Distributed version control allows developers to manage software evolution among distributed development teams. But it does not eliminate all consistency and concurrency issues, and instead introduces additional complexity when merging code. And resolving merge conflicts is nontrivial when automated merging fails. In such cases, developers are forced to inspect the...
Solvent extraction is an integral chemical and biochemical separation process that is drastically intensified in microfluidic systems. A novel high-throughput micro-separator was additively manufactured for the intensification of liquid–liquid separation. The micro-posts array within the flow plate generated a capillary pressure gradient on the non-wetting organic phase, enabling continuous, membrane-free,...
Over time, Open Source Software (OSS) has become indispensable in the creation and upkeep of software products, serving as the fundamental building block for widely used solutions in our daily lives, including applications that enable communication, entertainment, and productivity. A sustainable OSS ecosystem is one that attracts and retains a...
Toxin production by cyanobacterial harmful algal blooms (cyanoHABs) in freshwater systems has lasting ecological and human impacts. Nutrients, light availability, hydrology, and microbial community composition impact the frequency and intensity of toxic cyanoHABs. Climate change will exacerbate toxic cyanoHABs, making real time and predictive monitoring a vital tool for managing...
The focus of this thesis is to design, characterize, and apply novel computational methods and molecular systems to interrogate heterogeneous human gut microbiome-related phenomena. In Chapter 2, I design, implement, and characterize a method for embedding co-occurrence patterns derived from massive 16s amplicon datasets. I use this method to 1....
Analysis of observations on sequential events over time is common in real life. Sequential measurements over time describing the behavior of systems are usually called time series data, which have been collected in a wide range of disciplines. Over the years there have been multiple research areas in studying stochastic...
Energetic resources transferred between distinct habitats or ecosystems, referred to as allochthonous resources, can greatly subsidize consumers in the recipient habitat, and thus influence food web structure and dynamics. Such subsidies may allow the growth of the consumer population to be decoupled from in situ productivity with effects on consumer...
Given the many significant roles that bacteria play in modern food manufacturing, it is crucial that we have a fundamental understanding of how bacterial communities assemble and behave in the food manufacturing environment. The focus of this dissertation was to investigate both the spatial and temporal distributions of microbial communities...
The variety of natural disasters provide different sets of characteristics and properties with unique challenges. One significant difference between hazard types is prewarning lead time, the amount of time individuals have from a potential warning to the disaster occurring. Rapid onset disasters may not provide an official warning about a...
Listeria monocytogenes is a foodborne pathogen frequently associated with food processing environments. Its presence is particularly concerning in facilities handling minimally processed and ready-to-eat foods. Recent outbreaks associated with fresh produce, such as packaged salads and mushrooms, highlight the need to better understand and control these pathogens in environments that...
Managing agricultural diversity ensures a range of public services, such as genetic resource diversity, food security for subsistence-based economies, and landscape resilience in the context of climate change, among others. These agrobiodiversity conservation services are positive externalities from agrobiodiversity conservation. Whereas their value is not captured in market transactions, management...
The purpose of this thesis is to examine gender and historical bias in wind band music and related practices in the Pacific Northwest. This research was conducted via an IRB approved research study, Equity and Gender Bias in High School Music Programming in the Pacific Northwest: A Case Study, which...
Although computer science (CS) education researchers and practitioners have found ways to improve CS classroom inclusivity, few researchers have considered inclusivity of online CS education. We have begun developing a new approach that we term “embedded inclusive design” to address inclusive CS. The essence of the approach is to integrate...
It is desirable for complex engineered systems to perform missions efficiently and economically, even when these missions' complex, variable, long-term operational profiles make it likely for hazards to arise. It is thus important to design these systems to be resilient so that they will actively prevent and recover from hazards...
Software systems are becoming an essential part of the lives of both individuals and organizations, and as a consequence, these systems are getting bigger and more complex. Because of this, the tasks of maintaining the quality in these complex software systems are becoming increasingly difficult. Furthermore, these systems are subject...
Merge conflicts have long plagued software development. With larger and more dispersed teams comes greater risk of developers working on the same code at the same time. While merge conflicts are known to be painful, their exact impact on software is still largely unknown. Are merge conflicts an isolated problem,...
Newcomers’ seamless onboarding is important for open collaboration communi- ties, particularly those that leverage outsiders’ contributions to remain sustainable. Nevertheless, previous work shows that OSS newcomers often face several barriers to contribute, which lead them to lose motivation and even give up on contributing. A well-known way to help newcomers...
Although the need for gender-inclusivity in software itself is gaining attention among both SE researchers and SE practitioners, and methods have been published to help, little has been reported on how to make such methods work in real-world settings. For example, how do busy software practitioners use such methods in...
Most software systems today do not support cognitive diversity. Further, because of differences in problem-solving styles that cluster by gender, software that poorly supports cognitive diversity can also embed gender biases. To help software professionals fix gender bias “bugs” related to people’s problem-solving styles for information processing and learning of...
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B Information Processing Style (InfoProc Style
The Supreme Court Bar-the lawyers who argue before the US Supreme Court-has historically been an elite and exclusive group. This investigation examines the demographic make-up of the Supreme Court Bar in the Roberts Court and compares it to previous iterations of the Supreme Court Bar, as well as the national...
Age is a recognized risk factor for amyotrophic lateral sclerosis (ALS), a paralytic disease characterized by progressive loss of motor neurons and neuroinflammation. A hallmark of aging is the accumulation of senescent cells. Yet, the pathogenic role of cellular senescence in ALS remains poorly understood. In rats bearing the ALS-linked...
Background. Ampelisca eschrichtii Krøyer, 1842 of the Sakhalin Shelf of the Okhotsk Sea, Far Eastern Russia, comprise the highest known biomass concentration of any amphipod population in the world and are a critically important prey source for western gray whales. Growth and reproduction in this population has not been apparent...
Background. Ampelisca eschrichtii Krøyer, 1842 of the Sakhalin Shelf of the Okhotsk Sea, Far Eastern Russia, comprise the highest known biomass concentration of any amphipod population in the world and are a critically important prey source for western gray whales. Growth and reproduction in this population has not been apparent...
While the contemporary movement against sexual and domestic violence has roots in radical, feminist theory and anti-state, community-based modes of resistance, over the past several decades, advocates and activists have increasingly turned to corporations and the state for support through the non-profit, prison, and medical industrial complexes. This acceptance of...
Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our...
In recent years, many studies have focused on the molecular and biochemical mechanisms regulating the development of wine grapes. The course of grape berry development is directed by genetic design and is mediated by phytohormones, which regulate grape berry growth and development by orchestrating a complex network of interacting genes,...
Previous work introduced the GenderMag method, a software inspection method used to help software creators identify features within their software that are not gender-inclusive. Inclusiveness of software (gender or otherwise) matters because supporting diversity matters—it is well-known that the more diverse a group of problem-solvers, the higher the quality of...
Gender issues have recently received increased attention in human robot interaction (HRI). Because robots are becoming part of our homes and daily lives, it is important to understand how different groups of people use them. To the best of our knowledge, almost no research has been done that investigates gender...
The National Research Council has aggregated research evidence on the pedagogy of science teaching and learning (NRC, 2012), culminating in the Next Generation Science Standards (NGSS). These standards support emphasis on eight scientific practices as an important component for teaching science as inquiry to K-12 students. This latest framework for...
A great deal of research has been focused on the microbiomes of terrestrial angiosperms (flowering plants), but much less research has been performed on the microbiomes of aquatic angiosperms (Turner et al. 2013). Eelgrass beds are extremely productive ecosystems that provide habitat for many marine organisms, such as fish, shellfish,...
Limnology is undergoing a transition to high-throughput -omic analysis of freshwater
bacterial communities. An important first step in making the transition is to
characterize several genomes that can be used as references to guide metagenome
assembly and analysis. Here I characterize four new freshwater cyanobacterial
genomes, a pair of lake...
Ampelisca eschrichtii are among the most important prey of the Western North Pacific gray whales, Eschrichtius robustus. The largest and densest known populations of this amphipod occur in the gray whale’s Offshore feeding area on the Northeastern Sakhalin Island Shelf. The remote location, ice cover and stormy weather at the...
Ampelisca eschrichtii are among the most important prey of the Western North Pacific gray whales, Eschrichtius robustus. The largest and densest known populations of this amphipod occur in the gray whale’s Offshore feeding area on the Northeastern Sakhalin Island Shelf. The remote location, ice cover and stormy weather at the...
Quotient rings of Gaussian and Eisenstein-Jacobi(EJ) integers can be deployed to construct interconnection networks with good topological properties. In this thesis, we propose deadlock-free deterministic and partially adaptive routing algorithms for hexagonal networks, one special class of EJ networks. Then we discuss higher dimensional Gaussian networks as an alternative to...
Surface water quality is a growing concern in the Willamette River Basin and elsewhere. The region's growing population is dependent on the availability of clean water for drinking water, irrigation, wastewater dilution, and wildlife habitat. Watershed management to produce economic goods and environmental services requires an understanding of basic hydrologic...
This thesis focuses on the identification of ecohydrological processes in nested system of catchments in a tropical alpine (the wet Andean páramo) ecosystem. We accomplish this by conducting a water stable isotopic characterization of water sources, an evaluation of the mean transit time (MTT) of streams waters, and the investigation...
Ampelisca eschrichtii are among the most important prey of the Western North Pacific gray whales, Eschrichtius robustus. The largest and densest known populations of this amphipod occur in the gray whale’s Offshore feeding area on the Northeastern Sakhalin Island Shelf. The remote location, ice cover and stormy weather at the...
This thesis explores the experiences and negotiations of belonging for children of Mexican migrant farmworkers in Oregon. Ethnographic data was collected over the course of several months with Mexican migrant farmworkers and their children in agricultural fields in Oregon and at Oregon State University. The children in this project have...
Professional software engineers have an arsenal of techniques such as unit testing and assertions to check their specifications, but these techniques require tools, motivation, experience and training that programmers without professional software engineering training may not have. As a result, professionals in other fields, such as scientific modelers, face greater...
End-user programmers face many barriers in programming. Research has seen many programming environments that attempted to lower or remove the barriers but despite these efforts, empirical studies continue to report barriers users face. To investigate this issue, we took a theory-informed approach. Using theories from design, creativity, and problem solving...
Variation in cheese quality due to geographic location is important to cheese producers, consumers, and retailers on a global level. Understanding the impacts of geographic location of cheese plants may be useful to businesses for marketing, cost reduction, and quality improvement. Many aspects of variation due to geography have been...
Thesis explores the ways in which Information and Communication Technology (ICT)use, specifically that of telephones and the Internet, impacts the lives of Eritrean refugees in Rome, Italy. Informal interviews, semi-structured interviews, and participant observation were carried out in a 'center of second reception.' Results show that information obtained through the...
Although there has been significant research into gender regarding educational and workplace
practices, there has been little awareness of gender differences as they pertain to software tools,
such as spreadsheet applications, that try to support end users in problem-solving tasks. Although
such software tools are intended to be gender agnostic,...
The results of a machine learning from user behavior can be thought of as a program, and like all programs, it may need to be debugged. Providing ways for the user to debug it matters because without the ability to fix errors, users may find that the learned program’s errors...
End users' programs are fraught with errors, costing companies millions of dollars. One reason may be that researchers and tool designers have not yet focused on end-user debugging strategies. To investigate this possibility, this dissertation presents eight empirical studies and a new strategy-based end-user debugging tool for Excel, called StratCel....
Programmers spend a substantial fraction of their debugging time by navigating
through source code, yet little is known about how programmers navigate. With the
continuing growth in size and complexity of software, this fraction of time is likely to
increase, which presents challenges to those seeking both to understand and...
Long-run food price changes respond to long-run changes in food demand, quasi-fixed and variable production factors, and agricultural productivity. Recent global food-price volatility puts a renewed spotlight on the trends and sources of any agricultural productivity growth. Because food prices’ most critical effects are on human hunger, it is especially...
End-user programmers’ code (e.g., accountants’ spreadsheet formulas) is fraught with errors. To help mitigate this problem, end-user software engineering research is becoming established. However, most of this work has focused on feature usage, rather than debugging strategies. If a debugging tool were to support end-user programmers’ specific debugging strategy needs,...
Although there have been decades of research into how professional programmers debug, only recently has work begun to emerge about how end-user programmers attempt to debug their programs. Without understanding how end-user programmers approach debugging, we cannot build tools to adequately support their needs. To help fill this need, this...
End-user programmers’ code is notoriously buggy. This problem is amplified by the increasing complexity of end users’ programs. To help end users catch errors early and reliably, we employ a novel approach for the design of end-user debugging tools: a focus on supporting end users’ effective debugging strategies. This paper...