Displaying publications 1 - 20 of 148 in total

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  1. Gu C, Liang Y, Li J, Shao H, Jiang Y, Zhou X, et al.
    iScience, 2021 Dec 17;24(12):103439.
    PMID: 34988389 DOI: 10.1016/j.isci.2021.103439
    The highest plateau on Earth, Qinghai-Tibet Plateau, contains thousands of lakes with broad salinity and diverse and unique microbial communities. However, little is known about their co-occurring viruses. Herein, we identify 4,560 viral Operational Taxonomic Units (vOTUs) from six viromes of three saline lakes on Qinghai-Tibet Plateau, with less than 1% that could be classified. Most of the predicted vOTUs were associated with the dominant bacterial and archaeal phyla. Virus-encoded auxiliary metabolic genes suggest that viruses influence microbial metabolisms of carbon, nitrogen, sulfur, and lipid; the antibiotic resistance mediation; and their salinity adaption. The six viromes clustered together with the ice core viromes and bathypelagic ocean viromes and might represent a new viral habitat. This study has revealed the unique characteristics and potential ecological roles of DNA viromes in the lakes of the highest plateau and established a foundation for the recognition of the viral roles in plateau lake ecosystems.
  2. Li X, Abdullah LC, Sobri S, Md Said MS, Hussain SA, Aun TP, et al.
    Water Air Soil Pollut, 2023;234(5):328.
    PMID: 37200574 DOI: 10.1007/s11270-023-06279-8
    Currently, air quality has become central to global environmental policymaking. As a typical mountain megacity in the Cheng-Yu region, the air pollution in Chongqing is unique and sensitive. This study aims to comprehensively investigate the long-term annual, seasonal, and monthly variation characteristics of six major pollutants and seven meteorological parameters. The emission distribution of major pollutants is also discussed. The relationship between pollutants and the multi-scale meteorological conditions was explored. The results indicate that particulate matter (PM), SO2 and NO2 showed a "U-shaped" variation, while O3 showed an "inverted U-shaped" seasonal variation. Industrial emissions accounted for 81.84%, 58% and 80.10% of the total SO2, NOx and dust pollution emissions, respectively. The correlation between PM2.5 and PM10 was strong (R = 0.98). In addition, PM only showed a significant negative correlation with O3. On the contrary, PM showed a significant positive correlation with other gaseous pollutants (SO2, NO2, CO). O3 is only negatively correlated with relative humidity and atmospheric pressure. These findings provide an accurate and effective countermeasure for the coordinated management of air pollution in Cheng-Yu region and the formulation of the regional carbon peaking roadmap. Furthermore, it can improve the prediction accuracy of air pollution under multi-scale meteorological factors, promote effective emission reduction paths and policies in the region, and provide references for related epidemiological research.

    SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11270-023-06279-8.

  3. Chen W, Liao X, Wu Y, Liang JB, Mi J, Huang J, et al.
    Waste Manag, 2017 Mar;61:506-515.
    PMID: 28117129 DOI: 10.1016/j.wasman.2017.01.014
    Biochar, because of its unique physiochemical properties and sorption capacity, may be an ideal amendment in reducing gaseous emissions during composting process but there has been little information on the potential effects of different types of biochar on undesired gaseous emissions. The objective of this study was to examine the ability and mechanism of different types of biochar, as co-substrate, in mitigating gaseous emission from composting of layer hen manure. The study was conducted in small-scale laboratory composters with the addition of 10% of one of the following biochars: cornstalk biochar, bamboo biochar, woody biochar, layer manure biochar and coir biochar. The results showed that the cumulative NH3 production was significantly reduced by 24.8±2.9, 9.2±1.3, 20.1±2.6, 14.2±1.6, 11.8±1.7% (corrected for initial total N) in the cornstalk biochar, bamboo biochar, woody biochar, layer manure biochar and coir biochar treatments, respectively, compared to the control. Total CH4 emissions was significantly reduced by 26.1±2.3, 15.5±2.1, 22.4±3.1, 17.1±2.1% (corrected for the initial total carbon) for cornstalk biochar, bamboo biochar, woody biochar and coir biochar treatments than the control. Moreover, addition of cornstalk biochar increased the temperature and NO3(-)-N concentration and decreased the pH, NH4(+)-N and organic matter content throughout the composting process. The results suggested that total volatilization of NH3 and CH4 in cornstalk biochar treatment was lower than the other treatments; which could be due to (i) decrease of pH and higher nitrification, (ii) high sorption capacity for gases and their precursors, such as ammonium nitrogen from composting mixtures, because of the higher surface area, pore volumes, total acidic functional groups and CEC of cornstalk biochar.
  4. Gao X, Liu H, Li X, Fu S, Cao L, Shao N, et al.
    Vector Borne Zoonotic Dis, 2019 Jan;19(1):35-44.
    PMID: 30207876 DOI: 10.1089/vbz.2018.2291
    Japanese encephalitis virus (JEV) is a representative virus of the JEV serogroup in genus Flavivirus, family Flaviviridae. JEV is a mosquito-borne virus that causes Japanese encephalitis (JE), one of the most severe viral encephalitis diseases in the world. JEV is divided into five genotypes (G1-G5), and each genotype has its own distribution pattern. However, the distribution of different JEV genotypes has changed markedly in recent years. JEV G1 has replaced G3 as the dominant genotype in the traditional epidemic areas in Asia, while G3 has spread from Asia to Europe and Africa and caused domestic JE cases in Africa. G2 and G5, which were endemic in Malaysia, exhibited great geographical changes as well. G2 migrated southward and led to prevalence of JE in Australia, while G5 emerged in China and South Korea after decades of silence. Along with these changes, JE occurred in some non-traditional epidemic regions as an emerging infectious disease. The regional changes in JEV pose a great threat to human health, leading to huge disease burdens. Therefore, it is of great importance to strengthen the monitoring of JEV as well as virus genotypes, especially in non-traditional epidemic areas.
  5. Shiroiwa T, Murata T, Ahn J, Li X, Nakamura R, Teerawattananon Y, et al.
    Value Health Reg Issues, 2022 Nov;32:62-69.
    PMID: 36099801 DOI: 10.1016/j.vhri.2022.07.002
    OBJECTIVES: Almost all preference-based measures (PBMs) have been developed in Western countries, with none having been formulated in Asian countries. In this study, we construct a new generic PBM based on concept elicitation using interview surveys in East and Southeast Asian countries and qualitative analysis.

    METHODS: This cross-sectional study included 225 adults recruited from 9 East and Southeast Asian countries or regions (Indonesia, Japan, Korea, mainland China, Malaysia, the Philippines, Singapore, Taiwan, and Thailand). Trained interviewers conducted semistructured interviews with 25 participants from the general population of each country/region. Qualitative data were analyzed using a content analysis approach. The selection of items was determined based on interview surveys and team member discussions. The description of items was considered based on a detailed qualitative analysis of the interview survey.

    RESULTS: A new region-specific PBM-the Asia PBM 7 dimensions instrument-was designed. It reflects East and Southeast Asian values and comprises 7 items: pain, mental health, energy, mobility, work/school, interpersonal interactions, and burden to others.

    CONCLUSIONS: The new region-specific instrument is one of the first PBMs developed in the context of non-Western countries. The Asia PBM 7 dimensions contains 7 items that address the core concepts of health-related quality of life that are deemed important based on East and Southeast Asian health concepts.

  6. Li XP, Lin D, Zhang Y, Chen SQ, Bai HQ, Zhang SN, et al.
    Trop Biomed, 2020 Mar 01;37(1):116-126.
    PMID: 33612723
    Several bioactive molecules isolated from the saliva of blood-sucking arthropods, such as mosquitoes, have been shown to exhibit potential anticoagulant function. We have previously identified a 30kDa allergen named Aegyptin-like protein (alALP), which is highly homologous to Aegyptin, from the salivary glands of female Aedes albopictus (Asian tiger mosquito). In this study, we identified the conserved functional domain of alALP by using bioinformatic tools, and expressed the His-tagged alALP recombinant protein in sf9 insect cells by generation and transfection of a baculoviral expression plasmid carrying the fulllength cDNA of alALP. We purified this recombinant protein and examined its function on the inhibition of blood coagulation. The results showed that the purified His-alALP prolonged the Activated Partial Thromboplastin Time (APTT), Prothrombin Time (PT) and Thrombin Time (TT) in vitro as well as the Bleeding Time (BT) in vivo, which suggest that alALP could be a novel anticoagulant.
  7. Li S, Lu BP, Feng J, Zhou JJ, Xie ZZ, Liang C, et al.
    Trop Biomed, 2020 Dec 01;37(4):852-863.
    PMID: 33612738 DOI: 10.47665/tb.37.4.852
    Fructose-1,6-bisphosphate aldolase (FbA), a well characterized glycometabolism enzyme, has been found to participate in other important processes besides the classic catalysis. To understand the important functions of three fructose-1,6-bisphosphate aldolases from Clonorchis sinensis (CsFbAs, CsFbA-1/2/3) in host-parasite interplay, the open reading frames of CsFbAs were cloned into pET30a (+) vector and the resulting recombinant plasmids were transformed into Escherichia coli BL21 (DE3) for expression of the proteins. Purified recombinant CsFbAs proteins (rCsFbAs) were approximately 45.0 kDa on 12% SDS-PAGE and could be probed with each rat anti-rCsFbAs sera by western blotting analysis. ELISA and ligand blot overlay indicated that rCsFbAs of 45.0 kDa as well as native CsFbAs of 39.5 kDa from total worm extracts and excretory-secretory products of Clonorchis sinensis (CsESPs) could bind to human plasminogen, and the binding could be efficiently inhibited by lysine analog ε-aminocaproic acid. Our results suggested that as both the components of CsESPs and the plasminogen binding proteins, three CsFbAs might be involved in preventing the formation of the blood clot so that Clonorchis sinensis could acquire enough nutrients from host tissue for their successful survival and colonization in the host. Our work will provide us with new information about the biological function of three CsFbAs and their roles in hostparasite interplay.
  8. Zhang X, Deng T, Lu J, Zhao P, Chen L, Qian M, et al.
    Transbound Emerg Dis, 2020 May;67(3):1349-1355.
    PMID: 31943814 DOI: 10.1111/tbed.13477
    Infectious bronchitis virus (IBV), an ongoing emergence enveloped virus with a single-stranded positive-sense RNA genome, belongs to the Gammacoronavirus genus in the Coronaviridae family. IBV-associated tracheitis, nephritis, salpingitis, proventriculitis and egg drop have caused devastating economic losses to poultry industry worldwide. Since the end of 2018, a remarkably increasing number of commercial broilers and layers, vaccinated or not, were infected with IBV in China. Here, we described two IB outbreaks with severe respiratory system or kidney injury in IBV-vaccinated commercial poultry farms in central China. Other possible causative viral pathogens, including avian influenza virus (AIV), Newcastle disease virus (NDV) and Kedah fatal kidney syndrome virus (KFKSV), were excluded by reverse transcription-polymerase chain reaction (RT-PCR), and three virulent IBV strains, HeN-1/China/2019, HeN-2/China/2019 and HeN-101/China/2019, were identified. Although the gross pathologic appearance of these two IB outbreaks was different, the newly identified IBV strains were all closely related to the ck/China/I0529/17 strain and grouped into GI-19 genotype clade based on the sequencing and phylogenetic analysis of the complete S1 genes. Moreover, there are still some evolutionary distance between the newly identified IBV strains, HeN-101/China/2019 in particular, and other GI-19 strains, suggesting that Chinese IBV strains constantly emerge and evolve towards different directions. In conclusion, this study provided an insight of the recently emerging IBV outbreaks in IBV-vaccinated commercial poultry farms and identified the genetic characteristics of three virulent GI-19 IBV strains, which shows the need to carry out proper preventive measures and control strategies.
  9. Zhou X, Li Y, Wang W, Wang S, Hou J, Zhang A, et al.
    Theranostics, 2020;10(21):9443-9457.
    PMID: 32863938 DOI: 10.7150/thno.46078
    Objective: Esophageal squamous cell carcinoma (ESCC) is one of the most commonly diagnosed cancer types in China. Recent genomic sequencing analysis indicated the over-activation of Hippo/YAP signaling might play important roles for the carcinogenic process and progression for ESCC patients. However, little is known about the molecular mechanisms that controls Hippo signaling activity in ESCC. Our previous studies indicated that PLCE1-an important risk factor for ESCC-linked to ESCC progression through snail signaling, during this period, we found PARK2 was an important downstream target of PLCE1-snail axis. PARK2 was decreased in ESCC human samples, and correlated with good prognosis in ESCC patients. Further research showed that PARK2 could inhibit YAP, which functions as key downstream effectors of the Hippo pathway. Here, we aim to reveal the molecular mechanisms of PARK2 modulated Hippo pathway in ESCC. Methods: To evaluate the function of PARK2 in ESCC, we used a tissue microarray (TMA) of 223 human ESCC patients and immunohistochemistry to analyze the correlation between PARK2 expression and clinicopathologic variables. Depletion of endogenous PARK2 and YAP from ESCC cells using CRISPR/Cas9 technologies. Flow cytometry and EdU cell proliferation assay were used to detect proliferation of ESCC cells. Nude mice subcutaneous injection and Ki-67 staining were used to evaluate tumor growth in vivo. Migration and invasion assays were performed. In addition, lung metastasis models in mice were used to validate the function of PARK2 in vivo. Identification of PARK2 involved in hippo pathway was achieved by expression microarray screening, double immunofluorescence staining and co-immunoprecipitation assays. The RNA-seq analysis results were validated through quantitative real-time PCR (qRT-PCR) analysis. The protein half-life of YAP was analyzed by Cycloheximide assay, and the TEAD activity was detected by Luciferase reporter assays. Results: Clinical sample of ESCC revealed that low PARK2 expression correlated with late tumor stage (P < 0.001), poor differentiation (P < 0.04), lymph node (P < 0.001) and distant metastasis (P = 0.0087). Multivariate Cox proportional regression analysis further revealed that PARK2 expression (P = 0.032) is an independent prognostic factor for the overall survival of ESCC patients. Besides, the immunohistochemistry results showed that PARK2 negatively correlated with YAP protein level (P < 0.001). PARK2 depletion promotes ESCC progression both through Hippo/YAP axis, while PARK2 overexpression suppresses ESCC tumor progression by Hippo signaling. Co-IP and ubiquitination assays revealed that PARK2 could interact with YAP in the cytosol and promotes YAP K48-linked ubiquitination at K90 sites. Conclusion: Clinical sample analysis and mechanistic study have validated PARK2 as a tumor suppressor for ESCC. Multivariate Cox proportional regression analysis further revealed that PARK2 is an independent prognostic factor for the overall survival of ESCC patients. Cellular and molecular mechanisms in this study showed that PARK2 associated with YAP protein in the cytosol, promoted YAP ubiquitination and proteasome-dependent degradation in ESCC cells. Therefore, as a novel modulator for Hippo signaling, modulation of PARK2 activity or gene expression level could be an appealing strategy to treat esophageal.
  10. Miller V, Jenkins DA, Dehghan M, Srichaikul K, Rangarajan S, Mente A, et al.
    PMID: 38588684 DOI: 10.1016/S2213-8587(24)00069-X
    BACKGROUND: The association between the glycaemic index and the glycaemic load with type 2 diabetes incidence is controversial. We aimed to evaluate this association in an international cohort with diverse glycaemic index and glycaemic load diets.

    METHODS: The PURE study is a prospective cohort study of 127 594 adults aged 35-70 years from 20 high-income, middle-income, and low-income countries. Diet was assessed at baseline using country-specific validated food frequency questionnaires. The glycaemic index and the glycaemic load were estimated on the basis of the intake of seven categories of carbohydrate-containing foods. Participants were categorised into quintiles of glycaemic index and glycaemic load. The primary outcome was incident type 2 diabetes. Multivariable Cox Frailty models with random intercepts for study centre were used to calculate hazard ratios (HRs).

    FINDINGS: During a median follow-up of 11·8 years (IQR 9·0-13·0), 7326 (5·7%) incident cases of type 2 diabetes occurred. In multivariable adjusted analyses, a diet with a higher glycaemic index was significantly associated with a higher risk of diabetes (quintile 5 vs quintile 1; HR 1·15 [95% CI 1·03-1·29]). Participants in the highest quintile of the glycaemic load had a higher risk of incident type 2 diabetes compared with those in the lowest quintile (HR 1·21, 95% CI 1·06-1·37). The glycaemic index was more strongly associated with diabetes among individuals with a higher BMI (quintile 5 vs quintile 1; HR 1·23 [95% CI 1·08-1·41]) than those with a lower BMI (quintile 5 vs quintile 1; 1·10 [0·87-1·39]; p interaction=0·030).

    INTERPRETATION: Diets with a high glycaemic index and a high glycaemic load were associated with a higher risk of incident type 2 diabetes in a multinational cohort spanning five continents. Our findings suggest that consuming low glycaemic index and low glycaemic load diets might prevent the development of type 2 diabetes.

    FUNDING: Full funding sources are listed at the end of the Article.

  11. Di J, Xiong Y, Li D, Li X, Wang W, Cheng Y, et al.
    Malays J Pathol, 2022 Dec;44(3):509-516.
    PMID: 36591718
    Hyalinising clear cell carcinoma (HCCC) of the lung is an extremely rare tumour that is just recently recognised as one of the salivary gland-type tumours (SGTT) in the latest WHO classification of thoracic tumours. Eleven cases have been reported in English literature since Joaquín et al. reported the first case. Given the very limited number of cases, the clinical and histological features of pulmonary HCCC are equivocal. Herein, we present two cases of pulmonary HCCC. The patients were a 66-year-old man and a 48-year-old woman. The mass was located on the right main bronchus and right middle lobar bronchus separately. One was 2 cm and the other was 3.3 cm in the greatest dimension. The tumours were comprised of small monomorphic cells with clear or eosinophilic cytoplasm and infiltrated in a hyalinising stroma arranged in nests, cords, sheets and trabeculae. Their morphology resembled their head and neck counterparts. Immunohistochemically, the tumour cells were positive for AE1/AE3, P63, while negative for TTF1, Calponin, S-100, HMB45 and PAX8. Ki-67 labeling ranges from 3% to 10%. Fluorescence in situ hybridisation (FISH) demonstrated EWSR1 rearrangement and Next-generation sequencing (NGS) demonstrated EWSR1- ATF1 (exon 11: exon 3) fusion in case one and EWSR1- ATF1 (exon 2: exon 12) fusion in case two. This is the first time to report the EWSR1-ATF1fusion point other than exon 11: exon 3 in pulmonary HCCC. Case one recurred two years after local resection but didn't metastasise during follow-up 36 months. Case two is alive without disease after lobectomy during follow-up 14 months.
  12. Luo Y, Chang Y, Zhao Z, Xia J, Xu C, Bee YM, et al.
    Lancet Reg Health West Pac, 2023 Jun;35:100746.
    PMID: 37424694 DOI: 10.1016/j.lanwpc.2023.100746
    BACKGROUND: Technological advances make it possible to use device-supported, automated algorithms to aid basal insulin (BI) dosing titration in patients with type 2 diabetes.

    METHODS: A systematic review and meta-analysis of randomized controlled trials were performed to evaluate the efficacy, safety, and quality of life of automated BI titration versus conventional care. The literature in Medline, Embase, Web of Science, and the Cochrane databases from January 2000 to February 2022 were searched to identify relevant studies. Risk ratios (RRs), mean differences (MDs), and their 95% confidence intervals (CIs) were calculated using random-effect meta-analyses. Certainty of evidence was assessed using the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) approach.

    FINDINGS: Six of the 7 eligible studies (889 patients) were included in meta-analyses. Low- to moderate-quality evidence suggests that patients who use automated BI titration versus conventional care may have a higher probability of reaching a target of HbA1c <7.0% (RR, 1.82 [95% CI, 1.16-2.86]); and a lower level of HbA1c (MD, -0.25% [95% CI, -0.43 to -0.06%]). No statistically significant differences were detected between the two groups in fasting glucose results, incidences of hypoglycemia, severe or nocturnal hypoglycemia, and quality of life, with low to very low certainty for all the evidence.

    INTERPRETATION: Automated BI titration is associated with small benefits in reducing HbA1c without increasing the risk of hypoglycemia. Future studies should explore patient attitudes and the cost-effectiveness of this approach.

    FUNDING: Sponsored by the Chinese Geriatric Endocrine Society.

  13. Page DB, Broeckx G, Jahangir CA, Verbandt S, Gupta RR, Thagaard J, et al.
    J Pathol, 2023 Aug;260(5):514-532.
    PMID: 37608771 DOI: 10.1002/path.6165
    Modern histologic imaging platforms coupled with machine learning methods have provided new opportunities to map the spatial distribution of immune cells in the tumor microenvironment. However, there exists no standardized method for describing or analyzing spatial immune cell data, and most reported spatial analyses are rudimentary. In this review, we provide an overview of two approaches for reporting and analyzing spatial data (raster versus vector-based). We then provide a compendium of spatial immune cell metrics that have been reported in the literature, summarizing prognostic associations in the context of a variety of cancers. We conclude by discussing two well-described clinical biomarkers, the breast cancer stromal tumor infiltrating lymphocytes score and the colon cancer Immunoscore, and describe investigative opportunities to improve clinical utility of these spatial biomarkers. © 2023 The Pathological Society of Great Britain and Ireland.
  14. Thagaard J, Broeckx G, Page DB, Jahangir CA, Verbandt S, Kos Z, et al.
    J Pathol, 2023 Aug;260(5):498-513.
    PMID: 37608772 DOI: 10.1002/path.6155
    The clinical significance of the tumor-immune interaction in breast cancer is now established, and tumor-infiltrating lymphocytes (TILs) have emerged as predictive and prognostic biomarkers for patients with triple-negative (estrogen receptor, progesterone receptor, and HER2-negative) breast cancer and HER2-positive breast cancer. How computational assessments of TILs might complement manual TIL assessment in trial and daily practices is currently debated. Recent efforts to use machine learning (ML) to automatically evaluate TILs have shown promising results. We review state-of-the-art approaches and identify pitfalls and challenges of automated TIL evaluation by studying the root cause of ML discordances in comparison to manual TIL quantification. We categorize our findings into four main topics: (1) technical slide issues, (2) ML and image analysis aspects, (3) data challenges, and (4) validation issues. The main reason for discordant assessments is the inclusion of false-positive areas or cells identified by performance on certain tissue patterns or design choices in the computational implementation. To aid the adoption of ML for TIL assessment, we provide an in-depth discussion of ML and image analysis, including validation issues that need to be considered before reliable computational reporting of TILs can be incorporated into the trial and routine clinical management of patients with triple-negative breast cancer. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
  15. Jahangir CA, Page DB, Broeckx G, Gonzalez CA, Burke C, Murphy C, et al.
    J Pathol, 2024 Mar;262(3):271-288.
    PMID: 38230434 DOI: 10.1002/path.6238
    Recent advances in the field of immuno-oncology have brought transformative changes in the management of cancer patients. The immune profile of tumours has been found to have key value in predicting disease prognosis and treatment response in various cancers. Multiplex immunohistochemistry and immunofluorescence have emerged as potent tools for the simultaneous detection of multiple protein biomarkers in a single tissue section, thereby expanding opportunities for molecular and immune profiling while preserving tissue samples. By establishing the phenotype of individual tumour cells when distributed within a mixed cell population, the identification of clinically relevant biomarkers with high-throughput multiplex immunophenotyping of tumour samples has great potential to guide appropriate treatment choices. Moreover, the emergence of novel multi-marker imaging approaches can now provide unprecedented insights into the tumour microenvironment, including the potential interplay between various cell types. However, there are significant challenges to widespread integration of these technologies in daily research and clinical practice. This review addresses the challenges and potential solutions within a structured framework of action from a regulatory and clinical trial perspective. New developments within the field of immunophenotyping using multiplexed tissue imaging platforms and associated digital pathology are also described, with a specific focus on translational implications across different subtypes of cancer. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
  16. Lou Z, Xu Y, Xiang K, Su N, Qin L, Li X, et al.
    FEBS J, 2006 Oct;273(19):4538-47.
    PMID: 16972940
    The Nipah and Hendra viruses are highly pathogenic paramyxoviruses that recently emerged from flying foxes to cause serious disease outbreaks in humans and livestock in Australia, Malaysia, Singapore and Bangladesh. Their unique genetic constitution, high virulence and wide host range set them apart from other paramyxoviruses. These characteristics have led to their classification into the new genus Henpavirus within the family Paramyxoviridae and to their designation as Biosafety Level 4 pathogens. The fusion protein, an enveloped glycoprotein essential for viral entry, belongs to the family of class I fusion proteins and is characterized by the presence of two heptad repeat (HR) regions, HR1 and HR2. These two regions associate to form a fusion-active hairpin conformation that juxtaposes the viral and cellular membranes to facilitate membrane fusion and enable subsequent viral entry. The Hendra and Nipah virus fusion core proteins were crystallized and their structures determined to 2.2 A resolution. The Nipah and Hendra fusion core structures are six-helix bundles with three HR2 helices packed against the hydrophobic grooves on the surface of a central coiled coil formed by three parallel HR1 helices in an oblique antiparallel manner. Because of the high level of conservation in core regions, it is proposed that the Nipah and Hendra virus fusion cores can provide a model for membrane fusion in all paramyxoviruses. The relatively deep grooves on the surface of the central coiled coil represent a good target site for drug discovery strategies aimed at inhibiting viral entry by blocking hairpin formation.
  17. Ong P, Jian J, Li X, Zou C, Yin J, Ma G
    PMID: 37356390 DOI: 10.1016/j.saa.2023.123037
    The proliferation of pathogenic fungi in sugarcane crops poses a significant threat to agricultural productivity and economic sustainability. Early identification and management of sugarcane diseases are therefore crucial to mitigate the adverse impacts of these pathogens. In this study, visible and near-infrared spectroscopy (380-1400 nm) combined with a novel wavelength selection method, referred to as modified flower pollination algorithm (MFPA), was utilized for sugarcane disease recognition. The selected wavelengths were incorporated into machine learning models, including Naïve Bayes, random forest, and support vector machine (SVM). The developed simplified SVM model, which utilized the MFPA wavelength selection method yielded the best performances, achieving a precision value of 0.9753, a sensitivity value of 0.9259, a specificity value of 0.9524, and an accuracy of 0.9487. These results outperformed those obtained by other wavelength selection approaches, including the selectivity ratio, variable importance in projection, and the baseline method of the flower pollination algorithm.
  18. Ong P, Jian J, Li X, Yin J, Ma G
    PMID: 37804706 DOI: 10.1016/j.saa.2023.123477
    Spectroscopy in the visible and near-infrared region (Vis-NIR) region has proven to be an effective technique for quantifying the chlorophyll contents of plants, which serves as an important indicator of their photosynthetic rate and health status. However, the Vis-NIR spectroscopy analysis confronts a significant challenge concerning the existence of spectral variations and interferences induced by diverse factors. Hence, the selection of characteristic wavelengths plays a crucial role in Vis-NIR spectroscopy analysis. In this study, a novel wavelength selection approach known as the modified regression coefficient (MRC) selection method was introduced to enhance the diagnostic accuracy of chlorophyll content in sugarcane leaves. Experimental data comprising spectral reflectance measurements (220-1400 nm) were collected from sugarcane leaf samples at different growth stages, including seedling, tillering, and jointing, and the corresponding chlorophyll contents were measured. The proposed MRC method was employed to select optimal wavelengths for analysis, and subsequent partial least squares regression (PLSR) and Gaussian process regression (GPR) models were developed to establish the relationship between the selected wavelengths and the measured chlorophyll contents. In comparison to full-spectrum modelling and other commonly employed wavelength selection techniques, the proposed simplified MRC-GPR model, utilizing a subset of 291 selected wavelengths, demonstrated superior performance. The MRC-GPR model achieved higher coefficient of determination of 0.9665 and 0.8659, and lower root mean squared error of 1.7624 and 3.2029, for calibration set and prediction set, respectively. Results showed that the GPR model, a nonlinear regression approach, outperformed the PLSR model.
  19. Li X, Wang X, Ong P, Yi Z, Ding L, Han C
    Sensors (Basel), 2023 Oct 13;23(20).
    PMID: 37896537 DOI: 10.3390/s23208444
    Dragon fruit (Hylocereus undatus) is a tropical and subtropical fruit that undergoes multiple ripening cycles throughout the year. Accurate monitoring of the flower and fruit quantities at various stages is crucial for growers to estimate yields, plan orders, and implement effective management strategies. However, traditional manual counting methods are labor-intensive and inefficient. Deep learning techniques have proven effective for object recognition tasks but limited research has been conducted on dragon fruit due to its unique stem morphology and the coexistence of flowers and fruits. Additionally, the challenge lies in developing a lightweight recognition and tracking model that can be seamlessly integrated into mobile platforms, enabling on-site quantity counting. In this study, a video stream inspection method was proposed to classify and count dragon fruit flowers, immature fruits (green fruits), and mature fruits (red fruits) in a dragon fruit plantation. The approach involves three key steps: (1) utilizing the YOLOv5 network for the identification of different dragon fruit categories, (2) employing the improved ByteTrack object tracking algorithm to assign unique IDs to each target and track their movement, and (3) defining a region of interest area for precise classification and counting of dragon fruit across categories. Experimental results demonstrate recognition accuracies of 94.1%, 94.8%, and 96.1% for dragon fruit flowers, green fruits, and red fruits, respectively, with an overall average recognition accuracy of 95.0%. Furthermore, the counting accuracy for each category is measured at 97.68%, 93.97%, and 91.89%, respectively. The proposed method achieves a counting speed of 56 frames per second on a 1080ti GPU. The findings establish the efficacy and practicality of this method for accurate counting of dragon fruit or other fruit varieties.
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