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Fulltext Metabolomics approach for multibiomarkers determination to investigate dengue virus infection in human patients

Shahfiza N, Osman H, Hock TT, Abdel-Hamid AZ

Acta Biochim. Pol., 2017;64(2):215-219.
PMID: 28350402 DOI: 10.18388/abp.2015_1224

BACKGROUND: Dengue is one of the major public health problems in the world, affecting more than fifty million cases in tropical and subtropical region every year. The metabolome, as pathophysiological end-points, provide significant understanding of the mechanism and progression of dengue pathogenesis via changes in the metabolite profile of infected patients. Recent developments in diagnostic technologies provide metabolomics for the early detection of infectious diseases.
METHODS: The mid-stream urine was collected from 96 patients diagnosed with dengue fever at Penang General Hospital (PGH) and 50 healthy volunteers. Urine samples were analyzed with proton nuclear magnetic resonance (1H NMR) spectroscopy, followed by chemometric multivariate analysis. NMR signals highlighted in the orthogonal partial least square-discriminant analysis (OPLS-DA) S-plots were selected and identified using Human Metabolome Database (HMDB) and Chenomx Profiler. A highly predictive model was constructed from urine profile of dengue infected patients versus healthy individuals with the total R2Y (cum) value 0.935, and the total Q2Y (cum) value 0.832.
RESULTS: Data showed that dengue infection is related to amino acid metabolism, tricarboxylic acid intermediates cycle and β-oxidation of fatty acids. Distinct variations in certain metabolites were recorded in infected patients including amino acids, various organic acids, betaine, valerylglycine, myo-inositol and glycine.
CONCLUSION: Metabolomics approach provides essential insight into host metabolic disturbances following dengue infection.

Matched MeSH terms: Principal Component Analysis
Breeding habitat preference of preimaginal black flies (Diptera: Simuliidae) in Peninsular Malaysia

Ya'cob Z, Takaoka H, Pramual P, Low VL, Sofian-Azirun M

Acta Trop, 2016 Jan;153:57-63.
PMID: 26476394 DOI: 10.1016/j.actatropica.2015.10.007

To investigate the breeding habitat preference of black flies, a comprehensive black fly survey was conducted for the first time in Peninsular Malaysia. Preimaginal black flies (pupae and larvae) were collected manually from 180 stream points encompassing northern, southern, central and east coast of the Peninsular Malaysia. A total of 47 black fly species were recorded in this study. The predominant species were Simulium trangense (36.7%) and Simulium angulistylum (33.3%). Relatively common species were Simulium cheongi (29.4%), Simulium tani (25.6%), Simulium nobile (16.2%), Simulium sheilae (14.5%) and Simulium bishopi (10.6%). Principal Component Analysis (PCA) of all stream variables revealed four PCs that accounted for 69.3% of the total intersite variance. Regression analysis revealed that high species richness is associated with larger, deeper, faster and higher discharge streams with larger streambed particles, more riparian vegetation and low pH (F=22.7, d.f.=1, 173; P<0.001). Relationship between species occurrence of seven common species (present in >10% of the sampling sites) was assessed. Forward logistic regression analysis indicated that four species were significantly related to the stream variables. S. nobile and S. tani prefer large, fast flowing streams with higher pH, large streambed particles and riparian trees. S. bishopi was commonly found at high elevation with cooler stream, low conductivity, higher conductivity and more riparian trees. In contrast, S. sheilae was negatively correlated with PC-2, thus, this species commonly found at low elevation, warmer stream with low conductivity and less riparian trees. The results of this study are consistent with previous studies from other geographic regions, which indicated that both physical and chemical stream conditions are the key factors for black fly ecology.

Matched MeSH terms: Principal Component Analysis
Fulltext A genetic comparison of two alleged subspecies of Philippine cynomolgus macaques

Smith DG, Ng J, George D, Trask JS, Houghton P, Singh B, et al.

Am. J. Phys. Anthropol., 2014 Sep;155(1):136-48.
PMID: 24979664 DOI: 10.1002/ajpa.22564

Two subspecies of cynomolgus macaques (Macaca fascicularis) are alleged to co-exist in the Philippines, M. f. philippensis in the north and M. f. fascicularis in the south. However, genetic differences between the cynomolgus macaques in the two regions have never been studied to document the propriety of their subspecies status. We genotyped samples of cynomolgus macaques from Batangas in southwestern Luzon and Zamboanga in southwestern Mindanao for 15 short tandem repeat (STR) loci and sequenced an 835 bp fragment of the mtDNA of these animals. The STR genotypes were compared with those of cynomolgus macaques from southern Sumatra, Singapore, Mauritius and Cambodia, and the mtDNA sequences of both Philippine populations were compared with those of cynomolgus macaques from southern Sumatra, Indonesia and Sarawak, Malaysia. We conducted STRUCTURE and PCA analyses based on the STRs and constructed a median joining network based on the mtDNA sequences. The Philippine population from Batangas exhibited much less genetic diversity and greater genetic divergence from all other populations, including the Philippine population from Zamboanga. Sequences from both Batangas and Zamboanga were most closely related to two different mtDNA haplotypes from Sarawak from which they are apparently derived. Those from Zamboanga were more recently derived than those from Batangas, consistent with their later arrival in the Philippines. However, clustering analyses do not support a sufficient genetic distinction of cynomolgus macaques from Batangas from other regional populations assigned to subspecies M. f. fascicularis to warrant the subspecies distinction M. f. philippensis.

Matched MeSH terms: Principal Component Analysis
Prioritization of natural extracts by LC-MS-PCA for the identification of new photosensitizers for photodynamic therapy

Samat N, Tan PJ, Shaari K, Abas F, Lee HB

Anal Chem, 2014 Feb 4;86(3):1324-31.
PMID: 24405504 DOI: 10.1021/ac403709a

Photodynamic therapy (PDT) is an alternative treatment for cancer that involves administration of a photosensitive drug or photosensitizer that localizes at the tumor tissue followed by in situ excitation at an appropriate wavelength of light. Tumour tissues are then killed by cytotoxic reactive oxygen species generated by the photosensitizer. Targeted excitation and photokilling of affected tissues is achieved through focal light irradiation, thereby minimizing systemic side effects to the normal healthy tissues. Currently, there are only a small number of photosensitizers that are in the clinic and many of these share the same structural core based on cyclic tetrapyrroles. This paper describes how metabolic tools are utilized to prioritize natural extracts to search for structurally new photosensitizers from Malaysian biodiversity. As proof of concept, we analyzed 278 photocytotoxic extracts using a hyphenated technique of liquid chromatography-mass spectrometry coupled with principal component analysis (LC-MS-PCA) and prioritized 27 extracts that potentially contained new photosensitizers for chemical dereplication using an in-house UPLC-PDA-MS-Photocytotoxic assay platform. This led to the identification of 2 new photosensitizers with cyclic tetrapyrrolic structures, thereby demonstrating the feasibility of the metabolic approach.

Matched MeSH terms: Principal Component Analysis*
Genetic differentiation of water buffalo (Bubalus bubalis) populations in China, Nepal and south-east Asia: inferences on the region of domestication of the swamp buffalo

Zhang Y, Vankan D, Zhang Y, Barker JS

Anim. Genet., 2011 Aug;42(4):366-77.
PMID: 21749419 DOI: 10.1111/j.1365-2052.2010.02166.x

Data from three published studies of genetic variation at 18 microsatellite loci in water buffalo populations in China (18 swamp type, two river type), Nepal (one wild, one domestic river, one hybrid) and south-east Asia (eight swamp, three river) were combined so as to gain a broader understanding of genetic relationships among the populations and their demographic history. Mean numbers of alleles and expected heterozygosities were significantly different among populations. Estimates of θ (a measure of population differentiation) were significant among the swamp populations for all loci and among the river populations for most loci. Differentiation among the Chinese swamp populations (which was due primarily to just one population) was much less than among the south-east Asian. The Nepal wild animals, phenotypically swamp type but genetically like river type, are significantly different from all the domestic river populations and presumably represent the ancestral Bubalus arnee (possibly with some river-type introgression). Relationships among the swamp populations (D(A) genetic distances, principal component analysis and structure analyses) show the south-east Asian populations separated into two groups by the Chinese populations. Given these relationships and the patterns of genetic variability, we postulate that the swamp buffalo was domesticated in the region of the far south of China, northern Thailand and Indochina. Following domestication, it spread south through peninsular Malaysia to Sumatra, Java and Sulawesi, and north through China, and then to Taiwan, the Philippines and Borneo.

Matched MeSH terms: Principal Component Analysis
Fulltext Using Zoo Welfare Assessments to Identify Common Issues in Developing Country Zoos

Ward SJ, Williams E, Groves G, Marsh S, Morgan D

Animals (Basel), 2020 Nov 12;10(11).
PMID: 33198237 DOI: 10.3390/ani10112101

Zoo animal welfare is a high priority for many institutions worldwide, with modern zoos now ensuring that animals are housed and cared for to the highest standards. However, in countries where this knowledge is not as available or understood, standards may be lower. The aim of this research was to investigate if there were common zoo welfare concerns across developing country zoos. Wild Welfare is a charity working globally to improve welfare for zoo animals and has an independent welfare audit that is carried out before any intervention occurs. The Wild Welfare Audit, consisting of 110 questions, covering nine topics, was completed at 11 zoos in seven developing countries (Brazil, Egypt, Libya, Indonesia, Thailand, Malaysia and Vietnam) following a Likert scale score (1-3). A principal component analysis was also performed to evaluate the audit questions. The results suggest that common areas of concern were animal behaviour, positive animal mental states and human health and safety. These themes were likely due to the lack knowledge and understanding that may be linked to historical and cultural differences. This research has helped to revise the welfare audit as well as inform future intervention strategies for improving developing country zoo animal welfare.

Matched MeSH terms: Principal Component Analysis
Performance of Combined Support Vector Machine and Principal Component Analysis in recognizing infant cry with asphyxia

Sahak R, Mansor W, Lee YK, Yassin AM, Zabidi A

Annu Int Conf IEEE Eng Med Biol Soc, 2010;2010:6292-5.
PMID: 21097359 DOI: 10.1109/IEMBS.2010.5628084

Combined Support Vector Machine (SVM) and Principal Component Analysis (PCA) was used to recognize the infant cries with asphyxia. SVM classifier based on features selected by the PCA was trained to differentiate between pathological and healthy cries. The PCA was applied to reduce dimensionality of the vectors that serve as inputs to the SVM. The performance of the SVM utilizing linear and RBF kernel was examined. Experimental results showed that SVM with RBF kernel yields good performance. The classification accuracy in classifying infant cry with asphyxia using the SVM-PCA is 95.86%.

Matched MeSH terms: Principal Component Analysis/methods*
A probability distribution of shape for the dental maxillary arch using digital images

Rijal OM, Abdullah NA, Isa ZM, Noor NM, Tawfiq OF

Annu Int Conf IEEE Eng Med Biol Soc, 2012;2012:5420-3.
PMID: 23367155 DOI: 10.1109/EMBC.2012.6347220

Selected landmarks from each of 47 maxillary dental casts were used to define a Cartesian-coordinate system from which the positions of selected teeth were determined on standardized digital images. The position of the i-th tooth was defined by a line of length (l(i)) joining the tooth to the origin, and the angle (θ(i)) of this line to the horizontal Cartesian axis. Four teeth, the central incisor, lateral incisor, canine and first molar were selected and their position were collectively used to represent the shape of the dental arch. A pilot study using clustering and principal component analysis strongly suggest the existence of 3 groups of arch shape. In this study, the homogeneity of the 3 groups was further investigated and confirmed by the Dunn and Davies-Bouldein validity indices. This is followed by an investigation of the probability distribution of these 3 groups. The main result of this study suggests 3 groups of multivariate (MV) normal distribution. The MV normal probability distribution of these groups may be used in further studies to investigate the issues of variation of arch shape, which is fundamental to the practice of prosthodontics and orthodontics.

Matched MeSH terms: Principal Component Analysis
Exploring the structural insights on human laforin mutation K87A in Lafora disease--a molecular dynamics study

Srikumar PS, Rohini K

Appl Biochem Biotechnol, 2013 Oct;171(4):874-82.
PMID: 23904258 DOI: 10.1007/s12010-013-0393-x

Lafora disease (LD) is an autosomal recessive, progressive form of myoclonus epilepsy which affects worldwide. LD occurs mainly in countries like southern Europe, northern Africa, South India, and in the Middle East. LD occurs with its onset mainly in teenagers and leads to decline and death within 2 to 10 years. The genes EPM2A and EPM2B are commonly involved in 90 % of LD cases. EPM2A codes for protein laforin which contains an amino terminal carbohydrate binding module (CBM) belonging to the CBM20 family and a carboxy terminal dual specificity phosphatase domain. Mutations in laforin are found to abolish glycogen binding and have been reported in wet lab methods. In order to investigate on structural insights on laforin mutation K81A, we performed molecular dynamics (MD) simulation studies for native and mutant protein. MD simulation results showed loss of stability due to mutation K87A which confirmed the structural reason for conformational changes observed in laforin. The conformational change of mutant laforin was confirmed by analysis using root mean square deviation, root mean square fluctuation, solvent accessibility surface area, radius of gyration, hydrogen bond, and principle component analysis. Our results identified that the flexibility of K87A mutated laforin structure, with replacement of acidic amino acid to aliphatic amino acid in functional CBM domain, have more impact in abolishing glycogen binding that favors LD.

Matched MeSH terms: Principal Component Analysis
Signal Enhancement Evaluation of Laser-Induced Breakdown Spectroscopy of Extracted Animal Fats Using Principal Component Analysis Approach

Hanasil NS, Raja Ibrahim RK, Duralim M, Sapingi HHJ, Mahdi MA

Appl Spectrosc, 2020 Dec;74(12):1452-1462.
PMID: 32166979 DOI: 10.1177/0003702820915532

In this work, principal component analysis (PCA) was utilized to analyze laser-induced breakdown spectroscopy (LIBS) signals of the extracted chicken fat, lamb fat, beef fat, and lard froze using two different freezing methods. The frozen samples were ablated using a neodymium-doped yttrium aluminum garnet (Nd:YAG) laser with a wavelength of 1064 nm, 170 mJ pulse energy, and 6 ns pulse duration to produce plasma on target surfaces. The samples were ablated using 30-60 shots of the laser beam at different spots. Stronger LIBS signals from the extracted chicken fat and lamb fat were obtained with liquid nitrogen (LN2) method. However, LIBS signals obtained from the freezer freezing method were found to be stronger for extracted beef fat and lard. The PCA was then used to visualize the LIBS spectra of extracted animal fats into a score plot. Data points of each extracted animal fat were divided into three groups representing LIBS spectra collected at the early, middle, and end part of the ablation process. The score plot revealed that the data points of the three groups of frozen extracted animal fats using the LN2 method were more closely clustered than those frozen in the freezer. Good discrimination with 97% of the variance was achieved between the extracted chicken fat, lamb fat, beef fat, and lard using the LN2 method in the three-dimensional score plot. LIBS signals of the extracted animal fats produced from the LN2 method were found to be more stable than those from the freezer method.

Matched MeSH terms: Principal Component Analysis
Characterization and Risk Analysis of Metals Associated with Urban Dust in Rawang (Malaysia)

Praveena SM

Arch Environ Contam Toxicol, 2018 Oct;75(3):415-423.
PMID: 29802419 DOI: 10.1007/s00244-018-0537-7

This study was designed to determine the particle size distribution and develop road dust index combining source and transport factors involving road dust for dust pollution quantification in Rawang. Principal component analysis (PCA) was applied to identify possible sources of potentially toxic elements and spot major pollution areas in Rawang. The health risks (carcinogenic and noncarcinogenic) to adults and children were assessed using the hazard index and total lifetime cancer Risk, respectively. A total of 75 road dust samples were collected and particle sizes (1000, 500, 250, 160, 125 and 63 µm) were determined. Concentrations of potentially toxic elements (Cu, Cd, Co, Cr, Pb, Ni, Zn and As) in particle size of 63 µm were analyzed. The results demonstrated that the highest grain size of 250 µm has contributed almost more than 25% of atmospheric particulate pollution. The highest potentially toxic element concentration was Pb (593.3 mg/kg), whereas the lowest was Co (5.6 mg/kg). Road dust index output indicated that pollution risk fell into moderate levels in eastern and northern areas of Rawang. Similarly, PCA results revealed that potentially toxic elements (Cu, Cd, Pb, Zn, Ni and Cr) were linked with anthropogenic sources (urbanization process, industrial and commercial growth, urban traffic congestion) in northern and southern parts of Rawang. Cobalt and As concentrations were explained mainly from natural sources. Noncarcinogenic risk by hazard index value more than 1.0 was indicated for adults and children. Similarly, carcinogenic risk by total lifetime cancer risk value also showed carcinogenic risks among adults and children.

Matched MeSH terms: Principal Component Analysis
Factor Structure of Hospital Anxiety and Depression Scale in Malaysian patients with coronary artery disease

Kaur S, Zainal NZ, Low WY, Ramasamy R, Sidhu JS

Asia Pac J Public Health, 2015 May;27(4):450-60.
PMID: 24807887 DOI: 10.1177/1010539514533719

The Hospital Anxiety and Depression Scale (HADS) is a common screening instrument used to determine the levels of anxiety and depression experienced by a patient and has been extensively used in patients with coronary artery disease (CAD). This study aimed to establish the factor structure of HADS in a Malaysian sample of 189 patients with CAD. Factor analysis of HADS using principal component analysis with varimax rotation yielded 3 factors. Confirmatory factor analysis supported the use of HADS in assessing 3 distinct dimensions of psychological distress--namely, anxiety, anhedonia, and psychomotor retardation. The HADS showed good internal consistency and was found to be a valid measure of psychological distress among Malaysian patients with CAD. However, low mean scores on the original 2 factors--that is, anxiety and depression--and also on the 2 depression subscales--anhedonia and psychomotor retardation--suggests that the recommended cutoff score to screen for psychological distress among CAD patients be reevaluated. Further research to determine the generalizability and consistency for the tridimensional structure of the HADS in Malaysia is recommended.

Matched MeSH terms: Principal Component Analysis
Phases of female sexual response cycle among Malaysian women with infertility: a factor analysis study

Seen Heng Y, Sidi H, Nik Jaafar NR, Razali R, Ram H

Asia Pac Psychiatry, 2013 Apr;5 Suppl 1:50-4.
PMID: 23857837 DOI: 10.1111/appy.12044

This cross-sectional study aimed to determine the construct of the phases of the female sexual response cycle (SRC) among women attending an infertility clinic in a Malaysian tertiary center.

Matched MeSH terms: Principal Component Analysis
Fulltext Reliability and validity of the Malay Version of the Breast- Impact of Treatment Scale (MVBITS) in breast cancer women undergoing chemotherapy

Zainal NZ, Shuib N, Bustam AZ, Sabki ZA, Guan NC

Asian Pac J Cancer Prev, 2013;14(1):463-8.
PMID: 23534774 DOI: 10.7314/apjcp.2013.14.1.463

BACKGROUND: Body image dissatisfaction among breast cancer survivors has been associated with psychological stress resultant from breast cancer and resultant surgery. This study aimed to examine the psychometric properties of the Malay Version of the Breast-Impact of Treatment Scale (MVBITS) and to investigate the associations of retained factors with the Hospital Anxiety and Depression Scale (HADS) and the Rosenberg Self-Esteem Scale (RSES).

MATERIALS AND METHODS: The MVBITS was 'forward-backward' translated from English to Malay and then administered to 70 female breast cancer patients who came to the Oncology Clinic of University Malaya Medical Centre, Kuala Lumpur, Malaysia to undergo chemotherapy. Principal component analysis (PCA) with varimax rotation was performed to explore the factor structure of the MVBITS. Associations of retained factors were estimated with reference to Spearman correlation coefficients.

RESULTS: The internal consistency reliability of MVBITS was good (Cronbach's alpha 0.945) and showed temporal stability over a 3-week period. Principal component analysis suggested two factors termed as 'Intrusion' and 'Avoidance' domains. These factors explained 70.3% of the variance. Factor 1 comprised the effects of breast cancer treatment on the emotion and thought, while Factor 2 informed attempts to limit exposure of the body to self or others. The Factor 1 of MVBITS was positively correlated with total, depression and anxiety sub-scores of HADS. Factor 2 was positively correlated with total and anxiety sub-scores of HADS. MVBITS was also positively correlated with the RSES scores.

CONCLUSIONS: The results showed that the Malay Version of Breast-Impact of Treatment Scale possesses satisfactory psychometric properties suggesting that this instrument is appropriate for assessment of body change stress among female breast cancer patients in Malaysia.

Matched MeSH terms: Principal Component Analysis
Fulltext A preliminary study on automated freshwater algae recognition and classification system

Mosleh MA, Manssor H, Malek S, Milow P, Salleh A

BMC Bioinformatics, 2012;13 Suppl 17:S25.
PMID: 23282059 DOI: 10.1186/1471-2105-13-S17-S25

Freshwater algae can be used as indicators to monitor freshwater ecosystem condition. Algae react quickly and predictably to a broad range of pollutants. Thus they provide early signals of worsening environment. This study was carried out to develop a computer-based image processing technique to automatically detect, recognize, and identify algae genera from the divisions Bacillariophyta, Chlorophyta and Cyanobacteria in Putrajaya Lake. Literature shows that most automated analyses and identification of algae images were limited to only one type of algae. Automated identification system for tropical freshwater algae is even non-existent and this study is partly to fill this gap.

Matched MeSH terms: Principal Component Analysis
Fulltext 3-Dimensional facial expression recognition in human using multi-points warping

Agbolade O, Nazri A, Yaakob R, Ghani AA, Cheah YK

BMC Bioinformatics, 2019 Dec 02;20(1):619.
PMID: 31791234 DOI: 10.1186/s12859-019-3153-2

BACKGROUND: Expression in H-sapiens plays a remarkable role when it comes to social communication. The identification of this expression by human beings is relatively easy and accurate. However, achieving the same result in 3D by machine remains a challenge in computer vision. This is due to the current challenges facing facial data acquisition in 3D; such as lack of homology and complex mathematical analysis for facial point digitization. This study proposes facial expression recognition in human with the application of Multi-points Warping for 3D facial landmark by building a template mesh as a reference object. This template mesh is thereby applied to each of the target mesh on Stirling/ESRC and Bosphorus datasets. The semi-landmarks are allowed to slide along tangents to the curves and surfaces until the bending energy between a template and a target form is minimal and localization error is assessed using Procrustes ANOVA. By using Principal Component Analysis (PCA) for feature selection, classification is done using Linear Discriminant Analysis (LDA).
RESULT: The localization error is validated on the two datasets with superior performance over the state-of-the-art methods and variation in the expression is visualized using Principal Components (PCs). The deformations show various expression regions in the faces. The results indicate that Sad expression has the lowest recognition accuracy on both datasets. The classifier achieved a recognition accuracy of 99.58 and 99.32% on Stirling/ESRC and Bosphorus, respectively.
CONCLUSION: The results demonstrate that the method is robust and in agreement with the state-of-the-art results.

Matched MeSH terms: Principal Component Analysis
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
Fulltext Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation

Fornarino S, Pala M, Battaglia V, Maranta R, Achilli A, Modiano G, et al.

BMC Evol. Biol., 2009;9:154.
PMID: 19573232 DOI: 10.1186/1471-2148-9-154

Central Asia and the Indian subcontinent represent an area considered as a source and a reservoir for human genetic diversity, with many markers taking root here, most of which are the ancestral state of eastern and western haplogroups, while others are local. Between these two regions, Terai (Nepal) is a pivotal passageway allowing, in different times, multiple population interactions, although because of its highly malarial environment, it was scarcely inhabited until a few decades ago, when malaria was eradicated. One of the oldest and the largest indigenous people of Terai is represented by the malaria resistant Tharus, whose gene pool could still retain traces of ancient complex interactions. Until now, however, investigations on their genetic structure have been scarce mainly identifying East Asian signatures.

Matched MeSH terms: Principal Component Analysis
Fulltext Evidence of weak genetic structure and recent gene flow between Bactrocera dorsalis s.s. and B. papayae, across Southern Thailand and West Malaysia, supporting a single target pest for SIT applications

Aketarawong N, Isasawin S, Thanaphum S

BMC Genet, 2014;15:70.
PMID: 24929425 DOI: 10.1186/1471-2156-15-70

Bactrocera dorsalis s.s. (Hendel) and B. papayae Drew & Hancock, are invasive pests belonging to the B. dorsalis complex. Their species status, based on morphology, is sometimes arguable. Consequently, the existence of cryptic species and/or population isolation may decrease the effectiveness of the sterile insect technique (SIT) due to an unknown degree of sexual isolation between released sterile flies and wild counterparts. To evaluate the genetic relationship and current demography in wild populations for guiding the application of area-wide integrated pest management using SIT, seven microsatellite-derived markers from B. dorsalis s.s. and another five from B. papayae were used for surveying intra- and inter-specific variation, population structure, and recent migration among sympatric and allopatric populations of the two morphological forms across Southern Thailand and West Malaysia.

Matched MeSH terms: Principal Component Analysis
Fulltext A latent trait approach to measuring HIV/AIDS related stigma in healthcare professionals: application of mokken scaling technique

Ahmadi K, Reidpath DD, Allotey P, Hassali MAA

BMC Med Educ, 2016 May 30;16:155.
PMID: 27240562 DOI: 10.1186/s12909-016-0676-3

BACKGROUND: The attitudes of healthcare professionals towards HIV positive patients and high risk groups are central to the quality of care and therefore to the management of HIV/AIDS related stigma in health settings. Extant HIV/AIDS stigma scales that measure stigmatising attitudes towards people living with HIV/AIDS have been developed using scaling techniques such as principal component analysis. This approach has resulted in instruments that are often long. Mokken scale analysis is a nonparametric hierarchical scaling technique that can be used to develop unidimensional cumulative scales. This technique is advantageous over the other approaches; as the scales are usually shorter, while retaining acceptable psychometric properties. Moreover, Mokken scales also make no distributional assumptions about the underlying data, other than that the data are capable of being ordered by item and by person. In this study we aimed at developing a precise and concise measure of HIV/AIDS related stigma among health care professionals, using Mokken scale analysis.
METHODS: We carried out a cross sectional survey of healthcare students at the Monash University campuses in Malaysia and Australia. The survey consisted of demographic questions and an initial item pool of twenty five potential questions for inclusion in an HIV stigma scale.
RESULTS: We analysed the data using the mokken package in the R statistical environment providing a 9-item scale with high reliability, validity and acceptable psychometric properties, measuring and ranking the HIV/AIDS related stigmatising attitudes.
CONCLUSION: Mokken scaling procedure not only produced a comprehensive hierarchical scale that could accurately order a person along HIV/AIDS stigmatising attitude, but also demonstrated a unidimensional and reliable measurement tool which could be used in future studies. The principal component analysis confirmed the accuracy of the Mokken scale analysis in correctly detecting the unidimensionality of this scale. We recommend future works to study the generalisability of this scale in a new population.

Matched MeSH terms: Principal Component Analysis

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