Carbon dioxide (CO₂) is a greenhouse gas that traps radiation in the Earth’s atmosphere. Increasing levels of CO₂ in the atmosphere can lead to a warming of the Earth’s surface and can affect a number of processes that affect climate patterns. Terrestrial ecosystems contain 3 times more carbon than the atmosphere, and each year forests release more than 10 times the amount of CO₂ to the atmosphere through soil respiration than fossil fuel emissions. Although these large natural soil respiration fluxes tend to be balanced by fixation of atmospheric CO₂ through photosynthesis, the carbon balance of forests under future climate is still unknown. In order for scientists to better model the role of forests under future climate change, an improved understanding of the amount of carbon that is allocated and stored in different components of forest ecosystems is needed.This project aims to provide a more thorough understanding of whole-plant carbon allocation in temperate forests. While trees may allocate up to 50% of their photosynthetically fixed carbon belowground, carbon allocation belowground has been historically overlooked. In particular, very few studies have quantified the amount of carbon allocated to mycorrhizal fungi – the symbiotic fungi found on tree roots that provide the plant with water and nutrients in return for sugars (carbon). We employed three distinct methods (including new isotopic techniques) to quantify carbon allocation to mycorrhizal fungi across a range of New Hampshire forest types. Preliminary results show that in nutrient poor conifer forests, mycorrhizal fungi may receive as much as 30% of the total plant carbon. This is one of the first studies that will quantify carbon allocation to mycorrhizal fungi under a range of natural forests.

Current methods for staging chronic kidney disease are deficient because they lack specificity and sensitivity. Two potential renal biomarkers, cinnamoylglycine (CG) and hippuric acid (HA) are dietary metabolites cleared by the kidneys. These two compounds are potentially more sensitive indicators of kidney function because they are shown to require active secretion into the ultrafiltrate by the renal tubules. The purpose of this project was to develop and validate a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for determining the concentration of CG and HA in serum for use in future clinical research studies. Samples were prepared by precipitating serum proteins with acidified acetonitrile followed by phospholipid removal using solid phase extraction. Compound separation was achieved with ultra-high performance liquid chromatography utilizing a reverse-phase T3 column with a gradient mobile phase. Detection and quantification were accomplished by isotope dilution-tandem mass spectrometry operated in positive electrospray mode. The transitions monitored were 206.04>131.04m/z and 181.03>105.01m/z for CG and HA respectively. The lower limit of quantification (20% CV) for this multiplexed assay was established at 0.028 ng/mL and 1.2 ng/mL for CG and HA, respectively. Linearity studies achieved an r² value >0.97 for both analytes. The mean analytical recovery was 62% for CG and 64% for HA. The following studies used concentrations of CG and HA at 44.67 ng/mL and 7063.05 ng/mL respectively: intra-assay imprecision (CV, n=20) was 5.05% and 4.36%, inter-assay imprecision (CV, n=20) was 11.90% and 5.89%, and total error was 12.92% and 7.33% for CG and HA, respectively. This LC-MS/MS method demonstrates good performance and excellent analytical specificity for detecting and quantifying CG and HA in serum. The next phase is to implement this method into a clinical research study and explore these analytes as improved biomarkers for staging chronic kidney disease.

 The JMS Diaries is a collection of 16 original diaries and 30 transcriptions of Joseph Mathia Svoboda's original diaries. As an employee of the Lynch Brothers’ Tigris and Euphrates Steam Navigation Company, Svoboda wrote daily accounts of life on the Euphrates River between 1862 and 1908. These diaries give us insight into valuable cultural and social perspectives about Iraq during the late 19th Century. The NEH-funded Newbook Digital Texts in the Humanities project works to transform such valuable primary source documents into digital texts, making them easily accessible to scholars and the general public. As undergraduate researchers, we work with these primary texts to gain both research and digital archiving skills. Our editorial team works through a five phase process consisting of transcribing, editing, analyzing, encoding and formatting each text. First, we transcribe the texts from the original handwritten documents to plain text digital form, editing and proofreading them. We format the transcriptions in a standardized way for our work-flow manager to then apply a program, written by our technology team, which converts this format into XML-TEI markup (tags). XML (Extensible Markup Language) is a human and machine readable markup language used for encoding documents, which we use in a form standardized by TEI, the Text Encoding Initiative. We convert these to HTML (HyperText Markup Language) for web display and to LaTeX typesetting language for printing. Our history team extracts information from the texts thus produced to write our project "wiki" (the Svobodapedia. Svobodapedia serves as the basic annotation source for the final text, which is made available to readers on our website and as a print-on-demand book. Since beginning the project in September 2012, we have completed two diaries consisting of 400 pages each, and continue to work toward advancing this evolving, ongoing repository of primary source documents.

The diaries kept by Emma B. Andrews are an undervalued resource for learning about Egyptian culture, history and many turn of the century discoveries. Andrews (1837-1922) was the mistress of Theodore Davis, an archeologist responsible for the excavations in the Valley of the Kings. Andrews accompanied Davis on his trips and kept records of her life in Egypt. Her diaries provide readers with valuable insights into the social, cultural and scientific climate during her years in Egypt. However, these first-hand accounts have gone virtually unnoticed for years. Now, at the University of Washington, undergraduate students have the unique opportunity of working with the Andrews diaries to prepare them for online publication through the Newbook Digital Texts Project. The project allows for inexpensive publication of materials with less difficulty than traditional publication methods. Students work to translate, transcribe, edit and tag large amounts of texts in order to make them universally available on the web. Students researching the diaries have a variety of tasks to complete before the diaries will be ready for publication. During our presentation, we will focus on the process by which we are compiling these writings, which include: transcribing the diaries to an electronic textual format which must be completed and edited twice for accuracy; running the transcriptions through an auto-tagging program to create an online format for the texts; converting the auto-tagged version into XML format and adding new content, including historical research on people mentioned in the diaries; as well as how we hope this will change research in this area in the future. Undergraduates working on The Emma B. Andrews Diary Project are passionate about and committed to making this valuable resource available to the world with the hope that it will become a more widely recognized in the world of academia.

Cancer diagnostic immunoassays are widely used for the detection of disease in vitro, but low antigen concentrations may not be detected in an early stage or confused for baseline noise, leading to false negative or positive diagnoses. Poly(carboxybetaine methacrylate) (PCB) is a zwitterionic polymer that strongly resists biofouling while allowing simple functionalization and effective bioconjugation to proteins. Coating this polymer on iron oxide nanoparticles via a DOPA attachment group allows for easy antibody immobilization, to realize low nonspecific binding and high signal-to-noise ratio in one platform. Methods for nanoparticle construction include synthesis of MNPs (magnetic nanoparticles) coated with PCB-DOPA and PCB-DOPA2. The coated particles are functionalized with FITC-BSA and FITC-streptavidin using EDC/NHS chemistry to optimize conjugation parameters. A model antibody (ALCAM antibody) is then conjugated to test the platform’s sensitivity for immunoassays. The functionalized nanoparticles are characterized with Dynamic Light Scattering (DLS), fluorescence spectroscopy, flow cytometry, and Surface Plasmon Resonance (SPR). Control groups with bare beads, functionalized beads with no polymer coating, or no functionalization are also processed in the experiment to compare with experimental groups. In preliminary tests, the functionalized magnetic nanoparticles have a high level of immobilization of each tested protein or antibody (FITC-BSA, FITC-streptavidin, and ALCAM antibody). In the plasma stability test, the PCB-coated and beads show low nonspecific binding even with high levels of functionalization. The experimental immunoassay can detect a low concentration of the ALCAM cancer biomarker in bovine serum, with less baseline noise than a commercial immunoassay (Luminex MagPlex®). The functionalized magnetic nanoparticles have a low detection limit to an early-stage cancer biomarker and a high signal-to-noise ratio due to reduced nonspecific binding. This platform could be extended to many clinical immunoassays in which either false negative or false positive diagnostic readings are problem.

With the fifth largest proven crude oil reserves in the world and a government dependent on oil for 90% of its annual revenue, it is difficult for the 21st century individual to imagine what Iraq’s economy looked like before petroleum was discovered in 1923. In fact, relatively little is known about Iraq’s pre-oil economy, including the methods that were used to transport and trade commodities, what commodities were traded, and the prevalence of commercial travel. My research project focuses on the historical role of steamships in Iraqi commerce and travel, and how the Joseph M. Svoboda Diaries can illuminate the patterns of 19th century commercial trade and travel along the Tigris River in the part of the Ottoman Empire that is present-day Iraq. By examining Diaries 47 and 48 and cataloguing Svoboda’s descriptions of the commercial river voyages he takes as part of his job as a clerk on British steamships, my research seeks to illuminate what goods were traded, what kind of people used steamships as a mode of travel, and what places along the Tigris River functioned as commercial hubs. I plan to create a visual map of Svoboda’s river journeys, and to identify which river ports were significant and which ports typically provided what commodities. (Example: Coot as a hub for coal.) By superimposing Svoboda’s steamship routes on a map of present-day Iraq, I hope to investigate what impact, if any, this 19th century steamship traffic had on the modern-day river ports mentioned in the text and explore whether these commercial hubs retained their historical economic significance into the 20th and 21st centuries.

Exoplanets are planets outside our solar system. The discovery and characterization of exoplanet systems informs us of the types of worlds found in nature and whether they might support life. There have been an unprecedented number of exoplanet detections in recent years spurred in large part by the advanced observing capabilities of NASA’s Kepler Space Telescope. The Kepler Spacecraft continuously monitors a large, fixed set of stars and collects time series photometric data that are unparalleled in both quantity and precision. Plots of stellar brightness against time called lightcurves are the canonical representation of Kepler data. The goal of our research is to detect exoplanets from the characteristic features they produce in these lightcurves known as transits. A transit occurs when an orbiting planet partially eclipses its stellar host, reducing the brightness observed by the telescope and recorded in the lightcurve. To detect transits, we use the Quasi-Periodic Automated Transit Search Algorithm (QATS). As an automated tool, QATS is instrumental in reducing the effective size of the Kepler dataset. However, QATS is sensitive to variability of the target star and to systematic artifacts of the telescope just as it is to transits. Thus optimal detection efficiency requires removal of all non-transit signals prior to applying the algorithm. Determining the best way to do this is the present focus of our work because it bounds our ability to detect planets whose size, composition, and orbital parameters are conducive to life.

Due to small position uncertainties within internal systems, it is difficult to accurately predict the movement of cable-driven robots. By studying what happens within the pulley-cable system, we will be able to propose a model that accounts for the specific properties of the system, such as friction, tension, and viscosity. This model can be used for more accurate control of robot movement.

A pulley board was built with similar mechanical parameters (same pulleys, cables, tensions, and dynamics) as the RAVEN II surgical robot of the UW BioRobotics Lab. The board was fitted with velocity sensors which measured the movement of the cables when predetermined forces were applied to the ends. Position, velocity, and acceleration functions were obtained from these data. A proposed model was formed from physical predictions of the cables, and by fitting the data from the pulley board into the proposed model, functions for a viscous damping coefficient and friction force were found. From the findings, the model was refined and applied to the RAVEN II, transforming sensor inputs into a more accurate estimation of the robot pose.

College student drinking continues to be a concern due to high consumption rates and negative consequences associated with excess use. Both male and female students are at risk for heavy alcohol use and related consequences. Symptoms of depression are also reported frequently amongst college students, particularly female students who tend to be at higher risk than males for depression. Evidence suggests that depressive symptoms are often correlated with increased alcohol use. Alcohol consumption has also been related to perceived social norms of peer drinking, i.e. the perceived amount of drinking that other students and peers typically engage in. Injunctive norms, which refer to perceived approval or disapproval of a behavior by other students, may be highly regarded by students as important for decisions regarding their own behavior. Furthermore, it is hypothesized that this relationship may shift with an increase in depressive symptomology in females. Injunctive norms-indicating approval from others-have been linked to increased alcohol use in this population. Prior research also suggests that female drinking tends to be more strongly correlated with typical same-sex student alcohol injunctive norms more than their male counterparts. Thus the proposed study examines the moderating role of depressive symptoms and gender on the relationship between injunctive norms and alcohol use in college-age students. The goal of this study is to further understand the nature of the relationship between injunctive norms and alcohol use, and whether depressive symptoms enhance risk from injunctive norms in females more than males.

Superconducting Josephson Junctions may be an enabling technology for the next generation of supercomputers. Breakthroughs in nanotechnology have allowed for transistors to close in on their theoretical limit of several nm in size, allowing for tens of billions of transistors per square inch to be fabricated on integrated circuits. As the transistor count increases processor power consumption will become a limiting factor. Josephson Junctions are a promising candidate to replace silicon transistor based switching as they consume several orders of magnitude less power than current silicon transistors while promising even faster switching speeds. Furthermore Josephson Junctions have been shown to be a possible basis for a scalable quantum computing architecture, increasing their usefulness beyond advanced classical computing applications. We characterize Josephson Junctions fabricated at the University of Washington using both room temperature and cryogenic measurements as part of a preliminary effort to further develop this technology.