VictorJuiz/thesis huggingface dataset:
Augmented Low Index Guiding and Hybrid Plasmonic Waveguides: Properties and Applications for On-chip Polarization Management
Keywords: Photonics Integrated Circuits

In recent years, photonic integrated circuits (PICs) have attracted much interest. To achieve a compact size, most recent devices are based on the high index contrast waveguides; however, this high index contrast also introduces large polarization sensitivity. Consequently, there is a need for compact and broadband polarization manipulation elements to handle the polarization state of the optical signal on the chip. In this dissertation, a new guiding structure, dubbed augmented low index guiding (ALIG) waveguide, is introduced to design, fabricate, and characterize polarization manipulation devices. The purely dielectric nature of the structure allows the optical waves to propagate with low losses. In the ALIG structure, the transverse magnetic (TM) mode is mostly confined in the low-index silicon nitride region, while the transverse electric (TE) mode is confined in the high index silicon layer. Because the two orthogonal modes are confined in two separate layers, their properties can be controlled independently. A compact polarization beam splitter and a polarization rotator based on the ALIG waveguide have been proposed, fabricated, and characterized. The good performance of these devices demonstrates the usefulness of the ALIG platform. Another waveguide, which confines the two orthogonal TE and TM modes in separate layers, is the hybrid plasmonic waveguide (HPWG). While the HPWG, as a plasmonic waveguide, has a higher loss than the dielectric waveguide, here an integrated ultra-low loss TE-pass polarizer based on a directional coupler is designed, fabricated, and characterized. The device is compact and offers excellent polarization extinction ratio. I have also compared the integration density and losses associated with several typical waveguides. Results show that for the same propagation losses, the HPWG can achieve higher packing density than other plasmonic waveguides.
Reaction Dynamics at Surfaces
Keywords: Ab initio computations
Hot atom and molecule motion
Molecular Dynamics
Scanning Tunneling Microscopy
Single-molecule chemistry

The dynamics of electron-induced surface-reactions was studied a-molecule-at-a-time by scanning tunneling microscopy (STM) and density functional theory. The STM was used to characterize the intact physisorbed initial states, induce reaction by electrons from the tip, and characterize the resulting final states. The dynamics between the initial and final states was modeled by ab initio molecular dynamics trajectories on a semiconductor and a metal surface. The first study examined the electron-induced reaction of 1,2-dibromoethane (DBE) and 1,2-dichloroethane (DCE) on Si(100). We observed a long-lived physisorbed molecular state of DBE at 75 K and of DCE at 110 K. As a result we were able to characterize the dynamics of ethylene production in the electron-induced surface-reaction of these physisorbed species. For both DBE and DCE the ethylene product was observed to migrate across the surface. For our main exemplar of DBE, the recoil of the ethylene favored the silicon rows, migrating by an average distance of 22 Å, and up to 100 Å. Trajectory calculations were performed using an ‘Impulsive Two-State’ model involving an anionic excited state and a neutral ground-potential. The model agreed with experiment in reproducing both migration and desorption of the ethylene product. The computed migration exhibited a ‘ballistic’ launch and subsequent ‘bounces’, thereby accounting for the observed long-range migratory dynamics. The second study examined the electron-induced reaction of physisorbed vinyl bromide (ViBr) and allyl bromide (AllBr) on Cu(110) at 4.6 K. ViBr and AllBr were found to react by two pathways: ‘Direct’, in which the molecule reacted under the tip, and ‘Delayed’ in which reaction occurred spontaneously after the molecule had diffused across the surface away from the tip. The novel pathway of Delayed reaction constituted a major route for both vinyl bromide (70%) and allyl bromide (55%). The observed reaction dynamics for ViBr and AllBr pointed to a long-lived vibrationally-excited intermediate for both Direct and Delayed reaction. Molecular dynamics simulations with reagent excitation by way of selected vibrational normal modes resulted in either Direct or Delayed reaction, depending on the vibrational mode.
Whole brain imaging of learning, memory, and plasticity
Keywords: brain plasticity
learning
magnetic resonance imaging
memory
neuroimaging

Even in adulthood, experience can have a lasting impact on the brain. The processes of learning and memory formation engage disparate neural circuits and result in many structural and functional changes in the brain. This plasticity occurs at multiple scales, from changes in synaptic strength, to shifts in dendritic spine density, to cell genesis, and to mesoscopic changes in the size or shape of different brain regions. A major challenge has been visualizing this plasticity across the whole brain. Chapters 3 and 4 of this thesis present approaches to visualize neural activity, markers of synaptic plasticity, and mesoscopic structural plasticity across the entire mouse brain. These approaches are then used to investigate the behavioural requirements and cellular pathways driving a particular form of structural plasticity: changes in brain structure volume. Chapter 5 and 6 ask whether changes in brain anatomy induced by learning and experience require long-term memory formation and/or CREB-dependent transcription. Chapter 6 also characterizes the time course of these volume changes and shows that even two days of environmental enrichment can induce structural changes in the brain. Finally, chapter 7 uses hierarchical Bayesian modelling to perform a meta-analysis of several different studies of experience-dependent plasticity. This chapter shows that maze training, exercise, and environmental enrichment each have distinct and increasingly large effects on hippocampal volume. In summary, this thesis presents methods for visualizing plasticity at multiple scales and shows that MRI can be used to image subtle structural plasticity induced by learning and experience.
HIV-1 Vpu Oligomerization in Membrane Mimetics
Keywords: HIV
Membrane Protein
NMR
Oligomer
Vpu

HIV-1 is a pandemic virus that has a continuing impact on human society. As treatments for HIV-1 infection improve, new targets for viral inhibition have provided a means to reduce a once-lethal infection into a manageable chronic condition. Among other proteins, HIV-1 encodes the Vpu accessory protein which upregulates the process of viral release from infected cells, providing an enticing target for future anti-HIV-1 therapies. In this thesis, I outline a conserved AxxAxxxAxxxA motif responsible for the assembly of Vpu into its functional oligomeric form, probe the importance of conserved residues in the motif via mutagenesis, and assess the relative stability of each resulting Vpu complex. Utilizing dynamic light scattering experiments, I characterized the molecular size of the Vpu oligomer in sodium dodecyl sulfate (SDS) solutions. To examine the Vpu oligomeric complex in greater detail, I employed the use of explicit all-atom simulations of the Vpu transmembrane domain oligomer in a hydrated lipid bilayer, verified the importance of the conserved AxxAxxxAxxxA motif, and characterized the stability of several Vpu oligomeric arrangements both in the presence and absence of water channels. Finally, I utilized NMR techniques to probe the Vpu assembly in SDS, dodecyl phosphocholine, and lipid membrane mimetics, providing a comparison between these three environments, and propose further studies based on the results of solution state NMR and solid-state magic angle spinning NMR experiments. The findings of this work are interpreted in the context of Vpu oligomerization relative to previous molecular dynamics simulations, the effect of membrane mimetic environment, and implications for Vpu interactions with host cell target proteins.
Innervation of the Posterior Aspect of the Sacroiliac Joint: An Anatomical Basis for Diagnostic Blocks and Radiofrequency Ablation Techniques for Sacroiliac Joint Pain
Keywords: diagnostic blocks
innervation
radiofrequency ablation
sacroiliac joint
sacroiliac joint pain

The aims of this thesis were to: (1) investigate the innervation of the posterior aspect of the sacroiliac joint (SIJ), and based on the anatomical findings, propose a novel ultrasound-guided SIJ diagnostic block/radiofrequency ablation (RFA) technique; (2) evaluate the feasibility of the proposed technique; and (3) compare lateral branch (LB) capture rates among different SIJ RFA techniques. In the first study, the course of the LBs of the L5-S4 posterior rami that innervate the posterior aspect of the SIJ was documented and quantified in 3D, relative to bony landmarks identifiable using ultrasound and fluoroscopy, using dissection, digitization and 3D modeling of cadaveric specimens (n=25 SIJs). The S1-S3 ± L5/S4 LBs united to form a fine nerve plexus, the posterior sacral network (PSN), which consistently coursed over the lateral sacral crest between the first and third transverse sacral tubercles (TSTs). Based on these findings, a novel ultrasound-guided PSN lateral crest diagnostic block/RFA technique was proposed: a block/RFA strip lesion along the lateral sacral crest from TST1 to TST3. The second study evaluated the feasibility of the proposed technique in cadaveric specimens (n=20 SIJs). Needles were placed bilaterally using the proposed ultrasound-guided technique, and then needle placement and PSN capture rates were documented and quantified using dissection, digitization and 3D modeling. Bony landmarks were easily visualized using ultrasound, needles were consistently placed along the lateral sacral crest using ultrasound guidance, and most or all of the PSN would be captured. In the third study, LB capture rates were compared among 17 versions of 7 current SIJ RFA techniques, including the proposed technique, in the same cadaveric specimens (n=40 SIJs). LBs were exposed, radiopaque wires sutured to LBs, fluoroscopic images obtained, lesions mapped on the fluoroscopic images using ImageJ, and LB capture rates quantified. The bipolar techniques, including the proposed technique, had a greater mean LB capture rate than the monopolar techniques. The 3 studies of this thesis provided an anatomical basis for a 12 month clinical study of the proposed technique. Future clinical studies are required to compare the lesion morphology generated by different SIJ RFA techniques in correlation with clinical outcomes.
An exploration of the utility of augmented haptic feedback for learning a curve-tracing task
Keywords: autonomy-support
bandwidth
feedback
haptic assistance
haptic error-augmentation
motor learning

Technology for the field of robot-assisted rehabilitation (and haptic training, in general) is rapidly advancing. However, there is some concern among the rehabilitation community that the outcomes, in terms of motor recovery, have fallen short of expectations. One reason for this may be that--despite the understanding that motor learning is a key component of motor recovery--motor learning scientists are not always involved in the design, development and deployment of these systems. In this dissertation, I explored optimization of haptic feedback from a motor learning perspective. In the first study, I compared learning outcomes after participants practised a curve-tracing task with assistive, error-augmenting or no haptic feedback. In study two, I investigated whether learning outcomes were affected by the bandwidth (i.e., error tolerance) at which each of the two forms of haptic feedback were provided. For the third study, I explored whether and how self-controlled or experimenter-imposed assistive haptic feedback schedules influenced motor learning. In all experiments, motor learning was assessed using a composite measure of performance efficiency (the speed accuracy cost function) on retention tests conducted immediately (10 min) and 1 day after skill acquisition. Results showed that error-augmenting haptic feedback was the most effective for learning (study 1) but its superiority was not observed with a wider bandwidth (study 2). When learners could self-control their assistive haptic feedback schedule, a lower frequency of feedback across practice blocks appeared to enhance learning (study 3). This final study also showed that whether learners had self-control over their feedback frequency was associated with their views about the utility of assistive haptic feedback for performing and learning the task. Additionally, these expressed views were significantly associated with both self-chosen feedback frequency and motor learning outcomes. This research demonstrates that error-augmenting haptic feedback is indeed beneficial for tasks which rely on error-based learning mechanisms but that this effect is bandwidth-dependent. Further, it highlights the importance of and need for continuing research to explore how learners' views about the training environment impact motor learning. These principles are useful for researchers and practitioners using haptic training in both basic and applied domains.
Behavioural and Neurophysiological Consequences of Dysfunction in the Lateral Entorhinal Cortex in Rats
Keywords: hippocampus
local field potential
medial prefrontal cortex
tau
trace eyeblink conditioning

Entorhinal dysfunction is implicated in the pathogenesis of several diseases such as Alzheimer’s disease and medial temporal lobe epilepsy. The entorhinal cortex is also critically involved in memory formation, and in particular, the memory for events separated in time (temporal associative memory; TAM). These memory paradigms also depend on the integrity of the dorsal hippocampus (dHPC) and neocortical regions such as the prelimbic medial prefrontal cortex (PrL). The dHPC and PrL have a unique pattern of connectivity with the lateral portions of the entorhinal cortex (LEC). It may therefore be that the LEC acts as a hub for cortico-limbic communication necessary for TAM. To address this point, I compared the effect of three different types of entorhinal manipulations in rats on the acquisition of a TAM learned through trace eyeblink conditioning (TEBC) while I simultaneously monitored learning-related oscillatory activity in the dHPC and PrL. To induce dysfunction in the LEC, I reversibly inactivated it, induced partial cell loss, or over-expressed abnormal tau. I found that transient inactivation of the LEC, but not partial cell loss or tau over-expression, impaired learning of TEBC. Despite normal learning in animals with cell loss and tau over-expression, these animals had altered learning-related oscillatory activity; partial cell loss in the LEC altered stimulus-evoked oscillatory activity whereas entorhinal tau accumulations attenuated learning-related amplitude-amplitude, phase-phase, and phase-amplitude couplings between the dHPC and PrL. Both groups had increased activity in the PrL which may reflect compensatory activity. These results demonstrate that the LEC is used for the formation of a TAM in normal brains but that the brain can compensate for permanent dysfunction in the LEC. They also reveal that different types of entorhinal dysfunction induce distinct learning-related electrophysiological patterns of activity. Thus, task-related electrophysiological activity may be a more sensitive measure of entorhinal dysfunction than behavioural measures.
The Speech Movement Disorder and its Rehabilitation in Parkinson’s Disease Using Augmented Visual Feedback
Keywords: Augmented visual feedback
Parkinson's disease
Rehabiliation science
Speech intelligibility
Speech kinematics

This dissertation comprises three studies that address the goals of better understanding the effects of Parkinson’s disease (PD) on speech movements and the development of a novel rehabilitation approach using augmented visual feedback (AVF) for individuals with an articulatory disorder due to PD. The first study examined jaw and tongue movements during sentence production in PD with respect to speech intelligibility and across different speaking styles, which are often used as intervention approaches (e.g., loud, clear speech). The results revealed consistently smaller jaw movements in individuals with PD relative to a control group. The results further showed that smaller tongue movement size was associated with lower ratings of speech intelligibility. The verbal cues to increase loudness, improve clarity, and reduce speaking rate generally resulted in changes in movement size and speed for both speakers with PD and healthy controls but the extent of change was smaller for the patient as compared to the control group. Using Cochrane-based methods, the second study systematically reviewed the PD literature that pertained to the use of AVF in motor rehabilitation. The findings showed that AVF is an effective tool for motor rehabilitation in PD. Treatment success can be further enhanced by providing large amounts and a high intensity of treatment, gamifying feedback, and providing knowledge of performance feedback in real-time and on 100% of practice trials. Taken together, the results of the first two studies guided the development of a novel therapy aimed at increasing tongue movement size using AVF, which provided visual feedback regarding movement performance, in addition to verbal cues. The final study investigated the effects of this novel therapy on tongue movement size and speech intelligibility in five patients with PD. The results indicated that AVF (+ verbal cue) may be beneficial in training participants to use large speech movements, compared to a verbal cue alone. The treatment effect on intelligibility was, however, not beneficial in 4/5 patients. The optimal extent of articulatory expansion needed to elicit benefits in speech intelligibility requires further investigation. Overall, this body of work furthered our understanding of the speech movement disorder in PD, and laid the groundwork for expanding evidence-based treatment options for this population in the future.
Autonomy, Rights, and Parenting in Changing Chinese Cultural Contexts
Keywords: Autonomy
Children's Rights
China
modernization
Parenting
self-determination theory

Drawing on both a universalistic perspective (self-determination theory) and a cultural psychological perspective (Greenfield’s theory of cultural change), the papers presented in this dissertation examine the joint role of universal psychological processes and cultural transformation in accounting for variations and similarities in parenting, children’s rights attitudes, and their outcomes in diverse settings within China. One hundred and twenty-eight Chinese adolescents (12-16-year-olds) and their mothers from urban and rural China - two settings that have been rapidly changing at a different pace over the past decades with the rise of modernization - participated in the current study. The first paper focuses on how cultural parenting practices are transmitted across generations, and their impact on Chinese adolescents’ psychological well-being. The second paper narrows the focus and examines how the socialization environment and other socio-demographic factors may contribute to the development of children’s rights conceptions amongst Chinese mothers and adolescents. Comparing mothers and adolescents from different settings coexisting within the same nation, encompassing urban social ecologies of the Gesellschaft form to the rural social ecologies of the Gemeinschaft form (Greenfield, 2009), these studies provide insight into how the extent of urbanization impacts parenting practices, beliefs and attitudes, and consequently affects children’s development in a non-Western cultural setting. Overall, findings from both of the studies demonstrated converging evidence supporting the universalist claim that children in a variety of cultural contexts benefit from family environments which are responsive and promote children’s needs to exercise autonomy. Findings also suggested that there has been a shift in cultural parenting practices in China (with a different pace of change in urban versus rural areas), consistent with Greenfield’s theory of cultural change.
Adapting Voices: The Musical Lifeworld of Sean-nós Singing in Carna, Ireland
Keywords: ethnomusicology
Ireland
music and place
phenomenology
Sean-nós singing
song tradition

Carna, a small village in County Galway, Ireland, is a place that is synonymous with the Irish-language traditional song form called sean-nós (‘old style’). Throughout the 20th century, Carna has seen the emergence of particular local people – often singers who have won at national competitions or have hundreds of songs in their repertoire – as the interpreters and narrators of musical practice. In the past, such individuals would be considered exceptional within a diverse community practice that included many singers, musicians, dancers, and storytellers. Today, the situation is quite different. Carna is a community with a smaller, more educated, mobile, and technologically enveloped population and the importance of sean-nós and other traditional practices as everyday entertainment has collapsed. In the wake of declining community practice, the value placed on knowledgeable local singers has increased to the extent that they are considered specialists. This dissertation expands beyond specialists’ narratives of place and local practice by discussing and interpreting the broader musical lifeworld of sean-nós singing in Carna. In particular, it examines the experience of local people that feel excluded and therefore do not participate in organized sessions and events that include sean-nós. The dwindling participation at such events often leads specialists to characterize sean-nós as a practice in decline with a corresponding local rejection of its value to social life. Seeking to complicate this narrative, my study examines how the social value of sean-nós singing, songs, and listening practices remains vital to social engagement and community cohesion despite the outward appearance of decline and disinterest. I accomplish this by contrasting how sean-nós is meaningful to both specialists and people on the margins of local practice and discuss different moments when sean-nós does expressive work in the community. I describe a broad scope of local people, events, and experience to show that sean-nós is a practice that creates webs of significance in numerous aspects of everyday life in Carna. I argue that sean-nós is embedded in local people’s intersubjective experience of place, song, and each other in a way that challenges the frequent focus on specialist knowledge in Irish traditional music studies.