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Fulltext Getting the most out of RNA-seq data analysis

Khang TF, Lau CY

PeerJ, 2015;3:e1360.
PMID: 26539333 DOI: 10.7717/peerj.1360

Background. A common research goal in transcriptome projects is to find genes that are differentially expressed in different phenotype classes. Biologists might wish to validate such gene candidates experimentally, or use them for downstream systems biology analysis. Producing a coherent differential gene expression analysis from RNA-seq count data requires an understanding of how numerous sources of variation such as the replicate size, the hypothesized biological effect size, and the specific method for making differential expression calls interact. We believe an explicit demonstration of such interactions in real RNA-seq data sets is of practical interest to biologists. Results. Using two large public RNA-seq data sets-one representing strong, and another mild, biological effect size-we simulated different replicate size scenarios, and tested the performance of several commonly-used methods for calling differentially expressed genes in each of them. We found that, when biological effect size was mild, RNA-seq experiments should focus on experimental validation of differentially expressed gene candidates. Importantly, at least triplicates must be used, and the differentially expressed genes should be called using methods with high positive predictive value (PPV), such as NOISeq or GFOLD. In contrast, when biological effect size was strong, differentially expressed genes mined from unreplicated experiments using NOISeq, ASC and GFOLD had between 30 to 50% mean PPV, an increase of more than 30-fold compared to the cases of mild biological effect size. Among methods with good PPV performance, having triplicates or more substantially improved mean PPV to over 90% for GFOLD, 60% for DESeq2, 50% for NOISeq, and 30% for edgeR. At a replicate size of six, we found DESeq2 and edgeR to be reasonable methods for calling differentially expressed genes at systems level analysis, as their PPV and sensitivity trade-off were superior to the other methods'. Conclusion. When biological effect size is weak, systems level investigation is not possible using RNAseq data, and no meaningful result can be obtained in unreplicated experiments. Nonetheless, NOISeq or GFOLD may yield limited numbers of gene candidates with good validation potential, when triplicates or more are available. When biological effect size is strong, NOISeq and GFOLD are effective tools for detecting differentially expressed genes in unreplicated RNA-seq experiments for qPCR validation. When triplicates or more are available, GFOLD is a sharp tool for identifying high confidence differentially expressed genes for targeted qPCR validation; for downstream systems level analysis, combined results from DESeq2 and edgeR are useful.
The Kra Isthmus Canal: A New Strategic Solution for China's Energy Consumption Scenario?

Lau CY, Lee JW

Environ Manage, 2016 Jan;57(1):1-20.
PMID: 26280310 DOI: 10.1007/s00267-015-0591-0

This paper is a conceptual study that examines the viability of the construction of the Kra Isthmus within the context of the five dimensions of megaproject success of Sovacool and Cooper (The governance of energy megaprojects: politics, hubris, and energy security, 2013)-social (governance), technological (systems), democratic (politics), externalities (economics, ecology), and risks assessments (accountability), and its possible impact on China's strategic energy supply chain. One of the objectives of this study is also to discuss the current impacts, perceived benefits, and risks of China's dependence on its multinational and transnational pipelines. China could see the construction of Kra Canal as an alternative option for its strategic sourcing activities especially crude oil and gas at much lower costs. The megaproject would become a passageway that connects the Indian Ocean, Andaman Sea, and the Gulf of Siam at the choke point of Isthmus region in Thailand. However, this megaproject could also trigger the internal conflicts of Thailand, and affect the ASEAN countries' political and economic relationships.
Fulltext Branchial-Cleft Sinus Manifesting as Recurrent Neck Abscess

Lau CY, Wong HT

N Engl J Med, 2018 Feb 08;378(6):e9.
PMID: 29414266 DOI: 10.1056/NEJMicm1710539
Fulltext Rare left-sided presentation of internal jugular vein ectasia in an adult

Cheah SC, Wong HT, Lau CY

Ann Saudi Med, 2018 10 5;38(5):381-382.
PMID: 30284994 DOI: 10.5144/0256.4947.2018.381
The rate of progression of type 2 diabetes mellitus to end stage renal disease - A single centred retrospective study from Malaysia

Ng YP, Ahmed R, Ooi GS, Lau CY, Balasubramanian GP, Yap CH

Diabetes Metab Syndr, 2018 Nov;12(6):1025-1030.
PMID: 30168425 DOI: 10.1016/j.dsx.2018.06.018

INTRODUCTION: In Malaysia, 61% of dialysis cases are secondary to diabetes. To date, we are still lacking of data on the rate of progression of type 2 diabetes mellitus (T2DM) to end stage renal disease (ESRD) in Malaysia.
MATERIALS AND METHODS: This was a retrospective study conducted at nephrology unit of a tertiary hospital in Kedah. All diabetic ESRD patients who fulfilled the inclusion criteria were identified and recruited for analysis.
RESULTS: The mean duration of DM to ESRD was found to be 14.37 ± 4.42 years. Mean duration for the onset of diabetic nephropathy was 8.73 ± 3.37 years. There was a relative short duration from diabetic nephropathy to ESRD noted, which was 5.63 ± 2.06 years. The mean duration of DM to ESRD for patients receiving RAAS blocker was found to be 18.23 ± 2.38 years as compared to 11.41 ± 2.94 years for those who did not (95% CI: -0.64 to -2.46). For different type of RAAS blockers, namely ACE inhibitor and angiotensin receptor blocker (ARB), there was no significant difference observed pertaining to mean duration of DM to ESRD; 17.89 ± 1.97 years for ACEi and 19.00 ± 4.16 years for ARB (95% CI: -4.74 to 2.52).
DISCUSSION: Time frame from diabetic nephropathy to ESRF among Malaysian population was shorter as compared to findings from other countries with an average period of 15 to 25 years. RAAS blockers should be initiated early in diabetic patients.
Nutritional compositions and bioactivities of Dacryodes species: a review

Tee LH, Yang B, Nagendra KP, Ramanan RN, Sun J, Chan ES, et al.

Food Chem, 2014 Dec 15;165:247-55.
PMID: 25038673 DOI: 10.1016/j.foodchem.2014.05.084

Dacryodes species are evergreen, perennial trees with fleshy fruits and belong to the family Buseraseae. Many Dacryodes species are underutilized but are widely applied in traditional folk medicine to treat malaria, fever and skin diseases. The nutritional compositions, phytochemicals and biological activities of Dacryodes edulis, Dacryodes rostrata, Dacryodes buettneri, Dacryodes klaineana and Dacryodes hexandra are presented. The edible fruits of D. edulis are rich in lipids, proteins, vitamins, fatty acids and amino acids. Its extracts (leaf, fruit and resin) exhibit antioxidant, anti-microbial, anti-carcinogenic and other bioactivities. D. rostrata fruit has significant nutrient content, and is rich in proteins, lipids and minerals. These fruits are also highly rich in polyphenols, anthocyanins and antioxidant activities. This comprehensive review will assist the reader in understanding the nutritional benefits of Dacryodes species and in identifying current research needs.
Valorization of Dacryodes rostrata fruit through the characterization of its oil

Tee LH, Yang B, Tey BT, Chan ES, Azlan A, Ismail A, et al.

Food Chem, 2017 Nov 15;235:257-264.
PMID: 28554634 DOI: 10.1016/j.foodchem.2017.05.021

Dacryodes rostrata (kembayau) is an important food and oil resource for local communities in Borneo, but it is not commonly known to wider community. The objective of this work is to valorize kembayau fruit by evaluating the characteristics of the oil from the fruit. In this study, the physicochemical characteristics and the lipophilic essential nutrient; the fatty acid composition, vitamin E and beta-carotene content of oils obtained from the peel, pulp and seeds of kembayau fruits were studied. The pulp of the kembayau fruit contained highest proportion of oil, followed by peel and seed. Kembayau fruit contained vitamin E and had trace amount of beta-carotene. Besides, kembayau fruit oils were not toxic to BRL3A cells, provided hepatoprotection and reversed lipid peroxidation in paracetamol-induced toxicity. Our results suggest that kembayau can be a potential source for cooking oil as the physicochemical characteristics are comparable with commercial source such as oil palm.