Journal Articles

Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915

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Author: search.filters.author.Wang H

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Now showing 1 - 10 of 19
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    Comprehensive analysis of molecular characteristics between primary and breast-derived metastatic ovarian cancer
    (AME Publishing Company, 2025-03-30) Long J; Liu B; Li J; Ji X; Zhu N; Zhuang X; Wang H; Li L; Chen Y; Li X; Zhao S
    Background: The molecular basis for the disparities between primary ovarian cancer (POC) and ovarian cancer secondary to breast cancer (OCSTBC) remains poorly understood. This study aimed to explore the different characteristics between them through genomic analysis. Methods: We performed differentially expressed genes (DEGs) analysis between POC (n=96) and OCSTBC (n=44) groups with transcriptome data and revealed the enriched biological pathways with Kyoto Encyclopedia of Genes and Genomes (KEGG) and Hallmark gene sets between these two groups. Then, the Microenvironment Cell Populations (MCP)-counter and Cell-type Identification by Estimating Relative Subsets of RNA Transcript (CIBERSORT) algorithms were applied to evaluate the immune infiltration in tumor microenvironment (TME) between them. Finally, we performed the association analysis within single nucleotide polymorphism (SNP) data and obtained some meaningful SNPs and candidate genes for further transcriptomic analysis. Results: We identified a total of 13 cancer-related genes including GATA3, FOXA1, CCND1, and TTK between POC (n=96) and OCSTBC (n=44) groups with DEGs analysis. Integrated analysis revealed more significant immune-enriched pathways in the POC than in the OCSTBC group. Most immune cells had higher infiltration abundance in POC, except M2 macrophages, which was higher in OCSTBC. In SNP analysis, four SNP regions (8q12.1, 11q21, 11q24.3, and 17q25.3) were found to be significantly correlated with phenotypes (POC/OCSTBC), and importantly, some new susceptibility genes such as ETS1, CWC15, and XKR4 were revealed to potentially be associated with distinction between POC and OCSTBC. Conclusions: Our study provides a systematic molecular characteristic between POC and OCSTBC and suggests a pressing need to develop some specific therapeutic strategies in certain types of ovarian cancer.
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    Transformer-Based Explainable Model for Breast Cancer Lesion Segmentation
    (MDPI (Basel, Switzerland), 2025-01-27) Wang H; Wei L; Liu B; Li J; Li J; Fang J; Mooney C; Gegov A; Jafari R; Arabikhan F
    Breast cancer is one of the most prevalent cancers among women, with early detection playing a critical role in improving survival rates. This study introduces a novel transformer-based explainable model for breast cancer lesion segmentation (TEBLS), aimed at enhancing the accuracy and interpretability of breast cancer lesion segmentation in medical imaging. TEBLS integrates a multi-scale information fusion approach with a hierarchical vision transformer, capturing both local and global features by leveraging the self-attention mechanism. This model addresses the limitations of existing segmentation methods, such as the inability to effectively capture long-range dependencies and fine-grained semantic information. Additionally, TEBLS incorporates visualization techniques to provide insights into the segmentation process, enhancing the model’s interpretability for clinical use. Experiments demonstrate that TEBLS outperforms traditional and existing deep learning-based methods in segmenting complex breast cancer lesions with variations in size, shape, and texture, achieving a mean DSC of 81.86% and a mean AUC of 97.72% on the CBIS-DDSM test set. Our model not only improves segmentation accuracy but also offers a more explainable framework, which has the potential to be used in clinical settings.
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    Association of common and rare variants with Alzheimer's disease in more than 13,000 diverse individuals with whole-genome sequencing from the Alzheimer's Disease Sequencing Project.
    (Wiley Periodicals LLC on behalf of Alzheimer's Association, 2024-10-20) Lee W-P; Choi SH; Shea MG; Cheng P-L; Dombroski BA; Pitsillides AN; Heard-Costa NL; Wang H; Bulekova K; Kuzma AB; Leung YY; Farrell JJ; Lin H; Kunkle BW; Naj A; Blue EE; Nusetor F; Wang D; Boerwinkle E; Bush WS; Zhang X; De Jager PL; Dupuis J; Farrer LA; Fornage M; Martin E; Pericak-Vance M; Seshadri S; Wijsman EM; Wang L-S; Alzheimer's Disease Sequencing Project; Schellenberg GD; Destefano AL; Haines JL; Peloso GM
    INTRODUCTION Alzheimer's disease (AD) is a common disorder of the elderly that is both highly heritable and genetically heterogeneous. METHODS We investigated the association of AD with both common variants and aggregates of rare coding and non-coding variants in 13,371 individuals of diverse ancestry with whole genome sequencing (WGS) data. RESULTS Pooled-population analyses of all individuals identified genetic variants at apolipoprotein E (APOE) and BIN1 associated with AD (p < 5 × 10−8). Subgroup-specific analyses identified a haplotype on chromosome 14 including PSEN1 associated with AD in Hispanics, further supported by aggregate testing of rare coding and non-coding variants in the region. Common variants in LINC00320 were observed associated with AD in Black individuals (p = 1.9 × 10−9). Finally, we observed rare non-coding variants in the promoter of TOMM40 distinct of APOE in pooled-population analyses (p = 7.2 × 10−8). DISCUSSION We observed that complementary pooled-population and subgroup-specific analyses offered unique insights into the genetic architecture of AD. Highlights We determine the association of genetic variants with Alzheimer's disease (AD) using 13,371 individuals of diverse ancestry with whole genome sequencing (WGS) data. We identified genetic variants at apolipoprotein E (APOE), BIN1, PSEN1, and LINC00320 associated with AD. We observed rare non-coding variants in the promoter of TOMM40 distinct of APOE.
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    Integrative analysis identifies two molecular and clinical subsets in Luminal B breast cancer
    (Elsevier Inc, 2023-09-15) Wang H; Liu B; Long J; Yu J; Ji X; Li J; Zhu N; Zhuang X; Li L; Chen Y; Liu Z; Wang S; Zhao S
    Comprehensive multiplatform analysis of Luminal B breast cancer (LBBC) specimens identifies two molecularly distinct, clinically relevant subtypes: Cluster A associated with cell cycle and metabolic signaling and Cluster B with predominant epithelial mesenchymal transition (EMT) and immune response pathways. Whole-exome sequencing identified significantly mutated genes including TP53, PIK3CA, ERBB2, and GATA3 with recurrent somatic mutations. Alterations in DNA methylation or transcriptomic regulation in genes (FN1, ESR1, CCND1, and YAP1) result in tumor microenvironment reprogramming. Integrated analysis revealed enriched biological pathways and unexplored druggable targets (cancer-testis antigens, metabolic enzymes, kinases, and transcription regulators). A systematic comparison between mRNA and protein displayed emerging expression patterns of key therapeutic targets (CD274, YAP1, AKT1, and CDH1). A potential ceRNA network was developed with a significantly different prognosis between the two subtypes. This integrated analysis reveals a complex molecular landscape of LBBC and provides the utility of targets and signaling pathways for precision medicine.
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    Integrated computer vision algorithms and drone scheduling
    (Elsevier B.V., 2021-08-23) Yi W; Wang H; Jin Y; Cao J
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    Biochar and soil properties limit the phytoavailability of lead and cadmium by Brassica chinensis L. in contaminated soils
    (Springer Nature on behalf of the Shenyang Agricultural University, 2022-12) Houssou AA; Jeyakumar P; Niazi NK; Van Zwieten L; Li X; Huang L; Wei L; Zheng X; Huang Q; Huang Y; Huang X; Wang H; Liu Z; Huang Z
    The current study investigated the effect of biochars derived from cinnamomum woodchip, garden waste and mulberry woodchip on soil phytoavailable lead (Pb), cadmium (Cd) pools, and their uptake by Chinese cabbage (Brassica chinensis L.). The biochars were produced at 450 °C of pyrolysis temperature. The contaminated soils were collected from Yunfu (classified as Udept), Jiyuan (Ustalf) and Shaoguan (Udult) cities in China at the depth of 0–20 cm and amended with biochars at the rate of 3% w/w. After mixing the soil with biochar for 14 days, the Chinese cabbage was planted in the amended soils. Then, it was harvested on the 48th day after sowing period. In Udult soil, Chinese cabbage died 18 days after sowing period in control and soils amended with cinnamomum and mulberry biochars. Although only plants grown with the garden waste biochar treatment survived in Udult soil, amendment of garden waste or mulberry biochars at 3% w/w (450 °C) to Udult soil significantly increased (4.95–6.25) soil pH compared to other biochar treatments. In Udept and Ustalf soils, the application of garden waste and mulberry biochars significantly improved plant biomass compared to control, albeit it was dependent on both biochar and soil properties. Garden waste biochar significantly decreased soil Cd phytoavailable concentration by 26% in the Udult soil, while a decrease of soil Cd phytoavailable concentration by 16% and 9% was observed in Ustalf and Udept soils, respectively. The available phosphorus in biochar and soil pH were important factors controlling toxic metal phytouptake by the plant. Thus, the amendment of soil with biochar at 3% can effectively reduce the mobility of Cd and Pb in soil and plant uptake. However, biochar and soil properties should be well-known before being used for soil toxic metal immobilization.
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    Enhanced denitrification driven by a novel iron-carbon coupled primary cell: chemical and mixotrophic denitrification
    (Springer, 2024-01-10) Wu R; Jeyakumar P; Nanthi B; Zhai X; Wang H; Pan M; Lian J; Cheng L; Li J; Hou M; Cui Y; Yang X; Dai K
    Iron-carbon micro-electrolysis system is a promising method for promoting electron transfer in nitrate removal. However, many traditional approaches involving simple physical mixing inevitably suffered from the confined iron-carbon contact area and short validity period, leading to the overuse of iron. Here, a ceramsite-loaded microscale zero-valent iron (mZVI) and acidified carbon (AC) coupled-galvanic cell (CMC) was designed to support chemical, autotrophic and heterotrophic denitrification. Long-term experiments were conducted to monitor the nitrogen removal performance of denitrification reactors filled with CMC and thus optimized the denitrification performance by improving fabrication parameters and various operating conditions. The denitrification contributions test showed that the chemical denitrification pathway contributed most to nitrate removal (57.3%), followed by autotrophic (24.6%) and heterotrophic denitrification pathways (18.1%). The microbial analysis confirmed the significant aggregation of related denitrifying bacteria in the reactors, while AC promoted the expression of relevant nitrogen metabolism genes because of accelerated uptake and utilization of iron complexes. Meanwhile, the electrochemical analysis revealed a significantly improved electron transfer capacity of AC compared to pristine carbon. Overall, our study demonstrated the application of a novel mZVI-AC coupled material for effective nitrate removal and revealed the potential impact of CMC in the multipathway denitrification process. Graphical Abstract: [Figure not available: see fulltext.]
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    Dietary Supplementation of Yeast Culture Into Pelleted Total Mixed Rations Improves the Growth Performance of Fattening Lambs
    (Frontiers Media S.A., 2021-05) Song B; Wu T; You P; Wang H; Burke JL; Kang K; Yu W; Wang M; Li B; He Y; Huo Q; Li C; Tian W; Li R; Li J; Wang C; Sun X
    There is a growing interest in the use of yeast (Saccharomyces cerevisiae) culture (YC) for the enhancement of growth performance and general animal health. Grain-based pelleted total mixed rations (TMR) are emerging in intensive sheep farming systems, but it is uncertain if the process of pelleting results in YC becoming ineffective. This study aimed to examine the effects of YC supplemented to pelleted TMR at two proportions of corn in the diet on animal performance, feed digestion, blood parameters, rumen fermentation, and microbial community in fattening lambs. A 2 × 2 factorial design was adopted with two experimental factors and two levels in each factor, resulting in four treatments: (1) low proportion of corn in the diet (LC; 350 g corn/kg diet) without YC, (2) LC with YC (5 g/kg diet), (3) high proportion of corn in the diet (HC; 600 g corn/kg diet) without YC, and (4) HC with YC. Fifty-six 3-month-old male F2 hybrids of thin-tailed sheep and Northeast fine-wool sheep with a liveweight of 19.9 ± 2.7 kg were randomly assigned to the four treatment groups with an equal number of animals in each group. The results showed that live yeast cells could not survive during pelleting, and thus, any biological effects of the YC were the result of feeding dead yeast and the metabolites of yeast fermentation rather than live yeast cells. The supplementation of YC resulted in 31.1 g/day more average daily gain regardless of the proportion of corn in the diet with unchanged feed intake during the 56-day growth measurement period. The digestibility of neutral detergent fibre and acid detergent fibre was increased, but the digestibility of dry matter, organic matter, and crude protein was not affected by YC. The supplementation of YC altered the rumen bacterial population and species, but the most abundant phyla Bacteroidetes, Firmicutes, and Proteobacteria remained unchanged. This study indicates that YC products can be supplemented to pelleted TMR for improved lamb growth performance, although live yeast cells are inactive after pelleting. The improved performance could be attributed to improved fibre digestibility.