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  1. Deng S, Mai Y, Niu J
    Gene, 2019 Mar 20;689:131-140.
    PMID: 30576805 DOI: 10.1016/j.gene.2018.12.016
    Citrus maxima "seedless" is originally from Malaysia, and now is widely cultivated in Hainan province, China. The essential features of this cultivar are thin skin, green epicarp and seedless at the ripening stage. Here, using C. maxima "seedless" as experimental material, we investigated the physical and inclusion indicators, and found the accumulation of storage compounds during 120-210 DAF leading to inconsistent increase between volume and weight. Component analysis of soluble sugar indicated that arabinose and xylose have a high content in early development of pummelo juice sacs (PJS), whereas fructose, glucose and sucrose show a significant increase during PJS maturation. To clarify a global overview of the gene expressing profiles, the PJSs from four periods (60, 120, 180 and 240 DAF) were selected for comparative transcriptome analysis. The resulting 8275 unigenes showed differential expression during PJS development. Also, the stability of 11 housekeeping genes were evaluated by geNorm method, resulting in a set of five genes (UBC, ACT, OR23, DWA2 and CYP21D) used as control for normalization of gene expression. Based on transcriptome data, 5 sucrose synthases (SUSs) and 10 invertases (INVs) were identified to be involved in sucrose degradation. Importantly, SUS4 may be responsible for arabinose and xylose biosynthesis to form the cell wall in early development, while SUS3 and VIN2 may be important in the accumulation of soluble hexose leading to cell expansion through an osmotic-independent pathway in late development. The information provides valuable metabolite and genetic resources in C. maxima "seedless", and is important for achieving high fruit yield and quality.
  2. Fu C, Deng S, Koneski I, Awad MM, Akram Z, Matinlinna J, et al.
    J Mech Behav Biomed Mater, 2020 12;112:104082.
    PMID: 32979607 DOI: 10.1016/j.jmbbm.2020.104082
    OBJECTIVE: To investigate the effect of blue light photoactivated riboflavin modified universal adhesives on dentin collagen biodegradation resistance, dentin apparent elastic modulus, and resin-dentin bond strength with interfacial morphology.

    METHODS: Dentin slabs were treated with 0.1% riboflavin-5-phosphate modified (powder added slowly while shaking and then sonicated to enhance the dispersion process) Universal Adhesive Scotch Bond and Zipbond™ along with control (non-modified) and experimental adhesives, photoactivated with blue light for 20s. Hydroxyproline (HYP) release was assessed after 1-week storage. Elastic-modulus testing was evaluated using universal testing machine at 24 h. Resin-dentin interfacial morphology was assessed with scanning electron-microscope, after 6-month storage. 0.1% rhodamine dye was added into each adhesive and analyzed using CLSM. Detection of free amino groups was carried out using ninhydrin and considered directly proportional to optical absorbance. Collagen molecular confirmation was determined using spectropolarimeter to evaluate and assess CD spectra. For molecular docking studies with riboflavin (PDB ID file), the binding pocket was selected with larger SiteScore and DScore using Schrodinger PB software. After curing, Raman shifts in Amide regions were obtained at 8 μm levels. Data were analyzed using Two-way analysis of variance (ANOVA, p ≤ 0.05) and Tukey-Kramer multiple comparison post hoc tests.

    RESULTS: At baseline, bond strength reduced significantly (p ≤ 0.05) in control specimens. However, at 6 months' storage, UVA Zipbond™ had significantly higher μTBS. Resin was able to diffuse through the porous demineralized dentin creating adequate hybrid layers in both 0.1%RF modified adhesives in CLSM images. In riboflavin groups, hybrid layer and resin tags were more pronounced. The circular dichroism spectrum showed negative peaks for riboflavin adhesive specimens. Best fitted poses adopted by riboflavin compound are docked with MMP-2 and -9 proteases. Amide bands and CH2 peaks followed the trend of being lowest for control UA Scotch bond adhesive specimens and increasing in Amides, proline, and CH2 intensities in 0.1%RF modified adhesive specimens. All 0.1%RF application groups showed statistically significant (p 

  3. Hu Q, Ma F, Wei H, Yang W, Deng S, Yu X, et al.
    J Texture Stud, 2023 Aug;54(4):582-594.
    PMID: 37400374 DOI: 10.1111/jtxs.12785
    The aim of this study was to compare the investigations of various contents of egg white protein (2.0%-8.0%, EWP), microbial transglutaminase (0.1%-0.4%, MTGase), and konjac glucomannan (0.5%-2.0%, KGM) on the gelling properties and rheological behavior of Trachypenaeus Curvirostris shrimp surimi gel (SSG), and assessed the modification mechanisms through the analysis of structure characteristics. The findings suggested that all modified SSG samples (expect SSG-KGM2.0% ) had the higher gelling properties and the denser network structure than those of unmodified SSG. Meanwhile, EWP could give SSG a better appearance than MTGase and KGM. Rheological results showed that SSG-EWP6% and SSG-KGM1.0% had the highest G' and G″, demonstrating that the formation of higher levels of elasticity and hardness. All modifications could increase gelation rates of SSG along with the reduction of G″ during the degeneration of protein. According to the FTIR results, three modification methods changed SSG protein conformation with the increasing α-helix and β-sheet contents and the decreasing of random coil content. LF-NMR results indicated that more free water could be transformed into immobilized water in the modified SSG gels, which contributed to improve the gelling properties. Furthermore, molecular forces showed that EWP and KGM could further increase the hydrogen bonds and hydrophobic interaction in SSG gels, while MTGase could induce the formation of more disulfide bonds. Thus, compared with another two modifications, EWP modified SSG gels showed the highest gelling properties.
  4. Xu X, Deng S, Essawy H, Lee SH, Lum WC, Zhou X, et al.
    Int J Biol Macromol, 2024 Oct;277(Pt 1):133784.
    PMID: 39084972 DOI: 10.1016/j.ijbiomac.2024.133784
    In this study, various chitosan-based films such as chitosan (C), chitosan-condensed tannin (CT), chitosan-casein (CC), and chitosan-casein-condensed tannin (CCT) films were prepared for the purpose of food packaging. In order to improve the hydrophobicity of these films, carnauba wax was blended into CCT to produce CCTW film. Properties such as morphology, UV resistance, water solubility, barrier performance, tensile strength, antioxidant, antibacterial and its performance as food packaging were evaluated. Compared with other chitosan-based films, CCTW films exhibited higher UV resistance, tensile strength, thermal stability and hydrophobicity. The addition of both condensed tannin and carnauba wax has significantly decreased the water vapor and oxygen permeability of the CCTW films. The CCTW films were proved capable of repelling most daily consuming liquids. Besides, CCTW films displayed outstanding free radical scavenging rate and antibacterial properties. Meanwhile, bananas wrapped with CCTW films remained fresh for seven days without any mold growth and outperformed other types of films. Apart from that, the CCTW films also showed biodegradable characteristics after exposure to Penicillium sp. These distinguished characteristics made the CCTW films a promising packaging material for long-term food storage.
  5. Tan KY, Deng S, Tan TK, Hari R, Sitam FT, Othman RY, et al.
    PeerJ, 2023;11:e16002.
    PMID: 37810781 DOI: 10.7717/peerj.16002
    BACKGROUND: The Malayan pangolin (Manis javanica) is a placental mammal and is listed as Critically Endangered on the IUCN Red List of Threatened Species. Most previous attempts to breed pangolins in captivity have met with little success because of dietary issues, infections, and other complications, although a previous study reported breeding pangolins in captivity to the third generation. In our previous pangolin genome sequencing data analysis, we obtained a considerable amount of bacterial DNA from a pregnant female Malayan pangolin (named "UM3"), which was likely infected by Paraburkholderia fungorum-an agent of biodegradation and bioremediation in agriculture.

    METHODOLOGY: Here, we further confirmed and characterized this bacterial species using PCR, histological staining, whole-genome sequencing, and bioinformatics approaches. PCR assays with in-house designed primer sets and 16S universal primers showed clear positive bands in the cerebrum, cerebellum, lung, and blood of UM3 suggesting that UM3 might have developed septicaemia. Histological staining showed the presence of Gram-negative rod-shaped bacteria in the pangolin brain and lungs, indicating the colonization of the bacteria in these two organs. In addition, PCR screening of UM3's fetal tissues revealed the presence of P. fungorum in the gastrocnemius muscle, but not in other tissues that we examined. We also sequenced and reconstructed the genome of pangolin P. fungorum, which has a genome size of 7.7 Mbps.

    CONCLUSION: Our study is the first to present detailed evidence of the presence of P. fungorum in a pangolin and her fetus (although preliminary results were presented in our previous article). Here, we raise the concern that P. fungorum may potentially infect humans, especially YOPI (young, old, pregnant, and immunocompromised) people. Therefore, caution should be exercised when using this bacterial species as biodegradation or bioremediation agents in agriculture.

  6. Quan Y, Ahmed SA, Menezes da Silva N, Al-Hatmi AMS, Mayer VE, Deng S, et al.
    Fungal Biol, 2021 Apr;125(4):276-284.
    PMID: 33766306 DOI: 10.1016/j.funbio.2020.11.006
    Among ancestral fungi in Chaetothyriales, several groups have a life style in association with tropical ants, either in domatia or in carton-nests. In the present study, two strains collected from ant carton in Thailand and Malaysia were found to represent hitherto undescribed species. Morphological, physiological, phylogenetic data and basic genome information are provided for their classification. Because of the relatively large phylogenetic distances with known species confirmed by overall genome data, large subunit (LSU) and Internal Transcribed Spacer (ITS) ribosomal DNA sequences were sufficient for taxonomic circumscription of the species. The analyzed strains clustered with high statistical support as a clade in the family Trichomeriaceae. Morphologically they were rather similar, lacking sporulation in vitro. In conclusion, Incumbomyces delicatus and Incumbomyces lentus were described as new species based on morphological, physiological and phylogenetic analysis.
  7. Zhang L, Tao Y, Woodring J, Rattana K, Sovannarith S, Rathavy T, et al.
    Int J Epidemiol, 2019 08 01;48(4):1327-1339.
    PMID: 30879066 DOI: 10.1093/ije/dyz037
    BACKGROUND: The Regional Framework for Triple Elimination of Mother-to-Child Transmission (EMTCT) of HIV, Hepatitis B (HBV) and Syphilis in Asia and the Pacific 2018-30 was endorsed by the Regional Committee of WHO Western Pacific in October 2017, proposing an integrated and coordinated approach to achieve elimination in an efficient, coordinated and sustainable manner. This study aims to assess the population impacts and cost-effectiveness of this integrated approach in the Cambodian context.

    METHODS: Based on existing frameworks for the EMTCT for each individual infection, an integrated framework that combines infection prevention procedures with routine antenatal care was constructed. Using decision tree analyses, population impacts, cost-effectiveness and the potential reduction in required resources of the integrated approach as a result of resource pooling and improvements in service coverage and coordination, were evaluated. The tool was assessed using simulated epidemiological data from Cambodia.

    RESULTS: The current prevention programme for 370,000 Cambodian pregnant women was estimated at USD$2.3 ($2.0-$2.5) million per year, including the duration of pregnancy and up to 18 months after delivery. A model estimate of current MTCT rates in Cambodia was 6.6% (6.2-7.1%) for HIV, 14.1% (13.1-15.2%) for HBV and 9.4% (9.0-9.8%) for syphilis. Integrating HIV and syphilis prevention into the existing antenatal care framework will reduce the total time required to provide this integrated care by 19% for health care workers and by 32% for pregnant women, resulting in a net saving of $380,000 per year for the EMTCT programme. This integrated approach reduces HIV and HBV MTCT to 6.1% (5.7-6.5%) and 13.0% (12.1-14.0%), respectively, and substantially reduces syphilis MCTC to 4.6% (4.3-5.0%). Further introduction of either antiviral treatment for pregnant women with high viral load of HBV, or hepatitis B immunoglobulin (HBIG) to exposed newborns, will increase the total cost of EMTCT to $4.4 ($3.6-$5.2) million and $3.3 ($2.7-$4.0) million per year, respectively, but substantially reduce HBV MTCT to 3.5% (3.2-3.8%) and 5.0% (4.6-5.5%), respectively. Combining both antiviral and HBIG treatments will further reduce HBV MTCT to 3.4% (3.1-3.7%) at an increased total cost of EMTCT of $4.5 ($3.7-$5.4) million per year. All these HBV intervention scenarios are highly cost-effective ($64-$114 per disability-adjusted life years averted) when the life benefits of these prevention measures are considered.

    CONCLUSIONS: The integrated approach, using antenatal, perinatal and postnatal care as a platform in Cambodia for triple EMTCT of HIV, HBV and syphilis, is highly cost-effective and efficient.

  8. Wu D, Shen E, Jiang B, Feng Y, Tang W, Lao S, et al.
    Nat Commun, 2022 02 03;13(1):689.
    PMID: 35115514 DOI: 10.1038/s41467-022-28359-9
    As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.
  9. Choo SW, Chong JL, Gaubert P, Hughes AC, O'Brien S, Chaber AL, et al.
    Sci Total Environ, 2022 Jun 10;824:153666.
    PMID: 35176378 DOI: 10.1016/j.scitotenv.2022.153666
  10. Hayrapetyan A, Tumasyan A, Adam W, Andrejkovic JW, Bergauer T, Chatterjee S, et al.
    Phys Rev Lett, 2024 Nov 08;133(19):191902.
    PMID: 39576923 DOI: 10.1103/PhysRevLett.133.191902
    The first search for soft unclustered energy patterns (SUEPs) is performed using an integrated luminosity of 138  fb^{-1} of proton-proton collision data at sqrt[s]=13  TeV, collected in 2016-2018 by the CMS detector at the LHC. Such SUEPs are predicted by hidden valley models with a new, confining force with a large 't Hooft coupling. In events with boosted topologies, selected by high-threshold hadronic triggers, the multiplicity and sphericity of clustered tracks are used to reject the background from standard model quantum chromodynamics. With no observed excess of events over the standard model expectation, limits are set on the cross section for production via gluon fusion of a scalar mediator with SUEP-like decays.
  11. Hayrapetyan A, Tumasyan A, Adam W, Andrejkovic JW, Bergauer T, Chatterjee S, et al.
    Phys Rev Lett, 2024 Nov 15;133(20):201803.
    PMID: 39626745 DOI: 10.1103/PhysRevLett.133.201803
    Searches for pair-produced multijet signatures using data corresponding to an integrated luminosity of 128  fb^{-1} of proton-proton collisions at sqrt[s]=13  TeV are presented. A data scouting technique is employed to record events with low jet scalar transverse momentum sum values. The electroweak production of particles predicted in R-parity violating supersymmetric models is probed for the first time with fully hadronic final states. This is the first search for prompt hadronically decaying mass-degenerate higgsinos, and extends current exclusions on R-parity violating top squarks and gluinos.
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