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  1. Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, et al.
    Autophagy, 2021 Jan;17(1):1-382.
    PMID: 33634751 DOI: 10.1080/15548627.2020.1797280
    In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
  2. Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, et al.
    Autophagy, 2016;12(1):1-222.
    PMID: 26799652 DOI: 10.1080/15548627.2015.1100356
  3. Wang YH, Chen CB, Tassaneeyakul W, Saito Y, Aihara M, Choon SE, et al.
    Clin. Pharmacol. Ther., 2019 01;105(1):112-120.
    PMID: 29569740 DOI: 10.1002/cpt.1071
    Specific ethnic genetic backgrounds are associated with the risk of Stevens-Johnson syndrome / toxic epidermal necrolysis (SJS/TEN) especially in Asians. However, there have been no large cohort, multiple-country epidemiological studies of medication risk related to SJS/TEN in Asian populations. Thus, we analyzed the registration databases from multiple Asian countries who were treated during 1998-2017. A total 1,028 SJS/TEN cases were identified with the algorithm of drug causality for epidermal necrolysis. Furthermore, those medications labeled by the US Food and Drug Administration (FDA) as carrying a risk of SJS/TEN were also compared with the common causes of SJS/TEN in Asian countries. Oxcarbazepine, sulfasalazine, COX-II inhibitors, and strontium ranelate were identified as new potential causes. In addition to sulfa drugs and beta-lactam antibiotics, quinolones were also a common cause. Only one acetaminophen-induced SJS was identified, while several medications (e.g., oseltamivir, terbinafine, isotretinoin, and sorafenib) labeled as carrying a risk of SJS/TEN by the FDA were not found to have caused any of the cases in the Asian countries investigated in this study.
  4. Oyomopito RA, Chen YJ, Sungkanuparph S, Kantor R, Merati T, Yam WC, et al.
    Kaohsiung J. Med. Sci., 2015 Sep;31(9):445-53.
    PMID: 26362956 DOI: 10.1016/j.kjms.2015.07.002
    Human immunodeficiency virus (HIV)-1 epidemics in Asian countries are driven by varying exposures. The epidemiology of the regional pandemic has been changing with the spread of HIV-1 to lower-risk populations through sexual transmission. Common HIV-1 genotypes include subtype B and circulating recombinant form (CRF) 01_AE. Our objective was to use HIV-1 genotypic data to better quantify local epidemics. TASER-M is a multicenter prospective cohort of HIV-infected patients. Associations between HIV exposure, patient sex, country of sample origin and HIV-1 genotype were evaluated by multivariate logistic regression. Phylogenetic methods were used on genotypic data to investigate transmission relationships. A total of 1086 patients from Thailand, Hong Kong, Malaysia and the Philippines were included in analyses. Proportions of male patients within countries varied (Thailand: 55.6%, Hong Kong: 86.1%, Malaysia: 81.4%, Philippines: 93.8%; p 
  5. Pasion EG, Sivananthan SK, Kung AW, Chen SH, Chen YJ, Mirasol R, et al.
    J. Bone Miner. Metab., 2007;25(2):105-13.
    PMID: 17323180
    We evaluated adherence with raloxifene therapy compared with daily bisphosphonate in Asian postmenopausal women at increased risk of osteoporotic fractures. In this 12-month observational study conducted in Asia (Hong Kong, Malaysia, Pakistan, Philippines, Singapore, Taiwan), 984 postmenopausal women (aged 55 years or older) were treated with raloxifene 60 mg/day (n = 707; 72%) or daily bisphosphonate (alendronate 10 mg/day; n = 206; 21%, or risedronate 5 mg/day; n = 71; 7%) during their normal course of care. Patients were assessed at baseline, 6, and 12 months. Baseline characteristics (including age, race, education, menopausal status, and baseline fractures) were comparable between the raloxifene and bisphosphonate groups. More women on raloxifene completed the study compared with those on bisphosphonate (50.2% versus 37.5%; P < 0.001). Patients also took raloxifene for a longer period than bisphosphonate (median, 356 versus 348 days; P = 0.011). Compared with those taking bisphosphonate, significantly fewer patients taking raloxifene discontinued the study because of stopping treatment (5.7% versus 10.1%, P = 0.017) or changing treatment (2.8% versus 9.7%, P < 0.001). Inconvenient dosing was reported as a primary reason for discontinuation due to stopping or changing treatment in 19 (6.9%) bisphosphonate patients compared with 0 raloxifene patients. The percentage of patients who had consumed 80% or more of their study medication was similar for raloxifene patients (48-56 weeks; 95.2%) and bisphosphonate patients (48-56 weeks; 93.3%). More raloxifene patients responded that they were satisfied with their medication than bisphosphonate patients at 48-56 weeks (P = 0.002). We concluded that Asian postmenopausal women at increased risk of osteoporotic fractures showed a greater propensity to remain on raloxifene compared with bisphosphonate. The women on raloxifene exhibited lower discontinuation rates and higher treatment satisfaction.
  6. Chen YJ, Chang JC, Lai EL, Liao TL, Chen HH, Hung WT, et al.
    Semin Arthritis Rheum, 2020 06;50(3):451-457.
    PMID: 32115237 DOI: 10.1016/j.semarthrit.2020.01.014
    OBJECTIVES: Systemic lupus erythematosus (SLE) is an autoimmune disease that develops mainly in women of reproductive age. We aimed to explore the risk of pregnancy complications in Asian patients with SLE.

    METHODS: From January 2005 to December 2014, we conducted a nationwide case-control study, using Taiwan's National Health Insurance Research Database. Obstetric complications and perinatal outcomes in SLE patients were compared with those without SLE.

    RESULTS: 2059 SLE offspring and 8236 age-matched, maternal healthy controls were enrolled. We found increased obstetric and perinatal complications in SLE population compared with healthy controls. SLE patients exhibited increased risk of preeclampsia/eclampsia (8.98% vs.1.98%, odds ratio [OR]: 3.87, 95% confidence interval [95% CI]: 3.08-4.87, p<0.0001). Their offspring tended to have lower Apgar scores (<7) at both 1 min (10.7% vs. 2.58%, p<0.0001) and 5 min (4.25% vs. 1.17%, p<0.0001), as well as higher rates of intrauterine growth restriction (IUGR, 9.91% vs. 4.12%, OR: 2.24, 95% CI: 1.85-2.71, p<0.0001), preterm birth (23.70% vs 7.56%, OR: 3.00, 95% CI: 2.61-3.45, p<0.0001), and stillbirth (4.23% vs. 0.87%, OR: 3.59, 95% CI: 2.54-5.06, p<0.0001). The risks of preterm birth and stillbirth were markedly increased in SLE patients with concomitant preeclampsia/eclampsia or IUGR. Preterm birth of SLE patients was 1~4 gestational weeks earlier than that of healthy controls and the peak occurrence of stillbirth in SLE population was at 20~30 gestational weeks.

    CONCLUSIONS: Asian SLE patients exhibited increased risks of maternal complications and adverse birth outcomes. Frequent antenatal visits before 20 gestational weeks are recommended in high-risk SLE patients.

  7. Grey AC, Lin Q, Low TY, Wu W, Haynes PA, Chung MCM, et al.
    Mol Cell Proteomics, 2023 Sep;22(9):100627.
    PMID: 37532177 DOI: 10.1016/j.mcpro.2023.100627
    As the first in-person Asia Oceania Human Proteomics Organization (AOHUPO) congress since 2018, the 11th AOHUPO congress was an opportune time for the research community to reconnect and to renew friendships after the long period of restricted travel due to the global pandemic. Moreover, this congress was a great opportunity for the many AO regional proteomics and mass spectrometry scientists to meet in Singapore to exchange ideas and to present their latest findings. Cohosted by the Singapore Society for Mass Spectrometry and the Malaysian Proteomics Society and held in conjunction with the seventh Asia Oceania Agricultural Proteomics Organization Congress and Singapore Society for Mass Spectrometry 2023, the meeting featured both human and agricultural proteomics. Over five hundred scientists from the AO region converged on the MAX Atria @ Singapore EXPO, Changi, Singapore from May 8 to 10 for the main congress. The diverse program was made up of 64 invited speakers and panellists for seven plenary lectures, 27 concurrent symposia, precongress and postcongress workshops, and 174 poster presentations. The AOHUPO society were able to celebrate not only their 20th anniversary but also the outstanding academic research from biological and agricultural proteomics and related 'omics fields being conducted across the Asia-Oceania region.
  8. Ishihama Y, Chen YJ, Cho JY, Ming Chung MC, Cordwell SJ, Low TY, et al.
    Mol Cell Proteomics, 2021;20:100048.
    PMID: 33465491 DOI: 10.1016/j.mcpro.2021.100048
    The Asia-Oceania Human Proteome Organization (AOHUPO; www.aohupo.org) was officially founded on June 7, 2001, by Richard J. Simpson (Australia), Akira Tsugita (Japan), and Young-Ki Paik (Korea) and launched on October 1-4, 2001, at the second scientific meeting of the International Proteomics Conference held in Canberra, Australia. Inaugural council members of the AOHUPO elected were Richard J. Simpson (Australia, president), Qi-Chang Xia (China), Kazuyuki Nakamura (Japan), Akira Tsugita (Japan, VIce President), Young-Ki Paik (Korea, secretary general), Mike Hubbard (New Zealand), Max C. M. Chung (Singapore), Shui-Tien Chen (Taiwan), and John Bennett (Philippines). The first AOHUPO conference was held on March 26-27, 2002, at the Seoul National University, Seoul, Korea, conjointly with the second Annual Meeting of KHUPO. Since then, biennial AOHUPO conferences have been held in Taipei (2004), Singapore (2006), Cairns (2008), Hyderabad (2010), Beijing (2012), Bangkok (2014), Sun Moon Lake (2016), and Osaka (2018). The 10th AOHUPO conference is scheduled to be held in Busan on June 30 to July 2, 2021, to celebrate our 20th anniversary.
  9. Loo YC, Hu HC, Yu SY, Tsai YH, Korinek M, Wu YC, et al.
    Phytomedicine, 2023 Feb;110:154643.
    PMID: 36623444 DOI: 10.1016/j.phymed.2023.154643
    BACKGROUND: Skin aging is associated with degradation of collagen by matrix metalloproteinases (MMPs), which leads to loss of skin elasticity and formation of wrinkles. Cosmos caudatus Kunth (CC) has been traditionally claimed as an anti-aging agent in Malaysia. Despite its well-known antioxidant activity, the anti-aging properties of CC was not validated.

    PURPOSE: This study aimed to investigate the anti-aging potential of CC extracts and fractions, particularly their inhibition of collagenase, MMP-1 and MMP-3 activities in human dermal fibroblasts CCD-966SK, followed by isolation, identification and analysis of their bioactive constituents.

    STUDY DESIGN AND METHODS: DPPH assay was firstly used to evaluate the antioxidant activity throughout the bioactivity-guided fractionation. Cell viability was determined using MTS assay. Collagenase activity was examined, while MMP-1 and MMP-3 expression were measured using qRT-PCR and western blotting. Then, chemical identification of pure compounds isolated from CC fractions was done by using ESIMS, 1H and 13C NMR spectroscopies. HPLC analyses were carried out for bioactive fractions to quantify the major components.

    RESULTS: Throughout the antioxidant activity-guided fractionation, fractions CC-E2 and CC-E3 with antioxidant activity and no toxicity towards CCD-966SK cells were obtained from CC 75% ethanol partitioned layer (CC-E). Both fractions inhibited collagenase activity, MMP-1 and MMP-3 mRNA and protein expression, as well as NF-κB activation induced by TNF-α in CCD-966SK cells. 14 compounds, which mainly consists of flavonoids and their glycosides, were isolated. Quercitrin (14.79% w/w) and quercetin (11.20% w/w) were major compounds in CC-E2 and CC-E3, respectively, as quantified by HPLC. Interestingly, both fractions also inhibited the MMP-3 protein expression synergistically, compared with treatment alone.

    CONCLUSION: The quantified CC fractions rich in flavonoid glycosides exhibited skin anti-aging effects via the inhibition of collagenase, MMP-1 and MMP-3 activities, probably through NF-κB pathway. This is the first study reported on MMP-1 and MMP-3 inhibitory activity of CC with its chemical profile, which revealed its potential to be developed as anti-aging products in the future.

  10. Kukreti S, Hsieh MT, Liu CH, Chen JS, Chen YJ, Hsieh MT, et al.
    Inquiry, 2024;61:469580231225030.
    PMID: 38314649 DOI: 10.1177/00469580231225030
    The COVID-19 pandemic presented significant challenges for individuals who experienced stroke and their caregivers. It is essential to understand the factors affecting preventive behavior in these populations. Therefore, the present study examined the factors that influenced COVID-19 preventive behavior and motivation for COVID-19 vaccine uptake among patients with stroke and their caregivers. A cross-sectional study comprising 191 participants (81 patients with stroke and 110 caregivers) was carried out. Participants completed a survey assessing fear of COVID-19, stress, perceived susceptibility, problematic social media use, preventive behaviors, and motivation for vaccine uptake. Statistical analyses included descriptive statistics, Pearson correlations, and multiple linear regressions. Motivation for COVID-19 vaccine uptake was significantly positively correlated with problematic social media use (r = 0.225, P = .002), perceived susceptibility (r = 0.197, P = .008), and fear of COVID-19 (r = 0.179, P = .015), but negatively correlated with stress (r = -0.189, P = .010). Caregivers, compared to patients, showed a lower level of preventive behavior (standardized coefficient = -0.23, P = .017). Furthermore, higher levels of fear were associated with increased preventive behavior (standardized coefficient = 0.22, P = .006), while greater stress correlated with lower preventive behavior (standardized coefficient = -0.38, P 
  11. Chiang TY, Chiang YC, Chen YJ, Chou CH, Havanond S, Hong TN, et al.
    Mol Ecol, 2001 Nov;10(11):2697-710.
    PMID: 11883883
    Vivipary with precocious seedlings in mangrove plants was thought to be a hindrance to long-range dispersal. To examine the extent of seedling dispersal across oceans, we investigated the phylogeny and genetic structure among East Asiatic populations of Kandelia candel based on organelle DNAs. In total, three, 28 and seven haplotypes of the chloroplast DNA (cpDNA) atpB-rbcL spacer, cpDNA trnL-trnF spacer, and mitochondrial DNA (mtDNA) internal transcribed spacer (ITS) were identified, respectively, from 202 individuals. Three data sets suggested consistent phylogenies recovering two differentiated lineages corresponding to geographical regions, i.e. northern South-China-Sea + East-China-Sea region and southern South-China-Sea region (Sarawak). Phylogenetically, the Sarawak population was closely related to the Ranong population of western Peninsula Malaysia instead of other South-China-Sea populations, indicating its possible origin from the Indian Ocean Rim. No geographical subdivision was detected within the northern geographical region. An analysis of molecular variance (AMOVA) revealed low levels of genetic differentiation between and within mainland and island populations (phiCT = 0.015, phiSC = 0.037), indicating conspicuous long-distance seedling dispersal across oceans. Significant linkage disequilibrium excluded the possibility of recurrent homoplasious mutations as the major force causing phylogenetic discrepancy between mtDNA and the trnL-trnF spacer within the northern region. Instead, relative ages of alleles contributed to non-random chlorotype-mitotype associations and tree inconsistency. Widespread distribution and random associations (chi2 = 0.822, P = 0.189) of eight hypothetical ancestral cytotypes indicated the panmixis of populations of the northern geographical region as a whole. In contrast, rare and recently evolved alleles were restricted to marginal populations, revealing some preferential directional migration.
  12. Chen YJ, Lai HC, Lin CC, Neoh ZY, Tsai WS
    Plants (Basel), 2021 Nov 06;10(11).
    PMID: 34834759 DOI: 10.3390/plants10112396
    Cucurbits are important crops in the world. However, leaf curl disease constrains their production. Here, begomovirus diversity and pathogenicity associated with the disease in Malaysia were studied based on 49 begomovirus-detected out of 69 symptomatic plants from seven cucurbit crops in 15 locations during 2016 and 2017. The presence of Squash leaf curl China virus (SLCCNV) and Tomato leaf curl New Delhi virus (ToLCNDV) were confirmed by virus detection by polymerase chain reaction, viral DNA sequence analysis and specific detection of the viral components. ToLCNDV Malaysian isolates were further distinguished into strains A, B, C and D. Virus co-infection was detected in bitter gourd, bottle gourd and squash. Among them, eight bitter gourd samples were detected without SLCCNV DNA-A. However, one bottle gourd and five squash samples were without ToLCNDV DNA-B. Pseudorecombination of ToLCNDV DNA-A and SLCCNV DNA-B was detected in two bitter gourd samples. The pathogenic viruses and pseudorecombinants were confirmed by agroinoculation. The viral DNA-B influencing on symptomology and host range was also confirmed. The results strengthen the epidemic of cucurbit-infecting begomovirus in Malaysia as well as Southeast Asia. Especially, the natural pseudorecombinant of begomovirus that extends host range and causes severe symptom implies a threat to crops.
  13. Chen YJ, Liu WJ, Chen DN, Chieng SH, Jiang L
    Zhongguo Zhong Yao Za Zhi, 2017 Dec;42(23):4593-4597.
    PMID: 29376257 DOI: 10.19540/j.cnki.cjcmm.20171030.018
    To provide theoretical basis for the traceability and quality evaluation of edible bird's nests (EBNs), the Cytb sequence was applied to identify the origin of EBNs. A total of 39 experiment samples were collected from Malaysia, Indonesia, Vietnam and Thailand. Genomic DNA was extracted for the PCR reaction. The amplified products were sequenced. 36 sequences were downloaded from Gen Bank including edible nest swiftlet, black nest swiftlet, mascarene swiftlet, pacific swiftlet and germain's swiftlet. MEGA 7.0 was used to analyze the distinction of sequences by the method of calculating the distances in intraspecific and interspecific divergences and constructing NJ and UPMGA phylogenetic tree based on Kimera-2-parameter model. The results showed that 39 samples were from three kinds of EBNs. Interspecific divergences were significantly greater than the intraspecific one. Samples could be successfully distinguished by NJ and UPMGA phylogenetic tree. In conclusion, Cytb sequence could be used to distinguish the origin of EBNs and it is efficient for tracing the origin species of EBNs.
  14. Low TY, Chen YJ, Ishihama Y, Chung MCM, Cordwell S, Poon TCW, et al.
    Mol Cell Proteomics, 2022 Dec;21(12):100436.
    PMID: 36309314 DOI: 10.1016/j.mcpro.2022.100436
    In 2021, the Asia-Oceania Human Proteome Organization (AOHUPO) initiated a new endeavor named the AOHUPO Online Education Series with the aim to promote scientific education and collaboration, exchange of ideas and culture among the young scientists in the AO region. Following the warm participation, the AOHUPO organized the second series in 2022, with the theme "The Renaissance of Clinical Proteomics: Biomarkers, Imaging and Therapeutics". This time, the second AOHUPO Online Education Series was hosted by the UKM Medical Molecular Biology Institute (UMBI) affiliated to the National University of Malaysia (UKM) in Kuala Lumpur, Malaysia on three consecutive Fridays (11th, 18th and 25th of March). More than 300 participants coming from 29 countries/regions registered for this 3-days event. This event provided an amalgamation of six prominent speakers and all participants whose interests lay mainly in applying MS-based and non-MS-based proteomics for clinical investigation.
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