Displaying publications 201 - 220 of 271 in total

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  1. Fulltext The conformational dynamics of H2-H3n and S2-H6 in gating ligand entry into the buried binding cavity of vitamin D receptor
    Tee WV, Ripen AM, Mohamad SB
    Sci Rep, 2016 Oct 27;6:35937.
    PMID: 27786277 DOI: 10.1038/srep35937
    Crystal structures of holo vitamin D receptor (VDR) revealed a canonical conformation in which the ligand is entrapped in a hydrophobic cavity buried in the ligand-binding domain (LBD). The mousetrap model postulates that helix 12 is positioned away from the domain to expose the interior cavity. However, the extended form of helix 12 is likely due to artifacts during crystallization. In this study, we set out to investigate conformational dynamics of apo VDR using molecular dynamics simulation on microsecond timescale. Here we show the neighboring backbones of helix 2-helix 3n and beta strand 2-helix 6 of LBD, instead of the helix 12, undergo large-scale motion, possibly gating the entrance of ligand to the ligand binding domain. Docking analysis to the simulated open structure of VDR with the estimated free energy of -37.0 kJ/mol, would emphasise the role of H2-H3n and S2-H6 in facilitating the entrance of calcitriol to the LBD of VDR.
    Matched MeSH terms: Principal Component Analysis
  2. Cardiorespiratory fitness is positively associated with a healthy dietary pattern in New Zealand adolescents
    Howe AS, Skidmore PM, Parnell WR, Wong JE, Lubransky AC, Black KE
    Public Health Nutr, 2016 May;19(7):1279-87.
    PMID: 26347042 DOI: 10.1017/S1368980015002566
    OBJECTIVE: To examine the association between cardiorespiratory fitness and dietary patterns in adolescents.

    DESIGN: Food choice was assessed using the validated New Zealand Adolescent FFQ. Principal components analysis was used to determine dietary patterns. Trained research assistants measured participants' height and body mass. Cardiorespiratory fitness was assessed in a subset of participants using the multistage 20 m shuttle run. The level and stage were recorded, and the corresponding VO2max was calculated. Differences in mean VO2max according to sex and BMI were assessed using t tests, while associations between cardiorespiratory fitness and dietary patterns were examined using linear regression analyses adjusted for age, sex, school attended, socio-economic deprivation and BMI.

    SETTING: Secondary schools in Otago, New Zealand.

    SUBJECTS: Students (n 279) aged 14-18 years who completed an online lifestyle survey during a class period.

    RESULTS: Principal components analysis produced three dietary patterns: 'Treat Foods', 'Fruits and Vegetables' and 'Basic Foods'. The 279 participants who provided questionnaire data and completed cardiorespiratory fitness testing had a mean age of 15·7 (sd 0·9) years. Mean VO2max was 45·8 (sd 6·9) ml/kg per min. The 'Fruits and Vegetables' pattern was positively associated with VO2max in the total sample (β=0·04; 95%CI 0·02, 0·07), girls (β=0·06; 95% CI 0·03, 0·10) and boys (β=0·03; 95% CI 0·01, 0·05).

    CONCLUSIONS: These results indicate that increase in cardiorespiratory fitness was associated with a healthier dietary pattern, suggesting both should be targeted as part of a global lifestyle approach. Longitudinal studies are needed to confirm this association in relation to health outcomes in New Zealand adolescents.

    Matched MeSH terms: Principal Component Analysis
  3. Fulltext A novel investigation of the effect of iterations in sliding semi-landmarks for 3D human facial images
    Nazri A, Agbolade O, Yaakob R, Ghani AA, Cheah YK
    BMC Bioinformatics, 2020 May 24;21(1):208.
    PMID: 32448182 DOI: 10.1186/s12859-020-3497-7
    BACKGROUND: Landmark-based approaches of two- or three-dimensional coordinates are the most widely used in geometric morphometrics (GM). As human face hosts the organs that act as the central interface for identification, more landmarks are needed to characterize biological shape variation. Because the use of few anatomical landmarks may not be sufficient for variability of some biological patterns and form, sliding semi-landmarks are required to quantify complex shape.

    RESULTS: This study investigates the effect of iterations in sliding semi-landmarks and their results on the predictive ability in GM analyses of soft-tissue in 3D human face. Principal Component Analysis (PCA) is used for feature selection and the gender are predicted using Linear Discriminant Analysis (LDA) to test the effect of each relaxation state. The results show that the classification accuracy is affected by the number of iterations but not in progressive pattern. Also, there is stability at 12 relaxation state with highest accuracy of 96.43% and an unchanging decline after the 12 relaxation state.

    CONCLUSIONS: The results indicate that there is a particular number of iteration or cycle where the sliding becomes optimally relaxed. This means the higher the number of iterations is not necessarily the higher the accuracy.

    Matched MeSH terms: Principal Component Analysis
  4. Fulltext Dimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction
    Sakaue S, Hirata J, Kanai M, Suzuki K, Akiyama M, Lai Too C, et al.
    Nat Commun, 2020 03 26;11(1):1569.
    PMID: 32218440 DOI: 10.1038/s41467-020-15194-z
    The diversity in our genome is crucial to understanding the demographic history of worldwide populations. However, we have yet to know whether subtle genetic differences within a population can be disentangled, or whether they have an impact on complex traits. Here we apply dimensionality reduction methods (PCA, t-SNE, PCA-t-SNE, UMAP, and PCA-UMAP) to biobank-derived genomic data of a Japanese population (n = 169,719). Dimensionality reduction reveals fine-scale population structure, conspicuously differentiating adjacent insular subpopulations. We further enluciate the demographic landscape of these Japanese subpopulations using population genetics analyses. Finally, we perform phenome-wide polygenic risk score (PRS) analyses on 67 complex traits. Differences in PRS between the deconvoluted subpopulations are not always concordant with those in the observed phenotypes, suggesting that the PRS differences might reflect biases from the uncorrected structure, in a trait-dependent manner. This study suggests that such an uncorrected structure can be a potential pitfall in the clinical application of PRS.
    Matched MeSH terms: Principal Component Analysis
  5. Fulltext DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system
    Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M, Halidu J
    Sci Rep, 2021 Jul 15;11(1):14527.
    PMID: 34267249 DOI: 10.1038/s41598-021-93867-5
    As a new crop in Malaysia, forty-four Bambara groundnut (Vigna subterranea L. verdc.) genotypes were sampled from eleven distinct populations of different origins to explore the genetic structure, genetic inconsistency, and fixation index. The Bambara groundnut, an African underutilized legume, has the capacity to boost food and nutrition security while simultaneously addressing environmental sustainability, food availability, and economic inequalities. A set of 32 ISSRs were screened out of 96 primers based on very sharp, clear, and reproducible bands which detected a total of 510 loci with an average of 97.64% polymorphism. The average calculated value of PIC = 0.243, RP = 5.30, H = 0.285, and MI = 0.675 representing the efficiency of primer set for genetic differentiation among the genotypes. The ISSR primers revealed the number of alleles (Na = 1.97), the effective number of alleles (Ne = 1.38), Nei's genetic diversity (h = 0.248), and a moderate level of gene flow (Nm = 2.26) across the genotypes studied. The estimated Shannon's information index (I = 0.395) indicates a high level of genetic variation exists among the accessions. Based on Nei's genetic dissimilarity a UPMGA phylogenetic tree was constructed and grouped the entire genotypes into 3 major clusters and 6 subclusters. PCA analysis revealed that first principal component extracted maximum variation (PC1 = 13.92%) than second principal component (PC2 = 12.59%). Bayesian model-based STRUCTURE analysis assembled the genotypes into 3 (best ΔK = 3) genetic groups. The fixation-index (Fst) analysis narrated a very great genetic diversity (Fst = 0.19 to 0.40) exists within the accessions of these 3 clusters. This investigation specifies the effectiveness of the ISSR primers system for the molecular portrayal of V. subterranea genotypes that could be used for genetic diversity valuation, detection, and tagging of potential genotypes with quick, precise, and authentic measures for this crop improvement through effective breeding schemes.
    Matched MeSH terms: Principal Component Analysis
  6. Fulltext Genetic analysis and selection of Bambara groundnut (Vigna subterranea [L.] Verdc.) landraces for high yield revealed by qualitative and quantitative traits
    Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M
    Sci Rep, 2021 Apr 07;11(1):7597.
    PMID: 33828137 DOI: 10.1038/s41598-021-87039-8
    As a crop for the new millennium Bambara groundnut (Vigna subterranea [L.] Verdc.) considered as leading legumes in the tropical regions due to its versatile advantages. The main intent of this study was to find out the high yielding potential genotypes and considering these genotypes to develop pure lines for commercial cultivation in Malaysia. Considering the 14 qualitative and 27 quantitative traits of fifteen landraces the variation and genetic parameters namely, variability, heritability, genetic advance, characters association, and cluster matrix were determined. ANOVA revealed significant variation for all the agronomic traits (except plant height). Among the accessions, highly significant differences (P ≤ 0.01) were found for almost all the traits excluding fifty percent flowering date, seed length, seed width. The 16 traits out of the 27 quantitative traits had a coefficient of variation (CV) ≥ 20%. A positive and intermediate to perfect highly significant association (r = 0.23 to 1.00; P 
    Matched MeSH terms: Principal Component Analysis
  7. A description of two new species of Ligophorus Euzet & Suriano, (Monogenea: Ancyrocephalidae) from Malaysian mugilid fish using principal component analysis and numerical taxonomy
    Soo OY, Lim LH
    J Helminthol, 2015 Mar;89(2):131-49.
    PMID: 24148150 DOI: 10.1017/S0022149X13000655
    Ligophorus belanaki n. sp. and Ligophorus kederai n. sp. are described from Liza subviridis Valenciennes, 1836 and Valamugil buchanani Bleeker, 1854, respectively. Ligophorus kederai n. sp. has fenestrated ventral anchors, while in L. belanaki n. sp. the ventral anchor is not fenestrated. Ligophorus belanaki n. sp. is similar to L. careyensis, one of its coexisting congeners, in the overall shape and size of hard parts, but differs in having a flat median piece in the structure of the AMP (antero-median protuberance of the ventral bar), copulatory organ with non-ornamented initial part and longer vaginal tube, compared to raised median piece in the AMP, ornamented initial part and comparatively shorter vaginal tube in L. careyensis. Ligophorus kederai n. sp. is similar to L. fenestrum, a coexisting congener, in having fenestrated ventral anchors, but differs in having longer points and narrower base. Ligophorus fenestrum, unlike L. kederai n. sp., also possesses fenestrated dorsal anchors. The principal component analysis (PCA) scatterplots indicate that the two new and eight known Ligophorus species from Malaysian mugilids can be differentiated based on the morphometries of their anchors, ventral bars and copulatory organ separately and when combined together. Numerical taxonomy (NT) analyses based on Jaccard's Index of Similarity and neighbour-joining clustering, is used to facilitate comparison of these two new species with the 50 known Ligophorus based on morphological and metric characters. The two new species are different from each other and the other 50 species in the overall shapes and sizes of hard parts, as indicated by the NT analyses.
    Matched MeSH terms: Principal Component Analysis
  8. Fulltext Amino Acid and Secondary Metabolite Production in Embryogenic and Non-Embryogenic Callus of Fingerroot Ginger (Boesenbergia rotunda)
    Ng TL, Karim R, Tan YS, Teh HF, Danial AD, Ho LS, et al.
    PLoS One, 2016;11(6):e0156714.
    PMID: 27258536 DOI: 10.1371/journal.pone.0156714
    Interest in the medicinal properties of secondary metabolites of Boesenbergia rotunda (fingerroot ginger) has led to investigations into tissue culture of this plant. In this study, we profiled its primary and secondary metabolites, as well as hormones of embryogenic and non-embryogenic (dry and watery) callus and shoot base, Ultra Performance Liquid Chromatography-Mass Spectrometry together with histological characterization. Metabolite profiling showed relatively higher levels of glutamine, arginine and lysine in embryogenic callus than in dry and watery calli, while shoot base tissue showed an intermediate level of primary metabolites. For the five secondary metabolites analyzed (ie. panduratin, pinocembrin, pinostrobin, cardamonin and alpinetin), shoot base had the highest concentrations, followed by watery, dry and embryogenic calli. Furthermore, intracellular auxin levels were found to decrease from dry to watery calli, followed by shoot base and finally embryogenic calli. Our morphological observations showed the presence of fibrils on the cell surface of embryogenic callus while diphenylboric acid 2-aminoethylester staining indicated the presence of flavonoids in both dry and embryogenic calli. Periodic acid-Schiff staining showed that shoot base and dry and embryogenic calli contained starch reserves while none were found in watery callus. This study identified several primary metabolites that could be used as markers of embryogenic cells in B. rotunda, while secondary metabolite analysis indicated that biosynthesis pathways of these important metabolites may not be active in callus and embryogenic tissue.
    Matched MeSH terms: Principal Component Analysis
  9. Fulltext Image Processing for mHealth-Based Approach to Detect the Local Tissue Inflammation in Cutaneous Leishmaniasis: A Proof of Concept Study
    Silva H, Chellappan K, Karunaweera N
    Comput Math Methods Med, 2021;2021:4208254.
    PMID: 34873414 DOI: 10.1155/2021/4208254
    Skin lesions are a feature of many diseases including cutaneous leishmaniasis (CL). Ulcerative lesions are a common manifestation of CL. Response to treatment in such lesions is judged through the assessment of the healing process by regular clinical observations, which remains a challenge for the clinician, health system, and the patient in leishmaniasis endemic countries. In this study, image processing was initially done using 40 CL lesion color images that were captured using a mobile phone camera, to establish a technique to extract features from the image which could be related to the clinical status of the lesion. The identified techniques were further developed, and ten ulcer images were analyzed to detect the extent of inflammatory response and/or signs of healing using pattern recognition of inflammatory tissue captured in the image. The images were preprocessed at the outset, and the quality was improved using the CIE L∗a∗b color space technique. Furthermore, features were extracted using the principal component analysis and profiled using the signal spectrogram technique. This study has established an adaptive thresholding technique ranging between 35 and 200 to profile the skin lesion images using signal spectrogram plotted using Signal Analyzer in MATLAB. The outcome indicates its potential utility in visualizing and assessing inflammatory tissue response in a CL ulcer. This approach is expected to be developed further to a mHealth-based prediction algorithm to enable remote monitoring of treatment response of cutaneous leishmaniasis.
    Matched MeSH terms: Principal Component Analysis
  10. Classification of lower limb body shapes of paralysed female wheelchair users in Hebei, China: analysis of anthropometric data using clustering approach
    Xing L, Zakaria N, Ruznan WS
    Ergonomics, 2024 Sep;67(9):1190-1197.
    PMID: 38044671 DOI: 10.1080/00140139.2023.2289855
    Lower limb body shape is important in the design of functional pants. The skin, muscles, and body shapes of the lower limbs of wheelchair users may differ from healthy people because of the different shapes of their legs and the prolonged seating position. This study aimed to classify the shapes of the lower limbs of adult female wheelchair users. The lower body measurement of 384 female wheelchair users was obtained. The principal component analysis and two-step cluster analysis were used to categorise the body shapes into three different types and five different size standards. Based on the study findings, female wheelchairs have larger waist, belly, and hip circumferences than healthy individuals, with 89.3% of them having prominent hips. Therefore, the design and production of trousers for wheelchair users should take into consideration the classification of lower limb shapes and sizes reported in this study.Practitioner summary: This work initiated the investigation of human body size assessment of clothes for handicapped persons in China, allowing paraplegic female wheelchair users to wear adapted trousers.
    Matched MeSH terms: Principal Component Analysis
  11. Cardiovascular risk factors in pre-pubertal Malays: effects of diabetic parentage
    Choo KE, Lau KB, Davis WA, Chew PH, Jenkins AJ, Davis TM
    Diabetes Res Clin Pract, 2007 Apr;76(1):119-25.
    PMID: 16979774 DOI: 10.1016/j.diabres.2006.08.006
    Diabetes prevalence is increasing rapidly in Asian populations but the influence of a family history of diabetes on cardiovascular risk is unknown. To assess this relationship, 120 urban-dwelling Malays were recruited to a cross-sectional case-control study. Sixty were pre-pubertal children, 30 of diabetic parentage (Group 1) and 30 with no diabetes family history (Group 2). Group 1 and 2 subjects were the offspring of adults with (Group 3) or without (Group 4) type 2 diabetes. Subjects were assessed for clinical and biochemical variables defining cardiovascular risk. Principal component analysis assessed clustering of variables in the children. Group 1 subjects had a higher mean waist:hip ratio, diastolic blood pressure and HbA(1c) than those in Group 2, and a lower HDL:total cholesterol ratio (P<0.03). Although there were no correlations between Group 1 and 3 subjects for cardiovascular risk variables, significant associations were found in Groups 2 and 4, especially HbA(1c) and insulin sensitivity (P< or =0.004). Of five separate clusters of variables (factors) identified amongst the children, the strongest comprised diabetic parentage, HbA(1c), insulin sensitivity and blood pressure. Features of the metabolic syndrome are becoming evident in the young non-obese children of diabetic Malays, suggesting that lifestyle factors merit particular attention in this group.
    Matched MeSH terms: Principal Component Analysis/methods
  12. Source contribution of PM₂.₅ at different locations on the Malaysian Peninsula
    Ee-Ling O, Mustaffa NI, Amil N, Khan MF, Latif MT
    Bull Environ Contam Toxicol, 2015 Apr;94(4):537-42.
    PMID: 25652682 DOI: 10.1007/s00128-015-1477-9
    This study determined the source contribution of PM2.5 (particulate matter <2.5 μm) in air at three locations on the Malaysian Peninsula. PM2.5 samples were collected using a high volume sampler equipped with quartz filters. Ion chromatography was used to determine the ionic composition of the samples and inductively coupled plasma mass spectrometry was used to determine the concentrations of heavy metals. Principal component analysis with multilinear regressions were used to identify the possible sources of PM2.5. The range of PM2.5 was between 10 ± 3 and 30 ± 7 µg m(-3). Sulfate (SO4 (2-)) was the major ionic compound detected and zinc was found to dominate the heavy metals. Source apportionment analysis revealed that motor vehicle and soil dust dominated the composition of PM2.5 in the urban area. Domestic waste combustion dominated in the suburban area, while biomass burning dominated in the rural area.
    Matched MeSH terms: Principal Component Analysis
  13. Fears related to pregnancy and childbirth among primigravidae who requested caesarean versus vaginal delivery in Iran
    Matinnia N, Faisal I, Hanafiah Juni M, Herjar AR, Moeini B, Osman ZJ
    Matern Child Health J, 2015 May;19(5):1121-30.
    PMID: 25269852 DOI: 10.1007/s10995-014-1610-0
    Pregnancy- and childbirth-related fears are common psychological concerns and the primary reasons for requesting caesarean section (CS). We aimed to examine the content of maternal fear and the associated demographic factors in a sample of Iranian primigravidae. A randomly selected sample of primigravidae (n = 342) was recruited in four health care centres in Iran. Data were collected using a 30-item questionnaire. Principal components factor analysis was applied to identify the main factors of pregnancy- and childbirth-related fears. All primigravidae reported some degree of fear, 48.2 % presented severe fear, and 62.6 % requested a CS because of childbirth-related fear. Most of the employed primigravidae with higher education level, higher family income, and unplanned pregnancy requested CS. The items constructed to measure maternal fear were subjected to exploratory factor analysis. Six categories were identified, including 'process of labour and childbirth', 'life and well-being of the baby', 'competence and behaviour of maternity ward personnel', 'own capabilities and reactions', 'becoming a parent and family life after delivery' and 'general fear in pregnancy' that cumulatively explained 55.3 % of the variance. The most common factor was 'life and well-being of the baby'. Severe fear was found in 70.6 % of those who chose CS, while 10.9 % of those who chose vaginal delivery reported severe fear. The between-group differences for mean scores and levels of fear were statistically significant. Pregnancy- and childbirth-related fears were frequently experienced by all low-risk primigravidae. Better strategies to address women's psychological needs during pregnancy are necessary.
    Matched MeSH terms: Principal Component Analysis
  14. Assessment of gas chromatography time-of-flight accurate mass spectrometry for identification of volatile and semi-volatile compounds in honey
    Moniruzzaman M, Rodríguez I, Ramil M, Cela R, Sulaiman SA, Gan SH
    Talanta, 2014 Nov;129:505-15.
    PMID: 25127626 DOI: 10.1016/j.talanta.2014.06.019
    The performance of gas chromatography (GC) combined with a hybrid quadrupole time-of-flight (QTOF) mass spectrometry (MS) system for the determination of volatile and semi-volatile compounds in honey samples is evaluated. After headspace (HS) solid-phase microextraction (SPME) of samples, the accurate mass capabilities of the above system were evaluated for compounds identification. Accurate scan electron impact (EI) MS spectra allowed discriminating compounds displaying the same nominal masses, but having different empirical formulae. Moreover, the use of a mass window with a width of 0.005 Da provided highly specific chromatograms for selected ions, avoiding the contribution of interferences to their peak areas. Additional information derived from positive chemical ionization (PCI) MS spectra and ion product scan MS/MS spectra permitted confirming the identity of novel compounds. The above possibilities are illustrated with examples of honey aroma compounds, belonging to different chemical classes and containing different elements in their molecules. Examples of compounds whose structures could not be described are also provided. Overall, 84 compounds, from a total of 89 species, could be identified in 19 honey samples from 3 different geographic areas in the world. The suitability of responses measured for selected ions, corresponding to above species, for authentication purposes is assessed through principal components analysis.
    Matched MeSH terms: Principal Component Analysis
  15. Fulltext Genetic dissection of sympatric populations of brown planthopper, Nilaparvata lugens (Stål), using DALP-PCR molecular markers
    Latif MA, Rafii MY, Mazid MS, Ali ME, Ahmed F, Omar MY, et al.
    ScientificWorldJournal, 2012;2012:586831.
    PMID: 22593700 DOI: 10.1100/2012/586831
    Direct amplified length polymorphism (DALP) combines the advantages of a high-resolution fingerprint method and also characterizing the genetic polymorphisms. This molecular method was also found to be useful in brown planthopper, Nilaparvata lugens species complex for the analysis of genetic polymorphisms. A total of 11 populations of Nilaparvata spp. were collected from 6 locations from Malaysia. Two sympatric populations of brown planthopper, N. lugens, one from rice and the other from a weed grass (Leersia hexandra), were collected from each of five locations. N. bakeri was used as an out group. Three oligonucleotide primer pairs, DALP231/DALPR'5, DALP234/DALPR'5, and DALP235/DALPR'5 were applied in this study. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on genetic distances for the 11 populations of Nilaparvata spp. revealed that populations belonging to the same species and the same host type clustered together irrespective of their geographical localities of capture. The populations of N. lugens formed into two distinct clusters, one was insects with high esterase activities usually captured from rice and the other was with low esterase activities usually captured from L. hexandra. N. bakeri, an out group, was the most isolated group. Analyses of principal components, molecular variance, and robustness also supported greatly to the findings of cluster analysis.
    Matched MeSH terms: Principal Component Analysis
  16. Sugars, ascorbic acid, total phenolic content and total antioxidant activity in passion fruit (Passiflora) cultivars
    Devi Ramaiya S, Bujang JS, Zakaria MH, King WS, Shaffiq Sahrir MA
    J Sci Food Agric, 2013 Mar 30;93(5):1198-205.
    PMID: 23027609 DOI: 10.1002/jsfa.5876
    The levels of sugars, ascorbic acid, total phenolic content (TPC) and total antioxidant activity (TAA) were determined in fruit juices from seven passion fruit (Passiflora spp.) cultivars: P. edulis cultivars Purple, Frederick, Yellow, Pink, P. edulis f. flavicarpa, P. maliformis and P. quadrangularis (we also tested this cultivar's mesocarp).
    Matched MeSH terms: Principal Component Analysis
  17. 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.
    Matched MeSH terms: Principal Component Analysis
  18. Fulltext Expression profile of MicroRNAs in young stroke patients
    Tan KS, Armugam A, Sepramaniam S, Lim KY, Setyowati KD, Wang CW, et al.
    PLoS One, 2009;4(11):e7689.
    PMID: 19888324 DOI: 10.1371/journal.pone.0007689
    The methods currently available for diagnosis and prognosis of cerebral ischaemia still require further improvements. Micro-RNAs (small non-coding RNAs) have been recently reported as useful biomarkers in diseases such as cancer and diabetes. We therefore carried out microRNA (miRNA) profiling from peripheral blood to detect and identify characteristic patterns in ischaemic stroke.
    Matched MeSH terms: Principal Component Analysis
  19. Composition and source apportionment of surfactants in atmospheric aerosols of urban and semi-urban areas in Malaysia
    Wahid NB, Latif MT, Suratman S
    Chemosphere, 2013 Jun;91(11):1508-16.
    PMID: 23336924 DOI: 10.1016/j.chemosphere.2012.12.029
    This study was conducted to determine the composition and source apportionment of surfactant in atmospheric aerosols around urban and semi-urban areas in Malaysia based on ionic compositions. Colorimetric analysis was undertaken to determine the concentrations of anionic surfactants as Methylene Blue Active Substances (MBAS) and cationic surfactants as Disulphine Blue Active Substances (DBAS) using a UV spectrophotometer. Ionic compositions were determined using ion chromatography for cations (Na(+), NH4(+), K(+), Mg(2+), Ca(2+)) and anions (F(-), Cl(-), NO3(-), SO4(2-)). Principle component analysis (PCA) combined with multiple linear regression (MLR) were used to identify the source apportionment of MBAS and DBAS. Results indicated that the concentrations of surfactants at both sampling sites were dominated by MBAS rather than DBAS especially in fine mode aerosols during the southwest monsoon. Three main sources of surfactants were identified from PCA-MLR analysis for MBAS in fine mode samples particularly in Kuala Lumpur, dominated by motor vehicles, followed by soil/road dust and sea spray. Besides, for MBAS in coarse mode, biomass burning/sea spray were the dominant source followed by motor vehicles/road dust and building material.
    Matched MeSH terms: Principal Component Analysis
  20. Fulltext The anti-neuroinflammatory effects of Clinacanthus nutans leaf extract on metabolism elucidated through 1H NMR in correlation with cytokines microarray
    Ahmad Azam A, Ismail IS, Kumari Y, Shaikh MF, Abas F, Shaari K
    PLoS One, 2020;15(9):e0238503.
    PMID: 32925968 DOI: 10.1371/journal.pone.0238503
    Clinacanthus nutans (CN) (Acanthaceae) is well-known for its anti-inflammatory properties among Asian communities; however, there are currently no data specifically focused on the anti-inflammatory effects of CN on the brain tissue. Neuroinflammation is a common consequence of toxin intrusion to any part of the central nervous system (CNS). As an innate immune response, the CNS may react through both protective and/or toxic actions due to the activation of neuron cells producing pro- and/or anti-inflammatory cytokines in the brain. The unresolved activation of the inflammatory cytokines' response is associated with the pathogenesis of neurological disorders. The present study aimed to decipher the metabolic mechanism on the effects of 14 days oral treatment with CN aqueous extract in induced-lipopolysaccharides (LPS) rats through 1H NMR spectroscopic biomarker profiling of the brain tissue and the related cytokines. Based on the principal component analysis (PCA) of the nuclear magnetic resonance (NMR) spectral data, twenty-one metabolites in the brain tissue were profiled as biomarkers for the LPS (10 μL)-induced neuroinflammation following intracerebroventricular injection. Among the twenty-one biomarkers in the neuroinflammed rats, CN treatment of 1000 and 500 mg/kg BW successfully altered lactate, pyruvate, phosphorylcholine, glutamine, and α-ketoglutarate when compared to the negative control. Likewise, statistical isolinear multiple component analysis (SIMCA) showed that treatments by CN and the positive control drug, dextromethorphan (DXM, 5 mg/kg BW), have anti-neuroinflammatory potential. A moderate correlation, in the orthogonal partial least squares (OPLS) regression model, was found between the spectral metabolite profile and the cytokine levels. The current study revealed the existence of high levels of pro-inflammatory cytokines, namely IL-1α, IL-1β, and TNF-α in LPS-induced rats. Both CN dose treatments lowered IL-1β significantly better than DXM Interestingly, DXM and CN treatments both exhibited the upregulation of the anti-inflammatory cytokines IL-2 and 4. However, DXM has an advantage over CN in that the former also increased the expression of IL-10 of anti-inflammatory cytokines. In this study, a metabolomics approach was successfully applied to discover the mechanistic role of CN in controlling the neuroinflammatory conditions through the modulation of complex metabolite interactions in the rat brain.
    Matched MeSH terms: Principal Component Analysis
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