Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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Item MOTL: enhancing multi-omics matrix factorization with transfer learning(BioMed Central Ltd, 2025-12-01) Hirst DP; Térézol M; Cantini L; Villoutreix P; Vignes M; Baudot A; Cosgrove AJoint matrix factorization is popular for extracting lower dimensional representations of multi-omics data but loses effectiveness with limited samples. Addressing this limitation, we introduce MOTL (Multi-Omics Transfer Learning), a framework that enhances MOFA (Multi-Omics Factor Analysis) by inferring latent factors for small multi-omics target datasets with respect to those inferred from a large heterogeneous learning dataset. We evaluate MOTL by designing simulated and real data protocols and demonstrate that MOTL improves the factorization of limited-sample multi-omics datasets when compared to factorization without transfer learning. When applied to actual glioblastoma samples, MOTL enhances delineation of cancer status and subtype.Item Protein Intake and Protein Quality Patterns in New Zealand Vegan Diets: An Observational Analysis Using Dynamic Time Warping(MDPI (Basel, Switzerland), 2025-05-26) Soh BXP; Vignes M; Smith NW; Von Hurst PR; McNabb WC; Hayes M; Naik ASBackground/Objectives: Inadequate intake of indispensable amino acids (IAAs) is a significant challenge in vegan diets. Since IAAs are not produced or stored over long durations in the human body, regular and balanced dietary protein consumption throughout the day is essential for metabolic function. The objective of this study is to investigate the variation in protein and IAA intake across 24 h among New Zealand vegans with time-series clustering, using Dynamic Time Warping (DTW). Methods: This data-driven approach objectively categorised vegan dietary data into distinct clusters for protein intake and protein quality analysis. Results: Total protein consumed per eating occasion (EO) was 11.1 g, with 93.5% of the cohort falling below the minimal threshold of 20 g of protein per EO. The mean protein intake for each EO in cluster 1 was 6.5 g, cluster 2 was 11.4 g and only cluster 3 was near the threshold at 19.0 g. IAA intake was highest in cluster 3, with lysine and leucine being 3× higher in cluster 3 than cluster 1. All EOs in cluster 1 were below the reference protein intake relative to body weight, closely followed by cluster 2 (91.5%), while cluster 3 comparatively had the lowest EOs under this reference (31.9%). Conclusions: DTW produced three distinct dietary patterns in the vegan cohort. Further exploration of plant protein combinations could inform recommendations to optimise protein quality in vegan diets.Item Factors predicting parenting stress in the autism spectrum disorder context: A network analysis approach(PLOS, 2025-04-21) Buchwald K; Shepherd D; Siegert RJ; Vignes M; Landon J; Singh ASElevated levels of parenting stress have been reported in parents raising an Autistic child. Previous studies have identified a multitude of predictors of parenting stress, including both child-related and parent-related factors, though findings across studies are not always in agreement. In the present study we investigate the determinants of parenting stress using a Network Analysis approach, which is then used to inform a subsequent structural equation model. New Zealand parents (n = 490) of a child diagnosed with Autism Spectrum Disorder (ASD) provided data on their Autistic child (e.g., ASD core symptoms, problem behaviours) and themselves (i.e., parenting stress). The analysis revealed that both child and parent demographic factors were poor predictors of parenting stress, while the child’s current language and communication ability were correlated with diagnostic age and parenting stress. An earlier diagnostic age, in turn, suggested better behavioural and emotional outcomes for children. Overall, the Network Analysis showed itself to be an informative approach to understanding parenting stress in the ASD context. Findings further advocate for the implementation of ASD-related and language-related interventions as early as possible, and that language delays during early infancy justify prompt clinical assessment.Item Evaluation of protein intake and protein quality in New Zealand vegans(PLOS, 2025-04-16) Soh BXP; Vignes M; Smith NW; Von Hurst PR; McNabb WC; Tomaszewska EDietary protein provides indispensable amino acids (IAAs) that the body cannot synthesise. Past assessments of total protein intake from vegan populations in western, developed countries were found to be low but not necessarily below daily requirements. However, plant-sourced proteins generally have lower quantities of digestible IAAs as compared to animal-sourced proteins. Simply accounting for protein intake without considering AA profile and digestibility could overestimate protein adequacy among vegans. This study quantified protein intake and quality, as compared to reference intake values among 193 NZ vegans using a four-day food diary. Protein and IAA composition of all foods were derived from New Zealand FoodFiles and the United States Department of Agriculture and adjusted for True Ileal Digestibility (TID). Mean protein intakes for males and females were 0.98 and 0.80g/kg/day, respectively with 78.8% of males and 73.0% of females meeting the Estimated Average Requirement for protein. Plant-sourced proteins provided 52.9mg of leucine and 35.7mg of lysine per gram of protein and were below the reference scoring patterns (leucine: 59mg/g, lysine: 45mg/g). When adjusted to individual body weight, average IAA intakes were above daily requirements, but lysine just met requirements at 31.0mg/kg of body weight/day (reference: 30mg/kg/day). Upon TID adjustment, the percentage of vegans meeting adequacy for protein and IAA decreased and only approximately 50% of the cohort could meet lysine and leucine requirements. Hence, lysine and leucine were the most limiting IAAs in the vegan cohort’s diet. Legumes and pulses contributed most to overall protein and lysine intake. An increased proportion of legumes and pulses can potentially increase these intakes but must be considered in the context of the whole diet. AA composition and digestibility are important aspects of protein quality when assessing protein adequacy and is of particular importance in restrictive diets.Item Visual integration of GWAS and differential expression results with the hidecan R package(2023-04-03) Angelin-Bonnet O; Vignes M; Biggs PJ; Baldwin S; Thomson SItem Visual Integration of Genome-Wide Association Studies and Differential Expression Results with the Hidecan R Package.(MDPI (Basel, Switzerland), 2024-09-25) Angelin-Bonnet O; Vignes M; Biggs PJ; Baldwin S; Thomson S; Hojsgaard DBackground/Objectives: We present hidecan, an R package for generating visualisations that summarise the results of one or more genome-wide association studies (GWAS) and differential expression analyses, as well as manually curated candidate genes, e.g., extracted from the literature. This tool is applicable to all ploidy levels; we notably provide functionalities to facilitate the visualisation of GWAS results obtained for autotetraploid organisms with the GWASpoly package. Results: We illustrate the capabilities of hidecan with examples from two autotetraploid potato datasets. Conclusions: The hidecan package is implemented in R and is publicly available on the CRAN repository and on GitHub. A description of the package, as well as a detailed tutorial, is made available alongside the package. It is also part of the VIEWpoly tool for the visualisation and exploration of results from polyploids computational tools.Item Evaluation of the accuracy of the IDvet serological test for Mycoplasma bovis infection in cattle using latent class analysis of paired serum ELISA and quantitative real-time PCR on tonsillar swabs sampled at slaughter(Public Library of Science (PLoS), 2023-05-11) Marquetoux N; Vignes M; Burroughs A; Sumner E; Sawford K; Jones G; Qi YMycoplasma bovis (Mbovis) was first detected in cattle in New Zealand (NZ) in July 2017. To prevent further spread, NZ launched a world-first National Eradication Programme in May 2018. Existing diagnostic tests for Mbovis have been applied in countries where Mbovis is endemic, for detecting infection following outbreaks of clinical disease. Diagnostic test evaluation (DTE) under NZ conditions was thus required to inform the Programme. We used Bayesian Latent Class Analysis on paired serum ELISA (ID Screen Mycoplasma bovis Indirect from IDvet) and tonsillar swabs (qPCR) for DTE in the absence of a gold standard. Tested samples were collected at slaughter between June 2018 and November 2019, from infected herds depopulated by the Programme. A first set of models evaluated the detection of active infection, i.e. the presence of Mbovis in the host. At a modified serology positivity threshold of SP%> = 90, estimates of animal-level ELISA sensitivity was 72.8% (95% credible interval 68.5%-77.4%), respectively 97.7% (95% credible interval 97.3%-98.1%) for specificity, while the qPCR sensitivity was 45.2% (95% credible interval 41.0%-49.8%), respectively 99.6% (95% credible interval 99.4%-99.8%) for specificity. In a second set of models, prior information about ELISA specificity was obtained from the National Beef Cattle Surveillance Programme, a population theoretically free-or very low prevalence-of Mbovis. These analyses aimed to evaluate the accuracy of the ELISA test targeting prior exposure to Mbovis, rather than active infection. The specificity of the ELISA for detecting exposure to Mbovis was 99.9% (95% credible interval 99.7%-100.0%), hence near perfect at the threshold SP%=90. This specificity estimate, considerably higher than in the first set of models, was equivalent to the manufacturer's estimate. The corresponding ELISA sensitivity estimate was 66.0% (95% credible interval 62.7%-70.7%). These results confirm that the IDvet ELISA test is an appropriate tool for determining exposure and infection status of herds, both to delimit and confirm the absence of Mbovis.Item Centrality statistics of symptom networks of schizophrenia: a systematic review(Cambridge University Press, 2024-01-04) Buchwald K; Narayanan A; Siegert RJ; Vignes M; Arrowsmith K; Sandham MThe network theory of psychological disorders posits that systems of symptoms cause, or are associated with, the expression of other symptoms. Substantial literature on symptom networks has been published to date, although no systematic review has been conducted exclusively on symptom networks of schizophrenia, schizoaffective disorder, and schizophreniform (people diagnosed with schizophrenia; PDS). This study aims to compare statistics of the symptom network publications on PDS in the last 21 years and identify congruences and discrepancies in the literature. More specifically, we will focus on centrality statistics. Thirty-two studies met the inclusion criteria. The results suggest that cognition, and social, and occupational functioning are central to the network of symptoms. Positive symptoms, particularly delusions were central among participants in many studies that did not include cognitive assessment. Nodes representing cognition were most central in those studies that did. Nodes representing negative symptoms were not as central as items measuring positive symptoms. Some studies that included measures of mood and affect found items or subscales measuring depression were central nodes in the networks. Cognition, and social, and occupational functioning appear to be core symptoms of schizophrenia as they are more central in the networks, compared to variables assessing positive symptoms. This seems consistent despite heterogeneity in the design of the studies.Item Using network analysis to identify factors influencing the heath-related quality of life of parents caring for an autistic child(Elsevier Ltd., 2024-09-01) Shepherd D; Buchwald K; Siegert RJ; Vignes MBACKGROUND: Raising an autistic child is associated with increased parenting stress relative to raising typically developing children. Increased parenting stress is associated with lower parent wellbeing, which in turn can negatively impact child wellbeing. AIMS: The current study sought to quantify parenting stress and parent health-related quality of life (HRQOL) in the autism context, and further understand the relationship between them by employing a relatively novel statistical method, Network Analysis. METHODS AND PROCEDURES: This cross-sectional study involved 476 parents of an autistic child. Parents completed an online survey requesting information on parent and child characteristics, parent's perceptions of their autistic child's symptoms and problem behaviours, and assessed their parenting stress and HRQOL. OUTCOMES AND RESULTS: Relative to normative data, parent HRQOL was significantly lower in terms of physical health and mental wellbeing. The structure extracted by the Network Analysis indicated that child age and externalising behaviours were the main contributors to parenting stress, and that externalising behaviours, ASD core behavioural symptoms, and parenting stress predicted HRQOL. CONCLUSIONS AND IMPLICATIONS: Parental responses to child-related factors likely determine parent HRQOL. Findings are discussed in relation to the transactional model, emphasising the importance of both parent and child wellbeing.Item Validation of low-cost air quality monitoring platforms using model-based control charts(Elsevier Ltd, 2024-04-01) Boulic M; Phipps R; Wang Y; Vignes M; Adegoke NAThe SARS COVID-19 pandemic highlighted the importance of routine indoor air quality (IAQ) monitoring. Recent advances in IAQ sensors and remote logging technologies offer opportunities to use low-cost platforms to monitor indoor air. The sensor's accuracy and stability are critical for reliable monitoring and health protection. Data from our low-cost IAQ platform (SKOMOBO) was validated against a commercial platform for carbon dioxide, temperature, and relative humidity measurements to test the reliability of the low-cost instrument. The traditional statistical method to test the variability between two data sets is the coefficient of determination method. We identified that this traditional method did not detect drifts in measurements, when comparing data from two platforms, in a controlled and uncontrolled environment. In our paper, we propose two complementary methods to detect potential drifts in measurements (a modified Shewhart method and a cumulative sum control chart method). The traditional coefficient of determination method indicated strong consistency (between 0.70 and 0.99) in the measurements between SKOMOBO and the reference platforms for both tested environments. Our more sensitive methods detected 100 % data matching for the controlled environment between the SKOMOBO and the reference platform but detected some drifts for the uncontrolled environment (between 81 % and 100 % data matching). It was expected that the uncontrolled environment would create more drifts in measurements than the controlled environment. Our new statistical methods achieved two important results; namely it advanced the validation process and proved the reliability of our low-cost platform for IAQ monitoring and assurance.