Displaying publications 41 - 60 of 93 in total

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  1. Kamarudin KR, Rehan MM
    Trop Life Sci Res, 2015 Apr;26(1):87-99.
    PMID: 26868593 MyJurnal
    This preliminary study aimed to identify a commercial gamat species, Stichopus horrens Selenka, 1867, and a timun laut species, Holothuria (Mertensiothuria) leucospilota (Brandt, 1835), from Pangkor Island, Perak, Malaysia, employing morphological techniques based on the shape of the ossicles and molecular techniques based on the cytochrome c oxidase I (COI) mitochondrial DNA (mtDNA) gene. In Malaysia, a gamat is defined as a sea cucumber species of the family Stichopodidae with medicinal value, and timun laut refers to non-gamat species. S. horrens is very popular on Pangkor Island as a main ingredient in the traditional production of air gamat and minyak gamat, while H. leucospilota is the most abundant species in Malaysia. In contrast to previous studies, internal body parts (the respiratory tree and gastrointestine) were examined in this study to obtain better inferences based on morphology. The results showed that there were no ossicles present in the gastrointestine of H. leucospilota, and this characteristic is suggested as a unique diagnostic marker for the timun laut species. In addition, the presence of Y-shaped rods in the respiratory tree of S. horrens subsequently supported the potential to use internal body parts to identify the gamat species. Phylogenetic analysis of the COI mtDNA gene of the sea cucumber specimens using the neighbour-joining method and maximum likelihood methods further confirmed the species status of H. leucospilota and S. horrens from Pangkor Island, Perak, Malaysia. The COI mtDNA gene sequences were registered with GenBank, National Center for Biotechnology Information (NCBI), US National Library of Medicine (GenBank accession no.: KC405565-KC405568). Although additional specimens from various localities will be required to produce more conclusive results, the current findings provide better insight into the importance of complementary approaches involving morphological and molecular techniques in the identification of the two Malaysian sea cucumber species.
    Matched MeSH terms: Likelihood Functions
  2. Mohammad NA, Al-Mekhlafi HM, Anuar TS
    Trop Biomed, 2018 Dec 01;35(4):849-860.
    PMID: 33601835
    Blastocystis is one of the most common parasites inhabiting the intestinal tract of human and animals. Currently, human Blastocystis isolates are classified into nine subtypes (STs) based on the phylogeny of their small subunit ribosomal RNA (SSU rRNA) gene. Although its pathogenicity remains controversial, the possibility of zoonotic transmission was recognized since eight of the nine STs (except for ST9) have been reported in both humans and animals. A cross-sectional study was conducted to determine the prevalence and subtype distribution of Blastocystis isolated from humans and associated animals in an indigenous community with poor hygiene in Malaysia, where the risk of parasitic infection is high. A total of 275 stool samples were collected, subjected to DNA extraction and amplified by PCR assay. The Blastocystis-positive amplicons were then purified and sequenced. Phylogenetic tree of positive isolates, reference strains and outgroup were constructed using maximum likelihood method based on Hasegawa-KishinoYano+G+I model. The prevalence of Blastocystis infection among humans and domestic animals by PCR assay were 18.5% (45/243) and 6.3% (2/32), respectively. Through molecular phylogeny, 47 isolates were separated into five clusters containing isolates from both hosts. Among human isolates, ST3 (53.3%) was the predominant subtype, followed by ST1 (31.1%) and ST2 (15.6%). Chicken and cattle had lower proportions of ST6 (50%) and ST10 (50%), that were barely seen in humans. The distinct distributions of the most important STs among the host animals as well as humans examined demonstrate that there is various host-specific subtypes in the lifecycle of Blastocystis.
    Matched MeSH terms: Likelihood Functions
  3. Nayeri ND, Goudarzian AH, Herth K, Naghavi N, Nia HS, Yaghoobzadeh A, et al.
    Int J Health Sci (Qassim), 2020 9 22;14(5):50-57.
    PMID: 32952505
    Objective: The psychological construct of hope is an important determinant for mental health and well-being. The availability of valid and reliable instruments to measure hope is, therefore, critical. Despite a large number of psychometric studies on the Herth Hope Index (HHI), its construct validity has not yet been determined. Therefore, this paper aimed to conduct a systematic review of the psychometric properties of the HHI.

    Methods: Databases such as PubMed, Science Direct, Google Scholar, Magiran, SID, IranDoc, and IranMedex were evaluated systematically using the terms "HHI," "psychometric," "validity," "reliability," and related terms (with the use of OR and AND operators) and no restrictions on the year of publication. A total of 13 eligible studies were found published between 1992 and 2018 in the USA, Portugal, Switzerland, Iran, Germany, Petersburg, Japan, the Netherlands, Lima, Peru, and Norway. The methodology used in the available studies included principal component analysis (n = 6), maximum likelihood estimation (n = 5), and principal axis factoring (n = 1). One study did not point the methodology.

    Results: Four studies reported the total extracted variances to be less than 50%, six studies reported variance between 50% and 60%, and three papers reported variance that exceeded 60%. Of the papers that examined the factor structure of the HHI, two studies reported a one-factor solution, seven reported two factors, and four reported a three-factor solution. Although the HHI is the most widely translated and psychometrically tested tool in languages other than English, psychometric variations in factor solutions remain inconsistent.

    Conclusion: Findings highlight the need for future research that appraises the validity of the HHI in different countries, and how the measure relates to other scales that evaluate hope.

    Matched MeSH terms: Likelihood Functions
  4. Dai X, Mak YL, Lu CK, Mei HH, Wu JJ, Lee WH, et al.
    Harmful Algae, 2017 07;67:107-118.
    PMID: 28755713 DOI: 10.1016/j.hal.2017.07.002
    Recent molecular phylogenetic studies of Gambierdiscus species flagged several new species and genotypes, thus leading to revitalizing its systematics. The inter-relationships of clades revealed by the primary sequence information of nuclear ribosomal genes (rDNA), however, can sometimes be equivocal, and therefore, in this study, the taxonomic status of a ribotype, Gambierdiscus sp. type 6, was evaluated using specimens collected from the original locality, Marakei Island, Republic of Kiribati; and specimens found in Rawa Island, Peninsular Malaysia, were further used for comparison. Morphologically, the ribotype cells resembled G. scabrosus, G. belizeanus, G. balechii, G. cheloniae and G. lapillus in thecal ornamentation, where the thecal surfaces are reticulate-foveated, but differed from G. scabrosus by its hatchet-shaped Plate 2', and G. belizeanus by the asymmetrical Plate 3'. To identify the phylogenetic relationship of this ribotype, a large dataset of the large subunit (LSU) and small subunit (SSU) rDNAs were compiled, and performed comprehensive analyses, using Bayesian-inference, maximum-parsimony, and maximum-likelihood, for the latter two incorporating the sequence-structure information of the SSU rDNA. Both the LSU and SSU rDNA phylogenetic trees displayed an identical topology and supported the hypothesis that the relationship between Gambierdiscus sp. type 6 and G. balechii was monophyletic. As a result, the taxonomic status of Gambierdiscus sp. type 6 was revised, and assigned as Gambierdiscus balechii. Toxicity analysis using neuroblastoma N2A assay confirmed that the Central Pacific strains were toxic, ranging from 1.1 to 19.9 fg P-CTX-1 eq cell-1, but no toxicity was detected in a Western Pacific strain. This suggested that the species might be one of the species contributing to the high incidence rate of ciguatera fish poisoning in Marakei Island.
    Matched MeSH terms: Likelihood Functions
  5. Ali H, Muhammad A, Bala NS, Wang G, Chen Z, Peng Z, et al.
    Mol Phylogenet Evol, 2018 10;127:1000-1009.
    PMID: 29981933 DOI: 10.1016/j.ympev.2018.07.003
    Wolbachia pipientis is a diverse, ubiquitous and most prevalent intracellular bacterial group of alpha-Proteobacteria that is concerned with many biological processes in arthropods. The coconut hispine beetle (CHB), Brontispa longissima (Gestro) is an economically important pest of palm cultivation worldwide. In the present study, we comprehensively surveyed the Wolbachia-infection prevalence and mitochondrial DNA (mtDNA) polymorphism in CHB from five different geographical locations, including China's Mainland and Taiwan, Vietnam, Thailand, Malaysia and Indonesia. A total of 540 sequences were screened in this study through three different genes, i.e., cytochrome oxidase subunit I (COI), Wolbachia outer surface protein (wsp) and multilocus sequencing type (MLST) genes. The COI genetic divergence ranges from 0.08% to 0.67%, and likewise, a significant genetic diversity (π = 0.00082; P = 0.049) was noted within and between all analyzed samples. In the meantime, ten different haplotypes (H) were characterized (haplotype diversity = 0.4379) from 21 different locations, and among them, H6 (46 individuals) have shown a maximum number of population clusters than others. Subsequently, Wolbachia-prevalence results indicated that all tested specimens of CHB were found positive (100%), which suggested that CHB was naturally infected with Wolbachia. Wolbachia sequence results (wsp gene) revealed a high level of nucleotide diversity (π = 0.00047) under Tajima's D test (P = 0.049). Meanwhile, the same trend of nucleotide diversity (π = 0.00041) was observed in Wolbachia concatenated MLST locus. Furthermore, phylogenetic analysis (wsp and concatenated MLST genes) revealed that all collected samples of CHB attributed to same Wolbachia B-supergroup. Our results strongly suggest that Wolbachia bacteria and mtDNA were highly concordant with each other and Wolbachia can affect the genetic structure and diversity within the CHB populations.
    Matched MeSH terms: Likelihood Functions
  6. Yang Y, Li J, Yang S, Li X, Fang L, Zhong C, et al.
    BMC Evol. Biol., 2017 01 18;17(1):22.
    PMID: 28100168 DOI: 10.1186/s12862-016-0849-z
    BACKGROUND: A large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation.

    RESULTS: In this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods. Extremely small effective population size (Ne) was inferred in populations from both eastern and western Malay Peninsula (44 and 396, respectively), mirroring the fragility of mangrove plants and their paucity of robustness against future climate perturbations and human activity. Two major genetic lineages of high divergence were identified in the two mangrove biodiversity centres: the Indo-Malesia and Australasia regions. The estimated splitting time between these two lineages was 3.153 million year ago (MYA), suggesting a role for pre-Pleistocene events in shaping the major diversity patterns of mangrove species. Within the Indo-Malesia region, a subdivision was implicated between the South China Sea (SCS) and the remaining area with a divergence time of 1.874 MYA, corresponding to glacial vicariance when the emerged Sunda Shelf halted genetic exchange between the western and eastern coasts of the Malay Peninsula during Pleistocene sea-level drops. Notably, genetic admixture was observed in populations at the boundary regions, especially in the two populations near the Malacca Strait, indicating secondary contact between divergent lineages during interglacial periods. These interregional genetic exchanges provided ample opportunity for the re-use of standing genetic variation, which could facilitate mangrove establishment and adaptation in new habitats, especially in the context of global climate changes.

    CONCLUSION: Phylogeogrpahic analysis in this study reveal that Pleistocene sea-level fluctuations had profound influence on population differentiation of the mangrove tree S. alba. Our study highlights the fragility of mangrove plants and offers a guide for the conservation of coastal mangrove communities experiencing ongoing changes in sea-level.

    Matched MeSH terms: Likelihood Functions
  7. Nik Adib NA, Ibrahim MI, Ab Rahman A, Bakar RS, Yahaya NA, Hussin S, et al.
    PMID: 30400357 DOI: 10.3390/ijerph15112455
    BACKGROUND: A Malay version of Parent Satisfaction Scale (PSS-M) is needed to investigate the factors contributing to the Malay caregivers' satisfaction with health care management for children with autism spectrum disorder (ASD). The aim of the study is to translate and validate the questionnaire to assess the caregivers' satisfaction on health care services.

    METHODS: A cross-sectional study was conducted among 110 caregivers of children with ASD aged between 2 and 17 years old that received treatment at two tertiary care centres in Kelantan. Permission to use the original version of the PSS questionnaire was obtained. The original English version of the PSS was translated into a Malay version following the 10 steps proposed by an established guideline. Pre-testing of the PSS was carried out with 30 caregivers before confirmatory factor analysis (CFA) was established using 110 caregivers. They were asked to assess their understanding of the questionnaire. The one-dimensional questionnaire consists of 11 items, including staff attitudes, availability of staff, supportiveness, and helpfulness. The 5-point Likert scale provided ratings from 1 (strongly disagree) to 5 (strongly agree). Confirmatory factor analysis was performed using a robust maximum likelihood estimator.

    RESULTS: The analysis showed model fit data with good reliability.

    CONCLUSION: The PSS-M shows overall model fitness based on specific indices, with good construct validity and excellent absolute reliability to determine the satisfaction level of caregivers of children with ASD with respect to health care services.

    Matched MeSH terms: Likelihood Functions
  8. Balla SB, Banda TR, Galic I, N NM, Naishadham PP
    Forensic Sci Int, 2019 Apr;297:243-248.
    PMID: 30844636 DOI: 10.1016/j.forsciint.2019.02.009
    The aims of the present study were to validate the discriminatory potential of Cameriere's third molar maturity index (I3M) cut-off value of I3M 
    Matched MeSH terms: Likelihood Functions
  9. Liversidge HM, Peariasamy K, Folayan MO, Adeniyi AO, Ngom PI, Mikami Y, et al.
    J Forensic Odontostomatol, 2017 Dec 01;35(2):97-108.
    PMID: 29384741
    BACKGROUND: The nature of differences in the timing of tooth formation between ethnic groups is important when estimating age.

    AIM: To calculate age of transition of the mandibular third (M3) molar tooth stages from archived dental radiographs from sub-Saharan Africa, Malaysia, Japan and two groups from London UK (Whites and Bangladeshi).

    MATERIALS AND METHODS: The number of radiographs was 4555 (2028 males, 2527 females) with an age range 10-25 years. The left M3 was staged into Moorrees stages. A probit model was fitted to calculate mean ages for transitions between stages for males and females and each ethnic group separately. The estimated age distributions given each M3 stage was calculated. To assess differences in timing of M3 between ethnic groups, three models were proposed: a separate model for each ethnic group, a joint model and a third model combining some aspects across groups. The best model fit was tested using Bayesian and Akaikes information criteria (BIC and AIC) and log likelihood ratio test.

    RESULTS: Differences in mean ages of M3 root stages were found between ethnic groups, however all groups showed large standard deviation values. The AIC and log likelihood ratio test indicated that a separate model for each ethnic group was best. Small differences were also noted between timing of M3 between males and females, with the exception of the Malaysian group. These findings suggests that features of a reference data set (wide age range and uniform age distribution) and a Bayesian statistical approach are more important than population specific convenience samples to estimate age of an individual using M3.

    CONCLUSION: Some group differences were evident in M3 timing, however, this has some impact on the confidence interval of estimated age in females and little impact in males because of the large variation in age.

    Matched MeSH terms: Likelihood Functions
  10. Ramlee MH, Kadir MR, Murali MR, Kamarul T
    Med Eng Phys, 2014 Oct;36(10):1322-30.
    PMID: 25127377 DOI: 10.1016/j.medengphy.2014.05.015
    Pilon fractures are commonly caused by high energy trauma and can result in long-term immobilization of patients. The use of an external fixator i.e. the (1) Delta, (2) Mitkovic or (3) Unilateral frame for treating type III pilon fractures is generally recommended by many experts owing to the stability provided by these constructs. This allows this type of fracture to heal quickly whilst permitting early mobilization. However, the stability of one fixator over the other has not been previously demonstrated. This study was conducted to determine the biomechanical stability of these external fixators in type III pilon fractures using finite element modelling. Three-dimensional models of the tibia, fibula, talus, calcaneus, navicular, cuboid, three cuneiforms and five metatarsal bones were reconstructed from previously obtained CT datasets. Bones were assigned with isotropic material properties, while the cartilage was assigned as hyperelastic springs with Mooney-Rivlin properties. Axial loads of 350 N and 70 N were applied at the tibia to simulate the stance and the swing phase of a gait cycle. To prevent rigid body motion, the calcaneus and metatarsals were fixed distally in all degrees of freedom. The results indicate that the model with the Delta frame produced the lowest relative micromovement (0.03 mm) compared to the Mitkovic (0.05 mm) and Unilateral (0.42 mm) fixators during the stance phase. The highest stress concentrations were found at the pin of the Unilateral external fixator (509.2 MPa) compared to the Mitkovic (286.0 MPa) and the Delta (266.7 MPa) frames. In conclusion, the Delta external fixator was found to be the most stable external fixator for treating type III pilon fractures.
    Matched MeSH terms: Likelihood Functions
  11. Solarin SA, Al-Mulali U, Ozturk I
    Environ Sci Pollut Res Int, 2018 Nov;25(31):30949-30961.
    PMID: 30182312 DOI: 10.1007/s11356-018-3060-5
    We investigate the role of military expenditure on emission in USA during the period 1960-2015. To achieve the objectives of this study, two measures of military expenditure are utilised, while several timeseries models are constructed with the gross domestic product (GDP) per capita, population, energy consumption per capita, non-renewable energy consumption per capita, renewable energy consumption per capita, urbanisation, trade openness and financial development serving as additional determinants of air pollution. We also use ecological indicator as an alternative measure of pollution. Moreover, different timeseries methods are utilised including a likelihood-based approach with two structural breaks. The output of this research concluded that all the variables are cointegrated. It is found that military expenditure has mixed impact on CO2 emissions. Real GDP per capita, energy consumption per capita, non-renewable energy consumption per capita, population and urbanisation increase CO2 emissions per capita in the long-run, while renewable energy consumption, financial development and trade openness reduce it. There is also evidence for the mixed role of military expenditure, when ecological footprint is utilised as the environmental degradation index. From the output of this research, few policy recommendations are offered for the examined country.
    Matched MeSH terms: Likelihood Functions
  12. Parsons MT, Tudini E, Li H, Hahnen E, Wappenschmidt B, Feliubadaló L, et al.
    Hum Mutat, 2019 Sep;40(9):1557-1578.
    PMID: 31131967 DOI: 10.1002/humu.23818
    The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co-segregation, family cancer history profile, co-occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case-control information. Research and clinical data for multifactorial likelihood analysis were collated for 1,395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; and 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared with information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known nonpathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene-specific calibration of evidence types used for variant classification.
    Matched MeSH terms: Likelihood Functions
  13. Mustafa MB, Salim SS, Mohamed N, Al-Qatab B, Siong CE
    PLoS One, 2014;9(1):e86285.
    PMID: 24466004 DOI: 10.1371/journal.pone.0086285
    Automatic speech recognition (ASR) is currently used in many assistive technologies, such as helping individuals with speech impairment in their communication ability. One challenge in ASR for speech-impaired individuals is the difficulty in obtaining a good speech database of impaired speakers for building an effective speech acoustic model. Because there are very few existing databases of impaired speech, which are also limited in size, the obvious solution to build a speech acoustic model of impaired speech is by employing adaptation techniques. However, issues that have not been addressed in existing studies in the area of adaptation for speech impairment are as follows: (1) identifying the most effective adaptation technique for impaired speech; and (2) the use of suitable source models to build an effective impaired-speech acoustic model. This research investigates the above-mentioned two issues on dysarthria, a type of speech impairment affecting millions of people. We applied both unimpaired and impaired speech as the source model with well-known adaptation techniques like the maximum likelihood linear regression (MLLR) and the constrained-MLLR(C-MLLR). The recognition accuracy of each impaired speech acoustic model is measured in terms of word error rate (WER), with further assessments, including phoneme insertion, substitution and deletion rates. Unimpaired speech when combined with limited high-quality speech-impaired data improves performance of ASR systems in recognising severely impaired dysarthric speech. The C-MLLR adaptation technique was also found to be better than MLLR in recognising mildly and moderately impaired speech based on the statistical analysis of the WER. It was found that phoneme substitution was the biggest contributing factor in WER in dysarthric speech for all levels of severity. The results show that the speech acoustic models derived from suitable adaptation techniques improve the performance of ASR systems in recognising impaired speech with limited adaptation data.
    Matched MeSH terms: Likelihood Functions
  14. Nayak VC, Rastogi P, Kanchan T, Yoganarasimha K, Kumar GP, Menezes RG
    Forensic Sci Int, 2010 Apr 15;197(1-3):67-9.
    PMID: 20071110 DOI: 10.1016/j.forsciint.2009.12.055
    The fingerprints are very typical for a human being. The present study was undertaken to study the gender differences in fingerprint ridge density in Chinese and Malaysian population. The study done on 200 subjects (100 males and 100 females) of Chinese origin and 100 subjects (50 males and 50 females) of Malaysian origin revealed that significant gender differences occur in the finger ridge density. Fingerprint mean ridge density of 12 ridges/25 mm(2) or less is found to be more likely to be of males and a mean ridge count of more the 13 ridges/25 mm(2) is more likely of female origin in Chinese subjects. Fingerprint mean ridge density of 11 ridges/25 mm(2) or less is found to be more likely to be of males and a mean ridge count of more the 13 ridges/25 mm(2) is more likely of female origin in Malaysian subjects.
    Matched MeSH terms: Likelihood Functions
  15. Fiala I, Hlavničková M, Kodádková A, Freeman MA, Bartošová-Sojková P, Atkinson SD
    Mol Phylogenet Evol, 2015 May;86:75-89.
    PMID: 25797924 DOI: 10.1016/j.ympev.2015.03.004
    In order to clarify the phylogenetic relationships among the main marine myxosporean clades including newly established Ceratonova clade and scrutinizing their evolutionary origins, we performed large-scale phylogenetic analysis of all myxosporean species from the marine myxosporean lineage based on three gene analyses and statistical topology tests. Furthermore, we obtained new molecular data for Ceratonova shasta, C. gasterostea, eight Ceratomyxa species and one Myxodavisia species. We described five new species: Ceratomyxa ayami n. sp., C. leatherjacketi n. sp., C. synaphobranchi n. sp., C. verudaensis n. sp. and Myxodavisia bulani n. sp.; two of these formed a new, basal Ceratomyxa subclade. We identified that the Ceratomyxa clade is basal to all other marine myxosporean lineages, and Kudoa with Enteromyxum are the most recently branching clades. Topologies were least stable at the nodes connecting the marine urinary clade, the marine gall bladder clade and the Ceratonova clade. Bayesian inference analysis of SSU rDNA and the statistical tree topology tests suggested that Ceratonova is closely related to the Enteromyxum and Kudoa clades, which represent a large group of histozoic species. A close relationship between Ceratomyxa and Ceratonova was not supported, despite their similar myxospore morphologies. Overall, the site of sporulation in the vertebrate host is a more accurate predictor of phylogenetic relationships than the morphology of the myxospore.
    Matched MeSH terms: Likelihood Functions
  16. Jani J, Mustapha ZA, Ling CK, Hui ASM, Teo R, Ahmed K
    Data Brief, 2020 Dec;33:106388.
    PMID: 33102655 DOI: 10.1016/j.dib.2020.106388
    In 2019, 10 million new cases of tuberculosis have been reported worldwide. Our data reports genetic analyses of a Mycobacterium tuberculosis strain SBH321 isolated from a 31-year-old female with pulmonary tuberculosis. The genomic DNA of the strain was extracted from pure culture and subjected to sequencing using Illumina platform. M. tuberculosis strain SBH321 consists of 4,374,895 bp with G+C content of 65.59%. The comparative analysis by SNP-based phylogenetic analysis using maximum-likelihood method showed that our strain belonging to sublineage of the Ural family of Europe-America-Africa lineage (Lineage 4) and clustered with M. tuberculosis strain OFXR-4 from Taiwan. The whole genome sequence is deposited at DDBJ/ENA/GenBank under the accession WCJH00000000 (SRR10230353).
    Matched MeSH terms: Likelihood Functions
  17. Heckenhauer J, Abu Salim K, Chase MW, Dexter KG, Pennington RT, Tan S, et al.
    PLoS One, 2017;12(10):e0185861.
    PMID: 29049301 DOI: 10.1371/journal.pone.0185861
    DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses.
    Matched MeSH terms: Likelihood Functions
  18. Jani J, Mustapha ZA, Jamal NB, Stanis CS, Ling CK, Avoi R, et al.
    Data Brief, 2019 Oct;26:104445.
    PMID: 31534995 DOI: 10.1016/j.dib.2019.104445
    A Mycobacterium tuberculosis strain SBH162 was isolated from a 49-year-old male with pulmonary tuberculosis. GeneXpert MDR/RIF identified the strain as rifampicin-resistant M. tuberculosis. The whole genome sequencing was performed using Illumina HiSeq 4000 system to further investigate and verify the mutation sites of the strain through genetic analyses namely variant calling using bioinformatics tools. The de novo assembly of genome generated 100 contigs with N50 of 156,381bp. The whole genome size was 4,343,911 bp with G + C content of 65.58% and consisted of 4,306 predicted genes. The mutation site, S450L, for rifampicin resistance was detected in the rpoB gene. Based on the phylogenetic analysis using the Maximum Likelihood method, the strain was identified as belonging to the Europe America Africa lineage (Lineage 4). The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number SMOE00000000.
    Matched MeSH terms: Likelihood Functions
  19. Barki N, Choudhry FR, Munawar K
    PMID: 33500886 DOI: 10.47176/mjiri.34.159
    Background: The construct of satisfaction with life has been studied across various cultures through the Satisfaction with Life Scale. The Satisfaction with Life Scale (SWLS) has been validated across several populations and languages. There are no published psychometric properties of its Urdu version. Hence, the aim of this study was to ascertain the psychometric properties of the Urdu version of the SWLS among the Urdu speaking population of Pakistan. Methods: The SWLS has already been translated into Urdu, and the Urdu version is available on the author's website however there is no information about its psychometric properties. To establish the psychometric properties especially the factor structure of the already translated Urdu SWLS, the SWLS-Urdu was administered to Urdu speaking population residing in Pakistan. The statistical analyses (i.e., normality through skewness and kurtosis, Kaiser-Meyer-Olkin (KMO) and Bartlett's test of sphericity, and test and re-test reliability) were conducted through SPSS version 25.0. Structure Equation Modelling via maximum likelihood method of estimation was used to perform confirmatory factor analysis on the data using AMOS 20.0. The significance level was set at p < 0.05. Results: The study was completed by recruiting 120 participants from different universities in Lahore, Pakistan. The sample was equally divided between male and female participants. The mean age of participants was 22.7(3.6) years. Test of the adequacy of the sample through Kaiser-Mayer-Olkin showed KMO=0.88 and Bartlett's test of sphericity (p<0.001). The Cronbach's alpha reliability of the scale was 0.90 and Confirmatory Factor Analysis confirmed a one-factor model as a good fit with strong statistical evidence. No factorial group variances were noticed in male and female participants. Conclusion: This study shows that Urdu SWLS has sound psychometric properties, is linguistically and culturally acceptable, and equally useful in assessing satisfaction with life in the Urdu speaking population.
    Matched MeSH terms: Likelihood Functions
  20. Nur Aisyah Atikah Alizan, Sarah S. Zakaria
    MyJurnal
    Bacteria of the genus Komagataeibacter are described to be the most noteworthy for having several of its species being efficient and strong cellulose producers. The 16S ribosomal RNA (rRNA) gene analysis is often used for the identification and taxonomic classification of these bacteria species. In order to observe the phylogenetic relationship among Komagataeibacter sp., twelve sequences of the 16S rRNA gene with three sequences each for species namely Komagataeibacter europaeus, Komagataeibacter hansenii, Komagataeibacter intermedius and Komagataeibacter xylinus were retrieved from NCBI GenBank database. The sequences were aligned and analysed using PAUP, OrthoANI and BLAST, followed by the phylogenetic tree construction using a Maximum Likelihood method. The parsimony character diagnostic analysis showed very few numbers of parsimony- informative characters present in the aligned sequences which is only 1.5% of the total characters. The inferred phylogenetic relationships demonstrated the unexpected positioning of K. xylinus (GQ240638: Gluconacetobacter xylinus strain) and K. xylinus (KC11853: G. xylinus strain) into the clades of K. europaeus and K. hansenii respectively. The also very low bootstrap values of the branch points linking the K. europaeus species indicated low support for the produced topologies. The findings of this study indicate that more phylogenies information can be attained by increasing the taxon sampling. In addition, more robust molecular data are needed to infer the phylogenetic relationships between the Komagataeibacter species more accurately.
    Matched MeSH terms: Likelihood Functions
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