VictorJuiz/thesis huggingface dataset:
Investigation of Biological Process for the Conversion of Bark Biomass to Bio-based Polyphenols

Due to increasing waste production and disposal problems arising from synthetic polymer production, there is a critical need to substitute these materials with biodegradable and renewable resources. The concept of green polymers has become more appealing due to the presence of large volumes of processing residuals from the timber and pulp industries. This, in turn, supports the idea of developing new polymers based on bark extractives. In this thesis, three comparative treatments i.e., enzymatic, alkaline, and UV/H2O2, have been conducted for the extraction of beetle infested lodgepole pine (BILP) and mixed aspen barks polyphenolic extractives. Use of laccases as biocatalysts to affect and enhance the catalytic properties of enzymes has been shown to be a promising solution for bark depolymerization. Furthermore, laccases are suitable for biotechnological applications that transform bark biomass into high valued bark biochemicals. The industrial and biotechnological application of ligninases is constantly increasing due to their multiple uses and applications in a diversity of processes. Bark depolymerization was conducted in submerged fermentation (SF) and we identified polyphenols/polyaromatic compounds after four weeks when the production media (PM) was induced with 50mg/100ml of each type of bark during the lag-phase. During SF where honey was used as a natural mediator substitute (NMS) in the PM, laccase activities were about 1.5 times higher than those found in comparable cultures without honey in the PM. These samples were analyzed by GC-MS. The laccase enzyme was purified using UNO sphere Q-1 anion exchange chromatography and the molecular weight was determined to be ~50kDa on 10% SDS-PAGE and laccase kinetic parameters including maximal velocity (Vmax), Michaelis constant (Km), and turnover number (Kcat) were calculated from a Lineweaver Burk plot. All calculated kinetic parameters of the laccase activity are substrate (ABTS) specific. Py-GC-MS analysis of bark showed differing effects of fungal activity on bark composition. Polyphenolics were separated in reverse-phase mode using HPLC with two selected wavelengths of 290 and 340 nm to improve separation. The replacement of conventional natural mediators (NM) by monofloral honey in production media, and investigation of the effect of fungi-derived laccases on bark polyphenols are studied for the first time by this thesis work.

Keywords: Bark depolymerization
Laccases
Microbial strain selection
Monofloral honey
natural mediator substitute
Polyphenols and Polyaromatics
Advisor: Sain, Mohini M
Yan, Ning
Northern High Latitude Climate Variability of the Last Millenium

This work explores the causes of northern high-latitude climate variations over the last millennium, and industrial and future periods. Attribution studies are performed on a suite of global climate simulations, and four historical reconstructions of Greenland surface temperatures and precipitation (two of which are new to this work). The simulations followed the protocols of the Palaeoclimate Modelling Intercomparison Project 3 and Coupled Model Intercomparison Project 5. At least half of the multi-decadal variability in simulated Greenland climate variations over the last millennium is reproduced by a linear, empirically-generated model including terms for volcanic emissions, solar insolation changes (including total solar irradiance and orbital components) and an index associated with latitudinal shifts in the North Atlantic jet. Empirical model parameters are obtained by regressing simulated Greenland temperatures and precipitation against time series for each of the response variables. Greenhouse gas radiative forcing changes are unimportant to simulated Greenland conditions over the last millennium, although they dominate after the mid-20th century. Most of the historical Greenland climate reconstructions are restricted to the industrial period, due to a lack of spatially-comprehensive climate records. They exhibit substantial differences in the timing, phasing and amplitudes of past climate variations, due to regional sensitivities in the source data and the reconstruction methodologies. Reconstructions indicate that Greenland temperatures did not begin to follow hemispheric greenhouse gas warming patterns until the mid-1990s. This discrepancy indicates either that the warming hiatus was associated with internal climate variability, or that the simulations are missing processes important to Greenland climate. For example, indirect effects of anthropogenic aerosols are not captured in the climate model employed here. All of the external climate forcings included in the empirical models initiate significant simulated climate responses in a number of northern hemispheric regions over the last millennium. These forcing responses are not independent, however, except in Tropical regions. Particularly in the Arctic and North Atlantic, nonlinear interactions between the forcings work together to generate the transition between the Medieval Climate Anomaly and the Little Ice Age. Internal variability also plays an important role, even on hemispheric averages.

Keywords: attribution
climate change
climate variability
Greenland ice sheet
last millennium
simulation
Advisor: Peltier, W. R.
Signal Strength and SNR Enhancement Techniques for Frequency Domain Photoacoustic Radar Imaging

A method for improving photoacoustic imaging depth and signal-to-noise (SNR) ratio through an externally imposed thermal field has been developed. Uniform heating, microwave and ultrasound localized heating have been applied for PA image improvement. The microwave or ultrasound-induced elevated temperature was experimentally measured using thermocouples in ex-vivo bovine muscle. The measured temperature on the heated surface spot induced by microwaves and the temperature induced at the heated center of a HIFU (High Intensity Focused Ultrasound) focal area were compared with the theoretically estimated temperature. The analytical method showed excellent agreement with the measured results. The experimental results with uniform heating showed that the maximum imaging depth was increased by 20% by raising the temperature of absorbing biotissues uniformly from 37 to 43℃, and the SNR was increased by 8%. The microwave assisted localized heating can increase the imaging depth by 11%, and the SNR by 5%. The parameters making up the Gruneisen constant were also investigated. The studies showed that the Gruneisen constant of biotissues increases with temperature. The thermal expansion coefficient contributes to the increase of the Gruneisen constant with temperature more than other relevant parameters (the specific heat capacity and the speed of sound) of ex-vivo bovine muscle. In addition to the thermal method, wavelength modulated differential PA radar is proposed for improving signal-to-noise ratio and early cancer diagnosis. This method is based on harmonic wavelength modulation which results in differential PA radar signal to enhance early cancer detection. Two chirp-waveforms out-of-phase modulating 680 nm and 800 nm laser beams can effectively suppress the background noise, greatly enhance the SNR, detect small variations in hemoglobin oxygen saturation levels, and be able to distinguish malignant tumors. The experiments were conducted at different hemoglobin oxygen saturation (StO2) levels of fresh sheep blood. Experimental results demonstrated the superior sensitivity by the differential PA method over other methods.

Keywords: Frequency Domain Photoacoustic Radar
Gruneisen parameter
Imaging Depth
Photoacoustic Imaging
Signal to noise ratio
Temperature
Advisor: Mandelis, Andreas
Nanomedicines and Combination Therapy of Doxorubicin and Olaparib for Treatment of Ovarian Cancer

Ovarian cancer is the fourth leading cause of death in women of developed countries, with dismal survival improvements achieved in the past three decades. Specifically, current chemotherapy strategies for second-line treatment of relapsed ovarian cancer are unable to effectively treat recurrent disease. This thesis aims to improve the therapeutic outcome associated with recurrent ovarian cancer by (1) creating a 3D cell screening method as an in vitro model of the disease (2) developing a nanomedicine of doxorubicin (DOX) that is more efficacious than PEGylated liposomal doxorubicin (PLD / Doxil ® ) and (3) evaluating additional strategies to enhance treatment efficacy such as mild hyperthermia (MHT) and combination therapy with inhibitors of the poly(ADP-ribose) polymerase enzyme family (PARP). Overall, this work demonstrates the use of 3D multicellular tumor spheroids (MCTS) as an in vitro drug testing platform which more closely reflects the clinical presentation of recurrent ovarian cancer relative to traditional monolayer cultures. With the use of this technology, it was found that tissue penetration of drug is not only an issue for large tumors, but also for invisible, microscopic lesions that result from metastasis or remain following cytoreductive surgery. A novel block-copolymer micelle formulation for DOX was developed and fulfilled the goal of iicontrolling drug release while enhancing intratumoral distribution and MCTS bioavailability of DOX, which resulted in a significant improvement in growth inhibition, relative to PLD. MHT appeared to enhance drug accumulation in MCTS in the short term, but not after 48 h of drug treatment. Drug combination studies of DOX together with the PARP inhibitor, olaparib (OLP, Lynparza ® ) were conducted in 2D monolayers and 3D MCTS. In these studies, the effectiveness of the DOX:OLP combination therapy in monolayers and MCTS was found to be ratio dependent such that equimolar ratios resulted in an additive effect, while a greater level of synergy was observed with more extreme ratios. The synergistic effect observed bears promise for future evaluation in vivo which warrants an appropriate delivery method to ensure that the determined molar ratios of both drugs accumulate at the tumor as such, despite differences in the pharmacokinetic profile of each drug, respectively.

Keywords: doxorubicin
nanomedicine
olaparib
ovarian cancer
Advisor: Allen, Christine
Novel Mouse Models to Reveal Pathogenic Determinants that Contribute to Gonococcal Infection and Pelvic Inflammatory Disease

Neisseria gonorrhoeae (Ngo) is an obligate human pathogen that causes gonorrhea, one of the most prevalent sexually transmitted infections worldwide. In women, endocervical infections are often asymptomatic; however, bacterial progression into the uterus and oviducts can lead to pelvic inflammatory disease (PID), an umbrella term used to describe a spectrum of inflammatory conditions of the upper genital tract. Although a mouse model for long term colonization of the lower genital tract has been previously established, there has been little consideration of Ngo infections involving the upper genital tract. As a result, host factors that influence disease outcome, which can range from mild discomfort to severe inflammation, pain, reproductive tract scarring and even infertility, remain elusive. My thesis work first aimed to establish a mouse model that can be used to study upper genital tract infection by N. gonorrhoeae. I reveal that the immunopathology associated with ascendant Ngo infections, as well as the development of a humoral response in the long term, are largely determined by the stage of the female reproductive cycle. Next, to examine how gonococcal Opa protein-mediated association with human CEACAM receptor proteins impacts infection and disease, I took advantage of “humanized” transgenic mouse lines that express various combinations of human CEACAMs. I show that CEACAM expression within the female genital tract of mice reflects that seen in humans, and that the spectrum of CEACAMs expressed influences colonization, clearance, and PID symptoms associated with gonococcal infection. Taken together, my findings provide new models to study infection within the genital tract, and use these to provide novel insights regarding factors that affect colonization and disease development.

Keywords: female reproductive cycle
gonorrhea
mouse models
Opa-CEACAM interactions
pelvic inflammatory disease
Advisor: Gray-Owen, Scott D
Language Expressiveness and Quality of Service for Content-based Publish/Subscribe Systems

The publish/subscribe paradigm is known for its loosely coupled interactions and event filtering capabilities. Traditional applications using pub/sub systems require large-scale deployment and high event throughput. Thus, pub/sub has always put the emphasis on scalability and performance, to the detriment of filtering expressiveness and quality of service. The matching language is usually limited to topic-based or content-based event filtering and does not allow complex stream-based subscriptions to be expressed. Messages are delivered on a best-effort basis without any ordering or reliability guarantees. Recently, modern pub/sub applications such as online games, social networks, and sensor networks, have specifications which extend beyond the basic semantics provided by standard systems. Installing additional services and event processing systems at the endpoints can overcome these limitations. However, this thesis argues that such solutions are inefficient and put an avoidable strain on the pub/sub layer itself. Therefore, the focus of this thesis is to develop integrated solutions to extend pub/sub language expressiveness and quality of service, as well as demonstrate that this approach results in better performance from a holistic perspective. The different pub/sub extensions described are ranked data dissemination, fair subscription filtering, and total order. Each section first describes the application use cases which justify the support for the developed feature in pub/sub. Those requirements are then extracted from our use cases and a general solution is developed within the pub/sub layer. A theoretical analysis is also conducted to demonstrate the correctness of every approach. Finally, experiments are employed to compare the performance of our solution to baselines which rely on end-to-end services and holistic evaluations are performed to assess the impact of our work.

Keywords: content-based matching
distributed systems
event processing
publish/subscribe
top-k
total order
Advisor: Jacobsen, Hans-Arno
No Emissions Trading Scheme is an Island: Building a Global Linking Agreement from the "Bottom Up"

The global climate change regime is at a crossroads. There remains little prospect states will agree to urgently needed binding commitments through a "top down" climate agreement, but the ability of national and sub-national policies to produce sufficient emission reductions in its place faces significant challenges. This paper proposes a possible alternative model for building a centralised climate regime from the "bottom up" through linking national and sub-national emissions trading schemes in stages under a global linking agreement. This model is argued as preferable to waiting for a global carbon price to develop from decentralised linkages, or for a "top down" linking agreement to emerge. The paper then considers how the legal design of such an agreement could best facilitate linking of different schemes, concluding that parties should agree to "low end" mutual recognition of allowances under an umbrella treaty structure, with less essential elements left to non-binding arrangements.

Keywords: climate change
emissions trading schemes
public international law
Advisor: Brunnée, Jutta R
How Effective is the Right to Health at Improving Equity in the Levels of Access to Childhood Immunisations?

This thesis explores various inequities in children's levels of access to vaccinations and considers how the normative aims of the international human right to health are being implemented in order to address them. It is argued that the right to health is a transformative right that places obligations upon states to achieve health equity. In light of this objective, this thesis investigates ways in which the right to health, in reality, is serving to influence levels of access to childhood vaccinations - a health equity enhancing intervention - and the rights impact upon equity is assessed throughout. It concludes that applications of the right to health are effective at procuring the equitable levels of access to childhood vaccinations that, in theory; its framework has been designed to effect. Remaining inequities in levels of access to childhood vaccinations might be more effectively addressed, if further rights-oriented approaches to the issues are adopted.

Keywords: children
equity
immunisation
Law
Right to health
vaccines
Advisor: Flood, Colleen M
An Organizational Study of Mental Health in the Workplace

Workplace mental health is becoming of increasing importance, in part due to the rising social and economic costs of mental health issues in the workplace. Little is known about how the experience of workers with mental health issues is actively produced through their participation in workplace procedures and associated supports. The purpose of this research is to better understand how employees actively engage in institutional practices and associated social relations that ultimately coordinate and produce their workplace experience. Using institutional ethnography, I take up the standpoint of the employee living with mental health issues to explore the coordinating relations associated with workplace mental health. This approach sheds light on how employees' experiences are socially produced and coordinated across and between institutional processes and practices. Data collection included over 140 hours of ethnographic observations, the analysis of associated texts and documents, and interviews that were conducted with 17 informants. This research details some of the challenges experienced by one novice health science researcher while conducting ethnographic research, and provides techniques for addressing personal and professional boundaries, negotiating ethical dilemmas, and reconciling the emotional experience of transitioning back and forth between being an `outsider' and `insider'. In addition to these insights, the findings explicate the social relations and institutional processes that coordinate sick time utilization for workers experiencing mental health issues. We revealed that employee's work of managing workplace absence management programs while negotiating episodes of mental ill health was perceived as overwhelming, unfair, and even punitive. Employees would require formal and informal respite from work, and would often utilized vacation time when unwell in order to avoid institutional processes all together. The biomedical focus of the absence management program created uncertainty about what constitutes a bona fide illness, and caused managers to come to know their work activities as distinctively separate from the work of healthcare practitioners. This research contributes to the literature by highlighting how tensions are created through textually coordinated work activities within and between the corporate and healthcare sector. These insights are important in establishing where and how to enact change from the standpoint of the worker.

Keywords: Institutional Ethnography
Mental health
Mental Illness
Social organization
Stigma
Workplace
Advisor: Kirsh, Bonnie
Errors and Behaviour with the Introduction of Electronic Remote Blood Issue

The goal of Electronic Remote Blood Issue (ERBI) is to increase the safety and efficiency of blood issuing in surgery suites. Like many healthcare information technologies (HIT), there is limited evidence of the impact of ERBI on safety and efficiency, and relatively little information on factors affecting errors and adaptation of work practices during implementation. This dissertation describes a human factors approach, informed by socio-technical perspectives on HIT, to the study of ERBI in three hospital operating suites and (i) the impact of ERBI on safety and efficiency, (ii) learning, adaptation and use of ERBI, and (iii) staff perspectives on ERBI. Findings are that: nursing staff experience ERBI differently from other staff roles; staff develop adaptations in work practice in response to constraints imposed by the design of ERBI and task constraints; sites differ in areas (i and ii, above) except the time it took sites to adapt to ERBI (3-4 months); and, that there is evidence of efficiency gains for blood use with ERBI at one of three sites. In addressing the intended aims of ERBI systems to increase safety and efficiency of blood issue and delivery, this dissertation provides some evidence of efficiency and safety gains when ERBI is successfully implemented. It also highlights barriers and enablers to successful implementation, identifying areas where further study may be needed, including workload factors impacting nursing staff experiences and adaptation to new technology, factors impacting error recovery in critical safety situations such as blood issuing, and representing dimensions and dynamics of transactional processes such as blood issuing for inclusion in systems design. Reflecting on the approach taken for the study of ERBI in this dissertation, the research highlights adaptation behaviours and experiences of ERBI that suggest a resiliency approach to be appropriate for understanding and designing HIT for blood unit issue, and highlights the value of a socio-technical approach in providing proxy measures for error, revealing diversity of experiences of implementation, and providing actionable design recommendations for implementation and design of ERBI systems.

Keywords: Human error
Human Factors
Medical Informatics
Resiliency
Technology Acceptance
Technology Diffusion
Advisor: Chignell, Mark
The Art of Marimba in Tokyo: Emergence in the Twentieth Century

The marimba emerged as a leading voice in contemporary Western art music in the twentieth century. This is due to several key factors: principally the extraordinary contribution composers and performers made to marimba repertoire in Tokyo after 1960. In this paper I will briefly outline the evolution of Western classical music in Japan, from its initial introduction in the latter part of the nineteenth century, to the proliferation of performing arts organizations in the late twentieth century. I will also explore the origins of the xylophone and marimba in Japan and the rise of the marimba through virtuoso performers, competitive instrument manufacturers and (most importantly) leading composers including commissioning practices, funding models and repertoire development. Information to support this paper was gathered in November, 2014 through personal interviews conducted by the author with performers and composers in Tokyo, Japan. These participants include marimbists Keiko Abe, Mutsuko Fujii, Michiko Takahashi, Sumire Yoshihara and composers Norio Fukushi, Jo Kondo, Toshi Ichiyanagi, Tokuhide Niimi, Yasuo Sueyoshi and Katsuhiro Tsubonoh; all of whom were some of the most active contributors to the development of the marimba in Japan in the late twentieth century and whose work is internationally celebrated. Most importantly, connections are identified between these performers, composers, instrument manufacturers, presenting organizations and funding systems that nurtured an environment for these marimba works to be created.

Keywords: contemporary
Japan
keiko abe
marimba
music
percussion
Advisor: Hartenberger, Russell J