Historically, only clinicians and researchers have been involved with decisions about what research topics to pursue, and patients have been left out of the process. This creates a gap between clinical application of research and patients’ experience. By expanding the scope of how researchers and clinicians obtain patient data to include research topic priorities, we explore how to incorporate patient perspectives better. Although there are many studies that aim to analyze patient registries, there are limited studies that attempt to elucidate the degree of the participants’ interest, or willingness to get involved in providing input on research activities. Through a study funded by the Patient-Centered Outcomes Research Institute (PCORI), we developed a two-phase approach to prioritize topics for low back pain research. In phase one, we invited participants from a patient registry of older adults with back pain , and in phase two, invited participants using Amazon Mechanical Turk (MTurk), an online crowd-sourcing platform. Participants completed an initial screening survey comprised of the Roland Morris Disability Questionnaire, a standard tool to identify individuals experiencing back pain. Those scoring 7 or higher on the RMDQ were sent a research topic prioritization survey. 1966 people completed the screening survey, and 480 qualified, of which 353 completed the prioritization survey (completion rate: 74%). Using both recruitment strategies, we had a high response rate, and participants are diverse in terms of pain, gender, and age. Responses show participants’ effort to fully answer the survey and voice their opinion, including providing additional topics that had not been identified previously.This work highlights that recruiting from a patient registry or using MTurk are both effective tools to obtain patient input, and increases the flow of information from the public/patient to the researcher, and inevitably the clinician; we expect incorporating these methods will increase patient voice in research.

Animals and humans collect and process information from their environment using a host of sensory modalities to maintain control of movement. Such integration of information is exceedingly challenging for the control of flight in insects, which is inherently unstable. We use insects as a model system for understanding how multiple sensory inputs influence flight control. While vision is necessary for flight, its processing time is too slow for effective fight control. Thus insects use a faster sensory modality that encodes mechanical information (inertial forces). We use a combination of experimental and theoretical approaches to reveal the precision, sensitivity, and rapid processing speeds of inertial sensors in flying insects. In particular, we suggest that wings not only serve a role as propuslors, but by virtue of the mechanosensory neurons in them, provide a key sensory role for inertial forces. We hypothesize that the wing mechanoreceptors of the hawkmoth (Manduca sexta) rapidly and precisely extract mechanical information necessary for flight control. We further hypothesize that such encoding properties are similar to those in wing evolutionary predecessors, halteres (a sensory organ that is known to be a gyroscopic organ) in flies. To test our hypotheses, we recorded the electrical activity of wing neurons subject to a mechanical stimulus. We used methods from computational neuroscience to characterize the encoding properties (the stimulus features that drive neural responses). We found that nearly all neurons respond rapidly with 5 ms precision and they are extremely selective for the temporal pattern of the stimulus. These results are similar to those found for halteres, and suggest a novel finding that wings serve the dual function of both actuation and sensing. These results reveal a new interpretation of movement control in animals and can serve as inspiration for the next generation of flight systems.

 Glioblastoma multiforme (GBM) is the most common and deadliest cancer of the central nervous system. The existence of stem-like cells within GBM tumors - Glioblastoma stem cells (GSCs) - may explain some of the malignant features of Glioblastoma multiforme (GBM) owing to their rapid self renewal and diffuse migratory behavior. Increasingly apparent is the role ion channels play in many cancer cell properties, including regulation of cell cycle progression and proliferation, tumor cell motility and invasion, and regulation of metabolic rate. We hypothesize that ion channel dysregulation contributes to GSC malignancy, including increased viability, proliferation, and migration. To test this, multiple GSC isolates derived from human GBM tumors were maintained in culture over many passages while retaining stem cell properties. RNA-seq expression profiles revealed ion channel families that were highly enriched in GSC samples. Real-time qPCR was next used to confirm increased expression of voltage gated calcium, sodium, and potassium channels, ionotropic glutamate channels and inwardly-rectifying potassium channels. Identifying ion channels uniquely enriched in GSCs led to functional analyses to determine how ion channel blockers affected their proliferative and migratory properties. We performed MTT cell viability assays to assess how ion channel blockers altered the viability of GSCs compared to a control neural stem cell line. We were able to show a significant decrease in cell viability across GSC lines compared to control at a variety of drug concentrations. Utilizing live-image cell tracking, we determined decreased migratory behavior and rates of these GSC lines with the same blockers. Finally, to elucidate the role of the extrinsic tumour microenvironment on the proliferation and migration of GSCs, unique coculture models involving GSCs cultured on mouse organotypic brain slices were utilized, and showed the affects of stimulating and inhibitory DREADD receptors to modulate local neuronal activity.

A cell’s outer membrane displays a broad range of proteins and other biomolecules that play an essential role in mediating interactions between the cell and its environment. Some cell surface molecules, known as antigens, can be used by clinicians and researchers to identify specific cells for use in diagnostics and targeted therapies. Cell identification based on surface antigens is known as phenotyping, which is typically performed in the clinical laboratory using a flow cytometer. In flow cytometry, cells are labeled with fluorescently-labeled antibodies that bind to a specific antigen on the cell surface in order to identify the cell’s phenotype. Conventional platforms for flow cytometry are costly, and fluorescence-based phenotyping involves tedious labeling steps and advanced detection capabilities. For laboratory facilities without the resources or need for a flow cytometry platform, a method for simple, specific, and direct cell characterization is desirable. The Ratner Lab uses silicon photonic technology in biosensing applications to detect when mass binds to a sensing surface. In this project, the sensing region of the silicon photonic chip was coated with antibodies to target a specific antigen displayed by a cell. A silicon photonic sensor was functionalized to phenotype prostate carcinoma cell lines for prostate-specific membrane antigen (PSMA). The cells were fragmented to yield membrane microparticles that could be flowed across the antibody-coated photonic sensor in order to characterize the cells for the presence or absence of the cancer marker. This study employed model cell lines as a proof-of-concept for simple, label-free cell phenotyping, departing from traditional fluorescence-based methods for cellular analysis.

As computational processing speeds and algorithmic models for machine learning continue to advance, depictions of Artificial Intelligence (A.I.) in science fiction (SF) have accordingly increased in production. Such fictional narratives typically anthropomorphize A.I., which brings into question whether intrinsically human concepts, such as gender, can legitimately be mapped onto A.I in the direct manner said fictions tend to portray. If “true” A.I., defined here as any technology that accurately replicates a human consciousness, is created, but gender is a social construction derived from strictly biological sex differences, then can the idea of “gender” be said to maintain any relevance to artificially intelligent beings? This paper intends to investigate that question by first cross-examining convolutional neural network theory with models of consciousness from M.I.T. theorists to establish a working model of how a true A.I. could learn, and then using said model, alongside feminist SF critical theory, as a lens through which to compare several SF works which depict gendered A.I.s. Understanding the relation—or lack thereof—between the human concept of gender and A.I.s is highly relevant to the ongoing discussion concerning the rights of A.I.s as intelligent non-humans.

Regulation of metabolic pathways is often implicated in many normal as well as disease processes in organisms. Our previous work discovered changes in the metabolome associated with longevity in eleven different species of fruit flies. The metabolic pathways associated with longevity included gluconeogenesis, the Krebs Cycle, and amino acid degradation. However, it is still unknown how basic nutrient parameters influence metabolic pathways in flies. We used mass spectrometry coupled with liquid chromatography to quantify the small molecules present in whole fly tissue. After finding metabolites associated with age, we completed nutrition assays to determine if there were associations between nutrient parameters and metabolomic profiles. The measurement of basic nutrient parameters consisted of colorimetric assays for total glucose and protein levels. Data analysis revealed correlations between the levels of each nutrient found in whole fly tissue and corresponding metabolomic profiles. In our future work, we plan to manipulate metabolic pathways or nutrient parameters found to be significantly associated with age and observe whether there are changes in longevity.

Therapeutic gardens are a specific type of landscape designed to promote physical and psychological human health within a natural environment. Designs of therapeutic gardens vary depending on the user populations and the goal of my project is to understand the healing components of therapeutic gardens and apply them to specific circumstances. In this project, I will conduct a post evaluation on the Ichi-Go Ichi-E Garden, used primarily by Japanese American senior residents of a senior residential community, Nikkei Manor, and analyze the use patterns of residents and staff using observation, mapping, surveys and interviews. By analyzing the success of the project, I hope to answer the question of how therapeutic gardens can be effectively designed for specific users, site conditions and programs. These findings and knowledge will be integrated into the design for a new project: a capstone design & build project led by Professor Daniel Winterbottom for the Puget Sound Veteran’s Affairs Hospital. The garden will serve veterans suffering from post-traumatic stress disorder (PTSD) and other stress-related illnesses. Finally, after gaining feedback from clients and presenting the final design, my classmates and I will build the project by June 2016 when the garden will be dedicated.

Leigh Syndrome (LS), one of the most common childhood mitochondrial diseases, typically arises during the first year of life and results in a wide array of metabolic and motor deficiencies leading to death within a couple of years. LS is associated with mutations in any of several mitochondrially encoded genes, including NADH Dehydrogenase Subunit 2 (ND2). The ND2 gene codes for a subunit of complex I within the respiratory chain of the mitochondria. Among patients with the same ND2 mutation, the progression and pathology of LS varies widely. The variation might be due to the effects of variation at other genes that interact with ND2. To test this hypothesis, we have turned to a Drosophila model of LS, in which flies carry an ND2 loss-of-function mutation. Drosophila with the ND2 mutation experience LS-like symptoms, including decreased lifespan, metabolic dysfunction, and paralysis, when exposed to mechanical stress, termed ‘bang sensitivity’. To identify other genes that affect the ND2 mutation in Drosophila, we crossed female ND2 flies with males from the Drosophila Genetic Reference Panel (DGRP); a panel of 200 inbred, fully sequenced lines. The resulting offspring are aged 21 days and assayed for changes in bang sensitivity— the time it takes for individual flies to recover from paralysis. By comparing the effects of ND2 on the bang sensitivity phenotype in each DGRP background, we hope to identify specific genes that either worsen or ameliorate the phenotype. If successful, this study could help us identify genetic modifiers of this mitochondrial disease, and thus help us identify novel therapeutic targets.

Aging is characterized by time-dependent deterioration of cellular and physiological functions. Due to the numerous challenges and limitations of studying aging in humans, model organisms are used to further extend our understanding of basic mechanisms of aging. The Kaeberlein laboratory uses the single celled budding yeast Saccharomyces cerevisiae as one such model. Advantages of this model organism include the ability to measure the lifespan of great numbers of organisms under various environmental conditions. One method of measuring a yeast cell’s longevity is by assaying its replicative lifespan (RLS). The RLS model refers to the number of daughter cells that can be produced by a mother cell before senescence. The number of budded daughters can be determined by micro-dissection with fiber optic needles from mother cells after each round of incubation. This process is repeated until mother cells no longer generate daughters. Approximately 600 mother cells are assessed weekly and incubation cycles last one month. Yeast lifespan can be manipulated through genetic changes, altering media content, addition of pharmacological agents, and change of temperature. Data collected is compared to control groups and to past and expected results. These results clarify how senescence is regulated. RLS is thought to be a better representation of senescence in mitotically active cells, like certain tissues in multicellular organisms. By analyzing thousands of cells, a variety of genes and environmental conditions that impact aging have been identified. These genes and interventions can be further studied and applied to other organisms. Studying budding yeast enhances our understanding of the molecular basis of aging.​

Zooplankton serve as vital components to the marine food web, and their distributions implement limits on population growth for organisms of both higher and lower trophic levels. Many zooplankton species, such as Calanoid and Cyclopoid copepods, are the primary food source for the juvenile fishes that are part of the fisheries within the temperate coastal Northeast Pacific, including Chinook, Chum, Pink, and Coho salmon. A better understanding of the environmental parameters that influence zooplankton abundance and distribution is essential for the proper management of these economic and culturally valuable fisheries. This study investigates the correlation between the abundance and distribution of Oithona, other small copepods (<2mm), large copepods (>2mm), euphausiids, hyperiids, gammarids, ostracods, chaetognaths, and larvaceans to dissolved oxygen, salinity, and chlorophyll conditions to determine which parameters have the greatest impact on zooplankton distribution. The ultimate goal of this study is to generate a model to predict the distribution of zooplankton populations under different environmental conditions. It was expected that distribution would favor higher dissolved oxygen, more saline, and high chlorophyll conditions. Samples were collected in Nootka Sound, British Columbia, onboard the R/V Thomas G. Thompson during the Oceanography Senior Thesis Cruise at 4 stations using 211-micron closing net. Four samples were collected at each station from 100-75m, 75-50m, 50-25m, 25-0m depth ranges to observe vertical distribution within the upper 100m of the water column. Results identified significant correlation between dissolved oxygen and salinity and zooplankton abundance and distribution. However, abundance appeared to be greater at stations and depths with lower dissolved oxygen and salinity concentrations. We also tested an alternative method of measuring zooplankton abundance and distribution by constructing an underwater video profiler (UVP), designed to capture imaging data of zooplankton at 15m depths, and used video analysis software to quantify this data.

Factors such as temperature, pressure, presence of a catalyst, and reactant concentration are all known to affect the rate of chemical reactions and are well exploited in industry to drive chemical synthesis to favor certain mechanistic pathways. Here we consider the effect of using magnetism to control the rate of reaction for the Briggs Ruascher reaction. This reaction was chosen as a model for magnetic manipulation because it is mediated by both radical and non-radical pathways that compete with oscillatory behavior to produce the same product. Dramatic color changes serve as a visual cue to indicate which path is dominating. Here we put forth magnetic radical arrest hypothesis for the Brigg’s Ruascher reaction. It is known that electrons act like tiny magnets that pair with opposite spins. Because radical species carry a lone unpaired electron, presumably their magnetic fields are not concealed. We proposed that due to the exposed nature of the unpaired radical electrons in the Briggs Ruascher reaction, the progress of the reaction would be affected by the application of a magnetic field. Upon exposure to strong magnets, the radical intermediates of the Briggs Ruascher reaction were expected to aligned their spins with the applied magnetic field affecting their reactivity. Several types of neodymium magnets with various strengths were applied to the reaction in order to determine whether magnetism could prevent or greatly reduce the velocity of the color phase changes for the radical mediated portion of the reaction. We also built an electromagnet to expose the reaction to in order to achieve even greater field strength. The Brigg’s Rouscher reaction was found to be significantly robust and there was insufficient evidence to suggest that the reaction was affected by neodymium fields below a range of 5.8 mT. Results of exposure to the electromagnet are still in progress. The color changing cycles of the Briggs Ruascher reaction were found to follow a decreasing sigmoid mathematical model before going to completion after 9-10 oscillations.

Global Positioning System (GPS) technology has revolutionized the way we navigate our world, yet there remain many practical geolocalization problems for which the technology is not directly useful, such as in urban environments and scientific field work where GPS satellite L.O.S. (line-of-sight) obstructions are ubiquitous. Motivated by our collaborations with the LEAF School of Anthropology, our work is focused on providing technological solutions for cm-scale GPS-like geolocalization; particularly for researchers doing field work in prohibitive and complicated field topologies through the use of field-configurable ad-hoc geolocalization subnetworks. We present our work on and our methods to utilize time-of-flight measurements from GPS-enabled acoustic and radio frequency sources placed at the boundaries of the field of interest to determine the geographical coordinates of any number of locations within that field.

The principal technological problem of the renewable energy industry is how to supply energy at its rate of demand and at a marginal cost less than that of present energy storage systems. One of the greatest challenges of this problem is the necessity of storing a portion of total produced energy such that it can be used when the instantaneous rate of energy demand differs from the limits of its instantaneous rate of production to balance out the demand and supply for energy. Our research focuses on the storage problem of current Under Water Compressed Air Energy Storage (UW-CAES) systems; in particular on decreasing the costs and environmental impact of air storage by performing electrolysis in a deep-sea electrolyzer to capitalize on the extreme energy densities already-available at depth and increase the energy density of each storage vessel/balloon by storing both hydrogen and oxygen. We demonstrate a method that increases the efficiency of energy storage by performing electrolysis using the high pressures available at depth, thereby eliminating the use of costly compressors and create a condition for the apparatus to be as close to a thermo neutral state.

The ability of animals to detect minute chemical concentrations and locate odor sources is unparalleled in synthetic systems. This is especially true in the hawkmoth Manduca sexta which can track and find the source of chemical plumes with astonishing efficiency. Male moths, for example, can detect female pheromones at concentrations of 1 in 10¹⁷ molecules of air. In this work, I created a biological odor sensor by measuring the electrical activity of the neurons in a severed antenna in response to their odor detection, (a.k.a. an electroantennogram or EAG). By comparison, commercial gas sensors are incredibly inefficient, large, heavy, expensive, and have slow response times. I have developed a small quadrotor drone which uses an electroantennogram with the antenna of a Manduca sexta moth to track a chemical plume to its source. The EAG signal is measured as the voltage across the antenna and then amplified and filtered to reduce noise. The control module of the drone uses this signal in conjunction with a measurement of the ambient airflow to steer the vehicle. The drone uses a cast and surge search algorithm to follow the chemical plume upwind: flying crosswind until the chemical is sensed, flying upwind until the scent is lost, and then repeating the process. This experiment provides proof of concept that EAGs can be used to direct the flight of an aerial vehicle for the purpose of chemical localization. This provides an odor sensing platform that is many orders of magnitude lighter than commercial odor sensors. The applications of a small, reproducible, chemosensing drone are numerous, ranging from locating contraband to testing biological hypotheses of insect flight.

Copper-doped semiconductor nanocrystals (NCs) combine the large effective Stokes shifts and broad PL spectra of bulk copper-doped semiconductors with the solution-processability of colloidal semiconductor nanocrystals. These properties make copper-doped NCs attractive materials for applications such as luminescent solar concentrators and light-emitting diodes. Copper-doped CdSe NCs are particularly desirable materials because their tunable absorption spans the visible spectrum, and they provide a useful model system for studying the photophysics of copper-doped semiconductor NCs. However, both fundamental studies and applications of copper-doped CdSe NCs have been limited by the inability to simultaneously control the NC diameter, size dispersity and copper dopant concentration during synthesis, This poster reports a new one-pot synthesis of copper-doped CdSe NCs that enables precise control of NC size and copper concentration while maintaining a narrow size distribution. This level of synthetic control is achieved by separating the nanocrystal growth and copper-doping steps, and tuning the reactivity of the copper precursor. Post-synthetic treatments with various surface ligands are also used to tune copper dopant concentration. Fundamental photophysical studies enabled by access to the high-quality copper-doped CdSe NCs provided by this new synthetic method will also be discussed.