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Recent Submissions

Fine-tuning Oxford Nanopore basecalling models to improve single-read variant calling in antibody libraries
(The University of Waikato, 2026) Zhou, Kang; Kelton, William; Holmes, Geoffrey
Accurate nucleic acid sequencing is essential for analysing protein variant libraries composed of closely related sequences. Oxford Nanopore sequencing offers long reads, high depth, and comparatively lower cost, but its single-read error rate limits its routine use for variant calling, where sequencing errors can be mistaken for true mutations. This thesis investigates whether domain-specific fine-tuning of a nanopore basecalling model can improve single-read variant- calling performance in an antibody library context, using a dual-site IgA Fc deep mutational scanning library as an example. A series of nanopore basecalling models was fine-tuned using in-house wild-type IgA Fc nanopore data collected under different experimental sample-prep procedures. These models were evaluated on a held-out, variant-rich nanopore dataset against an orthogonal MGI-derived short-read reference dataset. The benchmarking framework assessed both read-level quality and population-level recovery, focusing on library-constrained variant detection and variant-abundance concordance. Fine-tuned models consistently outperformed the pretrained baseline, demonstrating that nanopore signals contain learnable domain-specific structure that can improve single-read variant calling. The best model, Alpha, achieved the best observed balance of low primary error rate, high read retention, low framework noise, and strong abundance-aware concordance with the ground truth. The results showed that the experimental procedure used to collect training data had a greater influence on the fine-tuning outcome than either training data volume or the stringency of quality control. Lower validation loss observed during training did not reliably predict better downstream performance, highlighting the need to evaluate basecalling models using biologically meaningful metrics rather than training diagnostics alone. Model-weight analysis further showed that successful fine-tuning involved small, structured recalibration of the signal-interface and decoding components rather than broad model-level drift. Overall, this thesis establishes a practical framework for fine-tuning and evaluating domain-specific nanopore basecallers for variant libraries. It shows that domain-specific fine-tuning can materially improve the recovery of variant populations from nanopore signals and supports future work on computational augmentation of WT IgA Fc nanopore signals, architecture-aware fine-tuning, UMI-linked molecule-level benchmarking, experimental validation, predictive modelling, and extension to longer antibody constructs.
Functional communication training and visual activity schedules: Support for neurodiverse students in an inclusive classroom
(The University of Waikato, 2026) Pandya, Mahi; Blackmore, Tania Louise
One boy with ASD and one girl with ASD and ADHD participated in a study to examine the effectiveness of Functional Communication Training (FCT) and a Visual Activity Schedule (VAS) to reduce challenging behaviours in an inclusive classroom. A Functional Behaviour Assessment (FBA) was conducted to determine the function of behaviours presented by each student. The Open Ended Functional Assessment Interview (O-FAI), ABC narrative observations and structured observations using a Functional Assessment Observation (FAO) form were conducted within the classroom. For student M, ‘non-participation’ emerged as a behaviour of concern, while student H engaged in ‘non-instructed activity’. It was hypothesised that both behaviours were maintained by escape from tasks. FCT was implemented for student M to reduce ‘non-participation’ and a VAS was implemented for student H to reduce ‘non-instructed activity’ and increase independence in following a schedule. Student M showed a moderate reduction in ‘non-participation’ compared to baseline while student H did not show any difference in occurrences of ‘non-instructed activity’ compared to baseline, however, she did achieve independent use of the VAS. Despite the lack of change in the target behaviours for both participants, FCT and VAS interventions were approved as socially valid interventions by the class teachers. The interventions also contributed to the overall learning experiences of both students in an inclusive classroom setting.
Love Letter : A study of South Asian Women, and their relationships with Māori and other racialised Women in Aotearoa
(The University of Waikato, 2025) Alam-Simmons, Ara; Waitoki, Waikaremoana; Rata, Arama; Roa, Thomas
This project records the experiences of South Asian women in Aotearoa, New Zealand, and what those experiences reveal about the possibilities and limits of solidarity with Māori and other racialised women under conditions of settler colonialism and white supremacy. This work is a response to my own relational experiences as a South Asian woman living in Aotearoa, and to the conversations that have emerged from years of active community involvement. This project centres women's voices through the lens of Indigenous, Black, and women-of-colour feminist thinking and praxis. Using a toolkit methodology comprising collaging, one-to-one conversations, found poetry, and autoethnography, the study engaged fifteen South Asian women across three interconnected sites of inquiry. The first explored how South Asian women make sense of their own experiences of colonisation and what it might mean to reclaim identity outside of colonial narratives. The second took a look at women's relationships with other racialised women, including Māori women, to understand what those relationships reveal about the conditions under which solidarity becomes possible, conditional, or foreclosed. The third drew on my own autoethnographic account to illuminate how deliberate acts of remembering, unsettling colonial narratives, resisting co-optation, and being in solidarity can function as a decolonial practice grounded in relational accountability to Māori sovereignty and Te Tiriti o Waitangi. The central empirical finding of this thesis is that solidarity among South Asian women and between South Asian women and Māori is not a natural outcome of shared marginalisation or identity. It is a relational practice that is structured, conditional, and sometimes foreclosed by the intersecting dynamics of settler colonialism, caste supremacy, heteropatriarchy, biculturalism, and internalised colonial narratives. Key findings demonstrate that solidarity requires, first, an internal reckoning: healing from internalised oppression, reclaiming ancestral histories, cultural practices, language, and knowledge systems, and developing critical consciousness of complicity within settler-colonial structures. Second, it requires an external and political commitment: confronting caste supremacy within South Asian communities, refusing model minority positioning, and grounding relationships that engages in a political committment to Te Ao Māori and Māori sovereignty, rather than in the false promise of inclusion within settler-colonial frameworks. Additionally, this thesis, locates caste supremacy in Aotearoa, New Zealand. This thesis makes both an empirical and methodological contribution to the Asian-Indigenous solidarities literature. Methodologically, it demonstrates that arts-based approaches can make visible the complexity and diversity of South Asian women's relational lives in ways that conventional qualitative research cannot, offering a practical toolkit that can be taken up in community and activist spaces beyond the university. Conceptually, it offers two frameworks as new contributions to the decolonial solidarities literature. The first extends the whakawhanaungatanga framework developed by Rata and Al-Asaad (2019) by adding two new dimensions. These are restoration, which centres the reclaiming of identity, healing, and spiritual practice as political acts; and reconstruction, which names the need for joint political struggle as the governing horizon of solidarity. The second is a decolonial framework developed through the autoethnographic inquiry. This is made up of four interconnected dimensions: historical remembering, unsettling settler colonial narratives, resisting co-optation, and being in solidarity that is led by Te Ao Māori and accountable to Māori sovereignty. Together, these frameworks offer South Asian and other tauiwi of colour communities practical and political pathways for building solidarities that refuse settler-colonial logics and actively contribute to creating more just and relational ways of living together in Aotearoa.
Outcomes of cemented and hybrid primary total hip arthroplasty in osteoarthritis: A New Zealand regional study
(The University of Waikato, 2026) Pearce, Amy; Hebert-Losier, Kim; Joshi, Chaitanya
Introduction: Primary total hip arthroplasty (THA) for osteoarthritis (OA) success is typically assessed using implant survival as the primary outcome; however, revision surgery alone underestimates the true burden of suboptimal outcomes (e.g., pain or poor function). Secondary outcomes, or patient-reported outcomes (PROMs), therefore provide a complementary assessment of THA success. During the last two decades, fully cemented THAs have been progressively replaced by uncemented ones, despite limited long-term comparative evidence. Although national registry data allow analysis of broad implant category types, they may lack implant and PROM detail compared to regional registries. This Thesis evaluates whether changes in implant design and fixation strategy have translated into significant and meaningful improvements in implant survival and patient outcomes in the Bay of Plenty region of Aotearoa New Zealand (NZ). Aims: This Thesis aimed to evaluate long-term survival and PROMs of an early generation cemented, modern cemented, and modern hybrid primary THA for OA, and identify patient factors or funding source associated with these outcomes. The work first synthesised existing evidence comparing cemented and hybrid fixation. It then compared survival between the earlier generation THA and its modern cemented successor of the same lineage. Thereafter, the work identified long-term PROMs in earlier generation cemented THA and then compared 10-year PROMs between the two cemented THA generations. Finally, survival and PROM outcomes of the hybrid THA were compared with the modern cemented. Influential patient and funding factors of primary and secondary outcomes were identified across all studies. Methods: This Thesis comprised a systematic literature review and linked retrospective cohort studies using prospectively collected arthroplasty survival and PROM data from the NZ joint registry (NZJR) and Tauranga Orthopaedic Research Inc. registry for the Bay of Plenty region. Patients undergoing primary THA for OA between 2003 to 2023 with earlier generation cemented, modern cemented, or modern hybrid THAs were included. PROMs included the Oxford Hip Score (OHS), McMaster University Osteoarthritis index (WOMAC), and Veterans Rand 12-item health survey (VR-12). Baseline differences were addressed using propensity score weighting. Implant survival was analysed using Cox regression, and PROMs were analysed longitudinally including changes from baseline. Multivariable models examined the influence of sex, ethnicity, age at surgery, body mass index (BMI), American Anesthesiologist Society (ASA) rating, and funding source (public versus private) on outcomes. Results: In the literature, five studies compared survival and three compared PROMs between cemented and hybrid primary THA for OA. Survival outcomes were no different between THAs in three studies, but cemented survival was superior in two studies. PROMs were no different in the three available studies.
Education in the Te Aroha district in the nineteenth century
(Historical Research Unit, University of Waikato, 2016) Hart, Philip
Establishing a school at Te Aroha was delayed while the Education Board waited to see whether the settlement would become permanent. In the interim, temporary arrangements were made. Although some praised the building finally erected, others noted such defects as being cold in winter, and residents met some of the costs of necessary improvements. Details are given of all the teachers, of the development of the school, of the number of pupils, and of the quality of the teaching. At Waiorongomai there was same sequence of erecting and improving the school, and details are given of all the teachers and their teaching. In both communities, residents had to raise money through holding entertainments to fund necessary improvements. Examples of the curriculum are given, along with school inspectors’ reports on the effectiveness of the teaching. Patriotism was emphasized, and corporal punishment was a normal method of control. Irregular attendance handicapped many children’s success, and some parents clearly did not care about sending their children to school regularly. To vary the school year, there were occasional events such as Arbor Day, and a ‘treat’ was held at the end of every year. Providing religious education provoked controversy; and some attempts were made to provide much needed adult education. To conclude, the life of a particularly popular teacher, James William Rennick, is given in as much detail as is available. (Note that ‘most of the early records’ of the Te Aroha school ‘were destroyed by fire’, making a complete history of its early years impossible.)