Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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Item Developing a Framework for Sustainable Management of Archaeological Site Parks: Cross-Case Analysis Based on Public Perception(MDPI, Basel, Switzerland, 2025-04) Xi Y; Liu T; Wang Y; Ying FJ; Han Y; Luo S; Zhang PAs official terms included in the International Council on Monuments and Sites (ICOMOS) documents, archaeological site parks have gradually emphasized the establishment of sustainable management frameworks for archaeological sites open to the public and enhancing public experiences. The management frameworks should be closely related to the goals of the United Nations and other international conventions on sustainable development. However, they lack implementation strategies to promote archaeological site protection and provide responsible tourism. This research adopts a multi-case study approach to analyze the management of representative archaeological site parks in the United States, Japan, and China to develop a framework for the sustainable management of archaeological site parks. Various values, heritage tourism activities, and public perceptions of each park are examined based on cross-case analysis, which identifies principal elements and strategies for the sustainable management of archaeological parks. The principal elements reflect the archaeological parks’ intrinsic value, utility value, and other values. The strategies are closely related to the design of heritage tourism activities and are in alignment with the UN’s sustainable development goals. The theoretical and practical contributions of this research include the reflection and explanation of the sustainable management practices of archaeological site parks in different national and cultural contexts, considering public perceptions. The proposed framework and strategy integrate management guidelines, theoretical knowledge, and practical experience of public archaeological site parks. The outcomes of this research provide a reference for the study of archaeological parks and the management of heritage landscapes.Item Dynamics of Porcine Circovirus Type 3 Detection in Pre-Weaning Piglets: Insight From Multiple Sampling Methods(John Wiley and Sons Ltd, 2025-01-24) Yang DA; Li M; Wang Y; Zhao K; Zhang Q; Laven RA; Yang Z; Chen N-HPorcine circovirus type 3 (PCV3) has been identified worldwide and is associated with reproductive and systemic diseases, yet the dynamics of PCV3 within pig farms remain unclear. Building upon our previous study, which initialised comparisons of different sample types for the detection of PCV3 in a sow farm, this study expanded both the range of sample types and the timeline of sampling in piglets and sows to better understand the PCV3 dynamics. This study collected two additional sample types—oropharyngeal swab (OS) and oral fluid (OF) along with placental umbilical cord (PUC) blood and processing fluid (PF) that were used in the previous study. Data were collected from July to August and October 2022; the aforementioned four sample types from 51 litters were collected, and additional OS samples were collected from two to three identified piglets per litter on days 1, 7, 14, and 21 post-farrowing. Besides, blood swabs were taken from 135 sows subject to both PCR test and oestrogen measurement. PF showed the highest detection rates (50/51), while OS and OF revealed 33/51 (95% confidence interval [CI]: 51.2%–76.8%) and 37/51 (95% CI: 59.5%–83.5%) detection rates; both were higher than that of PUC blood (22/51, 95% CI: 30.2%–56.8%). Despite the similarity between OS and OF samples, they did not identify the same population as infected, as the agreement between the samples was only fair at 90% level. The Bayesian generalised linear mixed model suggested PCV3 was more likely to be detected in both OS and OF compared to PUC blood, and PCV3 was present in the farrowing room throughout the pre-weaning period using an OS. Finally, we observed higher PCV3 detection rates in sows after farrowing; however, no evidence was found that such a pattern was associated with the decreased concentration of oestrogen.Item State of the Art in Parallel and Distributed Systems: Emerging Trends and Challenges(MDPI (Basel, Switzerland), 2025-02-10) Dai F; Hossain MA; Wang Y; Djenouri D; Rosaci DDriven by rapid advancements in interconnection, packaging, integration, and computing technologies, parallel and distributed systems have significantly evolved in recent years. These systems have become essential for addressing modern computational demands, offering enhanced processing power, scalability, and resource efficiency. This paper provides a comprehensive overview of parallel and distributed systems, exploring their interrelationships, their key distinctions, and the emerging trends shaping their evolution. We analyse four parallel computing paradigms—heterogeneous computing, quantum computing, neuromorphic computing, and optical computing—and examine emerging distributed systems such as blockchain, serverless computing, and cloud-native architectures. The associated challenges are highlighted, and potential future directions are outlined. This work serves as a valuable resource for researchers and practitioners aiming to stay informed about trends in parallel and distributed computing while understanding the challenges and future developments in the field.Item TFGNet: Frequency-guided saliency detection for complex scenes(Elsevier B.V., 2025-01-08) Wang Y; Wang R; Liu J; Xu R; Wang T; Hou F; Liu B; Lei NSalient object detection (SOD) with accurate boundaries in complex and chaotic natural or social scenes remains a significant challenge. Many edge-aware or/and two-branch models rely on exchanging global and local information between multistage features, which can propagate errors and lead to incorrect predictions. To address this issue, this work explores the fundamental problems in current U-Net architecture-based SOD models from the perspective of image spatial frequency decomposition and synthesis. A concise and efficient Frequency-Guided Network (TFGNet) is proposed that simultaneously learns the boundary details (high-spatial frequency) and inner regions (low-spatial frequency) of salient regions in two separate branches. Each branch utilizes a Multiscale Frequency Feature Enhancement (FFE) module to learn pixel-wise frequency features and a Transformer-based decoder to learn mask-wise frequency features, improving a comprehensive understanding of salient regions. TFGNet eliminates the need to exchange global and local features at intermediate layers of the two branches, thereby reducing interference from erroneous information. A hybrid loss function is also proposed to combine BCE, IoU, and Histogram dissimilarity to ensure pixel accuracy, structural integrity, and frequency distribution consistency between ground truth and predicted saliency maps. Comprehensive evaluations have been conducted on five widely used SOD datasets and one underwater SOD dataset, demonstrating the superior performance of TFGNet compared to state-of-the-art methods. The codes and results are available at https://github.com/yiwangtz/TFGNet.Item An in-depth survey on Deep Learning-based Motor Imagery Electroencephalogram (EEG) classification(Elsevier BV, Netherlands, 2024-01) Wang X; Liesaputra V; Liu Z; Wang Y; Huang ZElectroencephalogram (EEG)-based Brain–Computer Interfaces (BCIs) build a communication path between human brain and external devices. Among EEG-based BCI paradigms, the most commonly used one is motor imagery (MI). As a hot research topic, MI EEG-based BCI has largely contributed to medical fields and smart home industry. However, because of the low signal-to-noise ratio (SNR) and the non-stationary characteristic of EEG data, it is difficult to correctly classify different types of MI-EEG signals. Recently, the advances in Deep Learning (DL) significantly facilitate the development of MI EEG-based BCIs. In this paper, we provide a systematic survey of DL-based MI-EEG classification methods. Specifically, we first comprehensively discuss several important aspects of DL-based MI-EEG classification, covering input formulations, network architectures, public datasets, etc. Then, we summarize problems in model performance comparison and give guidelines to future studies for fair performance comparison. Next, we fairly evaluate the representative DL-based models using source code released by the authors and meticulously analyse the evaluation results. By performing ablation study on the network architecture, we found that (1) effective feature fusion is indispensable for multi-stream CNN-based models. (2) LSTM should be combined with spatial feature extraction techniques to obtain good classification performance. (3) the use of dropout contributes little to improving the model performance, and that (4) adding fully connected layers to the models significantly increases their parameters but it might not improve their performance. Finally, we raise several open issues in MI-EEG classification and provide possible future research directions.Item Reprocessable Epoxy-Anhydride Resin Enabled by a Thermally Stable Liquid Transesterification Catalyst.(MDPI (Basel, Switzerland), 2024-11-20) Liang H; Tian W; Xu H; Ge Y; Yang Y; He E; Yang Z; Wang Y; Zhang S; Wang G; Chen Q; Wei Y; Ji Y; Jang K-SIntroducing dynamic ester bonds into epoxy-anhydride resins enhances the reprocessability of the crosslinked network, facilitated by various types of transesterification catalysts. However, existing catalysts, such as metal salts and organic molecules, often struggle with dispersion, volatility, or structural instability issues. Here, we propose to solve such problems by incorporating a liquid-state, thermally stable transesterification catalyst into epoxy resins. This catalyst, an imidazole derivative, can be uniformly dispersed in the epoxy resin at room temperature. In addition, it shows high-temperature structural stability above at least 200 °C as the synergistic effects of the electron-withdrawing group and steric bulk can be leveraged. It can also effectively promote transesterification at elevated temperatures, allowing for the effective release of shear stress. This property enables the thermal recycling and reshaping of the fully crosslinked epoxy-anhydride resin. This strategy not only enhances the functionality of epoxy resins but also broadens their applicability across various thermal and mechanical environments.Item Identification of candidate novel production variants on the Bos taurus chromosome X(Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association, 2023-11) Trebes H; Wang Y; Reynolds E; Tiplady K; Harland C; Lopdell T; Johnson T; Davis S; Harris B; Spelman R; Couldrey CChromosome X is often excluded from bovine genetic studies due to complications caused by the sex specific nature of the chromosome. As chromosome X is the second largest cattle chromosome and makes up approximately 6% of the female genome, finding ways to include chromosome X in dairy genetic studies is important. Using female animals and treating chromosome X as an autosome, we performed X chromosome inclusive genome-wide association studies in the selective breeding environment of the New Zealand dairy industry, aiming to identify chromosome X variants associated with milk production traits. We report on the findings of these genome-wide association studies and their potential effect within the dairy industry. We identify missense mutations in the MOSPD1 and CCDC160 genes that are associated with decreased milk volume and protein production and increased fat production. Both of these mutations are exonic SNP that are more prevalent in the Jersey breed than in Holstein-Friesians. Of the 2 candidates proposed it is likely that only one is causal, though we have not been able to identify which is more likely.Item Characterization of two conserved cell death elicitor families from the Dothideomycete fungal pathogens Dothistroma septosporum and Fulvia fulva (syn. Cladosporium fulvum)(Frontiers Media S.A., 2022-09-08) Tarallo M; McDougal RL; Chen Z; Wang Y; Bradshaw RE; Mesarich CH; Wang YDothistroma septosporum (Ds) and Fulvia fulva (Ff; previously called Cladosporium fulvum) are two closely related Dothideomycete fungal species that cause Dothistroma needle blight in pine and leaf mold in tomato, respectively. During host colonization, these pathogens secrete virulence factors termed effectors to promote infection. In the presence of corresponding host immune receptors, however, these effectors activate plant defenses, including a localized cell death response that halts pathogen growth. We identified two apoplastic effector protein families, Ecp20 and Ecp32, which are conserved between the two pathogens. The Ecp20 family has four paralogues in both species, while the Ecp32 family has four paralogues in D. septosporum and five in F. fulva. Both families have members that are highly expressed during host infection. Members of the Ecp20 family have predicted structural similarity to proteins with a β-barrel fold, including the Alt a 1 allergen from Alternaria alternata, while members of the Ecp32 family have predicted structural similarity to proteins with a β-trefoil fold, such as trypsin inhibitors and lectins. Using Agrobacterium tumefaciens-mediated transient transformation assays, each family member was assessed for its ability to trigger cell death in leaves of the non-host species Nicotiana benthamiana and N. tabacum. Using this approach, FfEcp20-2, DsEcp20-3, and FfEcp20-3 from the Ecp20 family, and all members from the Ecp32 family, except for the Ds/FfEcp32-4 pair, triggered cell death in both species. This cell death was dependent on secretion of the effectors to the apoplast. In line with recognition by an extracellular immune receptor, cell death triggered by Ds/FfEcp20-3 and FfEcp32-3 was compromised in N. benthamiana silenced for BAK1 or SOBIR1, which encode extracellular co-receptors involved in transducing defense response signals following apoplastic effector recognition. We then investigated whether DsEcp20-3 and DsEcp20-4 triggered cell death in the host species Pinus radiata by directly infiltrating purified protein into pine needles. Strikingly, as in the non-host species, DsEcp20-3 triggered cell death, while DsEcp20-4 did not. Collectively, our study describes two new candidate effector families with cell death-eliciting activity from D. septosporum and F. fulva and provides evidence that members of these families are recognized by plant immune receptors.Item Comparative transcriptomes reveal geographic differences in the ability of the liver of plateau zokors (Eospalax baileyi) to respond and adapt to toxic plants(BioMed Central Ltd, 2023-12) Tan Y; Wang Y; Liu Q; Wang Z; Shi S; Su JBACKGROUND: Environmental changes are expected to intensify in the future. The invasion of toxic plants under environmental changes may change herbivore feeding environments. Herbivores living long-term in toxic plant-feeding environments will inevitably ingest plant secondary metabolites (PSMs), and under different feeding environments are likely to have unique protection mechanisms that support improved adaptation to PSMs in their habitat. We aimed to compare different subterranean herbivore population responses and adaptations to toxic plants to unveil their feeding challenges. RESULTS: Here, we investigated the adaptive capacity of the liver in two geographically separated populations of plateau zokors (Eospalax baileyi) before and after exposure to the toxic plant Stellera chamaejasme (SC), at the organ, biochemical, and transcriptomic levels. The results showed no significant liver granules or inflammatory reactions in the Tianzhu (TZ) population after the SC treatment. The transaminase level in the TZ population was significantly lower than that in the Luqu population. Transcriptome analysis revealed that the TZ population exhibited interactions with other detoxification metabolic pathways by oxytocin pathway-associated genes, including diacylglycerol lipase alpha (Dagla), calcium/calmodulin dependent protein kinase II Alpha (Camk2a), and CD38 molecule (Cd38). The phase II process of liver drug metabolism increased to promote the rate of metabolism. We found that alternative splicing (AS) and the expression of the cyclin D (Ccnd1) gene interact-a TZ population hallmark-reduced liver inflammatory responses. CONCLUSION: Our study supports the detoxification limitation hypothesis that differences in liver detoxification metabolism gene expression and AS are potential factors in herbivore adaptation to PSMs and may be a strategy of different herbivore populations to improve toxic plant adaptability.Item Non-additive QTL mapping of lactation traits in 124,000 cattle reveals novel recessive loci(BioMed Central Ltd, 2022-12) Reynolds EGM; Lopdell T; Wang Y; Tiplady KM; Harland CS; Johnson TJJ; Neeley C; Carnie K; Sherlock RG; Couldrey C; Davis SR; Harris BL; Spelman RJ; Garrick DJ; Littlejohn MDBACKGROUND: Deleterious recessive conditions have been primarily studied in the context of Mendelian diseases. Recently, several deleterious recessive mutations with large effects were discovered via non-additive genome-wide association studies (GWAS) of quantitative growth and developmental traits in cattle, which showed that quantitative traits can be used as proxies of genetic disorders when such traits are indicative of whole-animal health status. We reasoned that lactation traits in cattle might also reflect genetic disorders, given the increased energy demands of lactation and the substantial stresses imposed on the animal. In this study, we screened more than 124,000 cows for recessive effects based on lactation traits. RESULTS: We discovered five novel quantitative trait loci (QTL) that are associated with large recessive impacts on three milk yield traits, with these loci presenting missense variants in the DOCK8, IL4R, KIAA0556, and SLC25A4 genes or premature stop variants in the ITGAL, LRCH4, and RBM34 genes, as candidate causal mutations. For two milk composition traits, we identified several previously reported additive QTL that display small dominance effects. By contrasting results from milk yield and milk composition phenotypes, we note differing genetic architectures. Compared to milk composition phenotypes, milk yield phenotypes had lower heritabilities and were associated with fewer additive QTL but had a higher non-additive genetic variance and were associated with a higher proportion of loci exhibiting dominance. CONCLUSIONS: We identified large-effect recessive QTL which are segregating at surprisingly high frequencies in cattle. We speculate that the differences in genetic architecture between milk yield and milk composition phenotypes derive from underlying dissimilarities in the cellular and molecular representation of these traits, with yield phenotypes acting as a better proxy of underlying biological disorders through presentation of a larger number of major recessive impacts.