CORA
Cork Open Research Archive (CORA) is UCC’s Open Access institutional repository which enables UCC researchers to make their research outputs freely available and accessible.
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Recent Submissions
‘You can do anything, but not everything’: using UCC’s Service Principles to optimise services in UCC Library’s Client Services
(2025-05-28) Harrington, Elaine
In summer 2024, UCC Library’s Client Services adopted UCC’s Service Principles to enhance service delivery, particularly for students. These principles - Trust, Connected & Responsive, Universally Designed, Sustainable & Innovative, and Continuously Improving - include social, economic and sustainability dimensions with 55 self-assessment questions. The poster details how the team evaluated these principles, identified areas for improvement, and integrated them into UCC Library’s Vision & Plan. By focusing on 6 key questions, the team improved communication, problem-solving, and accountability, ultimately enhancing service quality and sustainability. The approach underscores the importance of prioritising core practices for successful, agile service delivery.
Stratifying urban neighbourhoods by income: Comparison of a subjective participatory approach and an objective statistical analysis of deprivation indicators in Dar es Salaam, Tanzania
(SAGE Publishing, 2025-04-30) Msuya, Ibrahim; Boudou, Martin; Levira, Francis; Moshi, Irene; O’Dwyer, Jean; Killeen, Gerry; AXA Research Fund; UK Research and Innovation; Economic and Social Research Council; University College Cork
Mapping out geographic heterogeneities across urban neighbourhoods can inform urban planning and intervention targeting. Despite their subjectivity, intuitive participatory stratification approaches (PSAs) are becoming increasingly popular because of their affordability and practicality. In contrast, more objective statistical approaches, like latent profile analysis (LPA), typically require rich survey data and advanced capacities that are often lacking in low- and middle-income countries. This study therefore assessed these two distinct approaches, to compare their effectiveness, applicability, and complementarity for identifying geoeconomic heterogeneities of urban neighbourhoods in a typical contemporary African city. This study assessed a PSA to stratify neighbourhoods across the Tanzania city of Dar es Salaam in terms of income, by comparing it with a complementary LPA of national census data to stratify them in terms of deprivation. A consultative community-based workshop was used for the PSA, while 15 selected deprivation indicators from the census data were used to profile them using LPA. While the PSA allocated neighbourhoods to five income strata, six clear deprivation strata could be distinguished by LPA. A strong positive correlation was observed between the stratum identified by the LPA and that obtained through the PSA (ρ = 0.739, p < .0001). Furthermore, paired comparison of the two sets of correlation coefficients between each deprivation indicator and the stratum assigned by each stratification approach revealed no difference (V = 33, p-value = .1354), confirming that the two approaches yielded very similar patterns of stratification. Also, the two approaches yielded broadly comparable cartographic pictures of the city, depicting similar spatial distribution of wealth and poverty. Overall, this evidence indicates that subjective community knowledge and lived experience may be invaluable for understanding built environment and for mapping out pockets of poverty and affluence at fine scales with minimum resources.
Correlation between diplomatic visits and trade between the states of the EU and China
(University College Cork, 2024) Tynan, Neil; Duggan, Niall
Looking at diplomatic visits and trade between the EU27 and China during the period of 2001-2019, this thesis analyses the degree of correlation between these two variables on a country-to-country and annual basis. A further cross-sectional analysis looks at how a variety of sub-factors influence the overall degree of correlation between both variables. It finds that there is a high degree of correlation between trade and diplomatic across a series of different aggregation models. However, it notes that there are a number of caveats to this high degree of correlation, particularly related to the degree of correlation over time and how directionality (import/incoming visits vs exports/outgoing visits) can impact the degree of correlation.
Quorum sensing in the genus Hafnia - in vitro and in silico investigations
(University College Cork, 2024) O'Mahony, Amy Kate; Cotter, Paul; Gahan, Cormac G.; Filloux, Alain; Álvarez Ordòñez, Avelino; Science Foundation Ireland
Food production systems are subject to compounding anthropogenic pressures and understanding and managing their microbial components is more critical than ever. Food quality and safety are strongly influenced by the microbiota present in the raw materials from primary production as well as those that adapt over time to food processing environments. This doctoral thesis investigates the role of quorum sensing as a specific microbial adaptive mechanism in the context of food microbiology, and further interrogates quorum quenching or microbial interference with the quorum sensing strategies of other microbes for competitive advantage with a focus on the genus Hafnia within the order "Enterobacterales".
A comprehensive review on bacterial quorum sensing (QS) and quorum sensing inhibition (QSI) mechanisms was undertaken in Chapter 1, with particular focus on microbiomes associated with foods and the human gut. This was complemented with a general review of the genus Hafnia with a particular focus on food/gut microbiomes in Chapter 2, as Hafnia spp. emerged as promising hits in the screening work documented in Chapter 3. Here, in vitro high-throughput screening was undertaken to identify food-grade bacteria with potential applications in bioprotection as quorum quenching strains. In Chapter 4, the nature of the presumptive QSI activity of Hafnia spp. isolates towards acylated homoserine lactone (AHL) signalling was explored using a variety of in vitro approaches. Long-read sequencing of Hafnia spp. isolates was performed and a variety of basecalling and assembly tools were benchmarked in Chapter with the resulting assemblies being used to augment the pangenomic and phylogenomic investigation of the genus Hafnia undertaken in Chapter 6. Finally, Chapter 7 uses a combined vitro/in silico approach to interrogate the landscape of prophages within the genus Hafnia.
The review of literature regarding QS highlighted the need to disambiguate which strains merely possess QS genes from those that express them, and moreover to understand the environmental contexts influencing their expression. This guided the in vitro screening performed in Chapter 3 and the combination of bioinformatic and biochemical analysis in Chapter 4, resulting in the identification of QSI activity in dairy isolates across diverse genera, including several potentially food-grade isolates.
The focus was placed on Hafnia spp., reviewing the prevalence and diversity of the genus in Chapter 2. It was determined that QS activity was remarkably conserved in the expanded panel of strains assayed, but also that loss of QS activity has arisen at least once in the genus. Novel and improved assemblies of several Hafnia spp. isolates were generated using long-read sequencing, with a demonstration of the impact of choices in basecalling and assembly parameters and tools on the final assembly. High quality assemblies were fundamental for deciphering in vitro phenotypes in terms of QSI in Chapter 4 and prophages in Chapter 7 and also augment the quality of pangenomic analysis in Chapter 6. The curation and incorporation of MAGs complements the closed genomes by contributing important information on and insight into emerging and poorly understood clades, which are identified in this work.
This thesis demonstrates the ubiquity of quorum sensing in food-grade bacteria and provides evidence for its importance in governing microbial interactions with relevance to food production and human nutrition. Proposed taxonomic revisions are being prepared for submission to the International Committee on Systematics of Prokaryotes and SeqCode, providing clarification to taxonomy within the genus Hafnia. Outputs from the phylogenomic and pangenomic investigations provide a framework for future surveillance and risk analysis of Hafnia spp. in foods, while the pipelines developed may be deployed to conduct similar investigations on other microbial species of interest. Overall, it also demonstrates the potential for hybrid approaches which incorporate both wet lab and computational approaches to gain novel biological insights into microbiomes and validates the potential for the hybrid role of "damp-lab" microbiology in which researchers are trained in tenets of classical microbiology but also gain proficiency in the discipline of bioinformatics, while maintaining the sanctity of each discipline in its own right.
Enabling high baud rate terabit superchannels
(University College Cork, 2025) Canas Estrada, Natalia; Gunning, Fatima; Science Foundation Ireland
Internet service providers rely on optical systems to transmit and receive data through the optical fibre network, supporting applications ranging from video streaming to autonomous driving. To meet growing user demands, optical communication systems have evolved to maximize spectral efficiency and aggregated data rates by transmitting multiple closely-spaced optical carriers within a single fiber. However, opto-electronic components are reaching their performance limits in terms of electro-optic conversion, bandwidth, and frequency response. Innovative solutions are necessary. Superchannel systems offer a promising approach, utilizing off-the-shelf components to achieve high spectral efficiency by transmitting closely-spaced optical carriers that overlap. The optical carriers are treated as a single entity that collectively deliver multiple terabits per second. These systems, if designed for compact architectures, could be well-suited for integration into photonic integrated chips.
A critical component in superchannel systems is the Mach-Zehnder modulator (MZM), used to generate the optical carriers and encode data onto optical carriers through amplitude and phase modulation. However, MZMs are prone to bias drifts, requiring an effective DC bias control for stable operation. This work addresses the challenge of MZM bias drift by first characterizing the behavior of single and nested MZMs to understand their transfer functions. Based on the analysis and results, a simple DC bias monitoring method based on asymmetric dithering signals is proposed. The proposed method allows slope identification when the MZM is biased at quadrature. Time-interleaving is proposed to extend this approach to multiple devices using low-frequency dither signals of varying frequencies to monitor each MZM. This method successfully identifies bias point drifts by analyzing the peak-to-peak and mean power of the low-frequency components of the modulated signal.
The proposed technique was experimentally validated in an NRZ-OOK system transmitting at 10, 12.5, and 20 Gbit/s, demonstrating negligible impact on the bit error rate (BER) performance. Additionally, a DC bias control method based on the perturb-and-observe approach was developed and tested in simulations, effectively correcting bias drifts. These findings demonstrate a simple and feasible solution for stabilizing MZMs, ensuring reliable integration into advanced optical communication systems such as superchannels.