College of Science, Engineering and Food Science - Masters by Research Theses
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Item Evaluation of the microbial risks associated with duckweed cultivation on agro-industrial wastewaters(University College Cork, 2025-11-30) Bannon, Leah Bridgit; O'Leary, Niall; Department of Agriculture, Food and the Marine, IrelandIn Europe, the livestock sector is one of the biggest consumers of plant protein, with 70% being directed to pig and poultry feed alone. It is a challenge for the sector to meet this demand, resulting in a reliance on imported soy protein in several countries. Duckweed species are free floating freshwater plants belonging to the family Lemnaceae. These plants can be found worldwide and are characterized by high growth rates and high protein content (up to 35% per unit dry weight). In addition, these plants have been shown to grow on a range of high nutrient load, agricultural and municipal waste streams. Duckweed species therefore offer sustainable, circular economy opportunities to couple wastewater valorisation with high protein content plant growth for potential animal feed applications. However, a critical aspect of any such process would be to evaluate the potential microbiological risk of pathogenic bacterial associations with wastewater grown Duckweed. In this study, duckweed was cultivated on farmyard wastewater (dairy milking parlour and yard waste) and meat processing wastewater which underwent pre-treatment prior to duckweed growth. Duckweed was cultivated over a 28-day period, after which wastewater and frond associated bacteria were isolated via culture-based methods, and additional cultivation was conducted to allow for metagenomic sequencing of wastewater and duckweed associated communities. The dominant genera recovered from Duckweed contained several plant associated bacteria, including Pseudomonas, Comamonas, and Stenotrophomonas. These genera have previously been identified as common community members of duckweed associated microbiomes. While some pathogenic associations were observed within wastewater samples, a decrease was seen over time. Valuable fractions (protein and carbohydrate) were also extracted from duckweed following wastewater cultivation, and assessment of the microbiological safety was conducted. Significance of the findings are discussed within this thesis.Item Development of novel optical sensing-based digital stethoscopes and deep learning-based heart sound denoising algorithms(University College Cork, 2025-09-02) Duggan, Declan; Popovici, Emanuel; Factor, Andreea; QualcommThis thesis describes the design and evaluation of novel optical sensing-based digital stethoscopes and deep learning-based heart sound denoising algorithms. Cardiac auscultation is the act of listening non-invasively to the sounds of the heart. It provides insights into the mechanical activity of the heart, and the sounds produced by this activity can be recorded as a phonocardiogram (PCG) using a digital stethoscope. Cardiac auscultation using a digital stethoscope is an important method for diagnosis of cardiovascular diseases (CVDs), such as valvular heart diseases, heart failure, and congenital heart defects (CHD). Digitally recording heart sounds as PCGs also paves the way for automated or AI-assisted diagnosis of CVDs. A literature review is conducted, including the background of cardiac auscultation, digital stethoscopes, classical signal processing approaches to denoising heart sounds, deep learning approaches, and heart sound processing at the edge. New research into digital stethoscope design and heart sound denoising are highlighted, and the current limitations faced in these areas are also explored. Two novel optical sensing-based digital stethoscope designs developed in the embedded systems group are considered in this thesis: one based on a reflective stethoscope diaphragm, and the other using a beam-cutting design. The goal of these designs is to address the limitations of current commercially available digital stethoscopes. The reflective diaphragm device is presented in conjunction with a simulation framework which can be used to test the device without live patients. The device is tested to be capable of accurately capturing a PCG signal and improving on the challenges faced by traditional digital stethoscope designs. The beam-cutting design is considered as suitable for a future printed circuit board (PCB) implementation, and to this end a bespoke testing platform is presented which facilitates testing of multiple optical components for this device and tuning of important design parameters. A number of tests are performed to characterise the performance of the components, resulting in the best being selected, along with optimum values for the design parameters. A complete pipeline for the denoising of heart sounds using fully convolutional networks (FCNs) is proposed, along with a thorough investigation of its capabilities and robustness. Both the hardware and software systems developed in this thesis were designed under the guidance of its co-supervisor, a medical doctor with clinical experience. Finally, the proposed deep learning-based denoisers are implemented on relevant edge hardware, leveraging the hardware acceleration of a neural processing unit (NPU).Item Software defined networking for optical communications(University College Cork, 2025-12-31) Verbishchuk, Yuliya; Gunning, Fatima; Sreenan, Cormac J.; Gunning, PaulNetwork management has long relied on methods and tools conceived in the early days of the internet. The explosion in network usage due to the proliferation of mobile devices and round-the-clock internet access has revealed the inadequacy of these methods in providing fast and reliable services. Network growth struggles to keep pace with the ever-increasing demands of media consumption and mobile device usage. Consequently, the need for change is imperative to avoid vendor lock-in and introduce flexibility, reliability, and scalability to network management. The emergence of Software-Defined Networking (SDN) has revolutionized the landscape of network architecture, transforming the way networks and data centers are constructed and managed at scale. SDN’s fundamental principle of separating the control plane from the data plane, along with the ability to reprogram and reconfigure the data plane through a centralized controller, has reshaped network operations. As the demand for network services continues to grow, service providers face the challenge of meeting customer requirements for fast, reliable, and scalable services. Conventional network management methods fall short in adapting to this evolving landscape, and this is where SDN has made inroads, particularly in data center networks. In Telecommunications (TELCO) networks, a significant portion of the equipment is designed for specific functions, with a set-and-forget operational approach. The transition to incorporate SDN techniques necessitates a careful plan to enable the coexistence of legacy equipment with next-generation hardware and SDN capabilities. This transition allows network administrators and architects to design and manage networks with newfound flexibility, reliability, and scalability. In this thesis, I show for the first time, that hardware and dissagrgation is possible all the way to the physical layer (Layer 1), including management of legacy disagregated devices along with SDN-enabled devices. At the time this reasearch started, there were very few efforts in integrating SDN controls with open APIs in the physical layer, for example with minimal efforts to introduce wavelength tunability (e.g. Opendaylightv4.0). The research in this thesis demonstrates the use of NETCONF/YANG to monitor and reconfigure legacy dissagregated network devices within Dense Wavelength Division Multiplexing(DWDM) systems. It also explores the utilization of a SDN enabled optical switch to control the wavelength of transceivers. With an overall controll based on the Open Network Operating System (ONOS), employed for real-time control, monitoring, and on-demand device reconfiguration. While SDN techniques have advanced considerably in the realm of packet-based forwarding devices, such as Layer 2 Ethernet switches within data centers, their application to optical switches and optical transceivers has lagged behind. This thesis also shows development of methods for controlling and routing optical carriers to output ports of a open software whitebox optical Re-configurable Optical Add-Drop Multiplexer (ROADM) device. This enabled greater flexibility in optical management and the potential for improvement of quality of service in telecommunications networks. In summary, this thesis demonstrates, through experimental results, the feasibility of controlling a network including legacy disaggregated devices, using SDN tools.Item Dual active galactic nuclei within Romulus25(University College Cork, 2025-09-30) Sheehan, Ben; Tremmel, Michael; Bitsch, BertramDual active galactic nuclei (DAGN) trace the growth of supermassive black holes (SMBHs) during galaxy interactions, while also being an important electromagnetic precursor of SMBH mergers which are important for missions such as LISA. In this thesis, we aim to study the properties of DAGN within the Romulus25 simulation, which combines sub-kpc resolution with physically motivated prescriptions for SMBH seeds, dynamics, and accretion. We find that many observed DAGNs may merge prior to a Hubble time, making them incredibly important to the LISA mission. DAGNs preferentially occupy the most massive galaxies at all redshifts and are comprised of mostly low mass ratio SMBH pairs. We also investigate if DAGN activity is a good tracer of galaxy merger enhanced star formation or black hole accretion, and find that they only serve as a tracer at redshift greater than 3. We further find DAGNs in massive galaxies display a universal distribution of duty cycles regardless of the epoch which the DAGN underwent its active phase, and that the subpopulation of DAGNs that merge prior to a Hubble time tend to inhabit the larger end of this duty cycle distribution. Important for informing current DAGN observations, we provide estimates on the time since galaxy merger and time until SMBH merger for DAGNs, and find that on average most observed systems are rarely in post-merger galaxies and are > 1 Gyr away from their SMBHs merging. We also identify a novel in-situ formation channel for DAGNs that does not require any galaxy merger, which is afforded to the Romulus25 simulation due to its unique SMBH seeding prescription, and quantify how much this channel effects the results. These results provide insights into many fronts of research into DAGNs, including providing insights into the temporal connection between DAGN activity and the galaxy mergers that formed them and the SMBH mergers they may undergo, whilst also guiding future multi-messenger astrophysics missions which focus on DAGNs, and providing a general overview on the demographics and origins of DAGNs.Item An investigation into sustainable strawberry production using alternative growing systems(University College Cork, 2025-12-31) Bangash, Sana Batool; Doyle Prestwich, Barbara; Lettice, EoinStrawberry is a fruit propagated by runners who avoid direct seed plantation due to its low germination rate. The study aimed to explore the germination rate of strawberry seeds by considering two varieties, ‘Temptation’ and ‘Florian,’ in different growing substrates (rockwool with and without nutrients and compost). The outcomes revealed that the change in substrate positively affects seed germination. Rockwool with and without nutrients depicted better germination. The study aimed to explore the growth and development of strawberry runners in aeroponic towers and the effect of different concentrations of nutrients (A and B) on the growth and yield of strawberry plants. Tower 1 (50% nutrient A and B) showed the survival of three plants out of seven, tower 2 (70%nutrient A and 30% nutrient B) depicted the survival of two plants, and tower 3 (30%nutrient A and 70% nutrient B) showed the survival of six plants out of seven. The leaves taken from Tower 3 (Nutrient A 30% and Nutrient B 70%) were the largest among all. The effect of different light (red, dark, and white) temperatures and Ethephon on seed germination was observed for Temptation and Florian seeds. The statistical analysis revealed that light has no difference in seed germination in Temptation and Florian strawberry seeds. The temperature and ethephon treatment did not show any effect on Florian and temptation strawberry seed germination. Tissue culturing of Calypso strawberry plants revealed that tissue culturing in rockwool was difficult in comparison to agar gel medium, whereas charcoal can be used efficiently to reduce fungal contamination. This study's results indicated that Temptation strawberry seeds had higher germination rates compared to Florian seeds. Red light, temperature and ethephon showed no significant impact on seed germination. Tissue culture techniques for Calypso strawberry plants were effective, with shoot multiplication medium (SMM) and shoot propagation medium (SPM) media supporting plant growth. Charcoal significantly reduced contamination in tissue culture. Aeroponic towers positively impacted strawberry plant growth, as evidenced by improved leaf size and fruit yield. Healthy growth, flowering, and fruiting were observed in strawberry plants grown in aeroponic towers, with no fungal or bacterial diseases recorded. Data showed a total of 270 flowers and 193 fruits in parent plants and 245 flowers and 164 fruits in runners, with a total dry weight yield of 191.73 grams for parent plants and 186.32 grams for runners. Overall, the study was designed to examine how different factors (rockwool substrate, aeroponic towers, tissue culture, light, temperature and ethephon) have a significant influence on strawberry seed germination and overall plant growth.