Displaying publications 41 - 55 of 55 in total

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  1. Zhou Q, Lin CW, Ng WL, Dai J, Denda T, Zhou R, et al.
    Front Plant Sci, 2019;10:1477.
    PMID: 31824528 DOI: 10.3389/fpls.2019.01477
    Sonerileae/Dissochaeteae (Melastomataceae) comprises ca. 50 genera, two thirds of which occur in Southeast Asia. Phylogenetic relationships within this clade remain largely unclear, which hampers our understanding of its origin, evolution, and biogeography. Here, we explored the use of chloroplast genomes in phylogenetic reconstruction of Sonerileae/Dissochaeteae, by sampling 138 species and 23 genera in this clade. A total of 151 complete plastid genomes were assembled for this study. Plastid genomic data provided better support for the backbone of the Sonerileae/Dissochaeteae phylogeny, and also for relationships among most closely related species, but failed to resolve the short internodes likely resulted from rapid radiation. Trees inferred from plastid genome and nrITS sequences were largely congruent regarding the major lineages of Sonerileae/Dissochaeteae. The present analyses recovered 15 major lineages well recognized in both nrITS and plastid phylogeny. Molecular dating and biogeographical analyses indicated a South American origin for Sonerileae/Dissochaeteae during late Eocene (stem age: 34.78 Mya). Two dispersal events from South America to the Old World were detected in late Eocene (33.96 Mya) and Mid Oligocene (28.33 Mya) respectively. The core Asian clade began to diversify around early Miocene in Indo-Burma and dispersed subsequently to Malesia and Sino-Japanese regions, possibly promoted by global temperature changes and East Asian monsoon activity. Our analyses supported previous hypothesis that Medinilla reached Madagascar by transoceanic dispersal in Miocene. In addition, generic limits of some genera concerned were discussed.
  2. Lee SY, Ng WL, Mahat MN, Nazre M, Mohamed R
    PLoS One, 2016;11(4):e0154631.
    PMID: 27128309 DOI: 10.1371/journal.pone.0154631
    The identification of Aquilaria species from their resinous non-wood product, the agarwood, is challenging as conventional techniques alone are unable to ascertain the species origin. Aquilaria is a highly protected species due to the excessive exploitation of its precious agarwood. Here, we applied the DNA barcoding technique to generate barcode sequences for Aquilaria species and later applied the barcodes to identify the source species of agarwood found in the market. We developed a reference DNA barcode library using eight candidate barcode loci (matK, rbcL, rpoB, rpoC1, psbA-trnH, trnL-trnF, ITS, and ITS2) amplified from 24 leaf accessions of seven Aquilaria species obtained from living trees. Our results indicated that all single barcodes can be easily amplified and sequenced with the selected primers. The combination of trnL-trnF+ITS and trnL-trnF+ITS2 yielded the greatest species resolution using the least number of loci combination, while matK+trnL-trnF+ITS showed potential in detecting the geographical origins of Aquilaria species. We propose trnL-trnF+ITS2 as the best candidate barcode for Aquilaria as ITS2 has a shorter sequence length compared to ITS, which eases PCR amplification especially when using degraded DNA samples such as those extracted from processed agarwood products. A blind test conducted on eight agarwood samples in different forms using the proposed barcode combination proved successful in their identification up to the species level. Such potential of DNA barcoding in identifying the source species of agarwood will contribute to the international timber trade control, by providing an effective method for species identification and product authentication.
  3. Yap LPP, Sani FM, Chung E, Gowdh NFM, Ng WL, Wong JHD
    Singapore Med J, 2024 Feb 02.
    PMID: 38305361 DOI: 10.4103/singaporemedj.SMJ-2021-461
    INTRODUCTION: Multiphase computed tomography (CT) using fixed volume contrast media may lead to high radiation exposure and toxicity in patients with low body weight. We evaluated a customised weight-based protocol for multiphase CT in terms of radiation exposure, image quality and cost savings.

    METHODS: A total of 224 patients were recruited. An optimised CT protocol was applied using 100 kV and 1 mL/kg of contrast media dosing. The image quality and radiation dose exposure of this CT protocol were compared to those of a standard 120 kV, 80 mL fixed volume protocol. The radiation dose information and CT Hounsfield units were recorded. The signal-to-noise ratio, contrast-to-noise ratio (CNR) and figure of merit (FOM) were used as comparison metrics. The images were assessed for contrast opacification and visual quality by two radiologists. The renal function, contrast media volume and cost were also evaluated.

    RESULTS: The median effective dose was lowered by 16% in the optimised protocol, while the arterial phase images achieved significantly higher CNR and FOM. The radiologists' evaluation showed more than 97% absolute agreement with no significant differences in image quality. No significant differences were found in the pre- and post-CT estimated glomerular filtration rate. However, contrast media usage was significantly reduced by 1,680 mL, with an overall cost savings of USD 421 in the optimised protocol.

    CONCLUSION: The optimised weight-based protocol is cost-efficient and lowers radiation dose while maintaining overall contrast enhancement and image quality.

  4. Hishamuddin MS, Lee SY, Ng WL, Ramlee SI, Lamasudin DU, Mohamed R
    Sci Rep, 2020 Aug 03;10(1):13034.
    PMID: 32747724 DOI: 10.1038/s41598-020-70030-0
    Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.
  5. Pang T, Wong JHD, Ng WL, Chan CS, Wang C, Zhou X, et al.
    Phys Med Biol, 2024 Feb 19.
    PMID: 38373345 DOI: 10.1088/1361-6560/ad2a95
    OBJECTIVE: Generally, due to a lack of explainability, radiomics based on deep learning has been perceived as a black-box solution for radiologists. Automatic generation of diagnostic reports is a semantic approach to enhance the explanation of deep learning radiomics (DLR).

    APPROACH: In this paper, we propose a novel model called radiomics-reporting network (Radioport), which incorporates text attention. This model aims to improve the interpretability of deep learning radiomics in mammographic calcification diagnosis. Firstly, it employs convolutional neural networks (CNN) to extract visual features as radiomics for multi-category classification based on Breast Imaging Reporting and Data System (BI-RADS). Then, it builds a mapping between these visual features and textual features to generate diagnostic reports, incorporating an attention module for improved clarity.

    MAIN RESULTS: To demonstrate the effectiveness of our proposed model, we conducted experiments on a breast calcification dataset comprising mammograms and diagnostic reports. The results demonstrate that our model can: (i) semantically enhance the interpretability of deep learning radiomics; and, (ii) improve the readability of generated medical reports.

    SIGNIFICANCE: Our interpretable textual model can explicitly simulate the mammographic calcification diagnosis process.

  6. Pern YC, Lee SY, Ng WL, Mohamed R
    3 Biotech, 2020 Mar;10(3):103.
    PMID: 32099744 DOI: 10.1007/s13205-020-2072-2
    Tree species in the Aquilarieae tribe of the Thymelaeaceae family produce agarwood, a natural product highly valued for its fragrance, but the species are under threat due to indiscriminate harvesting. For conservation of these species, molecular techniques such as DNA profiling have been used. In this study, we assessed cross-amplification of microsatellite markers, initially developed for three Aquilaria species (A.crassna, A.malaccensis, and A.sinensis), on ten other agarwood-producing species, including members of Aquilaria (A.beccariana, A.hirta, A.microcarpa, A.rostrata, A.rugosa, A.subintegra, and A.yunnanensis) and Gyrinops (G.caudata, G.versteegii, and G.walla), both from the Aquilarieae tribe. Primers for 18 out of the 30 microsatellite markers successfully amplified bands of expected sizes in 1 sample each of at least 10 species. These were further used to genotype 74 individuals representing all the 13 studied species, yielding 13 cross-amplifiable markers, of which only 1 being polymorphic across all species. At each locus, the number of alleles ranged from 7 to 23, indicating a rather high variability. Four markers had relatively high species discrimination power. Our results demonstrated that genetic fingerprinting can be an effective tool in helping to manage agarwood genetic resources by potentially supporting the chain-of-custody of agarwood and its products in the market.
  7. Lee SY, Ng WL, Hishamuddin MS, Mohamed R
    Mitochondrial DNA B Resour, 2019;4(1):19-20.
    PMID: 33365402 DOI: 10.1080/23802359.2018.1535848
    Known for its durable timber quality, Neobalanocarpus heimii (King) Ashton is a highly sought after tree species endemic to the Malay Peninsula. Due to its scarcity and high value, the tree is classified under the IUCN Red List categories of Vulnerable. In this study, we assembled the complete chloroplast (cp) genome of N. heimii using data from high-throughput Illumina sequencing. The Chengal cp genome is 151,191 bp in size and includes two inverted repeat regions of 23,721 bp each, which is separated by a large single copy region of 83,801 bp and a small single copy region of 19,948 bp. A total of 130 genes were predicted, including 37 tRNA, 8 rRNA, and 85 protein-coding genes. Phylogenetic analysis placed N. heimii within the order Malvales.
  8. Lee SY, Ng WL, Mohamed R, Terhem R
    Mitochondrial DNA B Resour, 2018 Oct 29;3(2):1120-1121.
    PMID: 33474439 DOI: 10.1080/23802359.2018.1519382
    Known for its valuable agarwood, Aquilaria malaccensis Lam. is an evergreen tropical forest tree species endemic to the Indo-malesian region. Indiscriminate damaging and harvesting of the trees in the wild have resulted in it being listed in the CITES Appendix II for controlled trade and in the IUCN Red List as 'Vulnerable (VU)'. In this study, the complete chloroplast genome of A. malaccensis was assembled using data from high-throughput Illumina sequencing. The chloroplast genome was 174,832 bp in size, which included two inverted repeat regions of 42,091 bp each, separated by a large single copy region of 87,302 bp and a small single copy region of 3,348 bp. A total of 139 genes were predicted, including 39 tRNA, 8 rRNA, and 92 protein-coding genes. Phylogenetic analysis placed A. malaccensis within the family Thymelaeaceae. The chloroplast genome sequence of A. malaccensis offers a useful resource for future studies on the taxonomy and conservation of the threatened Aquilaria trees.
  9. Pang T, Wong JHD, Ng WL, Chan CS
    Comput Methods Programs Biomed, 2021 May;203:106018.
    PMID: 33714900 DOI: 10.1016/j.cmpb.2021.106018
    BACKGROUND AND OBJECTIVE: The capability of deep learning radiomics (DLR) to extract high-level medical imaging features has promoted the use of computer-aided diagnosis of breast mass detected on ultrasound. Recently, generative adversarial network (GAN) has aided in tackling a general issue in DLR, i.e., obtaining a sufficient number of medical images. However, GAN methods require a pair of input and labeled images, which require an exhaustive human annotation process that is very time-consuming. The aim of this paper is to develop a radiomics model based on a semi-supervised GAN method to perform data augmentation in breast ultrasound images.

    METHODS: A total of 1447 ultrasound images, including 767 benign masses and 680 malignant masses were acquired from a tertiary hospital. A semi-supervised GAN model was developed to augment the breast ultrasound images. The synthesized images were subsequently used to classify breast masses using a convolutional neural network (CNN). The model was validated using a 5-fold cross-validation method.

    RESULTS: The proposed GAN architecture generated high-quality breast ultrasound images, verified by two experienced radiologists. The improved performance of semi-supervised learning increased the quality of the synthetic data produced in comparison to the baseline method. We achieved more accurate breast mass classification results (accuracy 90.41%, sensitivity 87.94%, specificity 85.86%) with our synthetic data augmentation compared to other state-of-the-art methods.

    CONCLUSION: The proposed radiomics model has demonstrated a promising potential to synthesize and classify breast masses on ultrasound in a semi-supervised manner.

  10. Ng WL, Wu W, Zou P, Zhou R
    AoB Plants, 2019 Apr;11(2):plz019.
    PMID: 31037213 DOI: 10.1093/aobpla/plz019
    Variation in gene expression has been shown to promote adaptive divergence, and can lead to speciation. The plant genus Melastoma, thought to have diversified through adaptive radiation, provides an excellent model for the study of gene expressional changes during adaptive differentiation and following interspecific hybridization. In this study, we performed RNA-seq on M. candidum, M. sanguineum and their F1 hybrid, to investigate the role of gene expression in species diversification within the genus. Reference transcriptomes were assembled using combined data from both parental species, resulting in 50 519 and 48 120 transcripts for the leaf and flower petal, after removing redundancy. Differential expression analysis uncovered 3793 and 2116 differentially expressed (DE) transcripts, most of which are between M. candidum and M. sanguineum. Differential expression was observed for genes related to light responses, as well as genes that regulate the development of leaf trichomes, a trait that among others is thought to protect plants against sunlight, suggesting the differential adaptation of the species to sunlight intensity. The analysis of positively selected genes between the two species also revealed possible differential adaptation to other abiotic stresses such as drought and temperature. In the hybrid, almost all possible modes of expression were observed at the DE transcripts, although at most transcripts, the expression levels were similar to that of either parent instead of being intermediate. A small number of transgressively expressed transcripts that matched genes known to promote plant growth and adaptation to stresses in new environments were also found, possibly explaining the vigour observed in the hybrid. The findings in this study provided insights into the role of gene expression in the diversification of Melastoma, which we believe is an important example for more cross-taxa comparisons in the future.
  11. Tan KE, Ng WL, Ea CK, Lim YY
    Bio Protoc, 2023 Sep 05;13(17):e4798.
    PMID: 37849784 DOI: 10.21769/BioProtoc.4798
    Circular RNA (circRNA) is an intriguing class of non-coding RNA that exists as a continuous closed loop. With the improvements in high throughput sequencing, biochemical analysis, and bioinformatic algorithms, studies on circRNA expression became abundant in recent years. However, functional studies of circRNA are still limited. Subcellular localization of circRNA may provide some clues in elucidating its biological functions by performing subcellular fractionation assay. Notably, circRNAs that are predominantly found in the cytoplasm are more likely to be involved in post-transcriptional gene regulation, e.g., acting as micoRNA sponge, whereas nuclear-retained circRNAs are predicted to play a role in transcriptional regulation. Subcellular fractionation could help researchers to narrow down and prioritize downstream experiments. The majority of the currently available protocols describe the steps for subcellular fractionation followed by western blot analysis for protein molecules. Here, we present a protocol for the subcellular fractionation of cells to detect circRNA via RT-qPCR with divergent primers. Moreover, detailed steps for the generation of specific circRNAs-enriched cDNA included in this protocol will enhance the amplification and detection of low-abundance circRNAs. This will be useful for researchers studying low-abundance circRNAs. Key features This protocol builds upon the method developed by Gagnon et al. (2014) and extends its application to circRNA study. Protocol for amplification of low levels of circRNA expression. Analysis takes into consideration the ratio of cytoplasmic RNA concentration to nuclear RNA concentration.
  12. Ng WL, Mohd Mohidin TB, Shukla K
    RNA Biol, 2018;15(8):995-1005.
    PMID: 29954251 DOI: 10.1080/15476286.2018.1486659
    Circular RNAs (circRNAs) are a large class of endogenously expressed non-coding RNAs formed by covalently closed loops through back-splicing. High throughput sequencing technologies have identified thousands of circRNAs with high sequence conservation and cell type specific expression in eukaryotes. CircRNAs play multiple important roles in cellular physiology functioning as miRNA sponges, transcriptional regulators, RBP binding molecules, templates for protein translation, and immune regulators. In a clinical context, circRNAs expression is correlated with patient's clinicopathological features in cancers including breast, liver, gastric, colorectal, and lung cancer. Additionally, distinct properties of circRNAs, such as high stability, exonuclease resistance, and existence in body fluids, show promising role for circRNAs as molecular biomarkers for tumor diagnosis, non-invasive monitoring, prognosis, and therapeutic intervention. Therefore, it is critical to further understand the molecular mechanism underlying circRNAs interaction in tumors and the recent progress of this RNA species in cancer development. In this review, we provide a detailed description of biological functions, molecular role of circRNAs in different cancers, and its potential role as biomarkers in a clinical context.
  13. Ng LS, Khor SY, Ng WL
    Cureus, 2022 Oct;14(10):e30237.
    PMID: 36381844 DOI: 10.7759/cureus.30237
    Hypertriglyceridemic pancreatitis (HTGP) is well-known but it is extremely rare, especially in younger patients. The main treatment modalities for HTGP are apheresis and intravenous insulin. However, apheresis in severe HTGP is not well established and the efficacy of the treatment is lacking. Herein, we discuss a case of a 17-year-old female patient with no significant past medical history who initially presented to the emergency department with severe diabetic ketoacidosis (DKA) and was intubated due to severe metabolic acidosis and impending respiratory failure on arrival. Further investigation showed evidence of HTGP. Initially, her condition did not improve with intravenous insulin. However, a course of apheresis along with supportive care improved her condition drastically. Hence, this is a case report which showed the efficacy of concomitant use of insulin infusion and plasmapheresis in regard to treating HTGP. Outcomes of HTGP based on different treatment modalities are discussed in this literature as well. However, to date, there are no randomized studies to draw a solid treatment algorithm, thus further research on the most efficient treatment regimes is required for the management of HTGP.
  14. Ng WL, Abdullah N
    Singapore Med J, 2020 Feb;61(2):81-85.
    PMID: 32152640 DOI: 10.11622/smedj.2020016
    INTRODUCTION: Medical emergencies occur at a rate of one in 604‒753 flights. Doctors travelling on commercial flights may encounter an in-flight medical emergency requiring their assistance. There is a paucity of studies on how confident primary care doctors are in managing in-flight medical emergencies. This study aimed to determine the knowledge, confidence and attitude of primary care doctors in managing in-flight medical emergencies.

    METHODS: A cross-sectional study was conducted on all primary care doctors working in government health clinics in Kuala Lumpur, Malaysia, from October 2016 to November 2016. A self-reported questionnaire was used, which included questions on demographic information, knowledge of in-flight medicine, and the attitude and confidence of primary care doctors in managing in-flight medical emergencies.

    RESULTS: 182 doctors completed the questionnaire (92.9% response rate). The mean knowledge score was 8.9 out of a maximum score of 20. Only 11.5% of doctors felt confident managing in-flight medical emergencies. The majority (69.2%) would assist in an in-flight medical emergency, but the readiness to assist was reduced if someone else was already helping or if they were not familiar with the emergency. Total knowledge score was positively associated with confidence in managing in-flight medical emergencies (p = 0.03).

    CONCLUSION: Only one in ten primary care doctors in this study felt confident managing in-flight medical emergencies. A higher total knowledge score of in-flight medical emergencies was positively associated with greater confidence in managing them. Educational programmes to address this gap in knowledge may be useful to improve doctors' confidence in managing in-flight medical emergencies.

  15. Ng, WL, Umi Kalthum MN, Jemaima CH, Norshamsiah MD
    MyJurnal
    Frontal mucocele is not commonly masked as upper lid abscess.A 72-year-old Chinese man with underlying hyperthyroidism complained of left upper eyelid swelling of 6 months duration. The swelling had persisted and worsen when intravenous antibiotic was changed oral type. Visual acuity on presentation was hand motion and reverse relative afferent pupillary defect was present. Because the swelling was large and resulted in mechanical ptosis and ophthalmoplegia, a CT imaging was performed, which showed huge left frontal mucocele eroding the supereromedial orbital rim. The left globe was displaced inferolaterally but there was no extension into brain parenchyma. Fundus examination showed pale optic disc with dull macula. Old laser marks were seen at peripheral fundus. Referral to ortholaryngologist was made and endoscopic sinus surgery and evacuation of mucopyocoele was done. Culture and sensitivity of the fluid showed no organism. He recovered well postoperatively with additional two weeks of antibiotics. We highlight the necessity of surgical drainage of mucocele, following a course of antibiotic.
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