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Fulltext Detecting Community Structure by Using a Constrained Label Propagation Algorithm

Chin JH, Ratnavelu K

PLoS One, 2016;11(5):e0155320.
PMID: 27176470 DOI: 10.1371/journal.pone.0155320

Community structure is considered one of the most interesting features in complex networks. Many real-world complex systems exhibit community structure, where individuals with similar properties form a community. The identification of communities in a network is important for understanding the structure of said network, in a specific perspective. Thus, community detection in complex networks gained immense interest over the last decade. A lot of community detection methods were proposed, and one of them is the label propagation algorithm (LPA). The simplicity and time efficiency of the LPA make it a popular community detection method. However, the LPA suffers from instability detection due to randomness that is induced in the algorithm. The focus of this paper is to improve the stability and accuracy of the LPA, while retaining its simplicity. Our proposed algorithm will first detect the main communities in a network by using the number of mutual neighbouring nodes. Subsequently, nodes are added into communities by using a constrained LPA. Those constraints are then gradually relaxed until all nodes are assigned into groups. In order to refine the quality of the detected communities, nodes in communities can be switched to another community or removed from their current communities at various stages of the algorithm. We evaluated our algorithm on three types of benchmark networks, namely the Lancichinetti-Fortunato-Radicchi (LFR), Relaxed Caveman (RC) and Girvan-Newman (GN) benchmarks. We also apply the present algorithm to some real-world networks of various sizes. The current results show some promising potential, of the proposed algorithm, in terms of detecting communities accurately. Furthermore, our constrained LPA has a robustness and stability that are significantly better than the simple LPA as it is able to yield deterministic results.
Fulltext Subacute oral toxicity study of ethanolic leaves extracts of Strobilanthes crispus in rats

Lim KT, Lim V, Chin JH

Asian Pac J Trop Biomed, 2012 Dec;2(12):948-52.
PMID: 23593574 DOI: 10.1016/S2221-1691(13)60005-2

To examine the oral toxicity of repeated dosing of Strobilanthes crispus (S. crispus) ethanol leaves extract on the liver and kidney functions in Sprague Dawley rats.
Fulltext Toxicity study of Orthosiphon stamineus Benth (Misai Kucing) on Sprague Dawley rats

Chin JH, Abas HH, Sabariah I

Trop Biomed, 2008 Apr;25(1):9-16.
PMID: 18600199

Orthosiphon stamineus Benth (Family: Lamiaceae) or locally known as Misai Kucing has been widely used in Malaysia for treating kidney problems, gout, and diabetes. This study aims to evaluate the possible toxic effect after following fourteen days oral administration of methanol extract of O. stamineus in female Sprague Dawley (SD) rats. Control groups were treated orally with distilled water (vehicle) while the four test groups were treated up to fourteen days with 0.5 g/kg, 1 g/kg, 3 g/kg and 5 g/kg body weight of methanol extract of O. stamineus respectively. Toxicity of the methanol extract of O. stamineus was evaluated by the incident of lethality, side-cage observation and blood serum biochemical parameters. No lethality or adverse toxic signs were seen during the experimental period. A significant decrease in several serum biochemical parameters i.e. AST and ALT and increase in liver weight was observed in young female SD rat after being fed fourteen days with methanol extract of O. stamineus. No delayed toxic effect and lethality was observed in all rats during fourteen days of recovery period. In conclusion, methanol extract of O. stamineus within these range and treatment duration would not cause any severe toxic effects and organ damages in rats.
Fulltext Evaluation of the toxic effect of star fruit on serum biochemical parameters in rats

Khoo ZY, Teh CC, Rao NK, Chin JH

Pharmacogn Mag, 2010 Apr;6(22):120-4.
PMID: 20668578 DOI: 10.4103/0973-1296.62899

The objective of the present study was to evaluate the toxic effect of Averrhoa carambola (star fruit) juice at different storage conditions in Sprague Dawley (SD) rats. Twenty female rats weighing 180 +/- 20 g were randomly assigned into four groups with five rats per group (n = 5). First group served as the control group, fed with distilled water (vehicle). Second, third and fourth groups were orally treated with juice of A. carambola stored for 0, 1 and 3 h respectively for 14 days. Cage-side observations were done daily after each treatment. Body weight, food consumption and water intake were recorded on day-0, day-3, day-7 and day-14. All rats were fasted overnight prior to blood collection through cardiac puncture on day-15. The levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), urea and creatinine in blood serum were measured. Data were analyzed using Dunnett's test. From the results obtained, there was no lethality found and LD(50) could not be determined. Increment of ALT levels (P<0.05) was reported in those rats treated with A. carambola juice stored for 3 h. On the basis of these results, we can conclude that A. carambola juice stored for 0 hand 1 h are safe to be consumed. However, juice stored for 3 h exerts toxic effect on rat liver at hepatocellular level.
Cloning and expression of a novel lipase gene from Bacillus sphaericus 205y

Rahman RN, Chin JH, Salleh AB, Basri M

Mol Genet Genomics, 2003 May;269(2):252-60.
PMID: 12756537

A Bacillus sphaericus strain (205y) that produces an organic solvent-tolerant lipase was isolated in Port Dickson, Malaysia. The gene for the lipase was recovered from a genomic library and sequenced. Phylogenetic analysis was performed based on an alignment of thirteen microbial lipase sequences obtained from the NCBI database. The analysis suggested that the B. sphaericus lipase gene is a novel gene, as it is distinct from other lipase genes in Families I.4 and I.5 reported so far. Expression in Escherichia coli under the control of the lacZ promoter resulted in an eight-fold increase in enzyme activity after a 3-h induction with 1 mM IPTG. The crude enzyme thus obtained showed a slight (10%) enhancement in activity after a 30-min incubation in 25% (v/v) n-hexane at 37 degrees C, and retained 90% of its activity after a similar period in 25% (v/v) p-xylene.
Fulltext Quantitating proteinuria using the urinary protein creatinine index

Norella Kong CT, Chin JH, Izham Cheong IK, Abu Bakar A

Med J Malaysia, 1988 Jun;43(2):134-7.
PMID: 3237129
Fulltext Safety and Efficacy of Dietary Epigallocatechin Gallate Supplementation in Attenuating Hypertension via Its Modulatory Activities on the Intrarenal Renin-Angiotensin System in Spontaneously Hypertensive Rats

Parn KW, Ling WC, Chin JH, Lee SK

Nutrients, 2022 Nov 01;14(21).
PMID: 36364864 DOI: 10.3390/nu14214605

This study aimed to identify the no-observed-adverse-effect level (NOAEL) of dietary epigallocatechin gallate (EGCG) supplementation and its possible antihypertensive and nutrigenomics effects in modulating intrarenal renin-angiotensin system (RAS) gene expression in spontaneously hypertensive rats (SHR). EGCG (50, 250, 500 or 1000 mg/kg b.w. i.g., once daily) was administered to SHR for 28 days. All the SHR survived with no signs of systemic toxicity. Increased alanine aminotransferase (ALT), aspartate aminotransferase (AST) and thiobarbituric acid reactive substances (TBARS) were evident in SHR supplemented with 500 and 1000 mg/kg b.w. but not in those supplemented with lower doses of EGCG. Subsequently, the NOAEL of EGCG was established at 250 mg/kg b.w., and the same protocol was replicated to assess its effects on blood pressure and renal RAS-related genes in SHR. The systolic blood pressure (SBP) of the EGCG group was consistently lower than the control group. The mRNA levels of cortical Agtr2 and Ace2 and medullary Agtr2, Ace and Mas1 were upregulated while medullary Ren was downregulated in EGCG group. Statistical analysis showed that SBP reduction was associated with the changes in medullary Agtr2, Ace, and Ren. Dietary EGCG supplementation exhibits antihypertensive and nutrigenomics effects through activation of intrarenal Ace and Agtr2 and suppression of Ren mediators, while a high dose of EGCG induced liver damage in SHR. In future clinical studies, liver damage biomarkers should be closely monitored to further establish the safety of the long-term use of EGCG.
The complete chloroplast genome of Pandanus amaryllifolius Roxb. ex Lindl. (Pandanaceae) and its phylogenetic relationship

Chin JH, Wong XJ, Chong TF, Muangkot P, Heng AT, Tanee T, et al.

Mitochondrial DNA B Resour, 2024;9(4):541-545.
PMID: 38665928 DOI: 10.1080/23802359.2024.2345773

Pandanus amaryllifolius of Pandanaceae, a plant native to Southeast Asia, has been domesticated for its health benefits and aromatic leaves. It is also used for phytoremediation and soil rehabilitation. However, genetic studies of this species are limited. This study aims to expand its genomic information by assembling and characterizing the complete chloroplast genome of P. amaryllifolius. The chloroplast genome, which was 157,839 bp long, contains a total of 133 genes, including 87 protein-coding (CDS), 38 tRNA, and eight rRNA genes. The overall G/C content was 37.7%. A phylogenetic analysis using 79 shared unique CDS revealed a monophyletic relationship in Pandanales. Based on the limited sampling size, Pandanus amaryllifolius was the first to diverge in Pandanaceae. The genomic data will be useful for future phylogenetic and evolutionary studies of Pandanaceae.
Fulltext Comparison of Preoperative Nutritional Indexes for Outcomes after Primary Esophageal Surgery for Esophageal Squamous Cell Carcinoma

Yoon JP, Nam JS, Abidin MFBZ, Kim SO, Lee EH, Choi IC, et al.

Nutrients, 2021 Nov 15;13(11).
PMID: 34836339 DOI: 10.3390/nu13114086

BACKGROUND: This study aimed to compare the controlling nutritional status (CONUT) score, prognostic nutritional index (PNI), and geriatric nutritional risk index (GNRI) for predicting postoperative outcomes in patients with esophageal squamous cell carcinoma undergoing esophagectomy.
METHODS: We retrospectively reviewed the data of 1265 consecutive patients who underwent elective esophageal surgery. The patients were classified into no risk, low-risk, moderate-risk, and high-risk groups based on nutritional scores.
RESULTS: The moderate-risk (hazard ratio [HR]: 1.55, 95% confidence interval [CI]: 1.24-1.92, p < 0.001 in CONUT; HR: 1.61, 95% CI: 1.22-2.12, p = 0.001 in GNRI; HR: 1.65, 95% CI: 1.20-2.26, p = 0.002 in PNI) and high-risk groups (HR: 1.91, 95% CI: 1.47-2.48, p < 0.001 in CONUT; HR: 2.54, 95% CI: 1.64-3.93, p < 0.001 in GNRI; HR: 2.32, 95% CI: 1.77-3.06, p < 0.001 in PNI) exhibited significantly worse 5-year overall survival (OS) compared with the no-risk group. As the nutritional status worsened, the trend in the OS rates decreased (p for trend in all indexes < 0.05).
CONCLUSIONS: Malnutrition, evaluated by any of three nutritional indexes, was an independent prognostic factor for postoperative survival.
ASO Visual Abstract: Impact of Body Mass Index and Sarcopenia on Short- and Long-Term Outcomes After Esophageal Cancer Surgery-An Observational Study

Kim GW, Nam JS, Abidin MFBZ, Kim SO, Chin JH, Lee EH, et al.

Ann Surg Oncol, 2022 Oct;29(11):6884-6885.
PMID: 35829801 DOI: 10.1245/s10434-022-12076-0