Displaying publications 21 - 40 of 92 in total

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  1. Jiruskova A, Motyka M, Bocek M, Bocak L
    PeerJ, 2019;7:e6511.
    PMID: 30863675 DOI: 10.7717/peerj.6511
    We investigated the spatial and temporal patterns of Cautires diversification on the Malay Peninsula and Sumatra to understand if the narrow and frequently dry Malacca Strait separates different faunas. Moreover, we analyzed the origin of Cautires in Malayan and Sumatran mountains. We sampled 18 localities and present the mtDNA-based phylogeny of 76 species represented by 388 individuals. The phylogenetic tree was dated using mtDNA evolution rates and the ancestral ranges were estimated using the maximum likelihood approach. The phylogeny identified multiple lineages on the Malay Peninsula since the Upper Eocene (35 million years ago, mya) and a delayed evolution of diversity in Sumatra since the Upper Oligocene (26 mya). A limited number of colonization events across the Malacca Strait was identified up to the Pliocene and more intensive faunal exchange since the Pleistocene. The early colonization events were commonly followed by in situ diversification. As a result, the Malacca Strait now separates two faunas with a high species-level turnover. The montane fauna diversified in a limited space and seldom took part in colonization events across the Strait. Besides isolation by open sea or a savannah corridor, mimetic patterns could decrease the colonization capacity of Cautires. The Malay fauna is phylogenetically more diverse and has a higher value if conservation priorities should be defined.
    Matched MeSH terms: Likelihood Functions
  2. Amin L, Hashim H, Mahadi Z, Ismail K
    BMC Med Res Methodol, 2018 12 05;18(1):163.
    PMID: 30518344 DOI: 10.1186/s12874-018-0619-2
    BACKGROUND: The demand in biobanking for the collection and maintenance of biological specimens and personal data from civilians to improve the prevention, diagnosis and treatment of diseases has increased notably. Despite the advancement, certain issues, specifically those related to privacy and data protection, have been critically discussed. The purposes of this study are to assess the willingness of stakeholders to participate in biobanking and to determine its predictors.

    METHODS: A survey of 469 respondents from various stakeholder groups in the Klang Valley region of Malaysia was carried out. Based on previous research, a multi-dimensional instrument measuring willingness to participate in biobanking, and its predictors, was constructed and validated. A single step Structural Equation Modelling was performed to analyse the measurements and structural model using the International Business Machines Corporation Software Package for Social Sciences, Analysis of Moment Structures (IBM SPSS Amos) version 20 with a maximum likelihood function.

    RESULTS: Malaysian stakeholders in the Klang Valley were found to be cautious of biobanks. Although they perceived the biobanks as moderately beneficial (mean score of 4.65) and were moderately willing to participate in biobanking (mean score of 4.10), they professed moderate concern about data and specimen protection issues (mean score of 4.33). Willingness to participate in biobanking was predominantly determined by four direct predictors: specific application-linked perceptions of their benefits (β = 0.35, p 
    Matched MeSH terms: Likelihood Functions
  3. 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
  4. 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
  5. 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
  6. Chan KO, Grismer LL, Brown RM
    Mol Phylogenet Evol, 2018 10;127:1010-1019.
    PMID: 30030179 DOI: 10.1016/j.ympev.2018.07.005
    The family Rhacophoridae is one of the most diverse amphibian families in Asia, for which taxonomic understanding is rapidly-expanding, with new species being described steadily, and at increasingly finer genetic resolution. Distance-based methods frequently have been used to justify or at least to bolster the recognition of new species, particularly in complexes of "cryptic" species where obvious morphological differentiation does not accompany speciation. However, there is no universally-accepted threshold to distinguish intra- from interspecific genetic divergence. Moreover, indiscriminant use of divergence thresholds to delimit species can result in over- or underestimation of species diversity. To explore the range of variation in application of divergence scales, and to provide a family-wide assessment of species-level diversity in Old-World treefrogs (family Rhacophoridae), we assembled the most comprehensive multi-locus phylogeny to date, including all 18 genera and approximately 247 described species (∼60% coverage). We then used the Automatic Barcode Gap Discovery (ABGD) method to obtain different species-delimitation schemes over a range of prior intraspecific divergence limits to assess the consistency of divergence thresholds used to demarcate current species boundaries. The species-rich phylogeny was able to identify a number of taxonomic errors, namely the incorrect generic placement of Chiromantis inexpectatus, which we now move to the genus Feihyla, and the specific identity of Rhacophorus bipunctatus from Peninsular Malaysia, which we tentatively reassign to R. rhodopus. The ABGD analysis demonstrated overlap between intra- and interspecific divergence limits: genetic thresholds used in some studies to synonymize taxa have frequently been used in other studies to justify the recognition of new species. This analysis also highlighted numerous groups that could potentially be split or lumped, which we earmark for future examination. Our large-scale and en bloc approach to species-level phylogenetic systematics contributes to the resolution of taxonomic uncertainties, reveals possible new species, and identifies numerous groups that require critical examination. Overall, we demonstrate that the taxonomy and evolutionary history of Old-World tree frogs are far from resolved, stable or adequately characterized at the level of genus, species, and/or population.
    Matched MeSH terms: Likelihood Functions
  7. 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
  8. King JL, Churchill JD, Novroski NMM, Zeng X, Warshauer DH, Seah LH, et al.
    Forensic Sci Int Genet, 2018 09;36:60-76.
    PMID: 29935396 DOI: 10.1016/j.fsigen.2018.06.005
    The use of single nucleotide polymorphisms (SNPs) in forensic genetics has been limited to challenged samples with low template and/or degraded DNA. The recent introduction of massively parallel sequencing (MPS) technologies has expanded the potential applications of these markers and increased the discrimination power of well-established loci by considering variation in the flanking regions of target loci. The ForenSeq Signature Preparation Kit contains 165 SNP amplicons for ancestry- (aiSNPs), identity- (iiSNPs), and phenotype-inference (piSNPs). In this study, 714 individuals from four major populations (African American, AFA; East Asian, ASN; US Caucasian, CAU; and Southwest US Hispanic, HIS) previously reported by Churchill et al. [Forensic Sci Int Genet. 30 (2017) 81-92; DOI: https://doi.org/10.1016/j.fsigen.2017.06.004] were assessed using STRait Razor v2s to determine the level of diversity in the flanking regions of these amplicons. The results show that nearly 70% of loci showed some level of flanking region variation with 22 iiSNPs and 8 aiSNPs categorized as microhaplotypes in this study. The heterozygosities of these microhaplotypes approached, and in one instance surpassed, those of some core STR loci. Also, the impact of the flanking region on other forensic parameters (e.g., power of exclusion and power of discrimination) was examined. Sixteen of the 94 iiSNPs had an effective allele number greater than 2.00 across the four populations. To assess what effect the flanking region information had on the ancestry inference, genotype probabilities and likelihood ratios were determined. Additionally, concordance with the ForenSeq UAS and Nextera Rapid Capture was evaluated, and patterns of heterozygote imbalance were identified. Pairwise comparison of the iiSNP diplotypes determined the probability of detecting a mixture (i.e., observing ≥ 3 haplotypes) using these loci alone was 0.9952. The improvement in random match probabilities for the full regions over the target iiSNPs was found to be significant. When combining the iiSNPs with the autosomal STRs, the combined match probabilities ranged from 6.40 × 10-73 (ASN) to 1.02 × 10-79 (AFA).
    Matched MeSH terms: Likelihood Functions
  9. Lim KK, Yoon SY, Mohd Taib NA, Shabaruddin FH, Dahlui M, Woo YL, et al.
    Appl Health Econ Health Policy, 2018 06;16(3):395-406.
    PMID: 29572724 DOI: 10.1007/s40258-018-0384-8
    OBJECTIVE: Previous studies showed that offering BRCA mutation testing to population subgroups at high risk of harbouring the mutation may be cost effective, yet no evidence is available for low- or middle-income countries (LMIC) and in Asia. We estimated the cost effectiveness of BRCA mutation testing in early-stage breast cancer patients with high pre-test probability of harbouring the mutation in Malaysia, an LMIC in Asia.

    METHODS: We developed a decision analytic model to estimate the lifetime costs and quality-adjusted life-years (QALYs) accrued through BRCA mutation testing or routine clinical surveillance (RCS) for a hypothetical cohort of 1000 early-stage breast cancer patients aged 40 years. In the model, patients would decide whether to accept testing and to undertake risk-reducing mastectomy, oophorectomy, tamoxifen, combinations or neither. We calculated the incremental cost-effectiveness ratio (ICER) from the health system perspective. A series of sensitivity analyses were performed.

    RESULTS: In the base case, testing generated 11.2 QALYs over the lifetime and cost US$4815 per patient whereas RCS generated 11.1 QALYs and cost US$4574 per patient. The ICER of US$2725/QALY was below the cost-effective thresholds. The ICER was sensitive to the discounting of cost, cost of BRCA mutation testing and utility of being risk-free, but the ICERs remained below the thresholds. Probabilistic sensitivity analysis showed that at a threshold of US$9500/QALY, 99.9% of simulations favoured BRCA mutation testing over RCS.

    CONCLUSIONS: Offering BRCA mutation testing to early-stage breast cancer patients identified using a locally-validated risk-assessment tool may be cost effective compared to RCS in Malaysia.

    Matched MeSH terms: Likelihood Functions
  10. Gan HM, Tan MH, Lee YP, Schultz MB, Horwitz P, Burnham Q, et al.
    Mol Phylogenet Evol, 2018 01;118:88-98.
    PMID: 28966124 DOI: 10.1016/j.ympev.2017.09.022
    To further understand the evolutionary history and mitogenomic features of Australia's highly distinctive freshwater crayfish fauna, we utilized a recently described rapid mitogenome sequencing pipeline to generate 24 new crayfish mitogenomes including a diversity of burrowing crayfish species and the first for Astacopsis gouldi, the world's largest freshwater invertebrate. Whole mitogenome-based phylogeny estimates using both Bayesian and Maximum Likelihood methods substantially strengthen existing hypotheses for systematic relationships among Australian freshwater crayfish with evidence of pervasive diversifying selection and accelerated mitochondrial substitution rate among the members of the clade representing strongly burrowing crayfish that may reflect selection pressures for increased energy requirement for adaptation to terrestrial environment and a burrowing lifestyle. Further, gene rearrangements are prevalent in the burrowing crayfish mitogenomes involving both tRNA and protein coding genes. In addition, duplicated control regions were observed in two closely related Engaeus species, together with evidence for concerted evolution. This study significantly adds to the understanding of Australian freshwater crayfish evolutionary relationships and suggests a link between mitogenome evolution and adaptation to terrestrial environments and a burrowing lifestyle in freshwater crayfish.
    Matched MeSH terms: Likelihood Functions
  11. 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
  12. Karafas S, Teng ST, Leaw CP, Alves-de-Souza C
    Harmful Algae, 2017 09;68:128-151.
    PMID: 28962975 DOI: 10.1016/j.hal.2017.08.001
    The genus Amphidinium is an important group of athecated dinoflagellates because of its high abundance in marine habitats, its member's ability to live in a variety of environmental conditions and ability to produce toxins. Furthermore, the genus is of particular interest in the biotechnology field for its potential in the pharmaceutical arena. Taxonomically the there is a history of complication and confusion over the proper identities and placements of Amphidinium species due to high genetic variability coupled with high morphological conservation. Thirteen years has passed since the most recent review of the group, and while many issues were resolved, some remain. The present study used microscopy, phylogenetics of the 28S region of rDNA, secondary structure of the ITS2 region of rDNA, compensatory base change data, and cytotoxicity data from Amphidinium strains collected world-wide to elucidate remaining confusion. This holistic approach using multiple lines of evidence resulted in a more comprehensive understanding of the morphological, ecological, and genetic characteristics that are attributed to organisms belonging to Amphidinium, including six novel species: A. fijiensis, A. magnum, A. paucianulatum, A. pseudomassartii, A. theodori, and A. tomasii.
    Matched MeSH terms: Likelihood Functions
  13. 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
  14. 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
  15. Lopes-Lima M, Froufe E, Do VT, Ghamizi M, Mock KE, Kebapçı Ü, et al.
    Mol Phylogenet Evol, 2017 01;106:174-191.
    PMID: 27621130 DOI: 10.1016/j.ympev.2016.08.021
    Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032bp (COI+28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies.
    Matched MeSH terms: Likelihood Functions
  16. 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
  17. Hashibah Hamid, Long MM, Sharipah Soaad Syed Yahaya
    Sains Malaysiana, 2017;46:1001-1010.
    The location model proposed in the past is a predictive discriminant rule that can classify new observations into one
    of two predefined groups based on mixtures of continuous and categorical variables. The ability of location model to
    discriminate new observation correctly is highly dependent on the number of multinomial cells created by the number
    of categorical variables. This study conducts a preliminary investigation to show the location model that uses maximum
    likelihood estimation has high misclassification rate up to 45% on average in dealing with more than six categorical
    variables for all 36 data tested. Such model indicated highly incorrect prediction as this model performed badly for
    large categorical variables even with large sample size. To alleviate the high rate of misclassification, a new strategy
    is embedded in the discriminant rule by introducing nonlinear principal component analysis (NPCA) into the classical
    location model (cLM), mainly to handle the large number of categorical variables. This new strategy is investigated
    on some simulation and real datasets through the estimation of misclassification rate using leave-one-out method. The
    results from numerical investigations manifest the feasibility of the proposed model as the misclassification rate is
    dramatically decreased compared to the cLM for all 18 different data settings. A practical application using real dataset
    demonstrates a significant improvement and obtains comparable result among the best methods that are compared. The
    overall findings reveal that the proposed model extended the applicability range of the location model as previously it
    was limited to only six categorical variables to achieve acceptable performance. This study proved that the proposed
    model with new discrimination procedure can be used as an alternative to the problems of mixed variables classification,
    primarily when facing with large categorical variables.
    Matched MeSH terms: Likelihood Functions
  18. Umar Suleiman Dauda, Nik Noordini Nik Abdl Malik, Mazlina Esa, Mohd Fairus Mohd Yusoff, Mohamed Rijal Hamid
    MyJurnal
    Parameter estimation of complex exponential signals corrupted by additive white
    Gaussian noise (AWGN) is crucial in the study of distributed beamforming in a practical
    scenario. Near zero (0) phase offset are expected at the receiver end which rely on the
    smoothing and correction of the frequency and phase estimates. Neither
    computational complexity nor the processing latency has an effect on the expected
    zero phase offset but the estimation accuracy does. Thus, the maximum likelihood
    estimator (MLE) using Fast Fourier Transform (FFT) approach is being considered for
    cases with none and post processing in locating of the maximum peaks. Details on how
    the phase estimates are arrived at is not always covered in literatures but explained in
    the article. Numerical results obtained showed that global maximum peaks are arrived
    at by employing a fine search with higher values of FFT.
    Matched MeSH terms: Likelihood Functions
  19. Nurkhairany Amyra Mokhtar, Yong Zulina Zubairi, Abdul Ghapor Hussin, Rossita Mohamad Yunus
    MATEMATIKA, 2017;33(2):159-163.
    MyJurnal
    Replicated linear functional relationship model is often used to describe
    relationships between two circular variables where both variables have error terms and
    replicate observations are available. We derive the estimate of the rotation parameter
    of the model using the maximum likelihood method. The performance of the proposed
    method is studied through simulation, and it is found that the biasness of the estimates
    is small, thus implying the suitability of the method. Practical application of the
    method is illustrated by using a real data set.
    Matched MeSH terms: Likelihood Functions
  20. Murshid MA, Mohaidin Z
    Pharm Pract (Granada), 2017 Apr-Jun;15(2):990.
    PMID: 28690701 DOI: 10.18549/PharmPract.2017.02.990
    To date, research on the prescribing decisions of physician lacks sound theoretical foundations. In fact, drug prescribing by doctors is a complex phenomenon influenced by various factors. Most of the existing studies in the area of drug prescription explain the process of decision-making by physicians via the exploratory approach rather than theoretical. Therefore, this review is an attempt to suggest a value conceptual model that explains the theoretical linkages existing between marketing efforts, patient and pharmacist and physician decision to prescribe the drugs. The paper follows an inclusive review approach and applies the previous theoretical models of prescribing behaviour to identify the relational factors. More specifically, the report identifies and uses several valuable perspectives such as the 'persuasion theory - elaboration likelihood model', the stimuli-response marketing model', the 'agency theory', the theory of planned behaviour,' and 'social power theory,' in developing an innovative conceptual paradigm. Based on the combination of existing methods and previous models, this paper suggests a new conceptual model of the physician decision-making process. This unique model has the potential for use in further research.
    Matched MeSH terms: Likelihood Functions
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