Displaying publications 61 - 80 of 92 in total

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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. Hossain MA, Roslan HA
    ScientificWorldJournal, 2014;2014:186029.
    PMID: 25165734 DOI: 10.1155/2014/186029
    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom.
    Matched MeSH terms: Likelihood Functions
  12. Ibrahim N, Rampal L, Jamil Z, Zain AM
    Prev Med, 2012 Nov;55(5):505-10.
    PMID: 22982947 DOI: 10.1016/j.ypmed.2012.09.003
    OBJECTIVE: Develop, implement and evaluate the effectiveness of a peer-led education program related to HIV/AIDS among university students.
    METHOD:
    DESIGN: randomized controlled trial with 276 university students at Faculty of Medicine and Health Sciences University Putra Malaysia (UPM), Serdang in 2011.
    INTERVENTION: A peer-led education program on HIV prevention by university students.
    OUTCOME: differences in knowledge, attitude and risk behavior practices related to HIV between baselines, immediate follow-up after intervention and after three months.
    RESULTS: Significant improvement in sound knowledge in the intervention group as compared to the control group (Odds ratio, 1.75; 95% CI 1.01, 3.00; p=0.04) and improvement in good attitude related to HIV (Odds ratio 2.22; 95% CI 1.37, 3.61; p=0.01). The odds of high substance risk behavior was significantly reduced in the intervention group as compared to the control group (Odds ratio 0.07; 95% CI 0.02, 0.34; p=0.01). The association between good knowledge and intervention was modified by the different time points (baseline, immediately after intervention and 3 months after intervention), ethnicity and gender.
    CONCLUSION:
    Peer-led education program in HIV prevention improves knowledge, attitude and substance risk behavior. Changes in sexual risk behavior may require a longer follow-up.
    Matched MeSH terms: Likelihood Functions
  13. Mohd-Sidik S, Arroll B, Goodyear-Smith F, Zain AM
    Int J Psychiatry Med, 2011;41(2):143-54.
    PMID: 21675346 DOI: 10.2190/PM.41.2.d
    OBJECTIVE: To determine the diagnostic accuracy of the two questions with help question (TQWHQ) in the Malay language. The two questions are case-finding questions on depression, and a question on whether help is needed was added to increase the specificity of the two questions.
    METHOD: This cross sectional validation study was conducted in a government funded primary care clinic in Malaysia. The participants included 146 consecutive women patients receiving no psychotropic drugs and who were Malay speakers. The main outcome measures were sensitivity, specificity, and likelihood ratios of the two questions and help question.
    RESULTS: The two questions showed a sensitivity of 99% (95% confidence interval 88% to 99.9%) and a specificity of 70% (62% to 78%), respectively. The likelihood ratio for a positive test was 3.3 (2.5 to 4.5) and the likelihood ratio for a negative test was 0.01 (0.00 to 0.57). The addition of the help question to the two questions increased the specificity to 95% (89% to 98%).
    CONCLUSION: The two qeustions on depression detected most cases of depression in this study. The questions have the advantage of brevity. The addition of the help question increased the specificity of the two questions. Based on these findings, the TQWHQ can be strongly recommended for detection of depression in government primary care clnics in Malaysia. Translation did not apear to affect the validity of the TQWHQ.
    Matched MeSH terms: Likelihood Functions
  14. Quek SP, Davies SJ, Ashton PS, Itino T, Pierce NE
    Mol Ecol, 2007 May;16(10):2045-62.
    PMID: 17498231
    We investigate the geographical and historical context of diversification in a complex of mutualistic Crematogaster ants living in Macaranga trees in the equatorial rain forests of Southeast Asia. Using mitochondrial DNA from 433 ant colonies collected from 32 locations spanning Borneo, Malaya and Sumatra, we infer branching relationships, patterns of genetic diversity and population history. We reconstruct a time frame for the ants' diversification and demographic expansions, and identify areas that might have been refugia or centres of diversification. Seventeen operational lineages are identified, most of which can be distinguished by host preference and geographical range. The ants first diversified 16-20 Ma, not long after the onset of the everwet forests in Sundaland, and achieved most of their taxonomic diversity during the Pliocene. Pleistocene demographic expansions are inferred for several of the younger lineages. Phylogenetic relationships suggest a Bornean cradle and major axis of diversification. Taxonomic diversity tends to be associated with mountain ranges; in Borneo, it is greatest in the Crocker Range of Sabah and concentrated also in other parts of the northern northwest coast. Within-lineage genetic diversity in Malaya and Sumatra tends to also coincide with mountain ranges. A series of disjunct and restricted distributions spanning northern northwest Borneo and the major mountain ranges of Malaya and Sumatra, seen in three pairs of sister lineages, further suggests that these regions were rain-forest refuges during drier climatic phases of the Pleistocene. Results are discussed in the context of the history of Sundaland's rain forests.
    Matched MeSH terms: Likelihood Functions
  15. Pua YH, Lim CK, Ang A
    Obesity (Silver Spring), 2006 Nov;14(11):1992-9.
    PMID: 17135616 DOI: 10.1038/oby.2006.233
    OBJECTIVE: To revisit cut-off values of BMI, waist circumference (WC), and waist-to-stature ratio (WSR) based on their association with cardiorespiratory fitness (CRF). The derived cut-off points were compared with current values (BMI, 25.0 kg/m(2); WC, 80 cm) as recommended by the World Health Organization.
    RESEARCH METHODS AND PROCEDURES: Anthropometric indices were measured in a cross sectional study of 358 Singaporean female employees of a large tertiary hospital (63% Singaporean Chinese, 28% Malays, and 9% Indians). CRF was determined by the 1-mile walk test. Receiver operating characteristic curves were constructed to determine cut-off points.
    RESULTS: The cut-off points for BMI, WC, and WSR were 23.6 kg/m(2), 75.3 cm, and 0.48, respectively. The areas under the curve of BMI, WC, and WSR were 0.68, 0.74, and 0.74, respectively. For a given BMI, women with low CRF had higher WSR compared with women with high CRF.
    DISCUSSION: These findings provide convergent evidence that the cut-off points for Singaporean women were lower than the World Health Organization's criteria but were in good agreement with those reported for Asians.
    Matched MeSH terms: Likelihood Functions
  16. Matsui M, Shimada T, Ota H, Tanaka-Ueno T
    Mol Phylogenet Evol, 2005 Dec;37(3):733-42.
    PMID: 15964212
    The genus Rana, notably diversified in Oriental regions from China to Southeast Asia, includes a group of cascade frogs assigned to subgenera Odorrana and Eburana. Among them, R. ishikawae and the R. narina complex represent the northernmost members occurring from Taiwan to the Ryukyu Archipelago of Japan. Relationships of these frogs with the continental members, as well as the history of their invasions to islands, have been unclear. The taxonomic status of Odorrana and related genera varies among authors and no phylogenetic reassessment has been done. Using partial sequences of mitochondrial 12S and 16S rRNA genes, we estimated phylogenetic relationships among 17 species of the section Hylarana including Odorrana and Eburana, and related species from the Ryukyus, Taiwan, China, Thailand, Malaysia, and Indonesia. We estimate that (1) Odorrana is monophyletic and encompasses species of Eburana and R. hosii, which is now placed in Chalcorana, (2) the ancestor of R. ishikawae separated from other Rana in the middle to late Miocene prior to its entry to the Ryukyu Archipelago, (3) the ancestor of the R. narina complex later diversified in continental Asia, and invaded the Ryukyu Archipelago through Taiwan, (4) the R. narina complex attained its current distribution within the Ryukyus through niche segregations, and (5) vicariance of R. hosii between Malay Peninsula and Borneo occurred much later than the divergence events in the R. narina complex. Current subgeneric classification of Rana, at least of Southeast Asian members, requires full reassessment in the light of phylogenetic relationships.
    Matched MeSH terms: Likelihood Functions
  17. Quek SP, Davies SJ, Itino T, Pierce NE
    Evolution, 2004 Mar;58(3):554-70.
    PMID: 15119439
    We investigate the evolution of host association in a cryptic complex of mutualistic Crematogaster (Decacrema) ants that inhabits and defends Macaranga trees in Southeast Asia. Previous phylogenetic studies based on limited samplings of Decacrema present conflicting reconstructions of the evolutionary history of the association, inferring both cospeciation and the predominance of host shifts. We use cytochrome oxidase I (COI) to reconstruct phylogenetic relationships in a comprehensive sampling of the Decacrema inhabitants of Macaranga. Using a published Macaranga phylogeny, we test whether the ants and plants have cospeciated. The COI phylogeny reveals 10 well-supported lineages and an absence of cospeciation. Host shifts, however, have been constrained by stem traits that are themselves correlated with Macaranga phylogeny. Earlier lineages of Decacrema exclusively inhabit waxy stems, a basal state in the Pachystemon clade within Macaranga, whereas younger species of Pachystemon, characterized by nonwaxy stems, are inhabited only by younger lineages of Decacrema. Despite the absence of cospeciation, the correlated succession of stem texture in both phylogenies suggests that Decacrema and Pachystemon have diversified in association, or codiversified. Subsequent to the colonization of the Pachystemon clade, Decacrema expanded onto a second clade within Macaranga, inducing the development of myrmecophytism in the Pruinosae group. Confinement to the aseasonal wet climate zone of western Malesia suggests myrmecophytic Macaranga are no older than the wet forest community in Southeast Asia, estimated to be about 20 million years old (early Miocene). Our calculation of COI divergence rates from several published arthropod studies that relied on tenable calibrations indicates a generally conserved rate of approximately 1.5% per million years. Applying this rate to a rate-smoothed Bayesian chronogram of the ants, the Decacrema from Macaranga are inferred to be at least 12 million years old (mid-Miocene). However, using the extremes of rate variation in COI produces an age as recent as 6 million years. Our inferred timeline based on 1.5% per million years concurs with independent biogeographical events in the region reconstructed from palynological data, thus suggesting that the evolutionary histories of Decacrema and their Pachystemon hosts have been contemporaneous since the mid-Miocene. The evolution of myrmecophytism enabled Macaranga to radiate into enemy-free space, while the ants' diversification has been shaped by stem traits, host specialization, and geographic factors. We discuss the possibility that the ancient and exclusive association between Decacrema and Macaranga was facilitated by an impoverished diversity of myrmecophytes and phytoecious (obligately plant inhabiting) ants in the region.
    Matched MeSH terms: Likelihood Functions
  18. 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
  19. Sanders KL, Malhotra A, Thorpe RS
    J Evol Biol, 2004 Jul;17(4):721-31.
    PMID: 15271071
    We analyse molecular and phenotypic evolution in a group of taxonomically problematic Indomalayan pitvipers, the Trimeresurus sumatranus group. Mitochondrial DNA sequencing provides a well-resolved phylogeny, with each species representing a distinct lineage. Multivariate morphological analysis reveals a high level of phenotypic differentiation, which is congruent between the sexes but does not reflect phylogenetic history. An adaptive explanation for the observed pattern of differentiation is supported by independent contrasts analysis, which shows significant correlations between current ecology and the characters that most account for the variation between taxa, including those that are presently used to identify the species. Reduced precipitation and altitude, and increased temperature, are correlated with higher numbers of scales on the head, body and tail. It is hypothesized that scale number plays an important role in heat and water exchange by influencing the area of exposed of interstitial skin, and that colour pattern variation reflects selection pressures involving camouflage and thermoregulation. Ecological convergence in traits used for classification is found to have important implications for species identification where taxa are distributed over varying environments.
    Matched MeSH terms: Likelihood Functions
  20. Mohd-Padil H, Mohd-Adnan A, Gabaldón T
    Mol Biol Evol, 2013 Apr;30(4):894-905.
    PMID: 23258311 DOI: 10.1093/molbev/mss325
    Transferrin is a protein super-family involved in iron transport, a central process in cellular homeostasis. Throughout the evolution of vertebrates, transferrin members have diversified into distinct subfamilies including serotransferrin, ovotransferrin, lactoferrin, melanotransferrin, the inhibitor of carbonic anhydrase, pacifastin, and the major yolk protein in sea urchin. Previous phylogenetic analyses have established the branching order of the diverse transferrin subfamilies but were mostly focused on the transferrin repertoire present in mammals. Here, we conduct a comprehensive phylogenetic analysis of transferrin protein sequences in sequenced vertebrates, placing a special focus on the less-studied nonmammalian vertebrates. Our analyses uncover a novel transferrin clade present across fish, sauropsid, and amphibian genomes but strikingly absent from mammals. Our reconstructed scenario implies that this novel class emerged through a duplication event at the vertebrate ancestor, and that it was subsequently lost in the lineage leading to mammals. We detect footprints of accelerated evolution following the duplication event, which suggest positive selection and early functional divergence of this novel clade. Interestingly, the loss of this novel class of transferrin in mammals coincided with the divergence by duplication of lactoferrin and serotransferrin in this lineage. Altogether, our results provide novel insights on the evolution of iron-binding proteins in the various vertebrate groups.
    Matched MeSH terms: Likelihood Functions
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