Mapping is a powerful tool to visualize space and data. However, working with historical data and maps is problematic as spaces change across time. Given this, the scope of this research is to create visual maps using GIS software that accurately represents the Baghdad-Basrah region of the Ottoman Empire in the late nineteenth century. Our key research question is: how can cholera data from primary sources in the nineteenth century be visualized through mapping? We gathered the data for this research from the diaries of Joseph Svoboda, a resident of the region who traveled frequently up and down the river system and recorded information about numbers of deaths and quarantines from cholera in the cities he passed. The method we used for mapping the data includes a comprehensive reading of the diaries currently being transcribed to assess which information is important for mapping purposes, including the location and time period of the event in question. We mapped the data using Geographic Information Systems (GIS), a software that is used to analyze and represent data through maps, to geocode locations and include cities and other features as they appeared in the nineteenth century. Anticipated results include an interactive choropleth and dot maps that are accurate to the specific time period and show deaths from cholera in specific locations over time. One key implication for further work would be a standardized way to map disease data from primary sources and to increase the number of individuals who use data visualization with historical data. Additionally, our mapped data can be used for other types of GIS analysis that may be of interest to those studying the history of cholera or historic epidemics.

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. 

The environment in which a molecule resides can drastically affect both its reactivity and its spectroscopic properties. These effects can be clearly seen in phenomena such as solvochromism or increased reactivity in a protein active site. The most accurate models that can capture these effects are purely quantum mechanical, but they also have a steep computational scaling cost that prohibits their use on large molecular systems. In order to circumvent this, less expensive models, such as molecular mechanics, can be used for the environment while maintaining the accurate model for the system of interest. In recent years, development of polarizable molecular mechanics has enhanced the accuracy of this technique for time-independent systems, but a gap still exists for time-dependent systems. In particular, the frequency dependence of polarizability has yet to be addressed. This research uses frequency dependent polarizabilities to parameterize a novel molecular mechanics scheme. Specifically, a machine learning model is trained to predict the best locations to place isotropic polarizabilities in order to recover the molecular, frequency-dependent polarizability.

Humans hear sound through two main pathways: air conduction (AC) and bone conduction (BC). The AC pathway is dominant under normal listening conditions, but conductive hearing loss (e.g. outer/middle ear diseases) impairs one’s ability to hear by AC. BC hearing aids can improve hearing under such conditions. To determine the presence of a conductive hearing loss, BC hearing thresholds must be compared to AC thresholds. For populations that cannot respond reliably to behavioral audiometric testing (e.g. infants, elderly, individuals with cognitive impairments), clinicians instead record sound-evoked brainstem activity through the auditory brainstem response (ABR) test. While AC ABR test results are clinically reliable, BC ABR test results suffer from electrical artefacts generated by the BC transducer and variable ABR waveform morphology. Therefore, determining the presence of a conductive hearing loss by comparing AC and BC ABRs is often unreliable. This study aimed to (1) reduce the severity of electrical artefacts present in the early BC ABR waveform (Wave I/II) by shielding bone-vibrating transducers (Radioear B81) with MuMETAL and (2) improve the quality of the ABR signal by using ‘chirp’ stimuli (ascending frequency sweep) to enhance the summating amplitude of auditory neural responses. Ongoing measurements leverage three transducer types in total (shielded and unshielded BC, earphone AC) and three stimulus types (chirps, constant-frequency tone bursts, and broadband “clicks”) to evaluate main and combinatorial effects of the transducer and stimulus on BC ABR data quality. Early indications show that shielding the BC transducer does not materially change its frequency response. Therefore, any observed changes in the BC ABR waveform can be attributed to electrical shielding and/or stimulus modifications per se and not to unintended changes in transducer acoustic output. Data will inform efforts to improve the clinical reliability and utility of BC ABR measures for detection and treatment of conductive hearing loss.

Electronic movement can be modeled using the Schrodinger equation. For many-electron systems, however, these equations are not algebraically solvable, which is why this research uses direct numerical integration of Schrodinger’s equation to model time dependent electronic characteristics of molecules. The choice of numerical integration scheme can drastically change the outcomes of the simulation – even causing qualitative changes in molecular behavior. First, an advanced numerical integration technique (4th order Magnus propagator) has been implemented in the ChronusQuantum software package. Next, the effects on molecular behavior of choosing this integration scheme over preexisting schemes are evaluated. The implemented integration algorithms can be used to model the elementary steps of chemical reactions, as well as analyzing the effects of light on electron movement. The research provides meaningful information about the impacts of different implementations of algorithms along with analyzing the simulated behavior of electrons.

This research explores 19th century Middle Eastern and European quarantine practices through the personal diaries of Joseph Mattias Svoboda, written in Iraq from 1862 to 1908. Joseph Mattias Svoboda’s diaries document a detailed account of daily life and information in the Basra and Baghdad regions of modern day Iraq. Joseph himself was from a prominent European family and worked for an English steamship company, traveling across Iraq during a time when cholera was prevalent and occasionally reached epidemic proportions. I used Joseph Svoboda’s notes as a basis to piece together common quarantine practices and procedures utilized in the 19th century by the Ottoman Empire. Using digital transcriptions of the diaries, I used data-mining techniques to extract references to cholera outbreaks, quarantine procedures, and numbers of people afflicted by disease before and after quarantines were put in place. Then, using contemporary European newspapers, medical journals, and historical records, I compared the Ottoman procedures to European quarantine practices. I examined the efficacy of quarantine procedures in both regions depending on the size of each given cholera outbreak. Ultimately, these early forms of public health governance may have influenced global trade patterns. Future projects stemming from this research could look into the influence of European public health practices on Ottoman medical thought, or the comparative role of physicians in the Ottoman Empire and in 19th century Europe. Regardless, hopefully this research encourages others to explore beyond the Eurocentric narrative of developing public health in the 19th and 20th centuries.

The Svoboda Diaries Project works with personal diaries written at the turn of the 19th century, capturing over 40 years of the life, politics, and landscape of Ottoman Iraq. Written through the unique lens of a British steamship purser with a rich family history and connections in the area, these texts provide a unique insight into a locale on which there exists minimal literature for this time period. Undergraduate interns transcribe these diaries and develop open-source tools to make the texts available in a variety of formats. We are currently redesigning our website to better serve the needs of its various users, and our main question is: How do we realize the needs of prospective users when creating a digital platform for viewing historical manuscripts? Our current website is not sufficient in meeting the needs of the project’s diverse users: historians/researchers, contributors, and the general public. Therefore we intend to create an engaging and interactive user interface. At its core, the Svoboda Diaries comprise a personal narrative. We also intend to infuse a storytelling approach to present these unique documents in a larger political and historical context, and allow the user to explore them in different ways. We utilize a variety of user-centered research and design methods, such as conducting user interviews with domain experts and other interested individuals, creating prototypes, and conducting pilot usability sessions to refine the website.We anticipate that our website redesign will allow users greater access to explore the diaries. In addition, the redesign will draw attention to the most important aspect of the website: the diaries themselves, and the fascinating and valuable accounts within them.

Joseph Mathia Svoboda, a European residing in Baghdad and working as a steamship officer, kept a detailed daily diary from 1861 to 1908, in which he recorded his trips on the Tigris, family events, and his medical and financial concerns, as well as each day’s weather. Working with the UW Svoboda Diaries Project, part of the Newbook Digital Texts Collective, I transcribe these diaries and help develop resources for their analysis and the promotion of digital humanities. Digital humanities work changes not only the literal, physical forms of texts but their literary forms as well, and digitizing a text such as a diary and opening it to public scholarship presents new questions about how we think about private writings. Literary scholarship on diaries addresses the unique psychological and philosophical aspects of keeping a diary and attempts to analyze its own position in relation to its object of study, as what is personal to a diarist is placed in plain view. Svoboda himself wrote in a largely impersonal, factual style, with little personal commentary, for instance, but scholars mine social and political sentiments from his choice of language or attention. In this project, I will consider the Svoboda diaries (focusing on three diaries written between 1897 and 1899) as textual objects and describe the transformations they have undergone since their writing, with a special focus on the transformation of the private nature of a diary. What do the diaries become as we study them? While digital humanities seeks faithfulness to the original contents of a text, drastic transformation of forms such as “making the private public” naturally opens those same contents to new uses, and understanding these changes is crucial to understanding the full extent of digital humanities scholarship.