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Detection of high-risk HPV 16 genotypes in cervical cancers using isothermal DNA amplification with electrochemical genosensor

Nakowong P, Chatchawal P, Chaibun T, Boonapatcharoen N, Promptmas C, Buajeeb W, et al.

Talanta, 2024 Mar 01;269:125495.
PMID: 38043336 DOI: 10.1016/j.talanta.2023.125495

Cervical cancer emerges as the third most prevalent types of malignancy among women on a global scale. Cervical cancer is significantly associated with the persistent infection of human papillomavirus (HPV) type 16. The process of diagnosing is crucial in order to prevent the progression of a condition into a malignant state. The early detection of cervical cancer through initial stage screening is of the utmost significance in both the prevention and effective management of this disease. The present detection methodology is dependent on quantitative polymerase chain reaction (qPCR), which necessitates the use of a costly heat cycler instrument. In this study, we report the development of an electrochemical DNA biosensor integrated with an isothermal recombinase polymerase amplification (RPA) reaction for the detection and identification of the high-risk HPV-16 genotype. The electrochemical biosensor exhibited a high degree of specificity and sensitivity, as evidenced by its limit of detection (LOD) of 0.23 copies/μL of HPV-16 DNA. The validity of this electrochemical platform was confirmed through the analysis of 40 cervical tissues samples, and the findings were consistent with those obtained through polymerase chain reaction (PCR) testing. Our straightforward electrochemical detection technology and quick turnaround time at 75 min make the assay suitable for point-of-care testing in low-resource settings.
Fulltext Using VigiBase to Identify Substandard Medicines: Detection Capacity and Key Prerequisites

Juhlin K, Karimi G, Andér M, Camilli S, Dheda M, Har TS, et al.

Drug Saf, 2015 Apr;38(4):373-82.
PMID: 25687792 DOI: 10.1007/s40264-015-0271-2

Substandard medicines, whether the result of intentional manipulation or lack of compliance with good manufacturing practice (GMP) or good distribution practice (GDP), pose a significant potential threat to patient safety. Spontaneous adverse drug reaction reporting systems can contribute to identification of quality problems that cause unwanted and/or harmful effects, and to identification of clusters of lack of efficacy. In 2011, the Uppsala Monitoring Centre (UMC) constructed a novel algorithm to identify reporting patterns suggestive of substandard medicines in spontaneous reporting, and applied it to VigiBase(®), the World Health Organization's global individual case safety report database. The algorithm identified some historical clusters related to substandard products, which were later able to be confirmed in the literature or by contact with national centres (NCs). As relevant and detailed information is often lacking in the VigiBase reports but might be available at the reporting NC, further evaluation of the algorithm was undertaken with involvement from NCs.
Fulltext Complete Genome Sequence of Salmonella enterica Bacteriophage PRF-SP1

Mutusamy P, Jaya Jothi S, Lee SY, Petersen B, Sicheritz-Ponten T, Clokie MRJ, et al.

Microbiol Resour Announc, 2021 Nov 24;10(47):e0096521.
PMID: 34817216 DOI: 10.1128/MRA.00965-21

We characterized the complete genome sequence of the lytic Salmonella enterica bacteriophage PRF-SP1, isolated from Penang National Park, a conserved rainforest in northern Malaysia. The novel phage species from the Autographiviridae family has a 39,966-bp double-stranded DNA (dsDNA) genome containing 49 protein-encoding genes and shares 90.96% similarity with Escherichia phage DY1.
Ultrasensitive pathogen detection with a rolling circle amplification-empowered multiplex electrochemical DNA sensor

Yeap CSY, Chaibun T, Lee SY, Zhao B, Jan Y, La-O-Vorakiat C, et al.

Chem Commun (Camb), 2021 Nov 16;57(91):12155-12158.
PMID: 34726213 DOI: 10.1039/d1cc05181d

We report a highly sensitive and selective multiplex assay by empowering an electrochemical DNA sensor with isothermal rolling circle amplification. The assay could simultaneously detect and discriminate three common entero-pathogens in a single reaction, with femtomolar sensitivity. It is useful for field- or resource-limited settings.
Understanding the role of gut microbiota in the pathogenesis of schizophrenia

Ghorbani M, Rajandas H, Parimannan S, Stephen Joseph GB, Tew MM, Ramly SS, et al.

Psychiatr Genet, 2021 Apr 01;31(2):39-49.
PMID: 33252574 DOI: 10.1097/YPG.0000000000000270

Schizophrenia is a chronic mental disorder with marked symptoms of hallucination, delusion, and impaired cognitive behaviors. Although multidimensional factors have been associated with the development of schizophrenia, the principal cause of the disorder remains debatable. Microbiome involvement in the etiology of schizophrenia has been widely researched due to the advancement in sequencing technologies. This review describes the contribution of the gut microbiome in the development of schizophrenia that is facilitated by the gut-brain axis. The gut microbiota is connected to the gut-brain axis via several pathways and mechanisms, that are discussed in this review. The role of the oral microbiota, probiotics and prebiotics in shaping the gut microbiota are also highlighted. Lastly, future perspectives for microbiome research in schizophrenia are addressed.
Fulltext Complete genome sequence of Sphingomonas paucimobilis AIMST S2, a xenobiotic-degrading bacterium

Ravintheran SK, Sivaprakasam S, Loke S, Lee SY, Manickam R, Yahya A, et al.

Sci Data, 2019 11 25;6(1):280.
PMID: 31767854 DOI: 10.1038/s41597-019-0289-x

Complete genomes of xenobiotic-degrading microorganisms provide valuable resources for researchers to understand molecular mechanisms involved in bioremediation. Despite the well-known ability of Sphingomonas paucimobilis to degrade persistent xenobiotic compounds, a complete genome sequencing is lacking for this organism. In line with this, we report the first complete genome sequence of Sphingomonas paucimobilis (strain AIMST S2), an organophosphate and hydrocarbon-degrading bacterium isolated from oil-polluted soil at Kedah, Malaysia. The genome was derived from a hybrid assembly of short and long reads generated by Illumina HiSeq and MinION, respectively. The assembly resulted in a single contig of 4,005,505 bases which consisted of 3,612 CDS and 56 tRNAs. An array of genes involved in xenobiotic degradation and plant-growth promoters were identified, suggesting its' potential role as an effective microorganism in bioremediation and agriculture. Having reported the first complete genome of the species, this study will serve as a stepping stone for comparative genome analysis of Sphingomonas strains and other xenobiotic-degrading microorganisms as well as gene expression studies in organophosphate biodegradation.
Fulltext Rapid electrochemical detection of coronavirus SARS-CoV-2

Chaibun T, Puenpa J, Ngamdee T, Boonapatcharoen N, Athamanolap P, O'Mullane AP, et al.

Nat Commun, 2021 02 05;12(1):802.
PMID: 33547323 DOI: 10.1038/s41467-021-21121-7

Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis of COVID-19 depends on quantitative reverse transcription PCR (qRT-PCR), which is time-consuming and requires expensive instrumentation. Here, we report an ultrasensitive electrochemical biosensor based on isothermal rolling circle amplification (RCA) for rapid detection of SARS-CoV-2. The assay involves the hybridization of the RCA amplicons with probes that were functionalized with redox active labels that are detectable by an electrochemical biosensor. The one-step sandwich hybridization assay could detect as low as 1 copy/μL of N and S genes, in less than 2 h. Sensor evaluation with 106 clinical samples, including 41 SARS-CoV-2 positive and 9 samples positive for other respiratory viruses, gave a 100% concordance result with qRT-PCR, with complete correlation between the biosensor current signals and quantitation cycle (Cq) values. In summary, this biosensor could be used as an on-site, real-time diagnostic test for COVID-19.
Fulltext Development and Asian-wide validation of the Grade for Interpretable Field Triage (GIFT) for predicting mortality in pre-hospital patients using the Pan-Asian Trauma Outcomes Study (PATOS)

Yu JY, Heo S, Xie F, Liu N, Yoon SY, Chang HS, et al.

Lancet Reg Health West Pac, 2023 May;34:100733.
PMID: 37283981 DOI: 10.1016/j.lanwpc.2023.100733

BACKGROUND: Field triage is critical in injury patients as the appropriate transport of patients to trauma centers is directly associated with clinical outcomes. Several prehospital triage scores have been developed in Western and European cohorts; however, their validity and applicability in Asia remains unclear. Therefore, we aimed to develop and validate an interpretable field triage scoring systems based on a multinational trauma registry in Asia.
METHODS: This retrospective and multinational cohort study included all adult transferred injury patients from Korea, Malaysia, Vietnam, and Taiwan between 2016 and 2018. The outcome of interest was a death in the emergency department (ED) after the patients' ED visit. Using these results, we developed the interpretable field triage score with the Korea registry using an interpretable machine learning framework and validated the score externally. The performance of each country's score was assessed using the area under the receiver operating characteristic curve (AUROC). Furthermore, a website for real-world application was developed using R Shiny.
FINDINGS: The study population included 26,294, 9404, 673 and 826 transferred injury patients between 2016 and 2018 from Korea, Malaysia, Vietnam, and Taiwan, respectively. The corresponding rates of a death in the ED were 0.30%, 0.60%, 4.0%, and 4.6% respectively. Age and vital sign were found to be the significant variables for predicting mortality. External validation showed the accuracy of the model with an AUROC of 0.756-0.850.
INTERPRETATION: The Grade for Interpretable Field Triage (GIFT) score is an interpretable and practical tool to predict mortality in field triage for trauma.
FUNDING: This research was supported by a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (Grant Number: HI19C1328).
Fulltext Notes on Amanita section Validae in Hainan Island, China

Huang T, Su LJ, Zeng NK, Lee SML, Lee SS, Thi BK, et al.

Front Microbiol, 2022;13:1087756.
PMID: 36741898 DOI: 10.3389/fmicb.2022.1087756

Hainan is the second largest island in China with the most extensive and well-preserved tropical forests and is also the largest island of the Indo Burma Biodiversity Hotspot. It provides in situ conservation for the unique ecosystem of the island. Recent studies have shown that there are diverse fungal species in Hainan. In this study, about 40 collections of the genus Amanita have been studied based on the morphology and molecular systematics, including 35 Chinese specimens (24 from Hainan, and eleven from other regions) and three specimens from other countries (Singapore and Malaysia). In total, five new species belonging to Amanita section Validae are described: A. cacaina, A. parvigrisea, A. pseudofritillaria, A. pseudosculpta, and A. yangii. Amanita parvifritillaria is recorded for the first time in Hainan. It is also the first report of this fungus occurring, outside Yunnan Province, China. Among the five new species, two are unique in this section because of the appendiculate pileus margin and the absence of an annulus. Based on these new findings, the diagnosis of the section Validae should be slightly modified to include a few species with appendiculate margin and the lack of annulus.
Dry-reagent gold nanoparticle-based lateral flow biosensor for the simultaneous detection of Vibrio cholerae serogroups O1 and O139

Yu CY, Ang GY, Chua AL, Tan EH, Lee SY, Falero-Diaz G, et al.

J Microbiol Methods, 2011 Sep;86(3):277-82.
PMID: 21571011 DOI: 10.1016/j.mimet.2011.04.020

Cholera is a communicable disease caused by consumption of contaminated food and water. This potentially fatal intestinal infection is characterised by profuse secretion of rice watery stool that can rapidly lead to severe dehydration and shock, thus requiring treatment to be given immediately. Epidemic and pandemic cholera are exclusively associated with Vibrio cholerae serogroups O1 and O139. In light of the need for rapid diagnosis of cholera and to prevent spread of outbreaks, we have developed and evaluated a direct one-step lateral flow biosensor for the simultaneous detection of both V. cholerae O1 and O139 serogroups using alkaline peptone water culture. Serogroup specific monoclonal antibodies raised against lipopolysaccharides (LPS) were used to functionalize the colloidal gold nanoparticles for dual detection in the biosensor. The assay is based on immunochromatographic principle where antigen-antibody reaction would result in the accumulation of gold nanoparticles and thus, the appearance of a red line on the strip. The dry-reagent dipstick format of the biosensor ensure user-friendly application, rapid result that can be read with the naked eyes and cold-chain free storage that is well-suited to be performed at resource-limited settings.
Fulltext Polygenic risk scores for prediction of breast cancer risk in Asian populations

Ho WK, Tai MC, Dennis J, Shu X, Li J, Ho PJ, et al.

Genet Med, 2022 Mar;24(3):586-600.
PMID: 34906514 DOI: 10.1016/j.gim.2021.11.008

PURPOSE: Non-European populations are under-represented in genetics studies, hindering clinical implementation of breast cancer polygenic risk scores (PRSs). We aimed to develop PRSs using the largest available studies of Asian ancestry and to assess the transferability of PRS across ethnic subgroups.
METHODS: The development data set comprised 138,309 women from 17 case-control studies. PRSs were generated using a clumping and thresholding method, lasso penalized regression, an Empirical Bayes approach, a Bayesian polygenic prediction approach, or linear combinations of multiple PRSs. These PRSs were evaluated in 89,898 women from 3 prospective studies (1592 incident cases).
RESULTS: The best performing PRS (genome-wide set of single-nucleotide variations [formerly single-nucleotide polymorphism]) had a hazard ratio per unit SD of 1.62 (95% CI = 1.46-1.80) and an area under the receiver operating curve of 0.635 (95% CI = 0.622-0.649). Combined Asian and European PRSs (333 single-nucleotide variations) had a hazard ratio per SD of 1.53 (95% CI = 1.37-1.71) and an area under the receiver operating curve of 0.621 (95% CI = 0.608-0.635). The distribution of the latter PRS was different across ethnic subgroups, confirming the importance of population-specific calibration for valid estimation of breast cancer risk.
CONCLUSION: PRSs developed in this study, from association data from multiple ancestries, can enhance risk stratification for women of Asian ancestry.