in immunized mice using both MHC class I and II tetramers, and also by intracellular cytokine staining. Immunized mice, or unimmunized controls, were then challenged with M. tuberculosis via the aerosol route. Mice immunized with the nanoparticles displayed T-cell responses to the relevant CD4 antigens, but this response did not lead to a lower bacterial burden in the lung when the mice were challenged with M. tuberculosis. Future studies are needed to further optimize protection provided bthe nanoparticle vaccine platform.

Between 1875 and 1918, the German Social Democratic Party grew from an isolated and persecuted sect to become one of the largest, most well-organized, and most prestigious socialist parties in the world. The party's theoretical foundation was Marxism. Its leaders, intellectuals, and many of its rank-and-file members espoused a doctrine that prophesied the inevitable collapse of capitalism and the global transformation of society through socialism. However, on August 4, 1914, the party's representatives in the Reichstag  stood side by side with their conservative and liberal opponents in voting to provide funding for the war that had recently broken out in Europe. Furthermore, in defiance of the party's ideology and tradition of intransigence, a number of influential writers and intellectuals within the party had begun to articulate theories that attempted to harmonize German imperialism and Marxism. Contrary to the principles of the international solidarity of the working class, these thinkers argued that the acquisition of overseas colonies was essential to secure Germany's continued prosperity and the well-being of German workers. Many equated the so-called noble and civilizing values of German culture with socialism. The triumph of German imperialism thus laid the foundation for the coming socialist order. My research concerns a critical reading of primary source documents from prominent socialist newspapers and treatises of the period in light of the relevant secondary source literature to reconstruct the party's transformation from intransigence to imperialism. I seek to analyze these theories of socialist imperialism within the context of the party's growth and bureaucratization, the rise of powerful trade unions, and the emergence of theories that challenged orthodox Marxism. Ultimately, these theories of socialist imperialism discredited the party following the war with the disastrous consequence of making its leaders and members unprepared to contest the rise of Nazism in the 1930s.

Glioblastoma Multiforme (GBM) is an aggressive type of primary brain tumor, which is treated by surgery followed by chemotherapy and radiation. A majority of cases prove to be highly resistant resulting in uniform fatality. At present, research has been moving towards developing a patient-centered model of treatment that is developed by finding the unique characteristics of a patient's tumor growth kinetics and response to therapy. GBM is a very heterogeneous disease despite having a generally poor prognosis. A promising method of investigating this heterogeneity has been through finding patterns in the molecular-genetic makeup of these tumors. Large-scale mathematical analysis on data from open-source repositories such as The Cancer Genome Atlas (TCGA) has already led to the discovery and validation of four GBM subclasses which point to characteristic areas of origination in the brain as well as differential growth behaviour. A limitation in this strictly data-oriented approach is the lack of meaningful clinical perspective applied which has resulted in the findings only being directed towards gauging patient survival. The focus of our research has been the discovery of information about individual characteristics of patients tumors that may have more clinical significance for each patient. Our hypothesis is that there is a correlation between the different biological subtypes classified by cluster analysis and the different kinetics of tumor growth measured by imaging. This work will be done by developing tools to investigate the genetic changes that may be driving different kinetics of disease progression (the proliferation and migration rates of the tumor cells) measured from actual patient imaging. This approach is guided by the belief that individual patient tumor biology can be used to inform the data analysis techniques and ultimately bring us closer to the goal of identifying the most discriminating treatment to effectively treat an individual's cancer.

Engineered vehicles capable of matching the performance of natural systems in collision avoidance have not yet been developed. The purpose of our research is to translate the collision avoidance capability of schooling fish to an algorithm that could be applied to engineered vehicles. We want to determine if collision avoidance in schooling fish is related to an engineering method of collision avoidance termed collision cones. The collision cone is a set of velocities for one fish (or agent) that indicates it will collide with another fish (or agent). In order to avoid collision, the fish’s velocity vector must lie outside all collision cones. Constraints with this method are that it only works under certain conditions: each vehicle has constant velocities, uniform and full view sensing, noiseless measurements, and planar motion. This method already works well for engineered systems under these conditions. Our research is exploring how to alter the conditions to encompass the biological characteristics of the fish. As of now, the data that has been collected has revealed promising results. If further research reveals that collision cones do not match schooling fish’s collision avoidance capability, other algorithms will be explored. This research is significant in that it will impact the development of UAVs (Unmanned Aerial Vehicles) and other autonomous technology.

We, the researchers in Dr. Wendy Stone’s Lab, examined the developmental trajectory of motor imitation from 12-18 months and its relation to social functioning and language ability at 24 months in younger siblings of children diagnosed with an Autism Spectrum Disorder (ASD; ASD-sibs), compared to younger siblings of typically developing children (TD-sibs). Motor imitation is the reproduction of a modeled presentation of a motor event and ASD refers to neurodevelopmental disorders characterized by impairments in social-communication and the presence of stereotyped, repetitive behaviors. It is important to study ASD-sibs because they are at an increased risk for developing an ASD or sub-clinical symptoms. Young children with ASD display motor imitation deficits, but currently, studies have not examined motor imitation in ASD-sibs within the first 18 months of life. Thus, the age at which impairments emerge remains unanswered. Further investigation of motor imitation is necessary given its importance for learning and social interactions. Using the Screening Tool for Autism in Toddlers (STAT) to measure motor imitation, the Mullen Scales of Early Learning to assess language, and the Autism Diagnostic Observation Schedule to determine ASD severity, we expect to find that: a) motor imitation will show significant growth between 12-18 months of age; b) ASD-sibs will have lower baseline levels and lower rates of growth than TD-sibs; c) baseline levels and rate of growth for motor imitation will predict ASD severity and language ability at 24 months. Hierarchical linear models will be used for the developmental trajectories of motor imitation from 12-18 months of age. Linear regressions will be used to examine whether baseline levels and growth predict later ASD diagnosis and language outcomes. This study may provide information leading to earlier detection of ASD. Earlier diagnosis of ASD allows for earlier intervention, which has been shown to improve children’s social-communicative outcomes.  

Hydrogel tissue scaffolds have emerged as a useful tool for extensively mimicking and reproducing the cues of the natural extracellular matrix (ECM) of native cell environments. Polyethylene glycol (PEG) is a synthetic compound that is often used as a hydrogel as it is nontoxic and exhibits strong mechanical properties. PEG, however, does not allow cell adhesion and cannot be degraded by cells. To resolve this issue, the incorporation of denatured collagen, or gelatin, was used. This process was completed via addition of methacrylated gelatin (GelMA) to photocrosslinkable PEG hydrogels. The addition of the polysaccharide hyaluronic acid (HA), which is an integral part of the ECM, is in part a novel approach to further provide chemical cues to activate specific receptors (i.e. CD44) within cells. Moreover, cells have also been known to respond to physical stimuli such as changes in the topographical environment. We have developed a technique to produce a nanotopographic pattern on hydrogel scaffolds via the use of a nanopattern mold. Here, we propose the novel integration of the chemical signals produced from the hydrogel in conjunction with a nanopattern for directing cell migration and proliferation in vitro. In this experiment, Wnt1-Cre derived dental pulp stem cells (DPSC) were cultured on these scaffolds. Cellular regulation was reflected in changes in morphology and migration due to exposure to the combined chemical and physical signals of the tissue construct. Cells cultivated on patterned scaffolds showed significant alignment along the pattern compared to flat controls. In addition, cells on HA-PEG-GelMA hydrogels exhibited aggregation over time to form spheroids that persisted for the duration of the experiment. These findings suggest that the microenvironment of HA-PEG-GelMA hydrogels plays a significant role in regulation of the spatial arrangement of cells.

Magellanic penguin morphology is likely to influence the survival and reproductive success of an individual. Although Magellanic penguin colonies are not genetically differentiated, there may be significant differences in the structural size of penguins among colonies, as suggested by Bergmann’s and Allen’s rules that appendage size changes with latitude. We used data collected on 792 Magellanic penguins at 12 colonies in Argentina, Chile and Falkland/Malvinas Islands to compare weight, bill length, bill depth, flipper and foot. We expected penguins to be larger at southern colonies and have longer flippers and bills at northern colonies to shed heat. We expected variation among colonies as morphology should reflect adaptation to the local environment. We matched the years, months and approximate gender ratio of the measurements collected from the colonies with a randomly selected sample of penguins from Punta Tombo, Argentina, a northern colony. We performed an ANOVA on these data using Stata. When ANOVAs were significant, we performed pairwise comparisons (Tukey HSD) among the colonies. All traits varied among colonies except flipper length for females. Average female flipper length was 14.6 cm. suggesting that flipper surface area may be more important for foraging success and survival than for shedding heat on land or conserving heat in the water. Bill length decreased with latitude for males and females (males: R2 = 0 .73, females: R2 = 0.58). Exploring the interactions between latitude and morphology suggests selection is favoring penguins with longer bills at lower latitudes. Does bill size reflect diet changes with latitude or changes in heat and cold stress? Penguin morphology changed with location but flipper size did not which is not consistent with Allen’s rule. Flipper size may be so important in foraging success that selection favors a “standard" flipper size regardless of latitude and temperature.

"The S.P.O.T.", which stands for Students in Partnership for Organizing Transformation, began constructing a physical space on the University of Washington Bothell (UWB) campus in the fall of 2011. This space is meant to serve as a multipurpose room for recognized student organizations (RSO) to collaborate in creating a campus culture inclusive of diversity, representation and open dialogue. The purpose of this study is to critically analyze how The S.P.O.T. exists as a site of struggle, produce by the complex interplay of passionate and influential social actors including The Office of Student Life, RSO leaders, and dedicated faculty. I also document how RSO leaders negotiate public space on campus in an effort to mobilize the wants and needs of their organization. I have conducted a series of in-depth interviews with RSO leaders, participated in several UWB Club and Innovation Forums, and spent months directly observing how students attempt to understand public space on campus. Through this research I argue that The S.P.O.T., designed with the purpose of igniting social change, has itself become a powerful social actor in shaping students understanding of UWB initiatives and policies. RSO leaders must continually employ a series of strategies to maintain visibility and legitimacy in a constantly shifing sociopolitical landscape. By unraveling the unseen forces behind the creation of student spaces, such as The S.P.O.T., and exposing the limitation, as well as the potential, we can better understand how students make sense of complex social issues. This research is necessary if students, RSO leaders, and faculty are committed to increasing awareness, respect, and understanding by transforming physical space on campus.

Polychlorinated Biphenyls (PCBs) are a group of man-made chemical species that were manufactured as refrigerants the mid 1900’s. Though now banned, PCBs are highly resistant to degradation and persist for many decades in the environment where they are known to have adverse affects on the health of organisms, and are a suspected carcinogen in humans. My research examines the impact of tidal cycles on the re-suspension and transport of PCBs adsorbed on sediments in the Duwamish River estuary. Aquatic systems contaminated with PCBs may lead to accumulation of the toxins in the tissues of aquatic organisms, such as shellfish and endangered Chinook salmon. Consumption of these valuable food resources poses a threat to human safety, and therefore it is critical to understand the spread of PCBs due to tidal oscillations in estuarine systems. In the Lower Duwamish Waterway, a salt wedge estuary with a sharp boundary between fresh and salt water, turbulence created by the relative motion of these bodies of water can move contaminated sediments to new areas. By testing a variety of water quality parameters, including total and dissolved organic carbon content, suspended solid content, salinity, pH, and PCB concentration, my work evaluates the likelihood that elevated PCB concentrations correspond to periods of maximum tidal turbulence and re-suspension of contaminated sediment from the river bottom. Aqueous and solid samples were collected from the estuary at different depths during various stages in the tidal cycle. I have measured key aforementioned water quality parameters according to standard methods, and developed a combined microwave-accelerated solvent and solid-phase extraction procedure for PCB recovery in particulate and aqueous phases. Using these methods, I will quantify the samples’ PCB concentrations using gas chromatography/mass spectrometry to determine sample composition, and attempt to correlate these measurements with suspended sediment and organic carbon concentrations.

High gradient mountain streams are characterized by drops known as steps, followed by depressions in the bed known as pools. This step-pool morphology governs habitat availability and sediment transport of many high gradient streams. A notable characteristic of most pools is the presence of clast-size based sorting on their bottoms. We seek to understand how this sorting forms, as it may provide more insight into the currently debated topic of how such pools are formed. We propose that there is a decrease in shear stress on the bed from the base of a step to the lip of a pool. We suspect the effects of this difference in shear stress are proportional to changes in stream gradient, as step height has been shown to increase with gradient. If our hypothesis is true, we suspect to see a range of sorting patterns from low gradient to high gradient mountain streams. We will survey a number of pools in streams of varying gradient to determine whether such a range can be documented. Preliminary field observations have indicated that such a range is present, although we seek to quantify that observation. For each pool, we will use a pebble count procedure accompanied by geometric measurements of the pool to quantify sorting patterns and evaluate the relationship between sorting and stream gradient. By understanding how sorting is affected by gradient, we can start to determine what aspects of stream hydraulics control pool formation.

The concept of dynamically causing physical distortion of molecular frameworks to influence reactivity offers an intriguing opportunity for synthetic polymer chemists and materials scientists. Strained rings have been shown to undergo chemical transformations under different stimuli but their mechanochemical behavior is a relatively newer field of study. We postulate that directing a reaction pathway mechanochemically may be a viable means to increasing the selectivity in the ring opening event. Before the mechanochemistry is investigated, the polymeric materials containing these ring systems must be designed and synthesized. The development of our strained ring system is multi-step synthesis starting from a commercially available small molecule. Once the strained ring small molecule is created, the final step of the synthesis is to incorporate it in the middle portion of a polymer. After the molecular framework has been built, its mechanochemical reactivity is studied via solution-based experiments using an ultrasound probe and processor (20 kHz) of variable power output (up to 750 watts). This approach will facilitate product characterization, mechanistic inquiries, and reactivity profiles. Collectively, the ambitious research objectives provide a fundamental basis of how mechanical forces may be used to guide and control reaction profiles.

Populus tremuloides, quaking aspen, is the most widespread tree species in North America and one of the most important. Because of its valuable ecological role, aspen is considered to be a keystone species, crucial to maintaining the structure of an ecosystem. Aspen populations have been steadily declining throughout the country, particularly in California. In response, Lassen Volcanic National Park in Northern California has implemented a mapping and assessment program to evaluate the health of aspen stands within the park. Forty-eight stands of aspen were mapped and assessed for risk during 2004-2007, 2009, and 2011. I hypothesize that a majority of the stands are at high risk of disappearing and that the decline can be tied to the influence of one or more features of the stand’s environment. I assigned a risk rating to each stand based on a rating system developed by the Aspen Delineation Project and used by the US Forest Service and National Park Service. Using a geographic information system, I looked for associations between the relative risk rating and environmental features such as proximity to roads, proximity to streams, fire history, and elevation. The results of this study will assist in the development of a strategy to prevent aspen loss in Lassen Volcanic National Park. In addition, the results of this study may help inform the management of aspen in other similar environments in the United States and will lead to a better understanding of the drivers of aspen decline.

The fossil record in western Montana and central Oregon of the late Oligocene-early Miocene period, about 20-30 million years ago, presents a rich fauna of gophers (Geomyidae) of the subfamily Entoptychinae. These burrowing creatures may represent up to 25% of the mammalian fauna of certain fossil assemblages. Understanding the ecology of this large population is thus important for interpreting community-wide ecological changes. Prior to investigating their ecology, it is necessary to understand the taxonomic and morphological diversity of these fossil gophers. Previous attempts have been made to differentiate these gophers by using cranial and dental material. However, skulls and dentaries of such small rodents are rarely preserved. Isolated teeth are sometimes the only material available for identification. As a consequence of their abrasive diet, geomyids wear down their teeth over time, erasing potentially diagnostic features of the occlusal surface of the tooth. Therefore, several authors have suggested that differences in the shape of the teeth could be used as a means of species differentiation. This hypothesis has yet to be quantitatively tested. Geometric morphometrics allows such analysis of shape independently of size. This method involves the statistical comparison of geometric coordinates of landmarks placed on an object of interest. I will apply this method to the enamel band of the last premolar and last molar of 140 fossil geomyids. The goal of this study is to test the hypothesis that the shape of Entoptychine teeth can be used as a tool for species differentiation. Preliminary results of the analysis of M3s reveal statistically significant differences between genera. More specifically, the angles of the tooth (tilted anteriorly or posteriorly), its shape (rectangular versus square), and the proximity of its two lophs, appear taxonomically diagnostic. This analysis will allow me to distinguish between gopher taxa, and allow the investigation of their ecology and potential roles in the community.

The purpose of this research is to gain insight into prosthetic sock thickness trends of multiple sock stacks. For amputee patients, stacked sock combinations are necessary to accommodate volume change of the residual limb in the short and long term. The thickness of these stacks is quantified by the total number of ply. For example, a 1-Ply sock and a 3-Ply sock make a 4-Ply “stack.” However, with this method of measurement, total sock thickness depends on how many socks are worn. The focus of this test is to evaluate existing standards by comparing the thickness of multiple socks to a single sock of the same total ply. The results from this research should provide useful information to prosthetists fitting patients with prosthetic limbs. As the residual limb matures after amputation and swelling decreases, there is a reduction in volume and a change in shape. From the first prosthesis, the practitioner optimizes the fit with the expectation of the residual limb size decreasing. The practitioner advises the patient to add socks to take up space when the residual limb feels loose in the socket. By adding socks, the patient can maintain a proper fit, and the practitioner can track limb change and socket modifications so as to appropriately time fabrication of a new socket. The present research brings quantitative information about sock thickness, both for single socks and for stacks of socks, to clinical care. This quantification should help the practitioner determine just how much larger the socket is than the patient’s residual limb, and should help guide design of a new socket. This research collected in the present study may also facilitate documentation to justify the need for a new socket.

Over the past few decades the budding yeast Saccharomyces cerevisiae has emerged as a prominent model for aging research. One method for measuring aging in yeast is to determine the replicative life span (RLS) of mother cells, defined as the number of daughter cells produced prior to irreversible cell cycle arrest. The Kaeberlein Lab Dissection Team has measured RLS for hundreds of thousands of yeast mother cells over the past few years. In addition to RLS, we have also recently began recording the budding pattern at end of life as an additional phenotype of interest since these mutations have been known to lead to irregular cell cycle regulation. 4 different categories are used to define the terminal morphology of yeast cells: unbudded (U), small bud (S), long bud (L), and clumped (C). From the data gathered thus far, a positive correlation has been made between the terminal budding pattern of cells with reduced RLS compared to their unbudded counterparts. Meaning contructs that stop replicating mid cell cycle (S, L, or C) live shorter lives. We speculate that genomic instability contributes to terminal arrest in the budded state, but further research needs to be conducted to confirm this theory. It will also be of interest to determine how specific genetic defects lead to altered frequencies of the 4 different terminal morphologies and their relationship to replicative life span.

This project demonstrates a new synthetic approach to tetrapod-shaped colloidal nano structures using a combination of Mn doped CdSe quantum dot cores and CdS rods. These structures are achieved using a variation in quantum dot hot injection synthesis in which Mn is added before the injection of the anionic precursors. Once the initial synthesis is complete the products are characterized by UV/VIS absorption, photo-luminescence, EPR, and TEM imaging. Once characterized the doped quantum dots are re-immersed for arm growth to achieve the tetrapod shape. Mn doping provides a magnetic probe in the nano particle that would allow us to probe the carriers during temperature dependent luminescence. Semiconductor quantum dots are believed to be useful materials in solar energy cell applications because their band-gap can be manipulated by changing the size of the particles. However, one of the limiting factors in the efficiency of these dots is the fast recombination of the carriers in the material. Tetrapod nano structure semiconductors have demonstrated the ability to extend the lifetime of exitonic emission which enables greater separation of the carriers and may potentially increase the efficiency of future solar applications. Preliminary results show that Mn doped tetrapods can be synthesized using this method; however yields need to be maximized in order for future applications to come to fruition.

The effect of evaporative cooling is a common experience that people can relate to. For example Sweat cools us as a result of evaporative cooling. However latent heat is released when liquid water condenses. This transition from gas to liquid brings with it a large amount of energy. This effect is important because it implies that heat is transferred to objects more readily in humid environments. I ran a series of experiments demonstrating this effect. For example, liquid in a soda can will heat almost twice as much in a humid environment as compared to a dry environment at the same temperature.

Precipitation varies naturally and with human-caused climate changes, and we are interested in the range of these changes. We use data from the Coupled Model Intercomparison Project Phase 5 (CMIP5) archive, which contains precipitation and energy flux data from 1850 to 2100 from climate model simulations. The comparison of model data from past years with the observed climate record can be used to test the simulations. We use matlab to calculate the mean of precipitation and energy fluxes of each model in CMIP5. The precipitation differences are interpreted with the energy budget. While the precipitation clearly increases in 21st century, there is model-to-model differences over the 20th century. The 20th century differences may be caused by different strengths of aerosol effects related to the second industrial revolution during that period. We will continue data analysis to find the reason for the differences in model predictions over both the 20th and 21st centuries. The differences in the comparision are helpful for validation of the prediction of precipitation in the future and to show the effect of global warming.

An animal’s particular level of dominance within the group that they live with has been observed by various studies on its impact in regards to obtaining food, finding sexual partners, and how conflict is dealt with. Macaca fascicularis is a species of primate found all over Southeast Asia in countries such as Malaysia, Indonesia, India, Vietnam, and Thailand. They are most commonly known as long-tailed macaques. Studies show that they are matrilineal the males leave tend to leave their groups upon sexual maturity, preserving an abundant of female to male ratio. Studies show that the more dominant males within groups containing multiple males are given higher priority for the access of essential elements such as food and mate selection, sustaining the fitness of the individual. The males who are dominant to the other males should displaying aggressive behavior such as biting, kicking, directed vocalization, lunging, chasing, and threatening gestures suggesting imminent attack whilst the submissive male must in turn perform a submissive behavior. These include lip smacking, fleeing, avoiding, vocalization, or grimacing. We found, through open field observance, that between the only two adult male long-tailed macaques that lived in the observed group, that there was a significant difference in perceived dominance based on agonistic and submissive interactions. Also, the dominant male spent significantly more time engaging in sexual behavior than the submissive male, which aids the supporting the hypothesis that there is a link between dominance and frequency of sexual behavior in groups of long-tailed macaques. The observations that made helped discern how aggressiveness impacts the lives of male animals and their ability to survive and reproduce and provided data on group dynamics, which is important to the overall management of the island population. Supported in part by the UW Center for Global Field Study; PSSP-IPB, Indonesia.

 Amongst other struggles, providing health care suitable for its population's needs remains a major challenge for Nigeria as a nation today. To assess the health of the population and the use of health care services, Nigeria's National Population Commission carried out Demographic and Health Surveys (DHS) in 1990, 1999, 2003, and 2008. Knowing that several states in Nigeria have populations dominated by one of the three major ethnic groups, my project used DHS data to examine how state of residence influences health measures, controlling for all other relevant factors. I used the ordinary least squares - multiple regression method in order to separately analyze the degree of influence each independent and control variable has on determining the aggregate health measures of each state. The health measures I focused on include child malnutrition and diarrhea, female circumcision, and maternal health behavior. In the past, studies have consistently revealed that amongst the three nationally dominant ethnic groups, Hausa people suffer the worst health measures for children and mothers; however, mixed results exist for how well Yoruba and Igbo communities fare relative to each other. This study aimed to clarify the relationship between Yoruba and Igbo dominated states using data from Nigeria's most recent and largest nationally representative sample yet - DHS 2008. I hypothesized that Igbo-dominated states fare worse than Yoruba-dominated states, because the Biafran War mostly damaged infrastructure in "Igboland", and reports indicate that the Yoruba region stands more highly urbanized today, which suggests greater postwar fitness. I also hypothesized that as the number of minority ethnic groups a state hosts increases, the worse the state-level health measures will be, according to predictions from social disorganization theory. If my results support my hypotheses, then Nigeria's future health initiatives should consider health disparities along lines of ethnicity and ethnic diversity within a state.

We consider a mathematical optimization problem that can be used to describe various physical situations that arise in physics and EE applications. In its general form, we study the following physical setting: There is some substance emanating from a source, which propagates through an inhomogeneous medium and reaches a drain. As a motivating application, we imagine a spark of fire igniting and spreading through a forest landscape. Alternately, light may be emitted from a point source and travel in a space with lenses of varying indices of refraction. In each case, we would like to influence the substance’s movement by optimally altering the medium in which it propagates. In the case of a forest fire, this corresponds to locating optimal places on the forest landscape to place water, in order to minimize the first arrival time of the fire at a specific location. To solve this convex optimization problem, we perform two tasks. In its general form, our first task relates to finding the shortest distance between a pair of points on a curved space, which is the solution to the Eikonal partial differential equation. Secondly, we take the derivative of the Eikonal solution with respect to a medium parameter. Due to the nature of our problem, these operations cannot be performed analytically. The results are approximated with the Subgradient Marching Algorithm. The unique element of this project has to do with the way we preform the algorithm. Once the shortest-path-length solution and its subgradient are known, we recognize a strategic location on the forest landscape to place a fire deterrent. In this work, we study and implement the overall optimization algorithm, and demonstrate an application to the forest fire problem.

This project uses commercially available CD printable inkjet printer with a chitosan solution as a replacement for ink to pattern chitosan nanofiber. Chitosan is a linear polysaccharide composed of randomly distributed β-(1-4)-linked D-glucosamine and N-acetyl-D-glucosamine derived from chitin. Chitin is the second most abundant polymer in the world. It mainly occurs in the cell walls of fungi and exoskeletons of arthropods (i.e. shrimp, crab, and insects). Chitosan and chitin are used in many applications, such as functional food, wound dressing and sutures, and most recently bionanoelectronics. Unlike chitin which is insoluble in most common solvents, maleic chitosan dissolves in water at mild conditions. Printing is the most widely used technology to deposit small particles onto various surfaces. Since printing enables the fabrication of large areas and arbitrarily high-accuracy patterns and scales well to nanoscopic sizes, we can use it to pattern nanostructures. In this fashion, self-assembled 3 nm chitosan nanofibers are printed.

In the aftermath of the 1916 Everett Massacre, the Industrial Workers of the World (I.W.W.), the City of Everett, and local newspapers struggled to control the story of this armed confrontation, and the ensuing trial of I.W.W. member Thomas Tracy. There has been a great deal written about the Massacre and trial, but limited research on the attempts of labor, political parties, industrialists, and the local community to control the story. To research this topic, I have examined a number of books, along with the Seattle Daily Times, the Everett Daily Herald, and various regional labor publications. I have also to conducted archival research in various documentary sites, as well as conducting informal interviews with archivists, and people in Everett. I argue that the rhetoric used by the attorneys at the trial, the I. W. W. literature, along with coverage in the local periodicals, provides an example of the larger battle waged for the control of the production of stories and historical memories. This paper uses the depictions of the massacre by various groups to raise broader questions about how memory is produced, and the lengths to which people will go to further their cause, and to have their views elevated to the story of history.

Since WWII there has not been a major intra-European war, with the very large exception of the 1992-1995 wars of Yugoslav Succession. These wars were a conflict between the different ethnicities of the republics of former Yugoslavia: Serbia, Croatia, Slovenia, Bosnia-Herzegovina, Macedonia, and Montenegro. The Serbs are widely viewed as the “aggressors” of this conflict, with their leader Slobodan Milošević responsible for inciting nationalism. However, importantly I argue that nationalism was already in place before Milošević rose to power. While most of the current scholarship focuses on the timeline of political developments, my paper moves beyond the political events to look at the cultural transformation of that nationalism from 1980-86 and the importance of nationalistic fervor.  I argue that after 1980, socio-economic and political circumstances reacted with historical revisionism and a resurgence of WWII memories by a group of Serbian intellectuals to produce this new form of nationalism that the Serbian state has been “victimized”.  This "victimized" feeling is crucial to understand the later events of the Yugoslav wars under Milošević.  This transformation is evident in the individual works produced by these Intellectuals culminating in 1986 SANU Memorandum, a dynamic list of grievances that Serbian Intellectuals had with the Yugoslav state. Because of this feeling of “victimization,” the Serbs felt that their group identity was being threatened by their “subordinate” position within the Yugoslav state.

The geographic ranges of species are strongly influenced by climate. As temperatures increase, species are expected to shift poleward in latitude and upward in elevation, a prediction supported by observations of range shifts in recent decades. Species interactions also play a crucial role in setting geographic ranges of global biomes, and could be critical in determining the response of species to climate change. Due to limited data on interspecific competition in the boreal biome, Earth's largest land biome, it is largely unclear how climate change will affect the range limits of the individual tree species that occupy it. In recent decades, spruce trees (Picea engelmannii) have increased in abundance at high elevation locations formerly dominated by larch trees (Larix lyallii). This change is thought to result from improved climatic conditions for spruce establishment but has not been tested. I hypothesize that spruce have higher establishment rates than larch where the two co-occur when temperatures are high. To test this hypothesis, I will harvest 120 stems of each species at locations in the North Cascade Mountains in the summer of 2012. I will then count the number of annual growth rings for each sapling to determine establishment year. Next, I will model the relationship between establishment rates and climate in different decades of the last ~100 years for each species. Finally, I will compare the establishment-climate relationships of the two species to infer how the relative abundances of the species might shift with warming. These results have large-scale implications for changes we should expect to see in global biomes as warming continues. In particular, this hypothesis suggests that spruce will replace larch as climate change progresses.

Following the Norman invasion of England in 1066, King William I instituted a new system of royal forests throughout England. Intended as royal hunting preserves, these areas were vast in extent, and a distinct system of law restricting land usage and hunting rights applied within their bounds. While information on baronial reactions to this change is readily available, the attitudes of commoners and the lesser gentry are more obscure. I argue that the primary audience of the ballads of the famed English outlaw Robin Hood was non-noble, and examines their earliest editions – and the activities of historical outlaws in the 15th century – in the context of both forest law and the appearance of a non-noble “middle class” concurrent with the tales’ apparent origins. Beginning with the origins of forest law and its departures from Anglo-Saxon precedent, I focus on the symbolic significance of the deer-hunt as a royal or noble privilege and the way deer-poachers, fictional and historical, both mocked and mimicked noble hunting rituals – a tendency inexplicable by the mere need for food. Most Robin Hood scholars seek either to identify the tales’ primary audience, or to identify a “historical” Robin Hood; those few that address forest law do not seek to tie these tales’ popularity to the resentment of noble privilege rife at the time of their inception. Robin Hood’s portrayal as a paragon of justice, coupled with his direct defiance of forest law, reveals a complex view of the matter: the stories’ hero defies laws that are specifically royal while upholding the status quo values of his time, up to and including the concept of kingship itself. Resentment is focused against the attempted royal monopoly of a symbolically-charged resource, rather than against the hierarchical structure of society as a whole.

Double stranded DNA (dsDNA) viruses such as herpesviruses, adenoviruses, and many bacteriophages, have common development pathways. In these cases, a packaging motor (the terminase enzyme) inserts the viral genome into a capsid shell. We study the DNA packaging motor from phage lambda as a model system. Lambda terminase plays four critical roles: (1) It has a site specific DNA binding activity where it binds to the cos site on the lambda genome, (2) it has an endonuclease activity where it cleaves the lambda genome at the cos site, (3) it has a “helicase” activity where it then separates the cleaved DNA strands, and (4) it has “packaging” activity where it translocates the “matured” viral DNA genome into a capsid shell through a portal ring structure. The lambda gpFI protein is required for virus assembly but the function remains unknown. In this study, we use a defined in vitro system to study the effects of gpFI on the endonuclease, helicase, and DNA packaging activities of lambda terminase as our first steps towards an understanding the function of gpFI in virus assembly. The information obtained from these experiments will be useful in understanding similar processes in the eukaryotic herpesviruses and adenoviruses.

Aging is a process that causes decline in normal biological function, eventually leading to disease and death. Aging is influenced by a number of factors, including stress-response pathways such as the hypoxic response. Over-expression of the hypoxic response pathway regulator, Hypoxia-inducible factor (HIF-1), increases lifespan in the nematode Caenorhabditis Elegans. Under atmospheric oxygen, HIF-1 is targeted for degradation by the Von Hippel Lindau (VHL-1) tumor suppressor protein, whose deletion increases nematode lifespan through increased HIF-1 activity. Since knocking out VHL-1 in mammals is known to cause disease, it is important to better understand the hypoxic pathway in nematodes to develop targeted therapies for age-related diseases in humans. The goal of this research is to determine the tissues and genes downstream of HIF-1 that modulate aging in C. elegans. To determine tissue specificity, we have developed vectors designed to reintroduce VHL-1 into VHL-1 knockout worms under the control of tissue specific promoters. Lifespan and other age-related parameters will be measured in these transgenic animals and compared to that of control groups. To further test tissue specificity, we are also developing vectors to overexpress a mutated non-degradable form of HIF-1 in specific tissues in wild-type worms, essentially the reverse of the reintroduction of VHL-1. To test for genes downstream of HIF-1 important for longevity, we have performed a screen and identified several genes that are important for HIF-1-induced lifespan extension. Our experiments will examine whether C. elegans lifespan is increased by the over-expression of these proteins, which would then suggest further characterization and a search for conserved proteins. Together, the results from these experiments will provide important information on how we might utilize the hypoxic response pathway to improve human health.

A spherical domed ceiling has been a proven artistic space since the era of Antonio da Correggio’s famous dome fresco, The Assumption of the Virgin. Mix that together with the University of Washington’s planetarium and an extremely fertile space for artistic collaboration and exploration is revealed. Today, brand-new digital projection technology at University of Washington’s planetarium provides a unique space for digital artwork in comparison to more classical, non-digital domes. However, because of a planetarium’s contextual history, a significantly greater amount of time has been spent continuing planetarium-like experiences rather than attempting more artistic and experimental explorations. Over the past year, I have worked in collaboration with the Astronomy and DXARTS departments to create a fully immersive and experimental film for fulldome projection. Through research, development, and testing, I have also produced a robust framework for future artists to create their own works in fulldome spaces, especially at the University of Washington. As Correggio has shown, being creative with illusionistic perspective on a dome can lead to impressive results. Even in the 21st century, his techniques can be applied towards scientific and artistic experiences as well as open up other unique avenues of exploration within a fulldome space.

Salmonella enterica serovar Typhimurium is a Gram-negative pathogen that causes gastroenteritis. Components of the outer and inner membrane, characteristic of Gram-negative bacteria, contribute to Salmonella’s mechanisms to avoid detection and killing by the host immune system. The anionic bacterial cell surface is disrupted by cationic antimicrobial proteins (CAMP) that increase outer membrane (OM) permeability and access to the inner membrane. To resist CAMP killing Salmonella activates the PhoPQ two-component system, which is essential for pathogenesis. Because many PhoPQ-regulated enzymes are dispensable during infection, we conducted a forward genetic screen that identified new components of the PhoPQ regulon involved in maintaining the OM permeability barrier. Sequencing revealed mutations in genes encoding a variety of membrane proteins including transporters, phospholipid and lipopolysaccharide biosynthetic enzymes and efflux pumps, as well as regulatory proteins. Amongst the results, yejM mutants expressed the highest levels of membrane damage. YejM is an inner membrane protein with a periplasmic enzymatic domain that is critically involved in maintaining the OM permeability barrier. Structural alignments suggest that YejM is a member of the alkaline phosphatase superfamily. Attempts at full length deletions of yejM were unsuccessful suggesting the transmembrane domain is essential for viability, whereas periplasmic deletion mutants were viable but expressed varied levels of OM damage. Complementation with periplasmic deletion mutants and plasmids carrying the periplasmic domain rescued the OM permeability defect. Using structural models generated by a Protein Homolog/analogy Recognition Engine (PHYRE), we located putative metal binding sites involved in catalysis. To investigate the enzymatic mechanism, specific metal-binding residues were mutated via Polymerase Chain Reaction. We aim to determine if these residues contribute to the OM permeability defect of the yejM mutant Salmonella.

Photolysis of chlorine under sunlight results in generation of hydroxyl radical. Hydroxyl radical can in turn sensitize chlorine-resistant forms microorganisms such as Bacillus subtilis spores or Cryptospordium spp. occysts, and can make those microorganisms more vulnerable to chlorine. If the photolysis rate of chlorine and quantum yield of hydroxyl radical are known, microorganisms’ exposure to hydroxyl radical and free chlorine during a photochemically-enhanced chlorination process can in turn be derived. It is known that the decay of chlorine follows a first-order decomposition reaction under sunlight. Therefore, the reaction constant and half-life of chlorine can be computed according to first-order reaction equations. Understanding how pH and temperature affect half-life of chlorine can improve accuracy of prediction on required chlorine dosage in order to achieve a certain extent of disinfection in this photochemically enhanced chlorination process. The photolysis rate of chlorine under sunlight was investigated by determining chlorine’s half-life under various temperature and pH. Reaction solutions were irradiated by a Newport-Oriel solar simulator. Chlorine samples were taken at different time points and residual chlorine concentration was measured by DPD method. The results to be reported here showed that at the same temperature, the decay of chlorine was slower in a more acidic solution, which was due to the increasing ratio of [HOCl]/[OCl-]. Temperature also influenced chlorine’s photolysis rate: chlorine decayed more slowly in 5 °C than it did in 25°C. These findings will help to optimize the application of this disinfection process for inactivation of chlorine-resistant microorganisms.

Harmful algal blooms (HABs) are an important, but generally not well understood topic in oceanography. The dinoflagellate, Alexandrium catenella, is a common HAB phytoplankton that can lead to a buildup of toxins in commercial shellfish and cause paralytic shellfish poisoning in humans that consume them. When conditions for growth in the water column are unfavorable, Alexandrium forms a protective cyst that sinks and lays dormant in the sediment. The goal of this project is to create a more efficient way to enumerate HAB species cysts in sediments around the Puget Sound to create a record of past HAB events. I propose to use density gradient centrifugation and rapid flow cytometry on sediment cores from Puget Sound to determine how cyst concentration has changed over time, using sediment depth as a proxy for age. Density gradient centrifugation will be used to separate cysts out of sediments by using variations in specific gravity, and provide concentrated cyst samples. Then rapid flow cytometry will be used to determine the cyst concentration in each sediment sample based on the specific fluorescent signature of cysts. Preliminary results indicate that the density centrifugation method is able capture at least 85% of cysts at any given sediment core depth. Using this method I will also estimate the frequency of HABs in the past 50 years using lead 210 isotope dating on sediment cores. These methods will allow HAB researchers to reconstruct past Alexandrium events to fine tune models that predict periodic Alexandrium occurrences. This coupled with performing germination experiments on cysts to understand their biology will help the research community understand the conditions that control Alexandrium blooms as well as their frequency and intensity. None of this can be achieved until a fast, simple, and reliable method for obtaining and enumerating cysts in sediments is created.

Significantly reducing caloric intake without malnutrition (calorie restriction) has been shown to extend lifespan in many organisms including yeast, nematodes, and mammals. Since calorie restriction (CR) can also result in the extension of healthspan, CR or CR mimetics may be useful in the prevention of aging related disorders such as cancer, neurodegenerative disease, and cardiovascular disease. However, before long-term CR or CR mimetics can be considered safe for humans, more information is needed on the molecular mechanisms responsible for the effects of CR. In addition, since long-term voluntary CR may prove difficult to endure in humans, the consequences of reinstating a normal or ad libitum (AL) diet after prolonged CR must be investigated. We hypothesized that switching back to an AL diet after prolonged CR would reactivate pro-aging molecular pathways, such as the target of rapamycin (TOR) pathway. To test this, we obtained kidney tissue from aged F344 rats that had been subjected to long-term CR. Some of the long-term CR treated rats had been gradually switched to an AL diet and the rest had been maintained on the CR diet. Proteins were extracted from the kidney tissue and then analyzed by Western blot. Switching to an AL diet after long-term CR resulted in a significant increase in the phosphorylation of downstream signaling proteins in the TOR pathway in kidney tissue. In addition, after switching to an AL diet, there were significant changes in autophagy, which is regulated by the TOR pathway, as indicated by increases in the autophagy markers LC3 and p62. These results indicate that reinstating an AL diet after prolonged CR results in an increase in the activation of the pro-aging TOR pathway. This suggests that the TOR pathway may regulate some of the physiological effects of reinstating a normal or ad libitum (AL) diet after prolonged CR.

Synthetic biology holds great promise regarding the production of important compounds, and the degradation of harmful ones. Last summer, we harnessed the power of synthetic biology to meet the world’s needs for fuel and medicine. We constructed a strain of Escherichia coli that produces a variety of alkanes, the main constituents of diesel fuel, by introducing a pair of genes recently shown convert fatty acid synthesis intermediates into alkanes. Using this method, we were able to produce on average 160 mg of alkanes per liter. Also, we identified a protease with gluten-degradation potential, and then reengineered it to have 100 times increased gluten-degrading activity, allowing for the breakdown of gluten in the digestive track when taken in pill form. Finally, to enable next-generation cloning of standard biological parts, BioBrick vectors optimized for Gibson assembly, an emerging DNA cloning technique, were constructed and used to construct the Magnetosome Toolkit: genes for biofabrication of magnetic particles.

The transport of heavy metals in the environment poses serious threats to ecological and human health. One major factor that influences the transport of heavy metals in the environment is interactions with microbial surfaces. To better understand the influence that endospores, a ubiquitous microbial surface in the environment, have on metal transport, we studied cadmium and uranium adsorption onto endospore surfaces. We focused on three main experiments: how fast metal adsorbs to spore surfaces (kinetics), the extent of metal adsorption, and the reversibility of metal-spore adsorption. These data are essential to deriving thermodynamic parameters that may quantify the interactions under conditions not directly studied in the laboratory. The ultimate goal of this research is to give environmental engineers the ability to incorporate microbe-metal interactions into geochemical models of contaminant transport and possibly aid in optimizing bioremediation strategies using endospores.

Plants use hormone-signaling pathways to regulate growth and development. Brassinosteroids (BRs) are critical plant hormones that regulate growth such as the elongation of the embryonic stem. We study the specific mechanism of this process by testing the hormone-induced growth responses of both wild type and mutant Arabidopsis seedlings. We are testing whether growth repressor SPATULA is involved in BR growth response. We hypothesized that the growth repressor SPATULA is downstream of the BR pathway. To test this hypothesis, we acquired mutants that lack SPATULA function. After confirming the genotype of the mutants by PCR, we used a high-resolution camera to observe growth throughout early development in response to hormone treatments. Data is recorded by the camera over the course of 132 hours. The images are then analyzed and growth rates are calculated. Using these data, we determined if SPATULA is involved in the BR growth response.

The study of chronological and replicative aging in Saccharomyces cerevisiae has provided both post-mitotic and mitotic aging models in this single-celled organism. In chronological aging, lifespan is determined by the length of time a yeast cell can survive in a non-dividing state, whereas in replicative aging, the lifespan is determined by the number of daughter cells produced by a mother cell prior to irreversible cell cycle arrest. The primary goals of this study were to observe how the chronological aging of yeast cells influences replicative lifespan (RLS) and to determine whether changes in the extracellular environment that influence chronological lifespan (CLS) would also influence subsequent RLS. By buffering the pH of the medium to 6.0 or reducing the concentration of available glucose (dietary restriction), we show that these manipulations were able to suppress the reduction in RLS associated with chronological aging, when compared with cells aged in synthetic complete medium with 2% glucose. The production of ethanol and acetic acid due to yeast fermentation may be responsible for cellular damage leading to reduced RLS, and it can be inferred that by buffering the pH to 6.0 or dietary restricting the cells, this damage is attenuated and replicative capacity is increased following chronological aging.

The nuclear transport pathway performs the fundamental function of moving cargo between the cytoplasm and nucleus in all eukaryotes. Nuclear transport is carried out through a highly conserved mechanism across all eukaryotes. Yet, in Drosophila, several components of the nuclear transport apparatus evolve rapidly under positive selection. Genetic conflict with selfish elements has been suggested as a possible cause for this pattern of rapid evolution. Here, we present a comprehensive phylogenomic analysis of importin gene evolution in Drosophila. Importins are adapter molecules that directly mediate the transport of cargo into the nucleus. Our analysis reveals a recurrent pattern of gain and loss of importin paralogs across independent lineages of Drosophila. Interestingly, we discovered that almost all new copies of importins have acquired a testes-specific expression pattern since their birth through gene duplication. This pattern of repeated gains of testes-specific copies of importins and signatures of episodic lineage-specific positive selection suggests a function in suppressing genetic conlifcts such as segregation distortion in the male germline.

Somali women immigrants have significant trauma histories related to their experiences of torture, rape, and displacement. They commonly present with somatic complaints for which there is no "medical explanation" and few acceptable or helpful treatment options. A community health program, Daryel, was started 3 years ago by a nurse at Harborview Medical Center to address somatic pain among Somali women through yoga and massage. Daryel primarily serves women over 50 years of age who are not fluent in English. This project consists of preparatory work for the development of a culturally congruent training manual for Health Care Practitioners working with Somali women. The following three methods will guide training manual development: 1) Conducting a literature review using databases such as ETHNOMED, CINHAL, PUBMED and gathering background on Somali traditional medicine, beliefs, and the cultural practices of Muslim women with regard to health; 2) Participating in individual conversations with Somali women and the Health Care Practitioners who serve them; and 3) Outreach to massage therapists who have stopped volunteering at Daryel with a set of questions on their volunteer experience. The results: 1) Findings based on the literature review show that taking time to establish rapport, understanding Somali culture and traditions, listening to their explanatory model of illness, and working skillfully with interpreters are important factors that will help gain success with Somali women patients; 2) Conversations with Somali women in Seattle confirm that a program such as Daryel is helpful for Somali women immigrants; 3) A survey of past and current volunteer Massage Therapists showed they want more training on Somali culture and language. In conclusion, a culturally congruent training manual will aid Health Care Practitioners in providing essential quality care to Somali women immigrants.

Antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) have been detected in many natural and engineered water systems, such as estuaries, surface waters, and drinking and waste water treatment plants. Although many ARB are likely to be inactivated during water treatment, their ARGs may survive treatment by means of protection with cell debris or adsorption on to particulate matter. This is a potential risk for human and animal health, as certain clinically-relevant bacterial populations can undergo horizontal gene transfer by means of natural transformation, which requires only intact, free DNA and a live recipient cell (no donor cell required). These risks can possibly be mitigated through optimization of disinfection processes. However, the current treatment processes focus on deactivating the viable microbes, not the ARGs. Our study focuses on the deactivation and degradation of ARGs in disinfection processes. Our data suggests that current CT (= oxidant concentration in mg/L * time of exposure in min) values for the use of free chlorine (10⁰ to 10¹) and ozone (10^-1 to 10⁰) in disinfection are sufficient to deactivate in vitro ARGs; however the CT values for chloramines (10² to 10³) are likely not able to deactivate the in vitro ARGs. In the case of in vivo ARGs, even higher CT values are likely to required, as cell debris can protect the genes. For example, our data show that a CT value of 90 mg/l*min of chlorine, which is a very high CT value, can deactivate all the cells, but has no effect on the genes inside.

This research examines the way Indigenous cultures and identities are represented at Tillicum Village, a Seattle-area tourist attraction. Recent changes in ownership and management at the site have proved controversial among the Indigenous populations represented, who perceive the focus as shifting away from cultural authenticity and toward economic profit. This project explores the issues of a corporation's responsibility in accurately and fairly representing the cultures it profits from. The concepts of staged authenticity and heterotopia are essential to the theoretical framework of this issue, as is placing Tillicum Village in the context of colonial tourism. Data are being collected using traditional ethnographic methods and historical research, and analyzed through critical theory. This research ultimately hopes to illuminate way in which Tillicum Village can better address the grievances of, and collaborate with, the Indigenous communities it portrays.

What is the effect of corporate environmental performance (EP) and social performance (SP) on financial performance (FP)? Conducting research on the effects of environmental performance and social performance on financial performance could encourage corporations to engage in more sustainable business operations. The potential benefits of better environmental performance and social performance range from a cleaner environment to healthier societies. Therefore, the goal of this research is to investigate the relationships among SP, EP, and FP. Freeman’s stakeholder theory (1984), defined as integrating (through who and what, processes, and allocating resources) multiple stakeholders, who affect and are affected by the firm on multiple issues (i.e. their “stakes”), is the basis for testing the following hypotheses. H1: Better environmental performance leads to higher financial performance. H2: Better social performance leads to higher financial performance. Our sample, which includes 90 Fortune 500 publically traded companies from the US, Europe, and Asia, represents a variety of industries. Environmental, social responsibility, and financial performance data were extracted from 2008 and 2009 annual financial and sustainability reports. We analyzed the data with descriptive statistics, exploratory factor analysis, and linear regression. If research findings reveal positive correlations among environmental, social responsibility, and financial performance, corporations will find it beneficial to be environmentally and socially responsible. The current study may contribute to the literature and managerial practices in two ways. First, reduced pollution, waste, and energy used can lower costs to corporations, thereby increasing profits, while benefiting the planet. Second, better relations with stakeholders can enhance the firm’s reputation thus financial performance.

Zebrafish have a defined striped pattern that results from pigment cell differentiation and migration during development, and this developmental process provides a good model for studying the process of boundary formation. Elucidating the mechanisms by which boundaries are formed is critical for understanding vertebrate development, and will give insight into what might cause them to malfunction during metastasis where cancer cells invade other tissue types, thus breaking the boundaries that have formed. While zebrafish have these defined patterns, a closely related species, the pearl danio, lacks stripes and instead has different pigment cell types intermingled. We hypothesize that the pearl danios have lost the mechanism for pigment cell boundary formation found in zebrafish and my goal is to identify genetic differences between the two species that could have caused this change pattern development. Preliminary RNA sequencing has identified candidate genes that appear to be differentially expressed. I am using in situ hybridization to compare the expression patterns of candidate genes between the two species. This is a technique where whole larval fish are incubated with RNA probes which are complimentary to the mRNAs of the genes I am screening for. Wherever the candidate genes are transcribed into mRNA, and thus expressed, the probe will hybridize. I am able to visualize this through labeling of the probe and staining with antibodies. I expect to find that some of the candidate genes will have different patterns of expression between the two species. This result will indicate that these genes are involved in the pigment pattern formation process, although it will not explain their specific function. However, once I know which genes are involved I will be able to manipulate their expression through knockdown or over-expression, which will provide further insight on the mechanisms of boundary formation in pigment patterns.

Our world is becoming increasingly integrated with motion sensor technology. However, the usefulness of motion sensor data is still vague and difficult to understand. Several applications using sensor infrastructure in the home, often referred to as smart homes, aim to support independence for older adults. The goal of this project is to try to understand smart homes for aging in place in general and complex motion sensor data within independent retirement communities. Our focus is in trying to understand how aggregated motion sensor data can be useful for clinicians, patients and family members, how to present aggregated motion sensor data, and how to proactively manage health to support aging in place. Our group is implementing ubiquitous motion sensors in independent retirement communities to assess mobility. Various parameters that influence mobility, including cognitive ability, psychosocial activity, and environmental characteristics, are noted and integrated into the data. The projects goal is to evaluate mobility in older adults and consider actions or treatments to prevent disease onset or discomfort. Preliminary findings from the ongoing longitudinal feasibility study provide strength to the argument that motion sensors may provide a supporting role for aging in place.

While research has focused on the presence of child disengagement during caregiver-child interaction, there is a gap in the literature analyzing the duration of time that a child is disengaged from an interaction and what implications this may have on the caregiver-child relationship. In addition, there is a gap in the literature that has examined the relationship between the duration of child disengagement and parenting behavior. One such behavior that has proven to be influential on a child’s developmental outcomes is caregiver sensitivity. A sensitive caregiver recognizes and responds appropriately to a child’s cues as well as provides a safe and stimulating environment in which the child can learn. The purpose of this study was to explore the relationship between caregiver sensitivity and the duration of time that a child exhibits potent disengagement cues during a caregiver-child interaction. Recorded caregiver-child interactions from a previous study were coded for the duration of time during the episode that the child displayed a potent disengagement cue. The definitions of the potent disengagement cues were taken from the NCAST Programs Caregiver/Parent-Child Interaction Teaching Manual. Caregivers’ sensitivity was assessed and scored using the NCAST Teaching Scales. Results demonstrated that as caregiver sensitivity increased, length of child disengagement decreased. The discovery of this relationship between caregiver sensitivity and duration of child disengagement serves as a gateway to new areas of research that could promote the quality of caregiver-child interactions and therefore have positive effects on the child’s developmental outcomes.

In recent years, electronic sensors, database technologies, and digital devices have been successful in improving the automated collection of personal activity data in a pervasive manner. Through these developments and advancements in mobile computing, the ability to accurately record and maintain complex health records has been realized. Yet, although an instrumental tool in preventative medicine, dietary assessment still lacks automated and objective means of data collection and analysis. Current methods of clinical dietary assessment are paper-based, burdensome, costly, and subject to bias, especially in terms of the estimation of food volume intake. To improve upon these deficiencies, we have developed the Dietary Data Recording System (DDRS). The DDRS incorporates a client-server architecture to efficiently collect, process, and store dietary data. The client is a mobile sensor package that is used for data collection, and the server runs image processing algorithms and maintains a database where organized and processed intake information can be accessed by clinicians through a specialized interface. The foundation of the sensor package is a Mobile Structured Light System (MSLS), which uses a laser to project patterns on viewed food and a mobile phone camera to capture video. The distinctive feature of the DDRS is the use of the MSLS and image processing techniques to determine the volume of food from recorded video without the aid of scale-identifying fiducial markers. Preliminary results prove the feasibility of this approach for assessing dietary intake with the DDRS, and future work will focus on automating and integrating the entire processing pipeline. The automated diet intake tracking resulting from this future development could provide clinicians with an invaluable tool in definitively correlating the long term intake of certain foods to cancer, heart-disease, diabetes, and various health disorders.

Our goal is to introduce a transgene into the plastid genome of maize instead of the nuclear genome because a plastid-localized transgene is not transfered via pollen. Plastid transformation will be performed using vectors based on plastid DNA (ptDNA) replication, terminal sequences, and and maintenance within plant tissues, work previously done in our lab. The first step is to extract ptDNA from maize seedlings. PCR is used with the ptDNA to get a product containing the plastid genome targeting left and right border sequences (LBS and RBS, respectively). To be more specific, the region amplified corresponds to nucleotides 128500 to 131000 of the maize plastid genome and designated 5'End2-to-3'End1. The second step is to insert 5'End2-to-3'End1 into the cloning plasmid pUC18, creating the plasmid, pZMCP101. It also must be mentioned that three other vectors will be tested, using slightly different LBS/RBS (3'End2-to-5'End1, 5'End2-to-5'End1, and 3'End2-to-3'End1). The next series of steps adds expression control regions and reporter genes between the LBS/RBS. We use the16s rRNA promoter and psbA 5'-and 3'-UTRs regions from maize ptDNA. For reporters the gfp gene, a visual marker, and pmi gene, metabolic selection, are used. PMI will be used because a plant without the pmi gene will not grow on mannose. So, after we combine gfp, pmi, and the control regions with pZMCP101, we now have pZMCP201-the final plasmid vector. Then we will shoot pZMCP201 into maize plastids using particle bombardment. We will use both the circular and linearized vectors and expect greater efficiency with the latter. We will be able to determine if the vector was incorporated into the chloroplast genome by visualization of GFP expression and growth of transgenic tissue on manose selection medium. 

Toxoplasma gondii (T. gondii), the parasite responsible for human Toxoplasmosis, has previously been shown to be inhibited by Bumped Kinase Inhibitors (BKIs) via inhibition of Calcium Dependent Protein Kinase 1 (CDPK1) in vivo. While BKIs inhibit T. gondii very well with high selectivity for parasite and not human functions, and have low toxicity, CDPK1 itself is significantly less inhibited by the compounds in vitro, suggesting that the observed inhibition may in part be due to other enzymes. Using genomic data, we selected three T. gondii kinases with similar gatekeeper regions to CDPK1 that could be structurally vulnerable to BKIs as well. In an effort to identify and understand these Off-target enzymes, two ongoing experiments were conducted. The first aim was to purify the suspected Off-target enzymes and assay them in vitro against the same BKI compounds that were so effective against CDPK1. The second aim was to genetically manipulate the protein structure of the Off-targets in the gatekeeper region of the enzyme to match that of the known CDPK1 enzyme, to verify the mechanism of action of the BKIs. The likely enzymes to be Off-targets were difficult to purify, and the project is in progress. Future work depends on new methods to purify the Off-targets, in order to make progress toward completing the goals of the project. CDPK1 is an attractive target for therapeutic development for Toxoplasmosis, and further knowledge of Off-target enzymes that are vulnerable in the same way in T. gondii can lead to much-needed low resistance therapeutics.

Motivated by recent interest in developing compact, inexpensive, and reliable eye-safe lasers, the effect of quantum confinement on a saturable absorber material, cobalt-doped zinc selenide (Co²⁺:ZnSe), was explored in colloidal quantum dots. Co²⁺:ZnSe diluted magnetic semiconductor quantum dots (DMS-QDs) are semiconducting nanocrystals with structural lattices that include substitutional magnetic ions in addition to the primary metal cations. While previous work has been conducted on the saturability of optical absorption in bulk Co²⁺:ZnSe, the research presented here focuses entirely on quantum-confined colloidal DMS-QDs. The ability of these particular DMS-QDs to behave as saturable absorbers was explored in depth. This property is directly related to the long lived ⁴T₂(F) excited state of the Co²⁺ dopants, which gives rise to bleaching of the Co²⁺ ligand field transitions, leading to increased transmission of light upon irradiation at high powers. Specifically, absorbance features associated with excitation of ground-state electrons localized in the d-orbitals of the dopants are lost. To examine the saturable absorber behavior of Co²⁺:ZnSe, we looked at the optical transmittance of the quantum dots as a function of photoexcitation power. This was done by slowly increasing the power of a pump laser exciting the sample and observing changes in the absorbance spectrum at characteristic Co²⁺ ligand-field transition features. The bleaching of the ligand field Co²⁺:ZnSe in its nanocrystal form demonstrates that these colloidal materials are candidates for saturable absorbers in Q-switched eye-safe lasers. From this point, it should also be possible to explore excitation of the electrons from the first excited state (⁴T₂(F)) into higher energy states (excited-state absorption).

Paleontological evidence has shown that during large scale extinction events, hydrogen sulfide (H2S) rises to abnormal levels in Earth’s atmosphere. To survive these extinction events, an organism would be required to counter-act the negative effects of H2S by evolving unique adaptations. It can be hypothesized that many of these unique adaptations still exist in present-day lineages. Modern plants, for example, may have developed a method of utilizing H2S in order to survive, and possibly thrive, in what would be considered a highly toxic atmosphere. Through experiments involving species Phaseolus vulgaris and Pisum sativum, it was discovered that applications of H2S to seedlings increased growth at rates of up to 200% within 1 week. In addition to the increases in growth, increases in plant mass and photosynthetic activity were also observed. In order to better understand the effects of H2S on P. vulgaris and P. sativum, seeds of the species were also exposed to H2S, under the same controlled conditions. The effects of the seed experiment were similar to the initial seedling tests. Time to germination decreased with exposure, and the overall rates of germination increased. Large scale implications of these findings present benefits such as greater crop yields and perhaps a more efficient method of bio-fuel production. Continuing research of H2S and its effects on plant life could someday create a powerful means to deal with our ever-expanding human population…and the ever-expanding human footprint that goes along with it.

Why do smokers with epilepsy suffer from cooking and not cigatte-induced burns? 21% of our patients smoke, yet cigarette-induced burns are uncommon. We studied whether nicotine might change seizure thresholds in patients undergoing video EEG telemetry (VEEG). We tested NP effects on duration of stay, rate of seizure aquisition and number of seizures collected in patients undergoing VEEG. 762 consecutive patients charts were screened for proven epilepsy (EPI) and NP use during their VEEG hospitalization (n=33). Randomized controls, EPI patients without NP (n=33), were also selected. Outcome variables included duration of stay number of seizures collected on day 2, and total number of seizures. T-test comparisons were done. Patients with psychogenic non-epileptic events (PNES) with NP (n=52) were compared to a randomized NP-free PNES group (n=52). The duration of VEEG in EPI patients with NP was 5.42 days (s.d=1.66) vs. 4.33 (s.d=1.74) days in patients without NP (p= 0.01). EPI patients with NP had a total of 3.88 (s.d.=8.82) seizures, while those without had 7.58 (s.d.=1.44, p=0.21). On day 2, 0.94 (s.d.=1.44) events were captured in patients with NP, and 2.18 (s.d.=5.38) events in patients without (p=0.21). PNES patients with NP spent 3.73 days for VEEG, those without 3.98 (p=0.46). No relationships were seen in PNES patients for day 2 or for total events captured. No differences in provider-specific stay durations were seen. In epilepsy subgroups, partial-onset EPI patients without NP stayed 4.41 days, those with NP 5.56 days (p < 0.05). Generalized EPI patients showed no differences. In conclusion, NP use during VEEG may prolong length of hospital stay in EPI patients, but not for those with PNES, this effect may be more notable in patients with partial onset epilepsy.

Reactive halogen species (RHS, e.g., X·, X2·- and HOX), which can be generated during solar irradiation of sea water, can abiotically produce organohalogen compounds by reacting directly with natural organic matter (NOM). In order to obtain a better understanding of the mechanism involved in these systems, a novel technique that allows monitoring RHS production in sea water is required. For this purpose, I have performed a variety of tests to aid in the development of a highly-sensitive method for measuring RHS yields using the probe compound 3,5-dimethylpyrazole (DMPZ), which can rapidly and selectively form monohalogenated products by interacting with certain RHS. In this work, samples of artificial sea water containing DMPZ were irradiated in a 1700-W Xe arc lamp solar simulator for 48 hours. The concentrations of the main photochemical reaction byproducts (4-bromo-3,5-dimethylpyrazole and 4-iodo-3,5-dimethylpyrazole), which are formed in proportion to the concentration of RHS generated during irradiation, were determined by liquid chromatography with mass spectrometry (LC-MS). From this work, we have demonstrated that DMPZ is suitable for use as a probe of RHS. In addition, we have used this method to study the influence different chemical species (NO2-, NO3- , Fe3+, I- and natural organic matter) present in the water matrix on yields of halogenated DMPZ. Results of these experiments will be presented, and discussed with respect to likely relevance for natural environmental systems.

Kaposi's Sarcoma-Associated Herpesvirus (KSHV) is a gamma2-herpesvirus that infects humans and can cause tumors in immunosuppressed individuals. Rhesus rhadinovirus (RRV) is a related herpesvirus of macaques that is similar to KSHV, but has significant differences as well. While KSHV infections are predominantly latent with only low levels of spontaneous replication, RRV replicates much more readily. For this reason, RRV is a useful tool in studying the mechanisms of reactivation and replication of rhadinoviruses. We sought to identify the regulatory promoter elements of the replication and transactivator (Rta) gene, which induces the lytic stage of the virus. To find this, we transfected cells with different length clones of the Rta promoter region and tested the activity using luciferase assays. We identified a potential binding site of the transcription factor Sp1 and tested its function through mutagenesis. Our results indicate that the Sp1 binding site is required for high level promoter activity suggesting that this is an important regulatory element within the promoter sequence. We also tested the activity of the RRV Rta promoter in the presence of the RRV latency associated nuclear antigen (LANA), a gene known to inhibit replication through suppression of Rta expression in KSHV. We found that with LANA present, the activity of the Rta promoter decreases significantly. Because Rta has a critical role in viral replication, the regulation of the Rta promoter by the cellular factor Sp1 and the viral gene LANA may have important implication on the RRV life cycle.

The Community Action Research and Empowerment Project (CARE), launched in September of 2010, is a participatory action research project where elders and youth work together to assess the strengths and needs of the Vietnamese community in Seattle, and develop a long-term plan to address those needs and advance the community. Data from 16 focus groups, 85 interviews, and 316 surveys were collected. We learned that the Vietnamese community members have a broad range of concerns, such as youth and education, housing, jobs, health and social services. During Phase 2 (2011-2012), a strategic action plan will be created with extensive input from community members to address the issues identified—thereby creating a shared vision for the Vietnamese community.

Chronic infections with Pseudomonas aeruginosa are a significant cause of deterioration of lung function in patients with cystic fibrosis (CF), and have substantial clinical importance due to their marked resistance to treatment with antibiotics. Furthermore, existing laboratory methods for testing bacterial susceptibility to antibiotics are poor indicators of clinical response to therapy, which further increase the difficulty associated with treating these infections. Current research shows that phenotypically diverse P. aeruginosa subpopulations evolve within a single patient during prolonged infection, and that clinical antibiotic therapy causes some of these subpopulations to change significantly in relative abundance. Observed changes in abundance following antibiotic treatment signify varying degrees of antibiotic susceptibility within each patient’s P. aeruginosa population as a whole, with an increase in a particular subpopulation abundance indicating resistance, and a decrease in a particular subpopulation abundance indicating sensitivity. As previous studies have only evaluated P. aeruginosa antibiotic sensitivity prior to antibiotic treatment, we attempted to demonstrate the correlation between an increase subpopulation abundance following clinical treatment and the degree of resistance to antibiotics in laboratory testing. This was done by evaluating the antibiotic minimum inhibitory concentration (MIC) of a range of isolates collected from CF patients who had undergone antibiotic therapy, using antibiotics which had been given to each patient in clinical treatment. Our results demonstrate a marked lack of correlation between relative subpopulation abundance and antibiotic MIC, with clinically resistant subpopulations showing the same or lower MIC than subpopulations which were clinically sensitive treatment. We conclude that isolates resisting treatment do not have a different MIC than isolates responding to treatment, suggesting that mechanisms other than classic antibiotic resistance are responsible for treatment resistance in the CF lung. Further studies to evaluate these mechanisms, such as biofilm formation and formation of persister cells, are currently under way.

 Mycobacterium tuberculosis infection is a leading cause of death worldwide, but the full details of how the human immune system responds to these bacteria are not known. Our lab studies CD1 proteins which allow T-cells to respond to bacterial lipids. We discovered that low expression of CD1A on dendritic cells is associated with an increased susceptibility to tuberculosis; however, the molecular details of CD1A-deficiency are not known. I cloned and analyzed the CD1A promoter from four CD1A-deficient and five control individuals. I identified twelve genetic variations in the CD1A promoter. Of these, eight were single nucleotide polymorphisms (SNPs), three were insertions or deletions, and one was a variable tandem repeat. One SNP (-199 T/C) and the variable tandem repeat showed an association with CD1A-deficiency. A T/T genotype at position -199 from the transcription start site correctly identified five out of five control subjects while a C/C genotype identified three out of four CD1A-deficient subjects. The variable tandem repeat was a string of 20 to 60 thymine bases. The CD1A-deficient subjects showed uniform repeat lengths, while the repeat lengths among control subjects were variable. These data identify two loci within the CD1A promoter that will be the target of future studies aimed at understanding the molecular mechanism of CD1A-deficiency.

Evolutionary conflicts involving mimicry are found throughout nature ranging in a multitude of levels from ecosystems to molecules. Moreover, structural mimicry is increasingly being recognized at the interface between viruses and hosts. The goal of my project is to provide structural and mechanistic insight into a newly discovered evolutionary ‘arms race’ between a viral protein and a host immunity protein. We have found that a poxviral protein IBP1 (IFIT Binding Protein 1) binds a host immunity protein, IFIT2, which represses viral mRNA translation. I hypothesize that IBP1 has convergently evolved to structurally mimic IFIT2’s binding partner, eIF3c, as a strategy to restore viral protein production. Because IBP1 has no known amino acid similarity to any other viral or host protein, the best way to test my hypothesis is to determine the molecular structure of IBP1 and compare it to eIF3c. I will biochemically engineer constructs to optimize the expression and amount of soluble IBP1 in E. coli and then utilize affinity columns to isolate IBP1, which will then be subjected to a myriad of crystallization conditions. Once optimized crystallization conditions have been found I will use X-ray diffraction techniques to solve the structure. Regardless of whether my hypothesis is correct, my work will provide atomic resolution detail for IBP1, which is a protein that is important for the fitness of the virus. If I find that IBP1 is indeed using molecular mimicry it will not only reveal the mechanism of IBP1 action, but it will also provide a case of molecular mimicry marked by the signature of convergent evolution. Furthermore, my work will make progress towards further understanding the interactions between hosts and viruses, which determine the results of potentially deadly infections in so many people.

The lymphatic system is essential to fluid and cell transport, immune function, and tumor metastasis. Lymph drains from body extremities into lymph nodes, via lymphatic vessels, to present antigens to lymphocytes. This can result in an immune response. The existence of tumor cells in lymph nodes is a sign that cellular metastasis has occurred from the primary tumor. I am studying lymphangiogenesis, a process in which lymphatic vessels and sinuses grow and dilate in response to antigens or tumors, thus increasing the lymph flow and capacity to transport tumor cells in lymph nodes. Recently an antibody, 10.1.1, has been discovered to recognize an antigen that is selectively and highly expressed in lymphatic endothelium. The 10.1.1 antibody specifically induces lymph node lymphangiogenesis. This binding also induces proliferation of an unknown cell type in the lymph node. In comparison to the 10.1.1 antibody, injecting a nonspecific antibody control has no effect on lymphatic sinus growth. I am therefore studying how the 10.1.1 antibody rapidly induces lymphatic sinus growth, as well as what cell types contribute to making the new sinuses. I am using the technique of immunostaining to study the effects of the 10.1.1 antibody. By taking a frozen slice of lymphatic tissue and staining it with various antibodies to detect proliferating cells and their cell type, I can identify the specific kinds of cells that are forming into lymphatic sinuses. An understanding of how these lymphatic sinuses grow could help generate therapeutic strategies for manipulation of the lymphatic or immune responses. By inhibiting sinus growth and thus limiting lymph flow, it could be possible to prevent the metastasis of cancer.

This paper critically analyzes the social and economic effects of a local business process outsourcing center, or BPO, B2R in three towns (Letybunga, Reetha, and Orakhan) in the state of Uttarakhand in India . This research intends to provide an understanding of the implications globalization has within rural communities, specifically for young women. Through participatory observation as well as qualitative and quantitative data gathered during semi-structured interviews, this project analyzed the changing perceptions of the community, employees, and the family members of employees towards B2R, its employees, and its effects on the community. Our primary goal was to better understand what people perceived as the positive and negative social and economic changes in the region brought on by development, specifically the addition of B2R. Our research sheds some light on changing gender and family dynamics in the region as young women increasingly enter the formal workforce.

Rhododendron is an aesthetically valuable plant genus primarily distributed in Northern hemisphere. Previous work by collectors and taxonomists has revealed that Rhododendron taxa have a scattered pattern of distribution around the globe. Yet, the evolutionary history that led to this modern distribution pattern is not well understood. Fossil records of once extant Rhododendron populations can be a key component for inferring the diversification and migration of Rhododendron. Macrofossils such as leaves and stems have more restricted requirements in their formation, and hence are rarely discovered. On the contrary, microfossils of pollen are more widely preserved and found. In this study, I explored the potential of using pollen microfossils of Rhododendron to understand how the modern distribution pattern of Rhododendrons came about. To that end, I compared and contrasted modern Rhododendron pollen from three subgenera and twenty four subsections in order to discover the degree of consistency in pollen morphology within and unique combination of traits of each taxon. All observations were performed under light microscopy. Experimental data include both structural differences and quantitative measurements. Preliminary results demonstrate promising level of variation in measurements such as the structure of apperture edges, pollen wall sculpture, overall size, and wall thickness. These palynological features are then fitted into a Rhododendron phylogeny based on molecular data to reveal any potential taxonomic significance of variation in pollen morphology. 

Within the previous year, over half of a million people died from malaria and ninety one percent of these deaths occurred in Africa. My research studies the living conditions of the Maasai tribe in correlation to the prevalence of malaria, intestinal parasites, and head fungus. During field research in Tanzania these were the three most widespread diseases among the three hundred patients treated. The life cycles and causes of each disease were studied individually to distinguish how specific environmental and household factors contributed to the transmission of the diseases. Relevant factors of the living conditions were identified. I hypothesized that the incidence of disease would be reflected in the prevalence of the elements relating to the transmission of disease. I collected data on the living conditions in Tanzania by visiting Maasai households and evaluating the following criteria: the presence of a fire inside the house, the presence of feces and/or garbage in the household, the number and size of the windows in each household, the number of people living there, the number of people who were sick living there, the presence of uncontained animals in the compound, the presence of mosquito nets, the type of material used to make the house, the presence of a toilet, and the presence of a cover on the toilet; if applicable. Analysis of the results suggests that for each disease, the relevant factors of living conditions matched expectations in all three diseases. These results suggest that by making certain improvements to the living conditions of the people in the Maasai village, it would be possible to reduce the prevalence of the tropical diseases of malaria, intestinal parasites, and head fungus.

Storm water pollution is a growing problem for the people of the Puget Sound. When contaminants are released into our environment they collect in storm drains and, for the most part, flow untreated into our precious streams, rivers, lakes, and oceans. Contaminants like copper from brake dust, nutrients from fertilizers, and detergents from washing cars, can cause adverse problems to the aquatic life in these water bodies. “Low Impact Development” designs like rain gardens and bio-retention systems are a viable option to reduce harmful effects, by filtering out many of the pollutants before they enter our aquatic systems. In order to improve the performance of rain gardens we propose adding various waste products from other treatment processes which have the potential to remove common storm water contaminants. In this research, we compared various soil mixes commonly used in systems with various amendments such as “Lodge Pole Pine and Water Treatment Residual (WTR)” to determine their ability to capture heavy metals and nutrients. To test the amended soil mixes we designed a series of columns packed with these mixes, saturated the columns with synthetic storm water, and monitored the concentrations of pollutants in the influent and effluent to determine contaminant removal capabilities. The constituents tested in this experiment include hydrologic conductivity, forms of Nitrogen and Phosphorus along with metals such as Aluminum, Arsenic, Cadmium, Copper, Lead, Nickel and Zinc. Our preliminary results have been very promising, with our WTR amendments showing an improvement of up to approximately 20% reduction in both total and dissolved forms of phosphorus and up to a 10% reduction in metals over standard soil mixes.

My research examines fairness and equity in the distribution of three wastewater treatment types across seven counties in the Puget Sound region. I begin my analysis with a thorough exploration into the concepts of fairness and equity, within the context of a variety of disciplines. Drawing on this analysis, I then look into the costs of these different systems, making sure to take into account all applicable considerations, including implementation, maintenance, and repair costs. Specifically, I investigate the costs of combined-sewer systems, separated sewer systems, and onsite septic systems at the household scale. Lastly, I use Geographical Information Systems and spatial analysis to compare the costs of these systems to their spatial distribution through the subject counties, and to the household median income within their respective census tracts. This methodology allows me to uncover any inequities in the way that the costs of these treatment types are distributed, and address a specific instance of fairness within urban planning that has yet to be investigated.

Currently, freight models at the state level use a four-step modeling approach, which generates trips based on origins, destinations, and land use. In the personal travel sector, models have started taking into consideration entire tours based on household demographics. Freight modeling uses this same approach despite situational differences. In an effort to improve freight modeling, this research aims to identify characteristics of freight carrier companies that determine distinct freight movements. A survey of licensed motor carriers was designed and conducted in Washington State and Oregon State. The identical surveys conducted in both states consisted of 33 questions. Respondents were asked questions regarding their vehicle fleet, locations served, times traveled, types of deliveries, and commodities. A total of 614 complete responses were gathered. An analysis of the data, using statistical software R and Excel, aims to reveal clusters of company types that can be distinguished by determining characteristics such as company size, commodity, and role in a supply chain. By identifying unique patterns among the dependent variable such as travel distance, travel times, and delivery style, the results can then be integrated into state models to more accurately predict freight vehicle routes.

Examining three of Booker prize winner Ian McEwan’s novels Atonement, At Chesil Beach and Saturday provides a passage into his exploration of changing attitudes and viewpoints regarding female sexuality during the later 20th and early 21st century. Utilizing the genre of historical fiction, McEwan explores the various sociological and cultural influences such as improving neonatal care, contraceptives and improved birth control options that severed the previously inescapable link between sexuality and motherhood. Additionally, the rise of women in higher education and sectors of the workforce beginning in the 1930s onwards contributed to the autonomy and, as these novels indicate, increasing sexual freedom of women. Each novel explores the 1930s, 1950s and 2000s respectively as critical turning points in British culture. In the 1935 pre-WWII setting of Atonement, the prevalence of women in college and independent professions challenge gender norms. Against this backdrop, McEwan examines reciprocal sexual desire against victimization and societal attitudes towards women as equally desirous individuals. At Chesil Beach explores the physical relationship of a newly married couple during the 1950s and the emergence of clinical contraceptives. Finally, Saturday examines the attitudes of a mother and daughter in a post-sexual revolution setting and explores issues of generational differences as well as the link between sexuality and victimization still present in a contemporary time period. Ultimately, critically examining the attitudes and historical contexts of each novel against other scholarly work provides a literary interpretation of the evolution of attitudes regarding female sexuality, and sub issues of autonomy, consensual desire, the role of women and victimization, spanning from a pre-WWII era to contemporary society.