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The effect of adipose tissue on transdermal monochromatic light presented to the human fetus using Monte Carlo simulations
(Springer Nature, 2025) Isaac, Zac; Heerikhuisen, Jacob; Reid, Vincent
The extent to which transdermal light sources illuminate the uterine environment is unknown. Recent work indicates the human fetus responds to external visual stimuli, such as laser diodes, and initial modeling suggests the fetus may not develop in a completely dark environment as previously assumed. Development of the human visual system begins within the womb, and there is motivation in fields such as developmental psychology, transabdominal oximetry, and photoacoustics to explore the extent to which light penetrates maternal abdominal tissue and understand how transdermal stimuli appear to the fetus. We develop and adapt a Monte Carlo model utilising third trimester histological properties of maternal tissue to simulate transdermal monochromatic collimated light sources, with particular focus on the 650 nm wavelength used in experimental applications. We determine approximate levels of third trimester uterine illumination from such stimuli, ranging from being comparable to an overcast night to a full moon in clear conditions. We further discuss the scope for multiple stimuli to be visibly distinct in utero for experimental applications. This modeling provides quantitative guidance on the interactions between transdermal monochromatic collimated source laser diode stimuli and maternal tissue to practitioners and researchers in the fields of fetal vision, ultrasound, and developmental psychology.
The effect of angular scattering imposed by charge exchange and elastic collisions on interstellar neutral hydrogen atoms
(American Astronomical Society, 2023-12-14) Rahmanifard, Fatemeh; Swaczyna, Paweł; Zirnstein, Eric J.; Heerikhuisen, Jacob; Galli, André; Sokół, Justyna M.; Schwadron, Nathan A.; Möbius, Eberhard; McComas, David J.; Fuselier, Stephen A.
Angular scattering (AS) in charge exchange and elastic collisions between interstellar ions and neutral (ISN) atoms has been assumed to be negligible in previous studies. Here, we investigate the momentum transfer associated with the AS of H atoms using Monte Carlo calculations to simulate their transport through the outer heliosheath. We consider two cases where charge exchange and elastic collisions between ISN H atoms and protons occur with and without AS in the outer heliosheath. We show that considering AS decelerates and heats primary ISN H, reducing the effect of selective charge exchange in the outer heliosheath. Secondary ISN H atoms, on the other hand, are not significantly affected by AS. We then simulate the transport of ISN H atoms inside the heliosphere to simulate count rates observed in the lowest energy bin of IBEX-Lo. We study the effect of radiation pressure on the ISN H measurements for the cases with and without AS and compare them with our previous findings. We find an effective radiation parameter (μeff, which represents force associated with radiation pressure relative to gravity) for the years 2009–2018 based on the longitudinal shift of the ISN H signal. The two cases with and without AS reproduce the longitudinal shift in accordance with variations in solar activity, in agreement with our previous results, and they result in similar values for the μeff, which is ∼22%–23% larger than the value found based on solar Lyα profile observations.
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.