VictorJuiz/thesis huggingface dataset:
Hummingbird Hovering Energetics and Flight Capacities Across Elevational Gradients
Keywords: elevation
energetics
flight
hovering
hummingbird
metabolism

High elevations are characterized by reductions in environmental parameters, including oxygen availability and air density. This can be problematic for volant species, as sustaining flight in hypodense air is more energetically demanding relative to normodensity. Animals meet these challenges by increasing wingbeat kinematics and mechanical power output, necessitating increased metabolic input, while at the same time aerobic metabolism is constrained by hypoxic conditions associated with increasing elevation. These limits may restrict the range of behaviours that can be aerobically sustained. This thesis explores the kinematic and aerobic capacities for exercise across an elevational gradient, and examines possible morphological adaptations associated with life at high elevations. Using hummingbirds, a group of animals with high hovering metabolic rates and wide elevational distributions, I examine the flight capacities and aerobic scopes across an 1800-m elevational gradient, as well as any morphological adaptations that permit high elevation flight. The angular velocity of the wings during hovering flight varies across elevations during hovering flight challenges, with higher elevations associated with higher angular velocities. Subsequently, the mechanical and metabolic power output of the muscles increases with rising elevation and challenge. Nonetheless, there is no relationship between aerobic scope and elevation. Overall, this suggests that hummingbirds are not metabolically limited and maintain the capacity to perform aerobic activities across their native ranges. Examination of morphology has previously indicated that high elevation species may have disproportionately larger wings than their lower elevation counterparts, hypothesized to be compensatory for high elevations. My analysis of hovering metabolic rate scaling has demonstrated that there is no relationship between elevation and morphological characteristics; there does not appear to be a compensatory effect of morphological variation upon hovering flight metabolic rates. However, there is a significant relationship between mass and mechanochemical efficiency of the flight muscles during hovering. Given that larger species tend to be overrepresented at higher elevations, greater efficiency may have permitted larger species to expand upwards because of their capacity to economize oxygen use. Overall, hummingbirds do not vary in flight scope across elevations, and many species are able to maintain large elevational ranges without apparent morphological or functional adaptation.
Designing Green Roofs for Low Impact Development: What Matters, and Why?
Keywords: Ecological Engineering
Green Roofs
Hydrology
Low Impact Development
Sustainable Urban Drainage
Urban Stormwater

This thesis assesses the performance of green roofs primarily as hydrologic systems and as components in biogeochemical cycles; asking: What are they made from? Which design parameters are most influential? What are the relative impacts? Can the findings be explained? A multivariate experiment (n = 24) at the Green Roof Innovation Testing laboratory (GRITlab) between May 2013 - April 2015 revealed that irrigation has the greatest effect on annual runoff coefficient, compared to type of planting medium or planting depth (đ ĽĚ = 0.5). Switching between Sedum. or native species planting made no significant difference. NRCS curve numbers (đ ĽĚ = 90) and peak runoff coefficients (đ ĽĚ = 0.1) were considered robust, unchanging with any of the design factors. Water extractable total phosphorus in 3.5-year-old media had been unaffected by irrigation, depth or planting compared to the overall difference between the compost or mineral basis (90 ppm and 46 ppm respectively). Electrical conductivity was higher in water discharged from the mineral media; in situ measurements are highly variable, complicated by the heterogeneity of the materials. Higher concentrations of humic acids were found at in the water discharged from the compost. The water retention curve (WRC) of ten media components and mixtures were used to explore the bi-modal distribution of inter-particle voids and intra-particle pore spaces and to explain why the non-linear storage capacity of the materials. The water retention capacity was inversely related to saturated hydraulic conductivity; both macroscale properties were highly dependent on the size of the lowest decile fraction of particle sizes. Media components with high organic matter content were assessed for wettability using contact angle measurements. Past and current practices in green roof construction were considered by sampling media from thirty-three green roofs. Most planting media were compost based with high organic matter (OM), or mineral based with very low OM. Bulk density, particle density and porosity were all dependent on OM, as were the hydrological properties of water retention capacity and permeability. An average 10% loss of depth was observed across all installations regardless of their age or organic matter content.
Maximizing feedback for language learning: English language learners' attention, affect, cognition and usage of computer-delivered feedback from an English language reading proficiency assessment
Keywords: Cognitive diagnostic assessment
Educational technology
Eye tracking
Feedback
Psychology of learning
Second language assessment

Attention to personalised feedback for language learning is increasing as computer-based assessment increases practicality, but little attention has been paid to how language learners interact with and use feedback from computer-based assessments. The purposes of the present research were two-fold: to investigate how adult immigrant English language learners engaged with and processed computer-based feedback on their English reading skills, and to explore how these learners used feedback depending on their processing outcomes, psychological characteristics, and English proficiency. To examine these issues, six data sources were analysed using mixed methods for complementary and developmental purposes through interviews, surveys, language assessments, and eye tracking with 102 adult immigrant English language learners in Canada. Data were analysed using qualitative coding and analysis and quantitative methods such as regression analyses and latent class profiling. Results were organized and synthesized by research questions. Study findings were that the personalised sections received most attention, particularly visual results, but detailed descriptive text was useful at intermediate stages of feedback processing and usage. Learnersâ cognitive and affective strategies for negotiating feedback included emotional reactions, deflecting responsibility for negative feedback, critically evaluating report content, negotiating comprehension difficulties, and relating the report to their own lives. Learners were generally positive about personalised feedback, adapted it for their own purposes, and used known affective and cognitive strategies, confirming earlier research in these areas. In addition, confirming other previous research, major factors impacting understanding and usage were external circumstances such as English language environment and language proficiency. A mastery goal orientation, trust in report content, reflection on English skills, and desire to use the report, were positively associated with report usage. Implications included an observed need to fully factor feedback design into test design where impact/effects/outcomes are a guiding principle in test validation processes. From an instructional perspective, a key implication was the need to embed feedback in a high-quality, regular, and social learning environment. Further research is required to understand how feedback design can be personalized to promote more constructive feedback usage in learners with different background characteristics.
Applications of blood biomarkers of traumatic brain injury across the severity spectrum---a focus on pathophysiological mechanisms
Keywords: coagulopathy
concussion
inflammation
SNS
TBI
trauma

INTRODUCTION. Traumatic Brain Injury (TBI) is a global health concern. Spanning mild cognitive disturbances to unsurvivable trauma, the clinical challenges of TBI range from acute life-saving predicaments to the management of chronic cognitive impairment. While the primary insult leading to injury is irreversible, the subsequent secondary manifestations are seemingly amenable to intervention. Yet, no effective therapies exist across the spectrum of brain injury, primarily owing to our inability to understand the multifaceted, complex, secondary manifestations that occur after the primary insult. While experimental animal research has been informative in this regard, our knowledge of these processes in humans is lacking. However, a growing body of evidence suggests blood biomarker analysis may be a useful tool to aid in the elucidation of important pathophysiological mechanisms across a range of severities in human TBI. OBJECTIVE. The aim of this thesis was to use blood biomarkers as a tool to advance knowledge of secondary injury processes across the severity spectrum of TBI. METHODS. To investigate moderate-to-severe injury, we evaluated patients over the first 24 h from hospital admission after isolated TBI. To investigate mild injury, we studied varsity athletes with a clinically diagnosed sport-related concussion (SRC), sampled from the subacute period throughout clinical recovery, and chronically up to years after injury. Using multiplex immunoassay techniques, we evaluated a total of 58 blood biomarkers associated with numerous previously defined secondary injury processes, including central nervous system (CNS) injury, sympathetic nervous system (SNS) activity, inflammation, vascular injury and hemostasis. RESULTS. In moderate-to-severe TBI, we found significant, dynamic pathological associations between SNS hyperactivity, inflammation, hemostasis, and vascular injury. In SRC, we found subacute alterations to numerous peripheral indices of CNS injury, inflammation and neuroinjury that persisted at medical clearance, as well as in ostensibly healthy athletes exposed to repetitive head impacts. CONCLUSION. Blood biomarkers are a useful tool to evaluate secondary injury processes across the spectrum of TBI. The results from these works necessitate future investigations into: (1) the potential therapeutic benefit of Î˛-blockers acutely after moderate-to-severe injury, and (2) the interrelationships between chronic inflammation and CNS injury after SRC, and their potential involvement in neurodegeneration.
High Stakes Technical Skill Assessments in Surgery: Development, Implementation and Predicting Performance
Keywords: assessment
competence
surgery
training

A paradigm shift in surgical training from an apprenticeship to a competency based model requires valid assessment platforms to assess surgical competence. Several domains of competence are currently formally assessed, however technical skill, despite being the hallmark of a surgeon, is not directly or formally assessed upon completion of surgical training. The development, evaluation and implementation of objective tools to evaluate technical skill are essential, as surgical bodies mandate the documentation of competence. The first manuscript describes the first key step in developing a high stakes examination, using a Delphi methodology to develop a blueprint for the General Surgery Objective Structured Assessment of Technical Skill (GOSATS) exam. An essential component of a high stakes exam is setting a pass score. The second and third manuscripts address this aspect of high stakes exam development. The second manuscript applies and compares three standard setting methodologies to the worldâ s largest Objective Structured Assessment of Technical Skill (OSATS) database to set passing scores for the OSATS exam. General surgery residents (n=133) from the University of Toronto between 2002 and 2012 were then assigned a pass/fail status allowing for comparison of the consistency of the pass/fail decision across the methodologies. The third manuscript investigates the validity of these set pass scores by evaluating the predictive ability of the OSATS pass/fail status. The general surgery residents that had passed the OSATS were compared to the residents that had failed the OSATS in terms of their PGY2 and PGY4 technical skill. The results indicate that passing the OSATS exam predicts technical skill in the PGY2 and PGY4 year. The final manuscript is a validation study investigating the results of the first North American technical skills certification examination. In 2014 the Colorectal Objective Structured Assessment of Technical Skill (COSATS) was a mandatory component of the American Board of Colon and Rectal Surgeons certification process and represents the last paper in this dissertation. The results indicate that individuals who failed the COSATS, passed both the oral and written ABCRS exams, suggesting that the current certification process may fail to identify individuals with technical deficiencies.
Search for Dark Gauge Bosons Decaying into Displaced Lepton-Jets in Proton-proton Collisions at 13 TeV with the ATLAS Detector
Keywords: ATLAS detector
beyond the Standard Model
dark matter
Higgs boson
Large Hadron Collider

The dark photon (A'), the gauge boson carrier of a hypothetical new force, has been proposed in a wide range of Beyond the Standard Model (BSM) theories, and could serve as our window to an entire dark sector. A massive A' could decay back to the Standard Model (SM) with a significant branching fraction, through kinetic mixing with the SM photon. If this A' can be produced from decays of a dark scalar that mixes with the SM Higgs boson, collider searches involving leptonic final states provide promising discovery prospects with rich phenomenology. This work presents the results of a search for dark photons in the mass range 0.2 ≤ mA' ≤ 10 GeV decaying into collimated jets of light leptons and mesons, so-called ``lepton-jets". It employs 3.57 fb–1 of data from proton–-proton collisions at a centre-of-mass energy of √s =13 TeV, collected during 2015 with the ATLAS detector at the LHC. No deviations from SM expectations are observed. Limits on benchmark models predicting Higgs boson decays to A's are derived as a function of the A' lifetime; limits are also established in the parameter space of mA' vs. kinetic mixing parameter ϵ . These extend the limits obtained in a similar search previously performed during Run 1 of the LHC, to include dark photon masses 2 ≤ mA' ≤ 10 GeV and to cover higher ϵ values for 0.2 ≤ mA' ≤ 2 GeV, and are complementary to various other ATLAS A' searches. As data-taking continues at the LHC, the reach of lepton-jet analyses will continue to expand in model coverage and in parameter space.
Co-registration of Ultrasound and Photoacoustic Radar Imaging and Image Improvement for Early Cancer Diagnosis
Keywords: Biomedical photoacoustic imaging
Differential imaging
Frequency modulation
Hypoxia
Spectroscopy
Ultrasound

Unlike mainstream biomedical photoacoustics, mostly based on pulsed laser excitation, this work explores the alternative photoacoustic radar (PAR) modality, using intensity-modulated continuous-wave laser sources driven by frequency-swept (chirp) waveforms. A one-dimensional, axisymmetric model, and quantitative blood oxygenation analysis were developed for analyzing experimental results. Signal processing tools are investigated to enhance system parameters such as signal-to-noise ratio (SNR), dynamic range and spatial resolution. Besides applying pulse compression through matched-filtering to generate high peak power cross-correlation response, SNR can be improved by leveraging the distinct phase channel to filter the PAR amplitude channel acquired by the cross-correlation of the PA response and the reference waveform. Phase-filtering is also investigated as a spatial-resolution improvement technique. An in-vivo study of a cancer cell-injected mouse recorded a 14-15 dB SNR gain for the phase-filtered image compared to the amplitude and phase independently, while the phase PAR image produced ~340 Îźm spatial resolution compared to ~840 Îźm for the amplitude image. Additionally, to accelerate clinical acceptance and use, the combination of the PAR system with clinically-accepted ultrasound is explored. PAR tomography is investigated toward in-vivo functional analysis and the effects of the number of scan lines on image quality, resolution and contrast, examined. Furthermore, addressing assumptions of linear fluence dependence in conventional multispectral photoacoustic imaging is crucial for obtaining accurate spatially-resolved quantitative functional information by exploiting known chromophore-specific spectral characteristics. A study conducted introduces the non-invasive phase-filtered wavelength-modulated differential photoacoustic radar technique to address this issue by eliminating the effect of the unknown wavelength-dependent fluence. It employs two laser wavelengths modulated out-of-phase to significantly suppress background absorption while amplifying the difference between the two photoacoustic signals. This facilitates (pre)malignant tumor identification and hypoxia monitoring with significant improvement in dynamic range, SNR and spatial resolution, as minute changes in total hemoglobin concentration and oxygenation are detectable.
An Archeology of Cryptography: Rewriting Plaintext, Encryption, and Ciphertext
Keywords: code
computation
cryptography
Goodman
Nelson
media
notation

This dissertation is an archeological study of cryptography. It questions the validity of thinking about cryptography in familiar, instrumentalist terms, and instead reveals the ways that cryptography can been understood as writing, media, and computation. In this dissertation, I offer a critique of the prevailing views of cryptography by tracing a number of long overlooked themes in its history, including the development of artificial languages, machine translation, media, code, notation, silence, and order. Using an archeological method, I detail historical conditions of possibility and the technical a priori of cryptography. The conditions of possibility are explored in three parts, where I rhetorically rewrite the conventional terms of art, namely, plaintext, encryption, and ciphertext. I argue that plaintext has historically been understood as kind of inscription or form of writing, and has been associated with the development of artificial languages, and used to analyze and investigate the natural world. I argue that the technical a priori of plaintext, encryption, and ciphertext is constitutive of the syntactic and semantic properties detailed in Nelson Goodman’s theory of notation, as described in his Languages of Art. I argue that encryption (and its reverse, decryption) are deterministic modes of transcription, which have historically been thought of as the medium between plaintext and ciphertext. By developing a new understanding of encryption as standing between two agents, I characterize the process in terms of media. As media, encryption technologies participate in historical desires for commodious and even “angelic” transmission, popular until the twentieth century. I identify how cryptanalysis, or “code-breaking,” is distinct from cryptography, and instead relates to language, being associated with the history of machine translation. Finally, I argue that ciphertext is the perspectival, ordered result of encryption—similar to computation—and resists attempts to be spoken. Since ciphertext resists being spoken, its application problematizes the category of language, and has, at least once in antiquity, been considered a means of creating silence. This dissertation is the first of its kind to offer a historically-rich, ontological analysis of cryptography, which therefore opens the topic to new fields of scholarship and humanistic forms of inquiry.
Imaging Fermionic Atoms in a Quantum Gas Microscope
Keywords: Atomic Physics
Quantum Gas Microscope
Quantum Simulation
Ultracold Atoms

This thesis describes the methods used to achieve single-atom and single-site resolved fluorescence imaging of a quantum gas of fermionic atoms held in an optical lattice. This kind of quantum gas microscopy has been previously applied to bosonic atoms in two experiments, and has allowed for extensive studies of many-body quantum systems. Here we detail methods to extend the techniques of quantum gas microscopy to fermionic species of atoms, opening the door to quantum simulation of electronic models of condensed matter physics. We prepare quantum degenerate gases of fermionic 40K through sympathetic cooling with a gas of \Rb. The gas prepared is trapped less than 1 mm away from a thin vacuum window, an experimental geometry which permits interrogation with a large Numerical Aperture microscope objective. The cloud is loaded into a 527 nm-period cubic optical lattice, ideal for quantum simulation of many-body models of fermionic particles such as the Hubbard model. The optical lattice is designed to allow for potential depths up to V/kB = 250 microKelvin, sufficient to strongly confine 40K atoms into individual lattice sites. EIT cooling --- a technique previously demonstrated in ion-trapping experiments --- is used to cool the fermionic atoms deeply towards the ground motional state of the lattice wells. We collect the photons scattered during continuous application of EIT cooling, while atoms are kept pinned in the lattice for many seconds. We strongly suppress all other sources of light with the use of a modulated cooling scheme and a spinning chopper wheel. Collecting the scattered light produced during 2 s of EIT cooling allows us to resolve single atoms in a fluorescence image. We demonstrate that the high resolution of our imaging apparatus also permits atom positions to be precisely identified on the length scale of the optical lattice. Thus we demonstrate the realisation of a quantum gas microscope for fermionic atoms, allowing for precise investigation of the ground states and dynamics of correlated quantum states of fermionic particles.