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Chemometric application in identifying sources of organic contaminants in Langat river basin

Osman R, Saim N, Juahir H, Abdullah MP

Environ Monit Assess, 2012 Jan;184(2):1001-14.
PMID: 21494831 DOI: 10.1007/s10661-011-2016-8

Increasing urbanization and changes in land use in Langat river basin lead to adverse impacts on the environment compartment. One of the major challenges is in identifying sources of organic contaminants. This study presented the application of selected chemometric techniques: cluster analysis (CA), discriminant analysis (DA), and principal component analysis (PCA) to classify the pollution sources in Langat river basin based on the analysis of water and sediment samples collected from 24 stations, monitored for 14 organic contaminants from polycyclic aromatic hydrocarbons (PAHs), sterols, and pesticides groups. The CA and DA enabled to group 24 monitoring sites into three groups of pollution source (industry and urban socioeconomic, agricultural activity, and urban/domestic sewage) with five major discriminating variables: naphthalene, pyrene, benzo[a]pyrene, coprostanol, and cholesterol. PCA analysis, applied to water data sets, resulted in four latent factors explaining 79.0% of the total variance while sediment samples gave five latent factors with 77.6% explained variance. The varifactors (VFs) obtained from PCA indicated that sterols (coprostanol, cholesterol, stigmasterol, β-sitosterol, and stigmastanol) are strongly correlated to domestic and urban sewage, PAHs (naphthalene, acenaphthene, pyrene, benzo[a]anthracene, and benzo[a]pyrene) from industrial and urban activities and chlorpyrifos correlated to samples nearby agricultural sites. The results demonstrated that chemometric techniques can be used for rapid assessment of water and sediment contaminations.
Fulltext Development of Chromatographic Fingerprints of Eurycoma longifolia (Tongkat Ali) Roots Using Online Solid Phase Extraction-Liquid Chromatography (SPE-LC)

Zaini NN, Osman R, Juahir H, Saim N

Molecules, 2016 Apr 30;21(5).
PMID: 27144555 DOI: 10.3390/molecules21050583

E. longifolia is attracting interest due to its pharmacological properties and pro-vitality effects. In this study, an online SPE-LC approach using polystyrene divinyl benzene (PSDVB) and C18 columns was developed in obtaining chromatographic fingerprints of E. longifolia. E. longifolia root samples were extracted using pressurized liquid extraction (PLE) technique prior to online SPE-LC. The effects of mobile phase compositions and column switching time on the chromatographic fingerprint were optimized. Validation of the developed method was studied based on eurycomanone. Linearity was in the range of 5 to 50 µg∙mL(-1) (r² = 0.997) with 3.2% relative standard deviation of peak area. The developed method was used to analyze 14 E. longifolia root samples and 10 products (capsules). Selected chemometric techniques: cluster analysis (CA), discriminant analysis (DA), and principal component analysis (PCA) were applied to the fingerprint datasets of 37 selected peaks to evaluate the ability of the chromatographic fingerprint in classifying quality of E. longifolia. Three groups were obtained using CA. DA yielded 100% correlation coefficient with 19 discriminant compounds. Using PCA, E. longifolia root samples were clearly discriminated from the products. This study showed that the developed online SPE-LC method was able to provide comprehensive evaluation of E. longifolia samples for quality control purposes.
Effect of Mobile Phase pH on the Electrospray Ionization Efficiency and Qualitative Analysis of Pharmaceuticals in ESI + LC-MS/MS

Kafeenah HIS, Osman R, Bakar NKA

J Chromatogr Sci, 2019 Oct 17;57(9):847-854.
PMID: 31512731 DOI: 10.1093/chromsci/bmz061

The effect of mobile phase pH on positive ionization process and retention time of nine pharmaceuticals on ultra-performance liquid chromatography-electrospray-tandem mass spectrometry (LC-MS/MS) was discussed. The effective use of high and low mobile phase pH in LC-MS/MS qualitative analyses method was also evaluated by comparing the instrument detection limit, quantification limit, precision, linearity and signal to noise (S/N) under low and high mobile phase pH. In this work, six mobile phase pH that ranged between pH 2 and pH 10 were used to evaluate the effect of the mobile phase pH changes on the ionization process in electrospray ionization. Results revealed that high mobile phase pH ionized more pharmaceuticals molecules and gave a higher signal than low mobile phase pH in positive ionization mode. The results proved that ammonium ion was better as a proton donor in high pH mobile phase than the hydronium ion in acidic mobile phase. The results revealed that the qualitative LC-MS/MS analyses method by using high mobile phase pH has better performance for most analytes in terms of sensitivity, precision, linearity and S/N than the low mobile phase pH.
Fulltext Combination of Sensory, Chromatographic, and Chemometrics Analysis of Volatile Organic Compounds for the Discrimination of Authentic and Unauthentic Harumanis Mangoes

Zakaria SR, Saim N, Osman R, Abdul Haiyee Z, Juahir H

Molecules, 2018 Sep 16;23(9).
PMID: 30223605 DOI: 10.3390/molecules23092365

This study analyzed the volatile organic compounds (VOCs) of three mango varieties (Harumanis, Tong Dam and Susu) for the discrimination of authentic Harumanis from other mangoes. The VOCs of these mangoes were extracted and analysed nondestructively using Head Space-Solid Phase Micro Extraction (HS-SPME) coupled to Gas Chromatography-Mass Spectrometry (GC-MS). Prior to the analytical method, two simple sensory analyses were carried out to assess the ability of the consumers to differentiate between the Harumanis and Tong Dam mangoes as well as their preferences towards these mangoes. On the other hand, chemometrics techniques, such as principal components analysis (PCA), hierarchical clustering analysis (HCA), and discriminant analysis (DA), were used to visualise grouping tendencies of the volatile compounds detected. These techniques were successful in identifying the grouping tendencies of the mango samples according to the presence of their respective volatile compounds, thus enabling the identification of the groups of substances responsible for the discrimination between the authentic and unauthentic Harumanis mangoes. In addition, three ocimene compounds, namely beta-ocimene, trans beta-ocimene, and allo-ocimene, can be considered as chemical markers of the Harumanis mango, as these compounds exist in all Harumanis mango, regardless the different sources of the mangoes obtained.
Fulltext Increased soluble HLA-DRB1in B-cell acute lymphoblastic leukaemia

Hassan N, Dhaliwal JS, Mohd Ibrahim H, Osman R, HIdris SZ, Lee le J, et al.

Malays J Pathol, 2015 Aug;37(2):83-90.
PMID: 26277663 MyJurnal

Soluble HLA (sHLA) are potential tumour markers released in order to counter immune surveillance. sHLA-class II is less known especially in acute lymphoblastic leukaemia (ALL). This study aimed to investigate soluble, surface and allelic expression of HLA Class II (sHLA-DR) in B-cell ALL patients and compare with soluble expression in normal individuals. A sandwich enzyme-linked immunosorbent assay (ELISA) was developed to measure soluble HLA-DRB1 in plasma. Flow cytometric analysis was performed to determine median fluorescence intensity in HLA-DR surface expression. HLA-DNA typing by polymerase chain reaction, sequence specific oligonucleotides, PCRSSO was performed to determine HLA-DRB1 type in ALL samples. Results showed sHLA-DRB1 (mean±SEM) was significantly increased (p=0.001) in plasma of ALL patients (0.260 ±0.057 μg/mL; n=30) compared to healthy controls (0.051 ± 0.007µg/mL; n=31) of Malay ethnicity. However, these levels did not correlate with percentage or median fluorescence intensity of HLA-DR expressed on leukemia blasts (CD19+CD34 ± CD45(lo)HLA-DR+) or in the normal B cell population (CD19+CD34- CD45(hi)HLA-DR+) of patients. No significant difference was observed in gender (male/female) or age (paediatric/adult). Only a trend in reduced sHLA was observed in patients carrying HLA-DR04. These results have to be validated with a larger number of samples.
Chemometric approach to validating faecal sterols as source tracer for faecal contamination in water

Saim N, Osman R, Sari Abg Spian DR, Jaafar MZ, Juahir H, Abdullah MP, et al.

Water Res, 2009 Dec;43(20):5023-30.
PMID: 19896157 DOI: 10.1016/j.watres.2009.08.052

Faecal sterols detection is a promising method for identifying sources of faecal pollution. In this study, faecal contamination in water samples from point source (sewage treatment plants, chicken farms, quail farms and horse stables) was extracted using the solid phase extraction (SPE) technique. Faecal sterols (coprostanol, cholesterol, stigmasterol, beta-sitosterol and stigmastanol) were selected as parameters to differentiate the source of faecal pollution. The results indicated that coprostanol, cholesterol and beta-sitosterol were the most significant parameters that can be used as source tracers for faecal contamination. Chemometric techniques, such as cluster analysis, principal component analysis and discriminant analysis were applied to the data set on faecal contamination in water from various pollution sources in order to validate the faecal sterols' profiles. Cluster analysis generated three clusters: coprostanol was in cluster 1, cholesterol and beta-sitosterol formed cluster 2, while cluster 3 contained stigmasterol and stigmastanol. Discriminant analysis suggested that coprostanol, cholesterol and beta-sitosterol were the most significant parameters to discriminate between the faecal pollution source. The use of chemometric techniques provides useful and promising indicators in tracing the source of faecal contamination.
Quality assessment and chemometrics application on physicochemical characteristics, antioxidant properties, and 5-HMF content of Malaysian stingless bee honey from different topographical origins

Manickavasagam G, Saaid M, Lim V, Saad MIZM, Azmi NAS, Osman R

J Food Sci, 2023 Apr;88(4):1466-1481.
PMID: 36922718 DOI: 10.1111/1750-3841.16535

The popularity of Malaysian stingless bee honey is rising among health-conscious individuals; thus, chemical and physical evaluations of Malaysian stingless bee honey are vital to ensure the honey has achieved the optimum limits set by Malaysian and international regulatory standards so that it can be commercialized locally and internationally. Therefore, in the present study, the physicochemical characteristics (moisture content, total dissolved solids, pH, free acidity, electrical conductivity, and ash content), antioxidant properties (total phenolic and flavonoid contents), and 5-hydroxymethylfurfural (5-HMF) of Heterotrigona itama (H. itama) honey from different sites in Peninsular Malaysia were investigated. Subsequently, the correlation between these chemical and physical parameters was studied using Spearman correlation coefficients. The significant difference between H. itama honey from different topographical origins was studied using univariate analysis (one-way ANOVA followed by post hoc Tukey's test). The discrimination pattern of 45 honey samples based on their topographical origins was evaluated using cluster analysis (heatmap and dendrogram) and chemometrics analysis (partial least squares-discriminant analysis). Results showed that some samples of certain parameters (electrical conductivity, free acidity, and moisture content) have exceeded the limit set by the international regulatory standard. However, the 5-HMF content of all samples was within the allowed range. A statistically significant difference (p
Increased regulatory T cells in acute lymphoblastic leukaemia patients

Idris SZ, Hassan N, Lee LJ, Md Noor S, Osman R, Abdul-Jalil M, et al.

Hematology, 2016 May;21(4):206-12.
PMID: 26907959 DOI: 10.1080/10245332.2015.1101965

INTRODUCTION: Regulation in adaptive immune response balances a fine line that prevents instigation of self-damage or fall into unresponsiveness permitting abnormal cell growth. Mechanisms that keep this balance in check include regulatory T cells (Tregs). Tregs consist of a small but heterogeneous population, which may be identified by the phenotype, CD3+CD4+CD25+CD127-. The role of Tregs in pathogenesis of cancers is thus far supported by evidence of increased Tregs in various cancers and may contribute to poorer prognosis. Tregs may also be important in acute leukaemias.
OBJECTIVE: A review of the literature on Tregs in acute leukaemias was conducted and Tregs were determined in B-cell acute lymphoblastic leukaemias (ALLs).
RESULTS: Studies on Tregs in B-cell ALL are few and controversial. We observed a significantly increased percentage of Tregs (mean±SD, 9.72 ± 3.79% vs. 7.05 ± 1.74%; P = 0.047) in the bone marrow/peripheral blood of ALL (n = 17) compared to peripheral blood of normal controls (n = 35). A positive trend between Tregs and age (R = 0.474, P = 0.055, n = 17) implicates this factor of poor prognosis in B-cell ALL.
DISCUSSION: Tregs in cancer are particularly significant in immunotherapy. The manipulation of the immune system to treat cancer has for a long time ignored regulatory mechanisms inducible or in place. In lymphoma studies, tumour-specific mechanisms that are unlike conventional methods in the induction of Tregs have been hypothesized. In addition, tumour-infiltrating Tregs may present different profiles from peripheral blood pictures. Tregs will continue to be dissected to reveal its mysteries and their impact on clinical significance.
Fulltext Medical image processing and COVID-19: A literature review and bibliometric analysis

Abumalloh RA, Nilashi M, Yousoof Ismail M, Alhargan A, Alghamdi A, Alzahrani AO, et al.

J Infect Public Health, 2022 Jan;15(1):75-93.
PMID: 34836799 DOI: 10.1016/j.jiph.2021.11.013

COVID-19 crisis has placed medical systems over the world under unprecedented and growing pressure. Medical imaging processing can help in the diagnosis, treatment, and early detection of diseases. It has been considered as one of the modern technologies applied to fight against the COVID-19 crisis. Although several artificial intelligence, machine learning, and deep learning techniques have been deployed in medical image processing in the context of COVID-19 disease, there is a lack of research considering systematic literature review and categorization of published studies in this field. A systematic review locates, assesses, and interprets research outcomes to address a predetermined research goal to present evidence-based practical and theoretical insights. The main goal of this study is to present a literature review of the deployed methods of medical image processing in the context of the COVID-19 crisis. With this in mind, the studies available in reliable databases were retrieved, studied, evaluated, and synthesized. Based on the in-depth review of literature, this study structured a conceptual map that outlined three multi-layered folds: data gathering and description, main steps of image processing, and evaluation metrics. The main research themes were elaborated in each fold, allowing the authors to recommend upcoming research paths for scholars. The outcomes of this review highlighted that several methods have been adopted to classify the images related to the diagnosis and detection of COVID-19. The adopted methods have presented promising outcomes in terms of accuracy, cost, and detection speed.
Fulltext Chromosomal Aberrations in ETV6/RUNX1-positive Childhood Acute Lymphoblastic Leukemia using 244K Oligonucleotide Array Comparative Genomic Hybridization

Zakaria Z, Ahid MF, Ismail A, Keoh TS, Nor NM, Kamaluddin NR, et al.

Mol Cytogenet, 2012;5(1):41.
PMID: 23151340 DOI: 10.1186/1755-8166-5-41