Displaying publications 181 - 200 of 283 in total

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  1. Lai K, Luo L, Kang T, Zhang F, Chen X
    Naunyn Schmiedebergs Arch Pharmacol, 2026 Feb;399(3):3619-3630.
    PMID: 41044440 DOI: 10.1007/s00210-025-04650-6
    Bisoprolol, a selective β₁-blocker, is widely prescribed for cardiovascular disease. Real-world pharmacovigilance can clarify adverse drug reactions (ADRs) across demographic strata and identify signals not fully characterized in trials. We analyzed bisoprolol-associated reports in the FDA Adverse Event Reporting System. Disproportionality was assessed using complementary algorithms-reporting odds ratio (ROR), proportional reporting ratio (PRR), information component (IC with IC025), and empirical Bayes geometric mean (EBGM with EBGM05). To stabilize sparse strata, we required a ≥ 3 and multi-algorithm concordance (EBGM05 > 2, IC025 > 0, lower95_ROR > 1). Multiple testing was controlled using Benjamini-Hochberg FDR and Bonferroni adjustments. Signals were summarized overall and stratified by sex and age (
    Matched MeSH terms: Bayes Theorem
  2. Leong SH, Ong SH
    PLoS One, 2017;12(7):e0180307.
    PMID: 28686634 DOI: 10.1371/journal.pone.0180307
    This paper considers three crucial issues in processing scaled down image, the representation of partial image, similarity measure and domain adaptation. Two Gaussian mixture model based algorithms are proposed to effectively preserve image details and avoids image degradation. Multiple partial images are clustered separately through Gaussian mixture model clustering with a scan and select procedure to enhance the inclusion of small image details. The local image features, represented by maximum likelihood estimates of the mixture components, are classified by using the modified Bayes factor (MBF) as a similarity measure. The detection of novel local features from MBF will suggest domain adaptation, which is changing the number of components of the Gaussian mixture model. The performance of the proposed algorithms are evaluated with simulated data and real images and it is shown to perform much better than existing Gaussian mixture model based algorithms in reproducing images with higher structural similarity index.
    Matched MeSH terms: Bayes Theorem
  3. Guure CB, Ibrahim NA, Adam MB, Said SM
    PLoS One, 2017;12(8):e0182873.
    PMID: 28813458 DOI: 10.1371/journal.pone.0182873
    BACKGROUND: Modified Mini-Mental State Examination (3MS) is an instrument administered by trained personnel to examine levels of participants' cognitive function. However, the association between changes in scores over time and the risk of death (mortality) is not known. The aims of this study are to examine the association between 3MS scores and mortality via cognitive impairment among older women and to determine individuals' risk of changes in scores to better predict their survival and mortality rates.

    METHODS: We propose a Bayesian joint modelling approach to determine mortality due to cognitive impairment via repeated measures of 3MS scores trajectories over a 21-year follow-up period. Data for this study are taken from the Osteoporotic Fracture longitudinal study among women aged 65+ which started in 1986-88.

    RESULTS: The standard relative risk model from the analyses with a baseline 3MS score after adjusting for all the significant covariates demonstrates that, every unit decrease in a 3MS score corresponds to a non-significant 1.059 increase risk of mortality with a 95% CI of (0.981, 1.143), while the extended model results in a significant 0.09% increased risk in mortality. The joint modelling approach found a strong association between the 3MS scores and the risk of mortality, such that, every unit decrease in 3MS scores results in a 1.135 (13%) increased risk of death via cognitive impairment with a 95% CI of (1.056, 1.215).

    CONCLUSION: It has been demonstrated that a decrease in 3MS results has a significant increase risk of mortality due to cognitive impairment via joint modelling, but insignificant when considered under the standard relative risk approach.

    Matched MeSH terms: Bayes Theorem
  4. Lithanatudom SK, Chaowasku T, Nantarat N, Jaroenkit T, Smith DR, Lithanatudom P
    Sci Rep, 2017 07 27;7(1):6716.
    PMID: 28751754 DOI: 10.1038/s41598-017-07045-7
    Dimocarpus longan, commonly known as the longan, belongs to the family Sapindaceae, and is one of the most economically important fruits commonly cultivated in several regions in Asia. There are various cultivars of longan throughout the Thai-Malay peninsula region, but until now no phylogenetic analysis has been undertaken to determine the genetic relatedness of these cultivars. To address this issue, 6 loci, namely ITS2, matK, rbcL, trnH-psbA, trnL-I and trnL-trnF were amplified and sequenced from 40 individuals consisting of 26 longan cultivars 2 types of lychee and 8 herbarium samples. The sequencing results were used to construct a phylogenetic tree using the neighbor-joining (NJ), maximum likelihood (ML) and Bayesian inference (BI) criteria. The tree showed cryptic groups of D. longan from the Thailand-Malaysia region (Dimocarpus longan spp.). This is the first report of the genetic relationship of Dimocarpus based on multi-locus molecular markers and morphological characteristics. Multiple sequence alignments, phylogenetic trees and species delimitation support that Dimocarpus longan spp. longan var. obtusus and Dimocarpus longan spp. malesianus var. malesianus should be placed into a higher order and are two additional species in the genus Dimocarpus. Therefore these two species require nomenclatural changes as Dimocarpus malesianus and Dimocarpus obtusus, respectively.
    Matched MeSH terms: Bayes Theorem
  5. Danderson CA, Downie SR, Hermann M
    Mol Phylogenet Evol, 2018 01;118:286-305.
    PMID: 29017853 DOI: 10.1016/j.ympev.2017.10.006
    The Arracacia clade (Apiaceae, Apioideae) is a heterogeneous assemblage of 12 genera, comprising 111 known species distributed in high montane temperate and sub-alpine habitats of meso- and South America. Previous studies have indicated that the genera Arracacia, Coulterophytum, and Prionosciadium are polyphyletic, but for the most part relationships among the members of the clade are largely unknown. Initially, cladistic analyses of nrDNA ITS sequences were carried out on 212 accessions (122 taxa), representing 92 species of the Arracacia clade and outgroups from the closely-related páramo genera Cotopaxia, Niphogeton, and Perissocoeleum and members of the Perennial Endemic North American clade and its allies. Using the ITS results to inform sampling of a small subset of taxa, a pilot study examining the phylogenetic utility of 20 noncoding chloroplast loci was subsequently performed to identify those regions most useful at resolving relationships. A cost-benefit analysis determined that five loci (trnQ-5'rps16, trnD-trnT, rpl32-trnL, psbD-trnT, ndhA intron) would maximize resolution and branch support in the clade. Cladistic analyses of four of these loci (trnQ-5'rps16, trnD-trnT, rpl32-trnL, ndhA intron) and the ITS region, separately and combined, revealed that Arracacia, Coaxana, Coulterophytum, Prionosciadium, and Rhodosciadium are each polyphyletic and that Donnellsmithia and Myrrhidendron are each monophyletic. Although most relationships in the Arracacia clade and among the closely-related genera Cotopaxia, Niphogeton, and Perissocoeleum are poorly resolved and supported, ten groups are recognized for future revisionary studies. Polyploidy and rapid species radiation have likely confounded generic circumscriptions and interpretation of relationships.
    Matched MeSH terms: Bayes Theorem
  6. Saffian SM, Duffull SB, Roberts RL, Tait RC, Black L, Lund KA, et al.
    Ther Drug Monit, 2016 12;38(6):677-683.
    PMID: 27855133
    BACKGROUND: A previously established Bayesian dosing tool for warfarin was found to produce biased maintenance dose predictions. In this study, we aimed (1) to determine whether the biased warfarin dose predictions previously observed could be replicated in a new cohort of patients from 2 different clinical settings, (2) to explore the influence of CYP2C9 and VKORC1 genotype on predictive performance of the Bayesian dosing tool, and (3) to determine whether the previous population used to develop the kinetic-pharmacodynamic model underpinning the Bayesian dosing tool was sufficiently different from the test (posterior) population to account for the biased dose predictions.

    METHODS: The warfarin maintenance doses for 140 patients were predicted using the dosing tool and compared with the observed maintenance dose. The impact of genotype was assessed by predicting maintenance doses with prior parameter values known to be altered by genetic variability (eg, EC50 for VKORC1 genotype). The prior population was evaluated by fitting the published kinetic-pharmacodynamic model, which underpins the Bayesian tool, to the observed data using NONMEM and comparing the model parameter estimates with published values.

    RESULTS: The Bayesian tool produced positively biased dose predictions in the new cohort of patients (mean prediction error [95% confidence interval]; 0.32 mg/d [0.14-0.5]). The bias was only observed in patients requiring ≥7 mg/d. The direction and magnitude of the observed bias was not influenced by genotype. The prior model provided a good fit to our data, which suggests that the bias was not caused by different prior and posterior populations.

    CONCLUSIONS: Maintenance doses for patients requiring ≥7 mg/d were overpredicted. The bias was not due to the influence of genotype nor was it related to differences between the prior and posterior populations. There is a need for a more mechanistic model that captures warfarin dose-response relationship at higher warfarin doses.

    Matched MeSH terms: Bayes Theorem
  7. Sharma R, Goossens B, Heller R, Rasteiro R, Othman N, Bruford MW, et al.
    Sci Rep, 2018 01 17;8(1):880.
    PMID: 29343863 DOI: 10.1038/s41598-017-17042-5
    The origin of the elephant on the island of Borneo remains elusive. Research has suggested two alternative hypotheses: the Bornean elephant stems either from a recent introduction in the 17th century or from an ancient colonization several hundreds of thousands years ago. Lack of elephant fossils has been interpreted as evidence for a very recent introduction, whereas mtDNA divergence from other Asian elephants has been argued to favor an ancient colonization. We investigated the demographic history of Bornean elephants using full-likelihood and approximate Bayesian computation analyses. Our results are at odds with both the recent and ancient colonization hypotheses, and favour a third intermediate scenario. We find that genetic data favour a scenario in which Bornean elephants experienced a bottleneck during the last glacial period, possibly as a consequence of the colonization of Borneo, and from which it has slowly recovered since. Altogether the data support a natural colonization of Bornean elephants at a time when large terrestrial mammals could colonise from the Sunda shelf when sea levels were much lower. Our results are important not only in understanding the unique history of the colonization of Borneo by elephants, but also for their long-term conservation.
    Matched MeSH terms: Bayes Theorem
  8. Jani J, Toor GS
    Water Res, 2018 06 15;137:344-354.
    PMID: 29571112 DOI: 10.1016/j.watres.2018.02.042
    Nitrogen (N) transport from land to water is a dominant contributor of N in estuarine waters leading to eutrophication, harmful algal blooms, and hypoxia. Our objectives were to (1) investigate the composition of inorganic and organic N forms, (2) distinguish the sources and biogeochemical mechanisms of nitrate-N (NO3-N) transport using stable isotopes of NO3- and Bayesian mixing model, and (3) determine the dissolved organic N (DON) bioavailability using bioassays in a longitudinal gradient from freshwater to estuarine ecosystem located in the Tampa Bay, Florida, United States. We found that DON was the most dominant N form (mean: 64%, range: 46-83%) followed by particulate organic N (PON, mean: 22%, range: 14-37%), whereas inorganic N forms (NOx-N: 7%, NH4-N: 7%) were 14% of total N in freshwater and estuarine waters. Stable isotope data of NO3- revealed that nitrification was the main contributor (36.4%), followed by soil and organic N sources (25.5%), NO3- fertilizers (22.4%), and NH4+ fertilizers (15.7%). Bioassays showed that 14 to 65% of DON concentrations decreased after 5-days of incubation indicating utilization of DON by microbes in freshwater and estuarine waters. These results suggest that despite low proportion of inorganic N forms, the higher concentrations and bioavailability of DON can be a potential source of N for algae and bacteria leading to water quality degradation in the estuarine waters.
    Matched MeSH terms: Bayes Theorem
  9. de Vries B, Narayan R, McGeechan K, Santiagu S, Vairavan R, Burke M, et al.
    Acta Obstet Gynecol Scand, 2018 Jun;97(6):668-676.
    PMID: 29450884 DOI: 10.1111/aogs.13310
    INTRODUCTION: Cesarean section rates continue to increase globally. Prediction of intrapartum cesarean section could lead to preventive measures. Our aim was to assess the association between sonographically measured cervical length at 37 weeks of gestation and cesarean section among women planning a vaginal birth. The population was women with a low-risk pregnancy or with gestational diabetes.

    MATERIAL AND METHODS: This was a prospective cohort study conducted in a tertiary referral hospital in Sydney, Australia. In all, 212 women with a low-risk pregnancy or with gestational diabetes were recruited including 158 nulliparous and 54 parous women. Maternal demographic, clinical and ultrasound characteristics were collected at 37 weeks of gestation. Semi-Bayesian logistic regression and Markov chain Monte Carlo simulation were used to assess the relation between cervical length and cesarean section in labor.

    RESULTS: Rates of cesarean section were 5% (2/55) for cervical length ≤20 mm, 17% (17/101) for cervical length 20-32 mm, and 27% (13/56) for cervical length >32 mm. These rates were 4, 22 and 33%, respectively, in nulliparous women. In the semi-Bayesian analysis, the odds ratio for cesarean section was 6.2 (95% confidence interval 2.2-43) for cervical length 20-32 mm and 10 (95% confidence interval 4.8-74) for cervical length >32 mm compared with the lowest quartile of cervical length, after adjusting for maternal age, parity, height, prepregnancy body mass index, gestational diabetes, induction of labor, neonatal sex and birthweight centile.

    CONCLUSIONS: Cervical length at 37 weeks of gestation is associated with intrapartum cesarean section.

    Matched MeSH terms: Bayes Theorem
  10. Kwong QB, Teh CK, Ong AL, Chew FT, Mayes S, Kulaveerasingam H, et al.
    BMC Genet, 2017 Dec 11;18(1):107.
    PMID: 29228905 DOI: 10.1186/s12863-017-0576-5
    BACKGROUND: Genomic selection (GS) uses genome-wide markers as an attempt to accelerate genetic gain in breeding programs of both animals and plants. This approach is particularly useful for perennial crops such as oil palm, which have long breeding cycles, and for which the optimal method for GS is still under debate. In this study, we evaluated the effect of different marker systems and modeling methods for implementing GS in an introgressed dura family derived from a Deli dura x Nigerian dura (Deli x Nigerian) with 112 individuals. This family is an important breeding source for developing new mother palms for superior oil yield and bunch characters. The traits of interest selected for this study were fruit-to-bunch (F/B), shell-to-fruit (S/F), kernel-to-fruit (K/F), mesocarp-to-fruit (M/F), oil per palm (O/P) and oil-to-dry mesocarp (O/DM). The marker systems evaluated were simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). RR-BLUP, Bayesian A, B, Cπ, LASSO, Ridge Regression and two machine learning methods (SVM and Random Forest) were used to evaluate GS accuracy of the traits.

    RESULTS: The kinship coefficient between individuals in this family ranged from 0.35 to 0.62. S/F and O/DM had the highest genomic heritability, whereas F/B and O/P had the lowest. The accuracies using 135 SSRs were low, with accuracies of the traits around 0.20. The average accuracy of machine learning methods was 0.24, as compared to 0.20 achieved by other methods. The trait with the highest mean accuracy was F/B (0.28), while the lowest were both M/F and O/P (0.18). By using whole genomic SNPs, the accuracies for all traits, especially for O/DM (0.43), S/F (0.39) and M/F (0.30) were improved. The average accuracy of machine learning methods was 0.32, compared to 0.31 achieved by other methods.

    CONCLUSION: Due to high genomic resolution, the use of whole-genome SNPs improved the efficiency of GS dramatically for oil palm and is recommended for dura breeding programs. Machine learning slightly outperformed other methods, but required parameters optimization for GS implementation.

    Matched MeSH terms: Bayes Theorem
  11. Krzemińska U, Morales HE, Greening C, Nyári ÁS, Wilson R, Song BK, et al.
    Heredity (Edinb), 2018 04;120(4):296-309.
    PMID: 29180719 DOI: 10.1038/s41437-017-0020-7
    The House Crow (Corvus splendens) is a useful study system for investigating the genetic basis of adaptations underpinning successful range expansion. The species originates from the Indian subcontinent, but has successfully spread through a variety of thermal environments across Asia, Africa and Europe. Here, population mitogenomics was used to investigate the colonisation history and to test for signals of molecular selection on the mitochondrial genome. We sequenced the mitogenomes of 89 House Crows spanning four native and five invasive populations. A Bayesian dated phylogeny, based on the 13 mitochondrial protein-coding genes, supports a mid-Pleistocene (~630,000 years ago) divergence between the most distant genetic lineages. Phylogeographic patterns suggest that northern South Asia is the likely centre of origin for the species. Codon-based analyses of selection and assessments of changes in amino acid properties provide evidence of positive selection on the ND2 and ND5 genes against a background of purifying selection across the mitogenome. Protein homology modelling suggests that four amino acid substitutions inferred to be under positive selection may modulate coupling efficiency and proton translocation mediated by OXPHOS complex I. The identified substitutions are found within native House Crow lineages and ecological niche modelling predicts suitable climatic areas for the establishment of crow populations within the invasive range. Mitogenomic patterns in the invasive range of the species are more strongly associated with introduction history than climate. We speculate that invasions of the House Crow have been facilitated by standing genetic variation that accumulated due to diversifying selection within the native range.
    Matched MeSH terms: Bayes Theorem
  12. Tan MH, Gan HM, Lee YP, Linton S, Grandjean F, Bartholomei-Santos ML, et al.
    Mol Phylogenet Evol, 2018 10;127:320-331.
    PMID: 29800651 DOI: 10.1016/j.ympev.2018.05.015
    The infraorder Anomura consists of a morphologically and ecologically heterogeneous group of decapod crustaceans, and has attracted interest from taxonomists for decades attempting to find some order out of the seemingly chaotic diversity within the group. Species-level diversity within the Anomura runs the gamut from the "hairy" spindly-legged yeti crab found in deep-sea hydrothermal vent environments to the largest known terrestrial invertebrate, the robust coconut or robber crab. Owing to a well-developed capacity for parallel evolution, as evidenced by the occurrence of multiple independent carcinization events, Anomura has long tested the patience and skill of both taxonomists attempting to find order, and phylogeneticists trying to establish stable hypotheses of evolutionary inter-relationships. In this study, we performed genome skimming to recover the mitogenome sequences of 12 anomuran species including the world's largest extant invertebrate, the robber crab (Birgus latro), thereby over doubling these resources for this group, together with 8 new brachyuran mitogenomes. Maximum-likelihood (ML) and Bayesian-inferred (BI) phylogenetic reconstructions based on amino acid sequences from mitogenome protein-coding genes provided strong support for the monophyly of the Anomura and Brachyura and their sister relationship, consistent with previous studies. The majority of relationships within families were supported and were largely consistent with current taxonomic classifications, whereas many relationships at higher taxonomic levels were unresolved. Nevertheless, we have strong support for a polyphyletic Paguroidea and recovered a well-supported clade of a subset of paguroids (Diogenidae + Coenobitidae) basal to all other anomurans, though this requires further testing with greater taxonomic sampling. We also introduce a new feature to the MitoPhAST bioinformatics pipeline (https://github.com/mht85/MitoPhAST) that enables the extraction of mitochondrial gene order (MGO) information directly from GenBank files and clusters groups based on common MGOs. Using this tool, we compared MGOs across the Anomura and Brachyura, identifying Anomura as a taxonomic "hot spot" with high variability in MGOs among congeneric species from multiple families while noting the broad association of highly-rearranged MGOs with several anomuran lineages inhabiting extreme niches. We also demonstrate the value of MGOs as a source of novel synapomorphies for independently reinforcing tree-based relationships and for shedding light on relationships among challenging groups such as the Aegloidea and Lomisoidea that were unresolved in phylogenetic reconstructions. Overall, this study contributes a substantial amount of new genetic material for Anomura and attempts to further resolve anomuran evolutionary relationships where possible based on a combination of sequence and MGO information. The new feature in MitoPhAST adds to the relatively limited number of bioinformatics tools available for MGO analyses, which can be utilized widely across animal groups.
    Matched MeSH terms: Bayes Theorem
  13. Nada Raja T, Hu TH, Zainudin R, Lee KS, Perkins SL, Singh B
    BMC Evol. Biol., 2018 04 10;18(1):49.
    PMID: 29636003 DOI: 10.1186/s12862-018-1170-9
    BACKGROUND: Non-human primates have long been identified to harbour different species of Plasmodium. Long-tailed macaques (Macaca fascicularis), in particular, are reservoirs for P. knowlesi, P. inui, P. cynomolgi, P. coatneyi and P. fieldi. A previous study conducted in Sarawak, Malaysian Borneo, however revealed that long-tailed macaques could potentially harbour novel species of Plasmodium based on sequences of small subunit ribosomal RNA and circumsporozoite genes. To further validate this finding, the mitochondrial genome and the apicoplast caseinolytic protease M genes of Plasmodium spp. were sequenced from 43 long-tailed macaque blood samples.

    RESULTS: Apart from several named species of malaria parasites, long-tailed macaques were found to be potentially infected with novel species of Plasmodium, namely one we refer to as "P. inui-like." This group of parasites bifurcated into two monophyletic clades indicating the presence of two distinct sub-populations. Further analyses, which relied on the assumption of strict co-phylogeny between hosts and parasites, estimated a population expansion event of between 150,000 to 250,000 years before present of one of these sub-populations that preceded that of the expansion of P. knowlesi. Furthermore, both sub-populations were found to have diverged from a common ancestor of P. inui approximately 1.5 million years ago. In addition, the phylogenetic analyses also demonstrated that long-tailed macaques are new hosts for P. simiovale.

    CONCLUSIONS: Malaria infections of long-tailed macaques of Sarawak, Malaysian Borneo are complex and include a novel species of Plasmodium that is phylogenetically distinct from P. inui. These macaques are new natural hosts of P. simiovale, a species previously described only in toque monkeys (Macaca sinica) in Sri Lanka. The results suggest that ecological factors could affect the evolution of malaria parasites.

    Matched MeSH terms: Bayes Theorem
  14. Rosli H, Batzer JC, Harrington TC, Gleason ML
    Mycologia, 2018 09 21;110(5):822-834.
    PMID: 30240341 DOI: 10.1080/00275514.2018.1486679
    Sooty blotch and flyspeck (SBFS) fungi infect the cuticle of fruit, including apple fruit, and produce pigmented colonies. A new member of this fungal complex in the genus Peltaster is described on the basis of molecular and morphological evidence. The SBFS complex is a diverse group of ectophytic fungi that reside primarily within the order Capnodiales. Sooty blotch and flyspeck isolates from apple orchards in the central United States were subjected to parsimony and Bayesian analyses based on the internal transcribed spacer regions of nuc rDNA, the partial translation elongation factor 1-α gene, and the partial mitochondrial small subunit rRNA gene. Phylogenetic analysis delineated a new species, Peltaster gemmifer, from P. cerophilus and P. fructicola. Peltaster gemmifer conidiophores bear primary conidia that produce secondary conidia either through budding or through microcyclic conidiation; these were not seen in cultures of P. cerophilus and P. fructicola. On cellulose membrane that was placed on water agar amended with apple juice, P. gemmifer produced brown to black pycnothyria in a superficial brownish mycelial mat, similar to the colonies produced on apple fruit. Findings from the present study add to the >80 named and putative SBFS species so far described worldwide.
    Matched MeSH terms: Bayes Theorem
  15. Saini S, Thakur CJ, Kumar V, Tandon S, Bhardwaj V, Maggar S, et al.
    Mol Biol Res Commun, 2018 Sep;7(3):107-118.
    PMID: 30426028 DOI: 10.22099/mbrc.2018.29577.1322
    Current re-emergence of Nipah virus (NiV) in India caused 11 deaths so far and many patients were kept in quarantine. A thorough study of previous outbreaks occurred in Malaysia, Bangladesh and India represents cases with high rate of fatality due to acute encephalitis. Our work involves genome analysis of NiV for prediction of miRNAs and their targeted genes in human in order to understand encephalitis origin. Ab-intio program-VMir was used for initial screening of genome, obtained nine pre-miRNAs was analyzed by ViralMir to check for any pseudo pre-miRNAs. Eighteen functional mature miRNAs were extracted from pre-miRNAs by using Mature-Bayes tool, which targets 669 genes in human genome as retrieved by miRDB. Gene ontology terms by PANTHER provide important pathways in which target genes were involved like Axon guidance, T cell activation, and nicotinic acetylcholine receptor signaling. Significant outcome was obtained after NCBI Gene and OMIM database mining and literature search for predicted target genes. TLR3, TJP1, NOTCH2, FHL1, and GRIA3 target genes obtained showed their involvement in host defense, blood brain barrier, neurogenesis, mental retardation and encephalitis. To conclude, we predicted significant genes in human that can be inhibited by miRNAs of NiV and results in etiology of encephalitis.
    Matched MeSH terms: Bayes Theorem
  16. Ng CH, Lee SL, Tnah LH, Ng KKS, Lee CT, Diway B, et al.
    J Hered, 2019 12 17;110(7):844-856.
    PMID: 31554011 DOI: 10.1093/jhered/esz052
    Southeast Asian rainforests at upper hill elevations are increasingly vulnerable to degradation because most lowland forest areas have been converted to different land uses. As such, understanding the genetics of upper hill species is becoming more crucial for their future management and conservation. Shorea platyclados is an important, widespread upper hill dipterocarp in Malaysia. To elucidate the genetic structure of S. platyclados and ultimately provide guidelines for a conservation strategy for this species, we carried out a comprehensive study of the genetic diversity and demographic history of S. platyclados. Twenty-seven populations of S. platyclados across its range in Malaysia were genotyped at 15 polymorphic microsatellite loci and sequenced at seven noncoding chloroplast DNA (cpDNA) regions. A total of 303 alleles were derived from the microsatellite loci, and 29 haplotypes were identified based on 2892 bp of concatenated cpDNA sequences. The populations showed moderately high genetic diversity (mean HE = 0.680 for microsatellite gene diversity and HT = 0.650 for total haplotype diversity) and low genetic differentiation (FST = 0.060). Bayesian clustering divided the studied populations into two groups corresponding to western and eastern Malaysia. Bottleneck analysis did not detect any recent bottleneck events. Extended Bayesian skyline analyses showed a model of constant size for the past population history of this species. Based on our findings, priority areas for in situ and ex situ conservation and a minimum population size are recommended for the sustainable utilization of S. platyclados.
    Matched MeSH terms: Bayes Theorem
  17. Wilcox JS, Kerschner A, Hollocher H
    Infect Genet Evol, 2019 11;75:103994.
    PMID: 31421245 DOI: 10.1016/j.meegid.2019.103994
    Plasmodium knowlesi is an important causative agent of malaria in humans of Southeast Asia. Macaques are natural hosts for this parasite, but little is conclusively known about its patterns of transmission within and between these hosts. Here, we apply a comprehensive phylogenetic approach to test for patterns of cryptic population genetic structure between P. knowlesi isolated from humans and long-tailed macaques from the state of Sarawak in Malaysian Borneo. Our approach differs from previous investigations through our exhaustive use of archival 18S Small Subunit rRNA (18S) gene sequences from Plasmodium and Hepatocystis species, our inclusion of insertion and deletion information during phylogenetic inference, and our application of Bayesian phylogenetic inference to this problem. We report distinct clades of P. knowlesi that predominantly contained sequences from either human or macaque hosts for paralogous A-type and S-type 18S gene loci. We report significant partitioning of sequence distances between host species across both types of loci, and confirmed that sequences of the same locus type showed significantly biased assortment into different clades depending on their host species. Our results support the zoonotic potential of Plasmodium knowlesi, but also suggest that humans may be preferentially infected with certain strains of this parasite. Broadly, such patterns could arise through preferential zoonotic transmission of some parasite lineages or a disposition of parasites to transmit within, rather than between, human and macaque hosts. Available data are insufficient to address these hypotheses. Our results suggest that the epidemiology of P. knowlesi may be more complicated than previously assumed, and highlight the need for renewed and more vigorous explorations of transmission patterns in the fifth human malarial parasite.
    Matched MeSH terms: Bayes Theorem
  18. Tilker A, Abrams JF, Mohamed A, Nguyen A, Wong ST, Sollmann R, et al.
    Commun Biol, 2019;2:396.
    PMID: 31701025 DOI: 10.1038/s42003-019-0640-y
    Habitat degradation and hunting have caused the widespread loss of larger vertebrate species (defaunation) from tropical biodiversity hotspots. However, these defaunation drivers impact vertebrate biodiversity in different ways and, therefore, require different conservation interventions. We conducted landscape-scale camera-trap surveys across six study sites in Southeast Asia to assess how moderate degradation and intensive, indiscriminate hunting differentially impact tropical terrestrial mammals and birds. We found that functional extinction rates were higher in hunted compared to degraded sites. Species found in both sites had lower occupancies in the hunted sites. Canopy closure was the main predictor of occurrence in the degraded sites, while village density primarily influenced occurrence in the hunted sites. Our findings suggest that intensive, indiscriminate hunting may be a more immediate threat than moderate habitat degradation for tropical faunal communities, and that conservation stakeholders should focus as much on overhunting as on habitat conservation to address the defaunation crisis.
    Matched MeSH terms: Bayes Theorem
  19. Jatoi MA, Kamel N, Musavi SHA, López JD
    Curr Med Imaging Rev, 2019;15(2):184-193.
    PMID: 31975664 DOI: 10.2174/1573405613666170629112918
    BACKGROUND: Electrical signals are generated inside human brain due to any mental or physical task. This causes activation of several sources inside brain which are localized using various optimization algorithms.

    METHODS: Such activity is recorded through various neuroimaging techniques like fMRI, EEG, MEG etc. EEG signals based localization is termed as EEG source localization. The source localization problem is defined by two complementary problems; the forward problem and the inverse problem. The forward problem involves the modeling how the electromagnetic sources cause measurement in sensor space, while the inverse problem refers to the estimation of the sources (causes) from observed data (consequences). Usually, this inverse problem is ill-posed. In other words, there are many solutions to the inverse problem that explains the same data. This ill-posed problem can be finessed by using prior information within a Bayesian framework. This research work discusses source reconstruction for EEG data using a Bayesian framework. In particular, MSP, LORETA and MNE are compared.

    RESULTS: The results are compared in terms of variational free energy approximation to model evidence and in terms of variance accounted for in the sensor space. The results are taken for real time EEG data and synthetically generated EEG data at an SNR level of 10dB.

    CONCLUSION: In brief, it was seen that MSP has the highest evidence and lowest localization error when compared to classical models. Furthermore, the plausibility and consistency of the source reconstruction speaks to the ability of MSP technique to localize active brain sources.

    Matched MeSH terms: Bayes Theorem
  20. Suhana O, Nazni WA, Apandi Y, Farah H, Lee HL, Sofian-Azirun M
    Heliyon, 2019 Dec;5(12):e02682.
    PMID: 31867449 DOI: 10.1016/j.heliyon.2019.e02682
    Chikungunya virus (CHIKV) is maintained in the sylvatic cycle in West Africa and is transmitted by Aedes mosquito species to monkeys. In 2006, four verified CHIKV isolates were obtained during a survey of arboviruses in monkeys (Macaca fascicularis) in Pahang state, Peninsular Malaysia. RNA was extracted from the CHIKV isolates and used in reverse transcription polymerase chain reactions (RT-PCR) to amplify PCR fragments for sequencing. Nucleic acid primers were designed to generate overlapping PCR fragments that covered the whole viral sequence. A total of 11,238 base pairs (bp) corresponding to open reading frames (ORFs) from our isolates and 47 other registered isolates in the National Center for Biotechnology Information (NCBI) were used to elucidate sequences, amino acids, and phylogenetic relationships and to estimate divergence times by using MEGA 7.0 and the Bayesian Markov chain Monte Carlo method. Phylogenetic analysis revealed that all CHIKV isolates could be classified into the Asian genotype and clustered with Bagan Panchor clades, which are associated with the chikungunya outbreak reported in 2006, with sequence and amino acid similarities of 99.9% and 99.7%, respectively. Minor amino acid differences were found between human and non-human primate isolates. Amino acid analysis showed a unique amino acid at position 221 in the nsP1region, at which a glycine (G) was found only in monkey isolates, whereas arginine (R) was found at the same position only in human isolates. The time to the most recent common ancestor (MRCA) estimation indicated that CHIKV probably started to diverge from human to non-human primates in approximately 2004 in Malaysia. The results suggested that CHIKV in non-human primates probably resulted from the spillover of the virus from humans. The study will be helpful in understanding the movement and evolution of CHIKV in Malaysia and globally.
    Matched MeSH terms: Bayes Theorem
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