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Light regulates many biological processes through light-sensitive proteins called opsins. Opsins are involved in vision, but they are also expressed in extraretinal tissue, where their roles are far less clear. Fish have large opsin repertoires, derived from a long history of gene duplication and divergence, making them useful models to study opsin diversity and function. I introduce the deep-sea sablefish (Anoplopoma fimbria) as a model for opsin research for three main reasons: i) the availability of a draft genome and transcriptome, simplifying the characterization of this species’ opsin repertoire, ii) the proximity of the only sablefish aquaculture facility in the world, providing exclusive access to a large number of individuals at all developmental stages, iii) the observation that sablefish occupy very different light environments during the course of development, ranging from well-lit shallow waters to the aphotic zone, which provides a light environment context for opsin gene expression data. My survey of the genome showed that sablefish have 36 distinct opsin genes (7 visual and 29 non-visual), even though they spend most of their lives in the dark. The sablefish opsin sequences and repertoire are similar to those of other teleost fish. To test the hypothesis that the sablefish opsin repertoire is being expressed/transcribed during the comparatively brief period of time when this species is exposed to light (the free-swimming larval stage through to the juvenile stage), I quantified the expression of five paralogous genes from a well-studied non-visual opsin family (OPN4’s) in the brain across life stages. Data show statistically stable expression of Opn4m1 and Opn4m3 among life stages, a rough association of Opn4x1 and Opn4m2 expression with age and light environment, and little-to-no expression of Opn4x2. I localized proteins encoded by the most highly expressed class of OPN4 genes in the brain, the Opn4m genes, to the surface of the optic tectum just below a cranial ‘window’; a zone that has been shown to express dozens of opsins in zebrafish (a distant relative, with their ancestor diverging more than 230 million years ago). Thus, in some cases, expression appears to be correlated with light exposure not only temporally, but also spatially. By studying non-visual opsins in sablefish, I have challenged and broadened the current understanding of opsin evolution and function in fish and provided the foundation for future studies to test brain regions for light-sensitivity, perform opsin gene knock-outs, and explore potential light-independent processes. / Graduate / 2023-09-06

Non-pulsatile and pulsatile flow in bent pipes and radial turbine has been assessed with numerical simulations. The flow field in a single bent pipe has been computed with different turbulence modelling approaches. A comparison with measured data shows that Implicit Large Eddy Simulation (ILES) gives the best agreement in terms of mean flow quantities. All computations with the different turbulence models qualitatively capture the so called Dean vortices. The Dean vortices are a pair of counter-rotating vortices that are created in the bend, due to inertial effects in combination with a radial pressure gradient. The pulsatile flow in a double bent pipe has also been considered. In the first bend, the Dean vortices are formed and in the second bend a swirling motion is created, which will together with the Dean vortices create a complex flow field downstream of the second bend. The strength of these structures will vary with the amplitude of the axial flow. For pulsatile flow, a phase shift between the velocity and the pressure occurs and the phase shift is not constant during the pulse depending on the balance between the different terms in the Navier- Stokes equations. The performance of a radial turbocharger turbine working under both non-pulsatile and pulsatile flow conditions has also been investigated by using ILES. To assess the effect of pulsatile inflow conditions on the turbine performance, three different cases have been considered with different frequencies and amplitude of the mass flow pulse and different rotational speeds of the turbine wheel. The results show that the turbine cannot be treated as being quasi-stationary; for example, the shaft power varies with varying frequency of the pulses for the same amplitude of mass flow. The pulsatile flow also implies that the incidence angle of the flow into the turbine wheel varies during the pulse. For the worst case, the relative incidence angle varies from approximately −80° to +60°. A phase shift between the pressure and the mass flow at the inlet and the shaft torque also occurs. This phase shift increases with increasing frequency, which affects the accuracy of the results from 1-D models based on turbine maps measured under non-pulsatile conditions. For a turbocharger working under internal combustion engine conditions, the flow into the turbine is pulsatile and there are also unsteady secondary flow components, depending on the geometry of the exhaust manifold situated upstream of the turbine. Therefore, the effects of different perturbations at the inflow conditions on the turbine performance have been assessed. For the different cases both turbulent fluctuations and different secondary flow structures are added to the inlet velocity. The results show that a non-disturbed inlet flow gives the best performance, while an inflow condition with a certain large scale eddy in combination with turbulence has the largest negative effect on the shaft power output. / QC 20101111

<p>Radial head arthroplasty (RHAP) is proposed as the treatment of choice of complex radial head fractures not amenable to reconstruction. With advances in the understanding of elbow biomechanics and subsequently implant designs, low morbidity, few complications and good success has been reported with RHAP compared to internal fixation. Much of the success/complication post RHAP has been attributed to the fracture pattern and presence of associated injuries. While these are important parameters to reflect on, however, the outcome of surgery cannot be solely attributed to the methods of dealing with the radial head fracture. Importantly, the outcomes of RHAP are also influenced by patient factors. Hence, the purpose of this thesis was to assess the existing knowledge of functional outcomes post RHAP and explore the role of acute post surgical pain as a predictor of those outcomes.</p> <p>The first manuscript in the thesis systematically examines the current available English literature regarding the functional outcomes of metal RHAP. Studies reviewed revealed significant heterogeneity in the study and patient characteristics. Likewise, the method of reporting fracture classification, clinician and patient reported outcomes are inconsistent. Based on the level 4 evidence studies in the review, we concluded that RHAP provides good to excellent outcomes in short-midterm follow up, with no evidence regarding the superiority of one implant over another.</p> <p>The second manuscript explored the role of acute post surgical pain in development of chronic functional impairment post RHAP using the EVOLVE (Wright Medical Technology, Arlington, Tennessee) implant at 2 years post surgery. A total of 59 adults with complex radial head fractures treated with EVOLVE metal radial head implant were followed for a period of two years. Demographics, American Shoulder and Elbow Surgeon's-Elbow (ASES-e) pain subscale and Disability of Arm, Hand and Shoulder Questionnaire (DASH) data were collected at baseline and two years. Regression analyses revealed that acute post operative pain post RHAP is significantly related to the functional outcome at 2 years post RHAP. An ASES-e pain cut off score of 32/50 predicted the development of chronic functional impairment two years post RHAP.</p> <p>The results of this thesis highlight the need for prospective longitudinal studies, comparative analyses and standardized methods of reporting concerning effectiveness of RHAP. It also emphasizes the significance of quantifying pain levels in the immediate post operative period and classifying the patient in high/low risk groups for developing chronic functional impairment based on the pain level.</p> / Master of Science (MSc)