Bioculture Journal
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1309 research outputs found
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Practical Verification of Safety-Critical Systems
No full textThesis (Ph.D.)--University of Washington, 2018Software-based control systems operate scientific equipment worth millions of dollars and even safety-critical medical devices, making them good targets for strong formal verification techniques. However, these systems are rarely verified in practice. We identify three key challenges hindering the application of verification to real-world control systems and present solutions to each. First, safety properties of control systems often rely on correct operation and interaction of several heterogeneous hardware and software components. No single analysis tool can reason about all types of components. We present techniques, based on the established practice of safety case construction, for building a machine-checkable safety case that combines concrete evidence about the system implementation derived from multiple analysis tools. Using these techniques, we uncovered safety-critical flaws in a prerelease version of control software for the Clinical Neutron Therapy System (CNTS), a radiotherapy installation. Second, software components of control systems are often developed using proprietary or domain-specific languages for which no formal semantics yet exist. We present a methodology for rapidly developing language semantics, allowing application of formal verification techniques in languages that have received little previous study. We used this methodology to develop semantics for Python and for the EPICS dataflow language, suitable for analyzing components of the CNTS control software. Third, for control system software written in specialized languages, often no verified language implementations are available. We present a new technique for developing verified compilers that combines a verified denotation function with a verified extraction procedure to achieve high run-time performance with low verification effort. We demonstrate the effectiveness of this technique by developing a verified compiler for a fragment of the EPICS dataflow language and using it to compile portions of the CNTS control software
A GIS-based Multi-Criteria Evaluation of Disaster Vulnerability in an Urban Space
No full textThe notions of resilience and vulnerability are rapidly gaining ground in the urban sustainability and planning literature. The series of recent natural disasters around the world such as earthquakes, tsunami, and hurricanes, highlights the need for planning around natural hazard prevention and mitigation in human settlements. Historically, efforts have concentrated on recovery efforts, but rather than public engagement with emergency planning. Traditionally, most policy regarding disaster puts emphasis on the impact of natural phenomena. This notion has led to the dominance of technical interventions concentrating on prediction of hazards or modifying their impact. Catastrophic natural disasters such as Hurricane Katrina in 2005 taught us a hard lesson that traditional methods of communicating emergency information often fall short from the goal of reaching everyone in a community (Bates and Swan 2010). Accordingly, the incorporation of the notions of vulnerability and resilience in city’s emergency preparedness and disaster management has become a new frontier. In this study, I employed a multi-criteria evaluation (MCE) method within a geographic information system (GIS) framework to evaluate the vulnerability at of the City of Bothell to natural disasters at the census block level
Shifting role of chemoautotrophic SUP05 bacteria in nitrogen, sulfur and carbon cycles across oxygen gradients in marine environments
No full textThesis (Ph.D.)--University of Washington, 2018Microbes make up a large percentage of the biomass within marine environments and play a key role in cycling of biogeochemical cycles. Despite this, majority of important species of bacteria and archaea remain poorly understood due to lack of cultured representatives. Ecological studies have utilized macromolecules like small subunit RNA (16S) to identify and enumerate important groups of microbes in the environment. An uncultivated group of thiotrophic gamma-proteobacteria from the clade SUP05 are ubiquitous and abundant at the interface at the boundaries of marine oxygen minimum zones (OMZs). Metagenomic studies have shown that they play an important role in the cycling of nitrogen, carbon and sulfur within OMZs. In this thesis, I present the first cultivated representative from the chemoautotrophic SUP05 subclade, Candidatus Thioglobus autotrophicus along with its complete and annotated genome. SUP05 bacteria have been long suspected as important players in the nitrogen, carbon and sulfur cycles within OMZs. Particularly in processes that involve loss of fixed nitrogen in the form of gases (denitrification) and fixation of carbon. Using laboratory experiments on T.autotrophicus, I show that SUP05 bacteria produce large amounts of nitrite by carrying out dissimilatory nitrate reduction and consuming ammonia. Furthermore, I use growth experiments, cryo-electron tomography and protein expression data T. autotrophicus in aerobic and anaerobic to show that SUP05 have the potential to assimilate more carbon and store large amounts of reduced sulfur when they are exposed to oxic environments. This thesis provides a cultured representative of the chemoautotrophic SUP05 and a working model of its growth and metabolic constraints
City of Seattle Digital Equity Evaluation Plan
No full textBuilding on 20 years of work, in 2016 the City of Seattle published a Digital Equity Action Plan to help ensure all residents and neighborhoods have access to and are proficient in using digital technologies. In order to monitor and assess progress toward the plan’s goals,
the City worked with researchers from the iSchool to develop a strategy and methodology for evaluating
and reporting on output and outcomes. The completed
evaluation plan includes a theory of change, indicator
framework, data collection and reporting strategy, and
recommendations for next steps
UW Symphony Orchestra David Alexander Rahbee, Music Director and Conductor with Ben Lulich, clarinet April 27, 2018
No full textConcert ProgramConcert Program for UW Symphony Orchestra David Alexander Rahbee, Music Director and Conductor with Ben Lulich, clarinet
April 27, 201
Spotlight UW Symphonic Band UW Wind Ensemble April 26, 2018
No full textConcert ProgramConcert Program for Spotlight UW Symphonic Band UW Wind Ensemble April 26, 201
Baffling Narrators: Barthes’s Neutral in Novels by Szabo, Sebastian, and Sebald
No full textThesis (Master's)--University of Washington, 2018This essay uses Roland Barthes’s concept of the Neutral to explore the narrative styles of three 20th century European novels: The Door by Magda Szabo, For Two Thousand Years by Mihail Sebastian, and The Rings of Saturn by W.G. Sebald. In each case, the essay locates some unwillingness on the part of the narrator to make affirmations about himself or herself or the world, or an effort to baffle others’ attempts to do so. Given that each of these novels, to varying degrees, deals with the persecution of Jewish people in mid-century Europe, the essay tests the limits of the Neutral as a narrative impulse
Adaptive Support for Face-to-Face Collaborative Learning at Tabletop Computers
No full textThesis (Ph.D.)--University of Washington, 2018Collaborative learning is a common practice in today's classrooms. Technology-supported collaborative learning environments are becoming increasingly sophisticated, enabling new ways for students to work together with technology. Research has shown that collaborative learning has many benefits, particularly for developing students' higher-order thinking and problemsolving skills. However, it has also been shown that students do not always know how to collaborate effectively, which can inhibit the success of collaborative learning. These findings suggest that collaboration itself is a skill that needs to be fostered and developed in the classroom. Tabletop computers have affordances for collaborative learning because of the large, shared interface that multiple people can see and interact with at once. Despite these affordances, small group work at a tabletop computer is just as susceptible to breakdowns in collaboration as group work using other kinds of tools. Through design-based research in classroom settings, I have investigated how tabletop computers can model social regulation—the processes that groups use to manage and monitor their collective work—in order to detect when a group of students is in need of support. While collaboration is driven by the verbal and gestural interactions between the learners, the tabletop is only able to capture direct interaction with the device. I have identified touch patterns that reflect the quality of social regulation and can be used to detect problems in the collaborative process. To enable the real-time use of these touch patterns, I developed a machine learning-based approach for distinguishing among simultaneous users at a tabletop computer. I also present software adaptations designed to encourage more effective collaboration that are triggered when breakdowns in collaboration are detected. A classroom evaluation of these adaptations showed that they deterred disruptive behavior and reduced the length of periods of sustained, low-quality collaboration. My dissertation demonstrates the following thesis: Interactive tabletop software that can automatically detect breakdowns in collaboration and adapt in real-time to scaffold effective social regulation can improve secondary school students' collaboration skills
Characterization of Coronary Arteries: Correlating Mechanical Stiffness with Staining for in vivo Imaging
No full textThesis (Master's)--University of Washington, 2018Widespread prevalence of cardiovascular disease (CVD) in the US is indisputable. Over 82.6 million adults (~30% of the US population) have been diagnosed with one or more forms of CVD. Coronary artery disease (CAD) is the most common form and constitutes nearly 50% of all cases. It remains the leading cause of death for individuals afflicted with CVD due to the critical role of the coronaries in myocardial function. In coronary arteries, the CAD manifests as a highly-active, immune-driven sequestration of lipids which eventually triggers calcification that is found in advanced CAD lesions. Calcification is thought to provide stability as an atheroprotective mechanism even though deposition results in gradual stenosis and angina. Unstable or ‘vulnerable’ lesions are characterized with very little calcium deposition, yet these lesions are thought to result in myocardial infarction. Vulnerable lesions are difficult to observe by traditional approaches and are differentiated by thin-cap fibroatheromas (TCFAs). TCFAs are large, eccentric, necrotized lipid cores that are contained within the arterial wall by a thin fibrotic cap. Vulnerable lesions do not occlude the lumen and are not evident under conventional, non- invasive imaging, thus monitoring their structural progression is paramount for improving clinical outcomes. Histopathology is the gold standard for assessing lesion grade through H&E and other more specific stains. These dyes are toxic which preclude their use in vivo interrogation. Several imaging modalities have thus been developed in lieu of conventional histology to circumvent this limitation. One of which is the Scanning Fiber Endoscope (SFE). Pilot SFE investigations on cadaveric specimens and biomarkers between the Human Photonics Lab (HPL) and the Center for CardioVascular Innovation (CCVI) led to the exploration and application of Evan’s blue as a contrast agent for fibrotic caps. Evan’s blue is an FDA-approved compound and is typically employed as an in vivo blood tracer for Boolean assessment of cardiac leakage, or output. The chemical compound also demonstrates increased affinity for fibrous cap components and exhibits spectral characteristics that permit SFE fluorescence imaging. Evan’s blue stains in a graded fashion reflecting fibrotic cap content. An increased fibrotic cap content is directly associated with an increase in mechanical stiffness. We therefore hypothesize that the optical intensity of Evan’s blue correlates with the mechanically stiff properties of diseased coronary arteries to support SFE detection for in vivo assessment. To test our hypothesis, the experimental histology laboratory at the CCVI was tailored to process human and porcine coronary specimens. This included all the classical steps in pathology along with high resolution imaging for quantification. Procured human (n = 7) and porcine (n = 10) specimens were first tested in a custom-designed mechanical apparatus assembled at HPL prior to histology. In proximity to the contracting myocardium, coronaries experience a greater amount of longitudinal stress during physiological activity and when coronaries are diseased. The mechanical apparatus thus measured displacements within specimens when a load (20-200 g) was applied to the sample. Coronary arteries were isolated and segmented (normal: n = 20, diseased: n = 14), and lengths/diameters were precisely measured. Segments were then mounted on a machined probe for testing. Vessel segments were loaded several times (n = 5) for a given mass and the experiment was repeated at least 5-8 times for fresh and frozen groups for both normal and diseased coronary segments. A knot in the suture line attaching the specimen to the calibrated mass provided a fiducial marker for vessel displacement. High resolution, high-speed cameras acquired video recordings of knot displacements where optical data were processed, and analyzed using ImageJ and MATLAB code. Displacement vs. force and stress vs. strain plots were produced for all experiments. Fresh, healthy segments displaced 500 um more than diseased samples and spanned a range of 1.5-3.3x. Frozen, healthy segments displaced an average of 400 um less than fresh segments suggesting the presence of a freezing-induced artifact. Comparisons between human and porcine segments revealed similarities in their displacements suggesting that porcine arteries can substitute for disease-free arteries during longitudinal uniaxial testing. Following mechanical characterization, coronary segments were processed into microscope slides for pathological evaluation. Sections (n > 10 slides/group) were stained (Verhoeff’s Hematoxylin - elastin/calcification, Aniline Blue - collagen, Evan’s Blue - fibrotic caps) and quantified via ImageJ to determine collagen-to-elastin (C/E) ratios and degree of Evan’s Blue staining. Although diseased tissue segments displaced less than normal segments, stress-strain analyses and the resulting Young’s modulus values did not confirm our hypothesis of an expected increase in stiffness. It is thought that the varying cross-sectional areas of diseased segments may have contributed to this effect as a diameters and hence cross-sectional areas between groups were different by nearly 3 fold
VIBRATION EXPOSURE FROM BUCKING BARS DURING PERCUSSIVE RIVETING IN THE AEROSPACE INDUSTRY
No full textThesis (Master's)--University of Washington, 2018A study was done on several bucking bars used during percussive riveting. First, a Simulink model was developed in order to predict a bucking bar’s behavior. The user can specify the gun input, the rivet type, the bucking bar’s mass, spring rate, and its damping coefficient. The simulation was able to predict the bucking bar’s displacement with a RMSD = 7.74%. Second, a spring-damper bucking bar handle was developed in order to absorb vibrations and isolate the operators from being exposed to high magnitude vibration. Third, 2 Boeing mechanics used 5 different bucking bar handles in order to install rivets on a test bench developed at the Boeing Advanced Research Center (BARC). The handles included a fixed plastic handle (P), spring and Sorbothane (T) handle, and 3 spring dampened handles (CS, CA, Y). The results showed that the spring dampened bucking bars handles reduced the vibration by 45% for mechanic 1 and by 16% for mechanic 2 compared to the P handle