Masters Degrees (Institute For Biomedical Engineering (IBE))

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    Nucleic acid capture and release device.
    (Stellenbosch : Stellenbosch University, 2022-04) Rabikoosun, Sagal; Nieuwoudt, MJ; Warren, R; Grobbelaar, M; Stellenbosch University. Faculty of Engineering. Institute of Biomedical Engineering.
    ENGLISH SUMMARY: This project research aims to design a prototype device to extract nucleic acids, mainly from lysed Mycobacterium Tuberculosis cells. The proposed device would be an industry asset that provides a time-saving preparatory step for downstream genome sequencing of Mycobacterium Tuberculosis and its drug-resistant variants. Existing literature indicates that using a positive potential will electrostatically attract nucleic acids due to the negatively charged phosphate backbone in the nucleic structure. The design process is divided into phases, including planning, concept design, embodiment design, detail design, testing, and production. This project focuses on aspects of project planning to detail design; however, recommendations for testing and production are indicated. A series of experiments were developed to demonstrate that a positive potential induces a migration of nucleic acids and to display that a usable quantity of nucleic acids is released when the voltage is reversed. The testing phase includes experiments to determine the impacts of material choice, presence of a coating, the applied voltage, capture/release times, device geometry, and the influence of biological contaminants. A prototype design is proposed from these results, with an acceptance testing plan and suggestions for refinement. The quality and quantity of captured nucleic acid can be determined using several processes. In this project, to quantify changes in nucleic acid concentration, a Qubit fluorometer was used. Observations include that gold and palladium remain viable material choices; however, collection with single uncoated probes with larger surface areas works best. Nafion-coated probes collect a comparable quantity of nucleic acids regardless of the surface area, number of probes, or geometric design. The presence of a surface coating during both capture and release and a buffer during collection improved experimental repeatability. During the release, Nafion coated probes repelled nucleic acids faster than uncoated probes. However, the mean quantity of nucleic acids released is lower than that of the uncoated probe. More rigid probes are less time-consuming to surface coat and are less likely to recapture nucleic acids during the sampling process and released the most nucleic acids. In the 2-probe setup, some of the released nucleic acids are recaptured on the secondary probe once polarity is reversed and voltage lowered by 0.5 V to reduce the power output. Saturation limits were reached during the +2.5 V capture experiment at the 6 min interval on uncoated probes. All probes also reached saturation limits during the Nafion release experiment at the 1 min, 30 s interval. Nafion coatings were found to degrade in 5 % NaClO in 30 min. It is apparent that a single rigid uncoated probe of as large as reasonably possible surface area will attract the most nucleic acid in 6 min. Reversing the polarity of the probe in a buffer capture solution will gradually repel nucleic acids from the probes until an eventual saturation limit is assumed to be released, after the 2 min, 15 s interval has passed. Using a surface coating on a probe and a 2-probe setup is not advised to optimise mass captured or experimental time.
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    Utilizing virtual reality as a therapeutic tool psychiatry
    (Stellenbosch : Stellenbosch University, 2022-04) Du Plessis, Stefan; Van den Heever, D. J.; Schreve, K.; Rosenstein, D.; Stellenbosch University. Faculty of Engineering. Institute of Biomedical Engineering.
    ENGLISH ABSTRACT: The mass production of modern cellphone technology has resulted in a dra matic cost reduction of producing Virtual Reality (VR) head-mounted dis plays. Although VR has been effective in the treatment of phobias, uptake is still far from mainstream. Fear of heights (i.e. acrophobia) is one of the more common forms of phobias in the general population. Up to 28% of people have distress and anxiety when exposed to heights (i.e. visual heights intoler ance (VHI)), with up to 6% of people meeting clinical criteria for the specific phobia. Virtual Reality Exposure Therapy (VRET) for acrophobia has been shown to be effective as early as the 1990s. There are, however, still relatively few randomized controlled studies that have looked at its effectiveness . Even fewer studies look at physiological responses associated with fear cessation. Biofeedback is the process of presenting participants with their physiological responses allowing them to gain a measure of control over them. Biofeedback shows promise as a treatment adjunct for specific phobias. We therefore aim to create a VR height exposure platform, that offers a graduated exposure, is optimized to avoid excessive motion sickness, is cost-effective for widespread use, and is validated by participant reports collected during the exposure. Here we developed and tested a cost effective VR acrophobia environment with biofeedback in a sample of 22 participants, 4 of whom had clinically measurable acrophobia. We constructed an Electrodermal Activity (EDA) biofeedback prototype using two Arduino boards, one being electrically isolated (Nano) to reduce noise and increase safety. The second Arduino (UNO R3) was con nected via USB to a VR workstation running the Unreal Engine 4.24.2. USB connectivity was established via the UE4duino plugin. All participants un derwent clinical screening, excluding for confounding psychopathology except acrophobia. Acrophobia symptoms were evaluated using the Visual Height Intolerance Severity Scale (vHISS) questionnaire. Participants were placed on a VR platform which ascended to 28 meters. Subjective stress responses were recorded during the task as well as VR related motion sickness. Data was en tered into a repeated measures ANOVA to check for within-subject differences in levels of stress, comparing when the platform was on the ground as well as in the air. Afterwards participants experiences were evaluated via a brief questionnaire. Biofeedback based on the mean of the signal consistently informed participants that they were stressed while the platform was elevated. Participants showed a significant increase in mean skin conductance signal while the platform was elevated. Continuous decomposition analysis as well as subjective responses confirmed the accuracy of the biofeedback provided. All participants reported a positive experience using the biofeedback, most perceiving it to be accurate. The present work indicates that biofeedback in VRET is a promising treatment adjunct, which should be explored in further clinical trials.