VictorJuiz/thesis huggingface dataset:
The Study of Interfacial Dynamics at Biochemically Modified Surfaces Using Acoustic Wave Physics and Molecular Simulations
Keywords: Biosensors
Acoustic wave device
bioanalytical chemistry
interfacial fluid dynamics
slip

Detection of conformational and structural shifts in biomolecules is of great importance in bioanalytical chemistry and pharmaceutical sciences. Transverse shear mode acoustic wave devices have been used as real-time, label-free detectors of conformational shifts in biomolecules on surfaces. However, material changes in the biochemical monolayer and coupling between the substrate and the surrounding liquid make it difficult to isolate the desired signal, so an understanding of these phenomena is required. In this thesis, interfacial slip, viscoelasticity, and structural changes are used to model acoustic signals due to surface adsorption of the protein neutravidin, immobilisation of HIV-1 TAR RNA, and subsequent interaction of the RNA with tat peptide fragments. Binding of tat peptides induces conformational changes in the TAR. Similar modelling is performed to describe experiments involving the binding of calcium to surface-attached calmodulin, which is also known to result in a conformational shift. The aim of the modelling is to isolate the sensor response due to conformational shifts. The biomolecules are described as hydrated, viscoelastic monolayers and slip is allowed at all interfaces. All models are numerically fit to experimental values using a two-parameter minimisation algorithm. Slip is found on the electrode surface prior to neutravidin adsorption. Neutravidin and TAR are described as distinct viscoelastic monolayers. Binding of tat peptide fragment to the TAR monolayer is modelled using a complex slip parameter and a change in length, corresponding to a straightening of the molecule. Similarly, numerical modelling of calmodulin results reveals a length change in the molecule upon calcium binding. Molecular dynamics (MD) simulations of the TAR-tat fragment system are performed to corroborate the modelling results. Starting structures are computed by molecular docking, and MD simulations of TAR complexed with various length tat fragments are described. The simulations are in general agreement with the modelling results and literature values from similar molecular dynamics experiment. A new parameter is introduced to describe biomolecule-solvent affinity, and is compared to interfacial coupling values obtained from modelling. This research demonstrates that acoustic wave devices can be used to detect conformational shifts in surface-attached biomolecules, provided molecular details about the shifts are known.
The Leadership Practices of Nurse Managers and the Association with Nursing Staff Retention and the Promotion of Quality Care in Two Saskatchewan Hospitals
Keywords: nursing leadership
nurse manager

Abstract The leadership practices of nurse managers and the association with nursing staff retention and the promotion of quality care in two Saskatchewan hospitals? Doctor of Philosophy, 2009, Karen Eisler Graduate Department of Faculty of Nursing, University of Toronto The purpose of this descriptive correlational study was to explore the relationship between nurse managers’ leadership practices as measured by Kouzes and Posners’ (2001) Leadership Practice Inventory and staff nurses’ intent to leave the job, absenteeism, medication errors and the quality of care. A total of 450 RNs and LPNs responded to a mailed survey. The respondents were representative of the target population; 54% were 46 years of age or older, 81% RNs and 19% LPNs, 95% female, over 65% had at least 11 years of nursing experience, and 65% worked fulltime. Staff nurses gave low ratings of their managers’ use of the five transformational leadership practices. There was a weak or non significant relationship between the five leadership practices and staff nurses’ intent to leave, absenteeism or medication errors. Results of hierarchical multiple regression analyses revealed that some of the leadership practices had a significant positive relationship with perceived quality of patient care and nursing care on the unit. The strongest predictors of quality of patient care (23% of the variance) were the leadership practices, Challenge the process, Inspire a shared vision, Enable others to act and Model the way. The strongest predictors of the quality of nursing care (16% of the variance) were the leadership practices, Model the way and Challenge the process. The results of this study indicated that managers’ use of transformational leadership practices can affect the staff nurses’ perception of the quality of patient care and nursing care on a unit. It is important that nurse managers develop leadership practices to promote high quality care in Saskatchewan hospitals.
Development and Evaluation of Whole Slide Hyperspectral Confocal Fluorescence and Brightfield Macroscopy
Keywords: hyperspectral
fluorescence
confocal
autofluorescence
linear unmixing
multi channel
pathology
tissue imaging
microscope
macroscope

Microscopic imaging in the biomedical sciences allows for detailed study of the structure and function of normal and abnormal (i.e., diseased) states of cells and tissues. The expression patterns of proteins and/or physiological parameters within these specimens can be related to disease progression and prognosis, and are often heterogeneously spread throughout the entire specimen. With conventional microscopy, a large number of individual image ‘tiles’ must be captured and subsequently combined into a mosaic of the entire specimen. This has the potential to introduce artefacts at the image seams, as well as introducing non-uniform illumination of the entire specimen. A further limitation often encountered in biomedical fluorescence microscopy is the high background due to the autofluorescence (AF) of endogenous compounds within cells and tissues. Often, AF can prevent the detection and/or accurate quantification in fluorescently- labelled tissues and, in general, can reduce the reliability of results obtained from such specimens. AF spectra are relatively broad and so can be present across a large number of image spectral channels. The intensity of AF also increases as the excitation wavelength is decreased, causing increasing amounts of autofluorescence when exciting in the blue and near-UV range of the spectrum (400 - 500 nm). This thesis reports the development of hyperspectral, fluorescence and brightfield imaging of entire, paraffin-embedded, formalin-fixed (PEFF) tissue slides using a prototype confocal scanner with a large field of view (FOV). This technology addresses the challenges of imaging large tissue sections through the use of a telecentric f-theta laser scan lens thus allowing an entire microscope slide (22x70 mm) to be imaged in a single scan at resolution equivalent to a 10x microscope objective. The development and optimization of brightfield and single-channel fluorescence imaging modes are discussed in the first half of this thesis, while the second half and appendices concentrate on the spectral properties of the system and removal of AF from PEFF tissue sections. The hyperspectral imaging mode designed for this system allows the fluorescence emission spectrum of each image pixel to be sampled at 6.7 nm/channel over a spectral range of 500-700 nm. This results in the ability to separate distinct fluorescence signatures from each other, and enables quantification even in situations where the AF completely masks the signal from the applied labels.
The Anthropomorphization of Law: Fictional Judges and Lawyers in Contemporary North American and European Settings
Keywords: (Treatment of) Law
Lawyer
Judge
Law and Literature

This dissertation examines the varying roles of lawyers and judges in Canada, the United States, England, France and Germany in a selection of “fictional legal narratives”: novels, movies, television shows and plays that explore legal themes. The study focuses on contemporary works after 1960, and explores the North American fascination with lawyers that saturates the major levels of culture, from the popular (including television shows, movies and novels) to the academic. Fictional images of lawyers and judges not only reflect but arguably also influence our attitudes toward the legal system, and offer a concrete way of conceptualizing abstract legal concepts. However, the vast differences between the Anglo-American adversarial legal system and the continental European inquisitorial legal system spawn very different fictional portraits of lawyers and judges. The differences between fictional legal narratives produced by each country, even those with similarly structured legal systems, are also striking. Chapter One begins by outlining a number of factors that contribute to the proliferation of fictional legal narratives in some countries, and their relative scarcity in other countries. Next, Chapter Two traces the wide range of lawyer images in American fictional legal narratives, which both glamourize and demonize the figure of the lawyer. Turning to anthropomorphizations of law in the United Kingdom, Chapter Three examines the British tendency to perpetuate the idea that, if correctly executed, the fundamental principles of British law would lead to a just and harmonious society. Chapter Four then explores the “anxiety of influence” reflected in Canadian images of law, which are more “soft-boiled” than the fictional legal figures of other countries. Moving to French fictional legal narratives, Chapter Five contemplates the predominance of the juge d’instruction figure and the prevalence of the investigatory mode. The dissertation then discusses the relative scarcity of fictional legal narratives in Germany, and the cynicism in existing German stories about law in Chapter Six. The study concludes by considering the future directions of the law and culture movement, as well as both the challenges and rewards of this interdisciplinary work.
Exploration of Autobiographical, Episodic, and Semantic Memory: Modeling of a Common Neural Network
Keywords: declarative memory
neural networks

The purpose of this thesis was to delineate the neural underpinning of three types of declarative memory retrieval; autobiographical, episodic, and semantic. Autobiographical memory was defined as the conscious recollection of personally relevant events, episodic memory as the recall of stimuli presented in the laboratory, and semantic memory as the retrieval of factual information and general knowledge about the world. Young adults participated in an event-related fMRI study in which pictorial stimuli were presented as cues for retrieval. By manipulating retrieval demands, autobiographical, episodic, or semantic memories were extracted in response to the same stimulus. The objective of the subsequent analyses was threefold: firstly, to delineate regional activations common across the memory conditions, as well as neural activations unique to each memory type (“condition-specific”); secondly, to delineate a functional network common to all three memory conditions; and, thirdly, to delineate functional network(s) of brain regions that show condition-specific activity and to assess their overlap with the common functional network. The results of the first analysis showed regional activations common to all three types of memory retrieval in the bilateral inferior frontal gyrus, left middle frontal gyrus, right caudate nucleus, bilateral thalamus, left hippocampus, and left lingual gyrus. Condition-specific activations were also delineated, including medial frontal increases for autobiographical, right middle frontal increases for episodic, and right inferior temporal increases for semantic retrieval. The second set of analyses delineated a functional network common to the three conditions that comprised 21 functionally connected neural areas. The final set of analyses further explored the functional connectivity of those brain regions that showed condition-specific activations, yielding two functional networks – one involved semantic and autobiographical conditions, and the other involved episodic and autobiographical conditions. Despite their recruiting some brain regions unique to the content of retrieved memories, the two functional networks did overlap to a degree with the common functional network. Together, these findings lend support to the notion of a common network, which is hypothesized to give rise to different types of declarative memory retrieval (i.e., autobiographical, episodic, or semantic) along a contextual continuum (i.e., highly contextualized or highly decontextualized).
Signal Processing Methodologies for Resource-efficient and Secure Communications in Wireless Networks
Keywords: signal processing, resource allocation, communication systems, biometric security

Future-generation wireless and mobile networks are expected to support a panoply of multimedia services, ranging from voice to video data. There is also a de facto "anytime anywhere" mentality that reliable communications should be ubiquitously guaranteed, irrespective of temporal or geographical constraints. However, the implicit catch is that these specifications should be achieved with only minimal infrastructure expansion or cost increases. In this thesis, various signal processing methodologies conducive to attaining these goals are presented. First, a system model that takes into account the time-varying nature of the mobile environment is developed. To this end, a mathematically tractable basis-expansion model (BEM) of the communication channel, augmented with multiple-state characterization, is proposed. In the context of the developed system model, strategies for enhancing the quality of service (QoS), while maintaining resource efficiency, are then studied. Specifically, dynamic channel tracking, adaptive modulation and coding, interpolation and random sampling, and spatiotemporal processing are examined as enabling solutions. Next, the question of how to appropriately aggregate these disparate methods is recast as a nonlinear constrained optimization problem. This enables the construction of a flexible framework that can accommodate a wide range of applications, to deliver practical network designs. In particular, the developed methods are well-suited for multi-user communication systems, implemented using spread-spectrum and multi-carrier solutions, such as code division multiple access (CDMA) and orthogonal frequency division multiplexing (OFDM). Moreover, privacy and security requirements are increasingly becoming essential aspects of the QoS paradigm in communications. Combined with the advent of novel security technologies, such as biometrics, the conventional communication infrastructure is expected to undergo fundamental modifications to support these new system components and modalities. Therefore, within the same framework for maximizing resource efficiency, several unique signal processing applications in network security using biometrics are also investigated in this thesis. It is shown that a resource allocation approach is equally appropriate, and productive, in delivering efficient and practical key distribution and biometric encryption solutions for secure communications.
Approximation and Refinement Techniques for Hard Model-checking Problems
Keywords: formal methods
model checking
software verification
hardware verification

Formal verification by model checking verifies whether a system satisfies some given correctness properties, and is intractable in general. We focus on several problems originating from the usage of model checking and from the inherent complexity of model checking itself. We propose approximation and iterative refinement techniques and demonstrate that they help in making these problems tractable on practical cases. Vacuity detection is one of the problems, relating to the trivial satisfaction of properties. A similar problem is query solving, useful in model exploration, when properties of a system are not fully known and are to be discovered rather than checked. Both of these problems have solution spaces structured as lattices and can be solved by model checking using those lattices. The lattices, in the most general formulation of these problems, are too complex to be implemented efficiently. We introduce a general approximation framework for model checking with lattices and instantiate this framework for the two problems, leading to algorithms and implementations that can obtain efficiently partial answers to the problems. We also introduce refinement techniques that consider incrementally larger lattices and compute even the partial answers gradually, to further abate the size explosion of the problems. Another problem we consider is the state-space explosion of model checking. The size of system models is exponential in the number of state variables and that renders model checking intractable. We consider systems composed of several components running concurrently. For such systems, compositional verification checks components individually to avoid composing an entire system. Model checking an individual component uses assumptions about the other components. Smaller assumptions lead to smaller verification problems. We introduce iterative refinement techniques that improve the assumptions generated by previous automated approaches. One technique incrementally refines the interfaces between components in order to obtain smaller assumptions that are sufficient to prove a given property. The smaller assumptions are approximations of the assumption that would be obtained without our interface refinement. Another technique computes assumptions as abstractions of components, as an alternative to current approaches that learn assumptions from counterexamples. Our abstraction refinement has the potential to compute smaller nondeterministic assumptions, in contrast to the deterministic assumptions learned by current approaches. We confirm experimentally the benefits of our new approximation and refinement techniques.
Probing Mesocorticolimbic Dopamine Function in Alcohol Dependence Using Dextroamphetamine: Behavioural and FMRI Studies
Keywords: Alcohol Dependence
Mesocorticolimbic
Dopamine
Dextroamphetamine
fMRI

Background: A dysfunctional mesocorticolimbic dopamine system has been reported in alcohol dependence and major depressive disorder. Probing mesocorticolimbic dopamine function in severe depression using dextroamphetamine revealed an altered behavioural response and a disrupted mesocorticolimbic circuitry in behavioural and functional magnetic resonance imaging (fMRI) studies. The purpose of this study was to use a similar approach in alcohol dependence. Behavioural Study: to assess dextroamphetamine subjective effects in alcohol-dependent and depressed alcohol-dependent participants. FMRI Study: to assess how the mesocorticolimbic circuitry would respond to a dextroamphetamine challenge in alcohol-dependent participants exposed to alcohol cues. Methods: In both studies, a single oral 30 mg dose of dextroamphetamine was the pharmacological intervention. Behavioural Study: randomized, double-blind, placebo-controlled, between-subject study. Eighteen alcohol-dependent and 22 depressed alcohol-dependent participants were compared using validated self-report drug effect tools (e.g. Addiction Research Center Inventory). FMRI Study: single-blind, between-subject study. FMRI blood oxygen level–dependent (BOLD) activation was measured in 14 alcohol-dependent and 9 healthy control participants during an alcohol-cue exposure task pre- and post-drug. Results: Behavioural Study: DRUG (F1,40=18.6; p<0.001) and GROUP (F1,40=16.6; p<0.001) main effects but no GROUPxDRUG interaction effects (F1,40=0.02; p=0.88) were detected, even when only severely depressed alcohol-dependent individuals were included (F1,30=0.04; p=0.84). FMRI Study: Alcohol-dependent participants exhibited greater ventral striatal activation compared to controls pre-drug and post-drug effect (F1,40=20.1; z=3.8; p<0.001; k>10; (x=10;y=-2;z=-14)). A GROUPxDRUG interaction effect was detected in the medial orbitofrontal cortex (mOFC) (F1,40=21.5; z=4.0; p<0.001; k>10; (x=-12;y=28;z=-20). The alcohol-dependent group exhibited a negligible mOFC response across both pre- and post-drug scanning sessions. In contrast, controls exhibited attenuation of mOFC response post-drug. Conclusion: The lack of significant GROUPxDRUG interaction effects in the Behavioural Study may suggest different neurobiological mechanisms underlying alcohol dependence and depression mesocorticolimbic dysfunction. Alcohol dependence appeared to mitigate the impact of depression severity on participants’ behavioural responses to dextroamphetamine. The FMRI Study data suggest there may be ventral striatal and mOFC disruption in alcohol-dependent participants. We suggest the mOFC may be involved in the reported loss of prefrontal modulation of dopamine cell activity in alcohol dependence. This supports a key role for the mOFC in mesocorticolimbic dysfunction in alcohol dependence.
Reshaping an Enduring Sense of Self: The Process of Recovery from a First Episode of Schizophrenia
Keywords: First Episode Schiophrenia
Recovery
Sense of Self
Process of Recovery

Although many advances in the treatment of schizophrenia have been made over the past decade, little is known about the process of recovery from a first episode of schizophrenia (FES). To date, the study of recovery in the field of mental health has focused on long-term mental illness. This in depth qualitative study drew upon Charmaz’s (1990) constructivist grounded theory methodology to address the following questions: How do individuals who have experienced a FES describe their process of recovery? How does an identified individual (e.g. friend, family member, teacher, or clinician) describe their role during the participant’s process of recovery, and their perception of the recovery process? Ten primary participants (who self-identified as recovering from a FES) had two interviews; in addition, there was a one-time interview with a secondary participant, for a total of 30 interviews. Data collection sources included participant semi-structured interviews, participant selected personal objects that symbolized their recovery, and clinical records. The results provide a substantive theory of the process of recovery from a FES. The emergent process of recovery model for these participants is comprised of the following phases: ‘Lives prior to the illness’, ‘Lives interrupted: Encountering the illness’, ‘Engaging in services and supports’, ‘Re-engaging in life’, ‘Envisioning the future’; and the core category, ‘Re-shaping an enduring sense of self,’ that occurred through all phases. A prominent distinctive feature of this model is that participants’ enduring sense of self were reshaped versus reconstructed throughout their recovery. The emergent model of recovery from a FES is unique, and as such, provides implications for clinical care, future research, and policy development specifically for these young people and their families.