Understanding an individual’s thought process as they encounter programming problems would enable the development of better techniques for teaching computer science and more comprehensive technical assessments. Prior work explored key stroke logging in writing research alongside the think-aloud study format using custom-built tools. We replicated this study format in the context of computer programming to gain insight into participant’s immediate thought process. We aimed to gain a better understanding of a participant’s mental model as they encounter computer science problems. In specific, we wanted to investigate pauses in coding and what students think before, during, and after these pauses. For this study, we used Codeitz, a custom programming tutor that allowed us to log all the participant’s timestamped input as they wrote code. We also collected audio and screen recordings of participants using the think-aloud strategy as they wrote code. We ran a pilot study that required participants (3) to answer eight programming questions, two of which involved writing code. We found some similarities in pause clustering for participants who answered the same questions. We also noticed that participants whose pauses were due to utilizing development environment affordances, identifying misconceptions, and identifying gaps in knowledge semantics exhibited more self-regulation as programmers.

The United States presence in Africa is mostly militaristic and oil-driven, whereas China's recent foray into the continent has rattled the traditional conventions for doing business and investing on the continent. Through a series of Foreign Direct Investments, International Trade, Government Funded Contractual Projects and loans by the Chinese government, China has taken direct action to infiltrate the internal economies, politics and societies of many African nations. To frame where China lays in terms of economic investments and involvement, my research examines the current state of three African nations in which China invests. The markers within a nation include the profitability of a particular industry sector, previous political relations with China, the market size of an economy or nation, political security of a nation and geopolitical strategy. I focus on three Sub-Saharan nations in which China has previous practices or a history of investments, Tanzania, Zambia and Angola. Statistical data provided by loans or investments and first-hand accounts of events are used to support my arguments about China’s involvement in the affairs of these three nations. I discuss multiple value factors for a superpower to invest in a nation and how this influences that nation’s economy and politics. The end result takes the form of a review of China’s influence on these three nations. My study gives context and poses questions for future research on the economies and political strategy behind the investments made by world powers in African countries.

Hybrid dynamical systems (HDS) are time dependent systems that have both discrete and continuous behavior, such as a bouncing ball or jumping leg. The BioRobotics Lab studies HDS in order to better understand locomotion and develop controls for robotics. As controllers are developed, they need to be tested in the hybrid dynamical system (HDS) either through simulation or implementing in physical robotics. While simulated system environments are useful in early controller development, they are unable to capture all the intricacies of a physical system. Thus, testing controllers in a physical system can provide better insights for future development. We developed a hopping robot for the purpose of easily implementing controllers through software. The hopping robot is designed to be modular and easily configured for different dynamics. Simulations of the robot were also developed so that researchers can use both simulated and physical environments. This tool will help researchers develop new controllers and could bring new insights to studying hybrid dynamical systems.

Increasingly, over the past half century, antibiotic resistant plasmids have spread to a large range of bacteria increasing the demand of new antibiotics. On average, once an antibiotic has been released into the public market, a strain that is antibiotic resistant evolves within a few years. Even though the constant production of new drugs and treatments provides some temporary solutions, a better solution would be to investigate and understand bacterial plasmid mechanisms. Through my research in the UW Biology Kerr Lab, I have been exploring how bacteria maintain plasmids that contain genes encoding for antibiotic resistance. Plasmids are extra-chromosomal pieces of DNA that require the host cell to allocate energy for their general maintenance. Prior theoretical research suggests that, to avoid this allocation of resources, the host should lose antibiotic resistant plasmids over time when the plasmid is no longer beneficial to the host’s fitness, for example when the antibiotic is no longer present. We found that many plasmids across multiple bacterial species persist in their hosts, even in the absence of selection for the plasmid. Currently, I am testing whether changing the environmental conditions experienced by the host/plasmid pairs, specifically from a nutrient-rich to minimal media, will affect the persistence of antibiotic resistant plasmids. This research provides important data that will allow us to have an easier time combating antibiotic resistance.  

International adoption in the United States began during World War II. It was developed as a humanitarian act to aid those orphaned due to the war. Since then international adoption has remained an option for Americans looking to expand their family. The Hague Convention is an international organization aimed at uniting countries in their laws regarding international adoption policy with the intent to ensure the welfare of the child. Since its founding in 1983, the Hague Convention has influenced a total of eighty - three countries including the United States. Despite the intention of the Hague Convention and its member's international adoption still places a child's welfare at higher risk than those of domestically adopted children. International adoptees are victims of human trafficking, abuse, and untimely death. Even the Hague Convention intended to improve international adoption does not advocate countries to use international adoption as a solution to aiding their orphaned population. Permitting an international adoption is promoted as a last resort for the most vulnerable of an already targeted community. The primary intent of this paper advocates for stricter enforcement and potential temporary stall on future international adoptions within the United States. This stance is taken due to issues of lack tracking of international adoptees, the failure of enforcement of international adoption laws currently in place, and the negative impact of the overtly positive marketing of international adoptions. This work intends to bring further awareness of the systemic issues of international adoption that put a child's welfare at risk. Concerning international adoption, this is highly important due to its primarily positive reputation with the general public. This research also intends to provide a solution society may advocate for or further build upon in order to take the measures necessary to ensure the welfare of a child.

Cleaning is a mutually beneficial relationship, where the cleaner removes and consumes ectoparasites from its clients. Among fishes, the cleaning behavior has evolved several times as a juvenile or facultative feeding strategy, and is often lost in adults. However, a minority of taxa clean almost exclusively across their ontogeny (obligate cleaners). The largest radiation of obligate cleaners are the Caribbean neon gobies (Elacatinus), that evolved with several congeneric non-cleaners, and in parallel with a closely related lineage of facultative cleaners (Tigrigobius). We suspect that obligate cleaning is a specialized trophic ecology tied to an equally specialized feeding morphology that facilitates improved cleaning performance. We coupled micro-CT scanning with the clearing and staining of museum specimens to compare several functional predictors of feeding performance between cleaner gobies and non-cleaners in a phylogenetic context. We also used geometric morphometrics to compare relative changes in head shape and mouth orientation. Obligate cleaning evolved once, and is characterized by a specialized scraping dentition, stouter cranial features, and a more subterminal mouth position relative to non-cleaners. Meanwhile, facultative cleaning evolved at least 2-3 times, and while some species display similar tooth morphologies as the obligate cleaners, they share more in common with non-cleaners. Obligate cleaners also exhibit fewer sexual dimorphic differences, suggesting that the demand for an efficient cleaning morphology trumps sexual selection.

Nearly 22 million HIV-positive people are receiving antiretroviral therapy in order to suppress their HIV infections. They need consistent viral load monitoring to track viral suppression and detect the possibility of viral rebound. Nucleic acid amplification tests (NAATs) are used to measure the viral load in a patient's blood. Traditional, laboratory-based NAATs require complex robotic systems to automate HIV RNA purification, amplification, and detection from blood. Since the majority of those living with HIV are located in low and middle income countries, there is a need for rapid viral load monitoring at the point of care (POC). We aim to provide accessible HIV viral load testing through low-cost, integrated POC NAAT devices. These proof-of-concept devices operate as a two-step assay to extract and detect nucliec acids in blood. An electrophoretic separation technique called isotachophoresis (ITP) separates HIV RNA from other components in a blood sample. An isothermal nucleic acid amplification assay amplifies the purified, concentrated nucleic acids in order to detect and quantify their presence. We present our development of a novel ITP system to remove potent contaminants from Proteinase K (PK) digested serum and extract highly pure nucleic acids automatically. Through computational modelling, a dual trailing electrolyte (TE) buffer system was designed to exploit the isoelectric point of PK for its removal, while simultaneously concentrating nucleic acids away from serum components. We demonstrate system control through comparison of experimental observations to model predictions by performing dual-TE ITP on pH paper. We also show that the dual-TE system improves upon previous limits of detection for DNA extraction and detection from complex samples. Our system processes 40 microliters of blood in 20 minutes using only simple buffers, a paper strip and an electric field - making it an ideal tool for use in a rapid NAAT for HIV viral load testing. 

By the late 1520s, Henry VIII’s lack of a legitimate male heir had led to a succession crisis in England. Eventually this culminated into a procession of legal and scholarly battles broadly referred to as "The Great Matter", which was the quest for the annulment of Henry VIII's first marriage. Criticisms over these proceedings by historians often decontextualize the events of the Great Matter. Moreover, the Great Matter is often portrayed as a vanity project; one that was wholly unnecessary because Henry VIII had a legitimate daughter from his first marriage. There are many flaws with this presentation of history. For one, it ignores most of the historic precedent up to the point of Henry VIII's reign for how female leadership was received, and what that reception could lead to– namely rebellion, usurpation, forced abdication, civil war, and instability. I argue that, rather than a vanity project, the Great Matter was absolutely understandable within the context of the time and place it occurred. I also argue that, rather than the near and distant future proving Henry’s anxiety over the reception of female leadership as unwarranted; such anxiety demonstrated a remarkable sense of awareness and an extraordinary prescience. My research includes the Letters and Papers of Henry VIII and a collection of other various primary source quotes relevant to the matter of female succession in the sixteenth century, and the Great Matter in particular. These were analyzed through a social and cultural lens, and also analyzed through contextualization and comparison to later relevant events.

 Twelve replicate populations of the bacterium Escherichia coli have been evolving in Lenski's Long-Term Evolution Experiment (LTEE) for over 67,000 generations in a shared nutrient limited environment. The evolved bacteria grow 70% faster than their ancestor but experience a decrease in number produced during a growth cycle. This is consistent with a trade-off between growth rate and yield (here defined numerically). We explore if populations are constrained by their previous ecolution, and if populations with high growth rate can evolve to have a higher yield (and if so, does this happen at a cost to growth rate?). We do this by adding population structure to growing populations, where selection is relaxed on growth rate and strengthened on yield. Water-in-oil emulsions provide a structured environment where millions of nutrient-filled droplets are isolated by an oil phase. We manipulate population structure by inoculating droplets with either one bacterial cell (low starting density) or more than two bacterial cells (high starting density). We observe that selection acts on faster growing cells in our high density emulsion treatment and higher yield cells in our low density emulsion treatment. We also observe a change in cell size: cells in the high density emulsion treatment get bigger over time, and cells in the low density emulsion treatment get smaller. We explore if there is a relationship between cell size and growth rate/yield trade-off.

Extra chromosomal pieces of DNA, called plasmids, exist within bacterial populations. Many scientists believe that the relationship between plasmids and their bacterial hosts is mutually beneficial. Plasmids use replication machinery from their host to ensure their continued persistence. Meanwhile, the plasmid carries genes that can benefit the bacteria, such as genes that can provide resistance to antibiotics. In environments that contain antibiotics, bacteria that contain plasmids with antibiotic resistance genes would have a higher fitness and be able to survive and reproduce at a higher rate compared to bacteria that don’t carry plasmids. Contrary to popular belief, research by members in our group showed that different plasmids actually persisted in bacterial populations when they were not under selection. The purpose of this project is to see if the trend of plasmid persistence would continue in a nutrient limited environment. We performed a long term evolution experiment on three types of bacteria containing plasmids in a nutrient limited environment. Next, grew the evolved descendants in an environment containing antibiotic to see what portion of the population is still containing the plasmid. The results of this experiment will help scientists have a more holistic understanding of plasmid biology which could have implications on antibiotic treatments.

Polycystic kidney disease (PKD) affects nearly 600,000 people in the United States and it is caused by mutations in the genes that encode polycystin-1 (PC1) and polycystin-2 (PC2). These modifications are responsible for the growth of fluid-filled renal cysts that can impair kidney function over time, and lead to end stage renal disease. PC1 and PC2 have also been localized to the mitochondria, suggesting that they are responsible for regulating cellular metabolism and energy production, which can lead to mitochondrial dysfunction and increased PKD progression. Our lab uses human pluripotent stem cells (hPSCs) to generate kidney organoids that can be used to study the advancement of PKD, which contain the major proximal structures of the nephron including podocytes, proximal tubules, distal tubules, and endothelial cells. Orgnaoids that lack both PC1 and PC2 will develop cysts that can grow large enough to be seen by eye. Unfortunately, these organoids lack a collecting duct (CD) system, a crucial component of the kidney that expands greatly in PKD. To address this need, we developed a protocol to differentiate hPSCs into ureteric bud (UB) cells, the precursors of CD cells. First, we identified Dolichos biflorus agglutinin (DBA) as a key CD lineage marker in developing kidneys through immunofluorescence analysis on human kidney tissue. Then, we took undifferentiated hPSCs and investigated their ability to express DBA by treating them with a concentration gradient of small molecules known to induce kidney lineage cells. The resulting cells were stained with DBA and GATA 3, an additional, early CD marker, and we found that both markers were expressed in vitro. We will continue modifying this protocol to better study the increased metabolic rates seen in PKD, its effects in CD cells, and the mechanism behind the PC1 and PC2 pathway that leads to cyst formation.

Polycystic kidney disease (PKD), commonly caused by defects in polycystin-1 or polycystin-2, results in the formation of fluid-filled cysts and progressive loss of kidney function. Our laboratory has established a cellular model for ADPKD using kidney organoids, multicellular tissue that functionally and structurally resembles the organ of interest, derived from gene-edited human pluripotent stem cells (hPSC). To address the need surrounding a cure for PKD, we have also discovered a basis for a form of treatment involving myosin. Non-muscle myosin is a protein that controls cell protrusion and adhesion; we have established that lack of adherence increases cystogenesis dramatically. We discovered blebbistatin, a non-muscle myosin (NMMII) inhibitor, is a robust inducer of cystogenesis. Our previous finding begged the question if activators of NMMII have the opposite effect and reduce cystogenesis in PKD organoids. To better understand the role of myosin, we differentiated kidney organoids from human PKD hPSCs in a 24-well plate coated with Matrigel. We proceeded with microdissecting the organoids at 3 weeks before they formed any cysts and transferred the organoids to suspension culture where they were treated with either DMSO as a control or a pharmacological myosin activator for one week. The organoids were then imaged and number of cystic organoids were quantified. The treatment using the myosin activator compound resulted in decreased cystogenesis, in terms of the size and number of cysts. Although we have yet to clarify myosin’s effect in the PKD pathway, we have identified a myosin activator as a potential inhibitor of cystogenesis. Further experimentation is to be done with other compounds such as actin activators, and proceeding with experimentation on ex vivo kidneys of mice. Our current findings suggest that the polycystin proteins positively regulate actomyosin’s contractility, therefore myosin may be an important factor for keeping kidney tubule integrity and preventing cystogenesis.

Understanding how genetic variation shapes phenotypic variation for complex quantitative traits is fundamental to developing more accurate disease prognoses and therapeutic interventions. Genes that are important in early development contribute to adult quantitative traits, such as height, vision, and health. The fruit fly Drosophila melanogaster is a model organism for studying complex traits, such as aging. Drosophila possesses many well-developed genetic tools and shares evolutionarily conserved age-regulating pathways with our species. One such conserved pathway is the mechanistic Target Of Rapamycin (mTOR) nutrient signaling pathway. Rapamycin is a specific allosteric inhibitor of mTOR signaling that extends lifespan in adult Drosophila melanogaster and delays development in larvae. However, the functional explanation for these effects is incomplete and a genetic association between development and lifespan is unknown. We used the Drosophila Genetic Reference Panel (DGRP), a highly inbred fruit fly population representing natural genetic variation, to measure rapamycin-mediated developmental delay. We used these data to carry out a Genome Wide Association Study (GWAS), and combined our data with data from a screen for the effects of rapamycin on lifespan in the DGRP, also carried out in our lab. GWAS analysis will help us to identify genetic variants associated with rapamycin efficacy and to discover novel variants associated with developmental timing. By connecting lifespan and development genetically, we identified shared candidate genes that modify these two very different molecular genetic programs. Accomplishing this is the first step towards identifying early life biomarkers that are predictive of rapamycin success as a longevity intervention in later years. These pharmacogenomic analyses advance a precision medicine approach where interventions are tailored towards genetic background to maximize human health.

 Antibiotic resistance is a growing threat to public health. This resistance, coupled with a dearth of new antibiotics, makes the study and development of antibiotics of critical importance. Many antibiotics derive from microbial pathways that synthesize complex natural products, and engineering these pathways to produce new antibiotics is an exciting prospect. I aim to use such a strategy to produce variants of the klebsidin lasso peptide, known for its distinct lariat knot structure and its antibiotic activity. Klebsidin is produced by three biosynthetic enzymes that modify and export a ribosomally-synthesized precursor peptide. We have developed an assay that relies on cellular growth to (1) investigate how mutation influences the antibiotic activity and biosynthesis of klebsidin, and to (2) identify variants of klebsidin that overcome a known resistance mutation. When expressed in E. coli, klebsidin inhibits growth of its host cell. I expressed a library of approximately 10,000 klebsidin variants, each within a single cell, and used next-generation DNA sequencing to count the frequency of each variant before and after a growth selection. Functional klebsidin variants should decrease in frequency after selection, whereas null variants should increase in frequency. Using these sequencing data, I generated functional scores for a majority of single amino acid mutations within klebsidin, identifying positions that tolerate mutation and positions for which mutation abolishes bioactivity. To better understand these trends, I am performing mass spectrometry experiments to study the biosynthesis of key variants. In addition, we are interested in how mutagenesis of klebsidin can combat known resistance to lasso peptides. By performing the same growth selection in an E. coli strain resistant to wild type klebsidin, we hope to identify variants that overcome this resistance. Together, these studies will provide a framework for understanding lasso peptide engineering and identifying novel peptide-based antibiotics.

Sexual dimorphism is a characteristic of many organisms that is genetically encoded and typically studied as a binary trait. Biomedical research routinely categorizes subjects into “male” and “female”, and the resulting data are used to establish sex-specific measures of good health and disease. However, this practice overlooks the existence of intersexual phenotypes and oversimplifies the overlapping variation between sex-specific groups. The phenotypic expression of sex is directed by a complex orchestration of many genes. As such, it is reasonable to consider that there are more than just two discrete expressions of sex, and furthermore that the dimorphism of so-called sex-specific traits resides along a continuum. Metabolomics studies the small molecules that make up all the molecular building blocks in the body, and offers a unique opportunity to quantify sex variation that is morphologically invisible. Doublesex (dsx) is a gene that plays a pivotal role in the sex development of Drosophila melanogaster, and its absence results in an intersexual morphological phenotype. This study models sex in Drosophila melanogaster as a continuous trait by comparing metabolomic profiles for wildtype females, males and dsx null mutants using statistical analysis of metabolome data. While many studies have been conducted to understand the role of dsx in sex determination, to our knowledge no one has attempted to use this novel approach to quantify sex variation as a complex trait. Here we measure over 1000 metabolites in fly samples and test a hypothesis that some metabolites exhibit continuity between male, intersex and female phenotypes. Future work could explore the degree to which these metabolic sexual continuities exist in natural fly populations, and provide a powerful model to study factors that are influenced by sex differences more comprehensively.

This research is aimed at improving the functionality and use of multi-robot control through several different aspects. One important aspect of this project is collision avoidance between multiple ASEA Brown Boveri (ABB) industrial robots. The active collision avoidance software is an efficient tool that detects potential collisions between multiple robots working in collaboration and the surrounding cell. The user can specify a safety net around each robot, which notifies the user if one or more robots are on a collision course. Each robot’s position is graphically displayed to the screen with respect to the user-defined world coordinate system, complete with logs of tool center point positions and time stamps, so collisions can be reproduced. This software is intended to be used in conjunction with automated scheduling as an external safety checker. Another important aspect of this research is the end effector, an attachment that is secured onto the end of the ABB robot and used to drill a series of holes in a given surface. The end effector has gone through numerous design improvements through which it became smaller and more cost efficient. The latest design incorporates the addition of a raspberry pi, a small single-board computer, which serves as a failure test. The pi is programmed to generate random failures which notifies the user to take the robot out of the running program. This system will eventually be used to detect real robot failures and alert the user of the malfunction. The end effector also has a separate attachment which is used to hold a camera in order to incorporate machine vision into the multi-robot system. Adding machine vision helps robot position calibration, along with detecting foreign objects other than the moving robots in the robot cell. This addition also improves security and liability of the system.

The study of the behavior of multiple agents, specifically human and machine, in a dynamic environment is challenging due to the unpredictable individual behaviors. Humans will naturally formulate beliefs about the machine’s behavior, which would directly affect their future decisions. Our research aims to develop a framework for the study of human-machine dynamic interactions. With the imperfect information humans and machines have about each other and their environment, a game-theoretic approach was done to study the natural model of their interactions. We derive theoretical models for steady-state (i.e. equilibrium) and transient (i.e. learning) behaviors of humans interacting with other agents (humans and machines). We also design experiments to validate our theory. A haptic testbench, in the shape of a robotic arm, is used as a dynamic simulation platform for studying the trajectories of the human/machine interaction, allowing us to study both theoretically and experimentally. The robotic arm has a position control system that supports a wide variety of human/machine experiments. The user is provided with visual and haptic feedback, which allows for experiments to be designed to study the sensorimotor learning processes. The robotic arm is built using direct-drive brushless motors, force sensors, an open-source ODrive motor controller, and an arm lever. The motor firmware is designed in C/C++, and integrated with a user-interface in Python. With the wide variety of potential applications, we hope our research will give insights into the different natures of human motion and be a fundamental platform for technological breakthroughs in the medical field.

Homo naledi is a species of hominin that lived in South Africa at between 335-236 ka, around the same time that anatomically modern humans were evolving in Africa. While the lower limb of Homo naledi shares many characteristics indicative of obligate bipedality with modern humans, the upper limb shows a more primitive morphology related to climbing. The distal humerus is one of the more common bony elements found in the fossil record and its morphology directly reflects the functional requirements of the limb, making it a good place to study upper limb function and adaptation. Using 3D geometric morphometrics, we compared seven distal humeri attributed to Homo naledi with distal humeri from great apes, modern humans, Neandertals, and other extinct hominins to place H. naledi in a functional context. We conducted a principal components analysis and partial least squares analysis on anatomical landmark data to investigate variation in distal humeral shape. Preliminary results indicate that H. naledi had a distal humeral morphology broadly similar to gorillas and unlike modern humans. Our results provide new insights into the upper limb mechanics and the role of climbing in the locomotion of Homo naledi, as well as clarify their phylogenetic relationship with other hominins.