Displaying publications 221 - 240 of 264 in total

Abstract:
Sort:
  1. 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
  2. Salarzadeh Jenatabadi H, Bt Wan Mohamed Radzi CWJ, Samsudin N
    PMID: 32708480 DOI: 10.3390/ijerph17145201
    As postpartum obesity is becoming a global public health challenge, there is a need to apply postpartum obesity modeling to determine the indicators of postpartum obesity using an appropriate statistical technique. This research comprised two phases, namely: (i) development of a previously created postpartum obesity modeling; (ii) construction of a statistical comparison model and introduction of a better estimator for the research framework. The research model displayed the associations and interactions between the variables that were analyzed using the Structural Equation Modeling (SEM) method to determine the body mass index (BMI) levels related to postpartum obesity. The most significant correlations obtained were between BMI and other substantial variables in the SEM analysis. The research framework included two categories of data related to postpartum women: living in urban and rural areas in Iran. The SEM output with the Bayesian estimator was 81.1%, with variations in the postpartum women's BMI, which is related to their demographics, lifestyle, food intake, and mental health. Meanwhile, the variation based on SEM with partial least squares estimator was equal to 70.2%, and SEM with a maximum likelihood estimator was equal to 76.8%. On the other hand, the output of the root mean square error (RMSE), mean absolute error (MSE) and mean absolute percentage error (MPE) for the Bayesian estimator is lower than the maximum likelihood and partial least square estimators. Thus, the predicted values of the SEM with Bayesian estimator are closer to the observed value compared to maximum likelihood and partial least square. In conclusion, the higher values of R-square and lower values of MPE, RMSE, and MSE will produce better goodness of fit for SEM with Bayesian estimators.
    Matched MeSH terms: Bayes Theorem
  3. 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
  4. Ferdowsi M, Kwan BH, Tan MP, Saedon NI, Subramaniam S, Abu Hashim NFI, et al.
    Biomed Eng Online, 2024 Mar 30;23(1):37.
    PMID: 38555421 DOI: 10.1186/s12938-024-01229-9
    BACKGROUND: The diagnostic test for vasovagal syncope (VVS), the most common cause of syncope is head-up tilt test (HUTT) assessment. During the test, subjects experienced clinical symptoms such as nausea, sweating, pallor, the feeling of palpitations, being on the verge of passing out, and fainting. The study's goal is to develop an algorithm to classify VVS patients based on physiological signals blood pressure (BP) and electrocardiography (ECG) obtained from the HUTT.

    METHODS: After 10 min of supine rest, the subject was tilted at a 70-degree angle on a tilt table for approximately a total of 35 min. 400 µg of glyceryl trinitrate (GTN) was administered sublingually after the first 20 min and monitoring continued for another 15 min. Mean imputation and K-nearest neighbors (KNN) imputation approaches to handle missing values. Next, feature selection techniques were implemented, including genetic algorithm, recursive feature elimination, and feature importance, to determine the crucial features. The Mann-Whitney U test was then performed to determine the statistical difference between two groups. Patients with VVS are categorized via machine learning models including Support Vector Machine (SVM), Gaussian Naïve Bayes (GNB), Multinomial Naïve Bayes (MNB), KNN, Logistic Regression (LR), and Random Forest (RF). The developed model is interpreted using an explainable artificial intelligence (XAI) model known as partial dependence plot.

    RESULTS: A total of 137 subjects aged between 9 and 93 years were recruited for this study, 54 experienced clinical symptoms were considered positive tests, while the remaining 83 tested negative. Optimal results were obtained by combining the KNN imputation technique and three tilting features with SVM with 90.5% accuracy, 87.0% sensitivity, 92.7% specificity, 88.6% precision, 87.8% F1 score, and 95.4% ROC (receiver operating characteristics) AUC (area under curve).

    CONCLUSIONS: The proposed algorithm effectively classifies VVS patients with over 90% accuracy. However, the study was confined to a small sample size. More clinical datasets are required to ensure that our approach is generalizable.

    Matched MeSH terms: Bayes Theorem
  5. NCD Risk Factor Collaboration (NCD-RisC)
    Lancet, 2020 Nov 07;396(10261):1511-1524.
    PMID: 33160572 DOI: 10.1016/S0140-6736(20)31859-6
    BACKGROUND: Comparable global data on health and nutrition of school-aged children and adolescents are scarce. We aimed to estimate age trajectories and time trends in mean height and mean body-mass index (BMI), which measures weight gain beyond what is expected from height gain, for school-aged children and adolescents.

    METHODS: For this pooled analysis, we used a database of cardiometabolic risk factors collated by the Non-Communicable Disease Risk Factor Collaboration. We applied a Bayesian hierarchical model to estimate trends from 1985 to 2019 in mean height and mean BMI in 1-year age groups for ages 5-19 years. The model allowed for non-linear changes over time in mean height and mean BMI and for non-linear changes with age of children and adolescents, including periods of rapid growth during adolescence.

    FINDINGS: We pooled data from 2181 population-based studies, with measurements of height and weight in 65 million participants in 200 countries and territories. In 2019, we estimated a difference of 20 cm or higher in mean height of 19-year-old adolescents between countries with the tallest populations (the Netherlands, Montenegro, Estonia, and Bosnia and Herzegovina for boys; and the Netherlands, Montenegro, Denmark, and Iceland for girls) and those with the shortest populations (Timor-Leste, Laos, Solomon Islands, and Papua New Guinea for boys; and Guatemala, Bangladesh, Nepal, and Timor-Leste for girls). In the same year, the difference between the highest mean BMI (in Pacific island countries, Kuwait, Bahrain, The Bahamas, Chile, the USA, and New Zealand for both boys and girls and in South Africa for girls) and lowest mean BMI (in India, Bangladesh, Timor-Leste, Ethiopia, and Chad for boys and girls; and in Japan and Romania for girls) was approximately 9-10 kg/m2. In some countries, children aged 5 years started with healthier height or BMI than the global median and, in some cases, as healthy as the best performing countries, but they became progressively less healthy compared with their comparators as they grew older by not growing as tall (eg, boys in Austria and Barbados, and girls in Belgium and Puerto Rico) or gaining too much weight for their height (eg, girls and boys in Kuwait, Bahrain, Fiji, Jamaica, and Mexico; and girls in South Africa and New Zealand). In other countries, growing children overtook the height of their comparators (eg, Latvia, Czech Republic, Morocco, and Iran) or curbed their weight gain (eg, Italy, France, and Croatia) in late childhood and adolescence. When changes in both height and BMI were considered, girls in South Korea, Vietnam, Saudi Arabia, Turkey, and some central Asian countries (eg, Armenia and Azerbaijan), and boys in central and western Europe (eg, Portugal, Denmark, Poland, and Montenegro) had the healthiest changes in anthropometric status over the past 3·5 decades because, compared with children and adolescents in other countries, they had a much larger gain in height than they did in BMI. The unhealthiest changes-gaining too little height, too much weight for their height compared with children in other countries, or both-occurred in many countries in sub-Saharan Africa, New Zealand, and the USA for boys and girls; in Malaysia and some Pacific island nations for boys; and in Mexico for girls.

    INTERPRETATION: The height and BMI trajectories over age and time of school-aged children and adolescents are highly variable across countries, which indicates heterogeneous nutritional quality and lifelong health advantages and risks.

    FUNDING: Wellcome Trust, AstraZeneca Young Health Programme, EU.

    Matched MeSH terms: Bayes Theorem
  6. Moretti B, Al-Sheikhly OF, Guerrini M, Theng M, Gupta BK, Haba MK, et al.
    Sci Rep, 2017 Jan 27;7:41611.
    PMID: 28128366 DOI: 10.1038/srep41611
    We investigated the phylogeography of the smooth-coated otter (Lutrogale perspicillata) to determine its spatial genetic structure for aiding an adaptive conservation management of the species. Fifty-eight modern and 11 archival (dated 1882-1970) otters sampled from Iraq to Malaysian Borneo were genotyped (mtDNA Cytochrome-b, 10 microsatellite DNA loci). Moreover, 16 Aonyx cinereus (Asian small-clawed otter) and seven Lutra lutra (Eurasian otter) were sequenced to increase information available for phylogenetic reconstructions. As reported in previous studies, we found that L. perspicillata, A. cinereus and A. capensis (African clawless otter) grouped in a clade sister to the genus Lutra, with L. perspicillata and A. cinereus being reciprocally monophyletic. Within L. perspicillata, we uncovered three Evolutionarily Significant Units and proved that L. p. maxwelli is not only endemic to Iraq but also the most recent subspecies. We suggest a revision of the distribution range limits of easternmost L. perspicillata subspecies. We show that smooth-coated otters in Singapore are L. perspicillata x A. cinereus hybrids with A. cinereus mtDNA, the first reported case of hybridization in the wild among otters. This result also provides evidence supporting the inclusion of L. perspicillata and A. cinereus in the genus Amblonyx, thus avoiding the paraphyly of the genus Aonyx.
    Matched MeSH terms: Bayes Theorem
  7. Too CW, Fong KY, Hang G, Sato T, Nyam CQ, Leong SH, et al.
    J Vasc Interv Radiol, 2024 May;35(5):780-789.e1.
    PMID: 38355040 DOI: 10.1016/j.jvir.2024.02.006
    PURPOSE: To validate the sensitivity and specificity of a 3-dimensional (3D) convolutional neural network (CNN) artificial intelligence (AI) software for lung lesion detection and to establish concordance between AI-generated needle paths and those used in actual biopsy procedures.

    MATERIALS AND METHODS: This was a retrospective study using computed tomography (CT) scans from 3 hospitals. Inclusion criteria were scans with 1-5 nodules of diameter ≥5 mm; exclusion criteria were poor-quality scans or those with nodules measuring <5mm in diameter. In the lesion detection phase, 2,147 nodules from 219 scans were used to develop and train the deep learning 3D-CNN to detect lesions. The 3D-CNN was validated with 235 scans (354 lesions) for sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) analysis. In the path planning phase, Bayesian optimization was used to propose possible needle trajectories for lesion biopsy while avoiding vital structures. Software-proposed needle trajectories were compared with actual biopsy path trajectories from intraprocedural CT scans in 150 patients, with a match defined as an angular deviation of <5° between the 2 trajectories.

    RESULTS: The model achieved an overall AUC of 97.4% (95% CI, 96.3%-98.2%) for lesion detection, with mean sensitivity of 93.5% and mean specificity of 93.2%. Among the software-proposed needle trajectories, 85.3% were feasible, with 82% matching actual paths and similar performance between supine and prone/oblique patient orientations (P = .311). The mean angular deviation between matching trajectories was 2.30° (SD ± 1.22); the mean path deviation was 2.94 mm (SD ± 1.60).

    CONCLUSIONS: Segmentation, lesion detection, and path planning for CT-guided lung biopsy using an AI-guided software showed promising results. Future integration with automated robotic systems may pave the way toward fully automated biopsy procedures.

    Matched MeSH terms: Bayes Theorem
  8. Ferdowsi M, Hasan MM, Habib W
    Comput Methods Programs Biomed, 2024 Sep;254:108289.
    PMID: 38905988 DOI: 10.1016/j.cmpb.2024.108289
    BACKGROUND AND OBJECTIVE: Cardiovascular disease (CD) is a major global health concern, affecting millions with symptoms like fatigue and chest discomfort. Timely identification is crucial due to its significant contribution to global mortality. In healthcare, artificial intelligence (AI) holds promise for advancing disease risk assessment and treatment outcome prediction. However, machine learning (ML) evolution raises concerns about data privacy and biases, especially in sensitive healthcare applications. The objective is to develop and implement a responsible AI model for CD prediction that prioritize patient privacy, security, ensuring transparency, explainability, fairness, and ethical adherence in healthcare applications.

    METHODS: To predict CD while prioritizing patient privacy, our study employed data anonymization involved adding Laplace noise to sensitive features like age and gender. The anonymized dataset underwent analysis using a differential privacy (DP) framework to preserve data privacy. DP ensured confidentiality while extracting insights. Compared with Logistic Regression (LR), Gaussian Naïve Bayes (GNB), and Random Forest (RF), the methodology integrated feature selection, statistical analysis, and SHapley Additive exPlanations (SHAP) and Local Interpretable Model-agnostic Explanations (LIME) for interpretability. This approach facilitates transparent and interpretable AI decision-making, aligning with responsible AI development principles. Overall, it combines privacy preservation, interpretability, and ethical considerations for accurate CD predictions.

    RESULTS: Our investigations from the DP framework with LR were promising, with an area under curve (AUC) of 0.848 ± 0.03, an accuracy of 0.797 ± 0.02, precision at 0.789 ± 0.02, recall at 0.797 ± 0.02, and an F1 score of 0.787 ± 0.02, with a comparable performance with the non-privacy framework. The SHAP and LIME based results support clinical findings, show a commitment to transparent and interpretable AI decision-making, and aligns with the principles of responsible AI development.

    CONCLUSIONS: Our study endorses a novel approach in predicting CD, amalgamating data anonymization, privacy-preserving methods, interpretability tools SHAP, LIME, and ethical considerations. This responsible AI framework ensures accurate predictions, privacy preservation, and user trust, underscoring the significance of comprehensive and transparent ML models in healthcare. Therefore, this research empowers the ability to forecast CD, providing a vital lifeline to millions of CD patients globally and potentially preventing numerous fatalities.

    Matched MeSH terms: Bayes Theorem
  9. Juhan N, Zubairi YZ, Khalid ZM, Mahmood Zuhdi AS
    Iran J Public Health, 2020 Sep;49(9):1642-1649.
    PMID: 33643938 DOI: 10.18502/ijph.v49i9.4080
    Background: Identifying risk factors associated with mortality is important in providing better prognosis to patients. Consistent with that, Bayesian approach offers a great advantage where it rests on the assumption that all model parameters are random quantities and hence can incorporate prior knowledge. Therefore, we aimed to develop a reliable model to identify risk factors associated with mortality among ST-Elevation Myocardial Infarction (STEMI) male patients using Bayesian approach.

    Methods: A total of 7180 STEMI male patients from the National Cardiovascular Disease Database-Acute Coronary Syndrome (NCVD-ACS) registry for the years 2006-2013 were enrolled. In the development of univariate and multivariate logistic regression model for the STEMI patients, Bayesian Markov Chain Monte Carlo (MCMC) simulation approach was applied. The performance of the model was assessed through convergence diagnostics, overall model fit, model calibration and discrimination.

    Results: A set of six risk factors for cardiovascular death among STEMI male patients were identified from the Bayesian multivariate logistic model namely age, diabetes mellitus, family history of CVD, Killip class, chronic lung disease and renal disease respectively. Overall model fit, model calibration and discrimination were considered good for the proposed model.

    Conclusion: Bayesian risk prediction model for CVD male patients identified six risk factors associated with mortality. Among the highest risks were Killip class (OR=18.0), renal disease (2.46) and age group (OR=2.43) respectively.

    Matched MeSH terms: Bayes Theorem
  10. Matsuda I, Kubo T, Tuuga A, Higashi S
    Am J Phys Anthropol, 2010 Jun;142(2):235-45.
    PMID: 20091847 DOI: 10.1002/ajpa.21218
    To understand the effects of environmental factors on a social system with multilevel society in proboscis monkey units, the temporal change of the local density of sleeping sites of monkeys was investigated along the Menanggul river from May 2005 to 2006 in Malaysia. Proboscis monkeys typically return to riverside trees for night sleeping. The sleeping site locations of a one-male unit (BE-unit) were recorded and the locations of other one-male and all-male units within 500 m of the BE-unit were verified. In addition, environmental factors (food availability, the water level of the river, and the river width) and copulation frequency of BE-unit were recorded. From the analyses of the distance from the BE-unit to the nearest neighbor unit, no spatial clumping of the sleeping sites of monkey units on a smaller scale was detected. The results of a Bayesian analysis suggest that the conditional local density around the BE-unit can be predicted by the spatial heterogeneity along the river and by the temporal change of food availability, that is, the local density of monkey units might increase due to better sleeping sites with regard to predator attacks and clumped food sources; proboscis monkeys might not exhibit high-level social organization previously reported. In addition, this study shows the importance of data analysis that considers the effects of temporal autocorrelation, because the daily measurements of longitudinal data on monkeys are not independent of each other.
    Matched MeSH terms: Bayes Theorem
  11. NCD Risk Factor Collaboration (NCD-RisC)
    Lancet, 2024 Nov 23;404(10467):2077-2093.
    PMID: 39549716 DOI: 10.1016/S0140-6736(24)02317-1
    BACKGROUND: Diabetes can be detected at the primary health-care level, and effective treatments lower the risk of complications. There are insufficient data on the coverage of treatment for diabetes and how it has changed. We estimated trends from 1990 to 2022 in diabetes prevalence and treatment for 200 countries and territories.

    METHODS: We used data from 1108 population-representative studies with 141 million participants aged 18 years and older with measurements of fasting glucose and glycated haemoglobin (HbA1c), and information on diabetes treatment. We defined diabetes as having a fasting plasma glucose (FPG) of 7·0 mmol/L or higher, having an HbA1c of 6·5% or higher, or taking medication for diabetes. We defined diabetes treatment as the proportion of people with diabetes who were taking medication for diabetes. We analysed the data in a Bayesian hierarchical meta-regression model to estimate diabetes prevalence and treatment.

    FINDINGS: In 2022, an estimated 828 million (95% credible interval [CrI] 757-908) adults (those aged 18 years and older) had diabetes, an increase of 630 million (554-713) from 1990. From 1990 to 2022, the age-standardised prevalence of diabetes increased in 131 countries for women and in 155 countries for men with a posterior probability of more than 0·80. The largest increases were in low-income and middle-income countries in southeast Asia (eg, Malaysia), south Asia (eg, Pakistan), the Middle East and north Africa (eg, Egypt), and Latin America and the Caribbean (eg, Jamaica, Trinidad and Tobago, and Costa Rica). Age-standardised prevalence neither increased nor decreased with a posterior probability of more than 0·80 in some countries in western and central Europe, sub-Saharan Africa, east Asia and the Pacific, Canada, and some Pacific island nations where prevalence was already high in 1990; it decreased with a posterior probability of more than 0·80 in women in Japan, Spain, and France, and in men in Nauru. The lowest prevalence in the world in 2022 was in western Europe and east Africa for both sexes, and in Japan and Canada for women, and the highest prevalence in the world in 2022 was in countries in Polynesia and Micronesia, some countries in the Caribbean and the Middle East and north Africa, as well as Pakistan and Malaysia. In 2022, 445 million (95% CrI 401-496) adults aged 30 years or older with diabetes did not receive treatment (59% of adults aged 30 years or older with diabetes), 3·5 times the number in 1990. From 1990 to 2022, diabetes treatment coverage increased in 118 countries for women and 98 countries for men with a posterior probability of more than 0·80. The largest improvement in treatment coverage was in some countries from central and western Europe and Latin America (Mexico, Colombia, Chile, and Costa Rica), Canada, South Korea, Russia, Seychelles, and Jordan. There was no increase in treatment coverage in most countries in sub-Saharan Africa; the Caribbean; Pacific island nations; and south, southeast, and central Asia. In 2022, age-standardised treatment coverage was lowest in countries in sub-Saharan Africa and south Asia, and treatment coverage was less than 10% in some African countries. Treatment coverage was 55% or higher in South Korea, many high-income western countries, and some countries in central and eastern Europe (eg, Poland, Czechia, and Russia), Latin America (eg, Costa Rica, Chile, and Mexico), and the Middle East and north Africa (eg, Jordan, Qatar, and Kuwait).

    INTERPRETATION: In most countries, especially in low-income and middle-income countries, diabetes treatment has not increased at all or has not increased sufficiently in comparison with the rise in prevalence. The burden of diabetes and untreated diabetes is increasingly borne by low-income and middle-income countries. The expansion of health insurance and primary health care should be accompanied with diabetes programmes that realign and resource health services to enhance the early detection and effective treatment of diabetes.

    FUNDING: UK Medical Research Council, UK Research and Innovation (Research England), and US Centers for Disease Control and Prevention.

    Matched MeSH terms: Bayes Theorem
  12. Golestan Hashemi FS, Rafii MY, Ismail MR, Mohamed MT, Rahim HA, Latif MA, et al.
    Gene, 2015 Jan 25;555(2):101-7.
    PMID: 25445269 DOI: 10.1016/j.gene.2014.10.048
    MRQ74, a popular aromatic Malaysian landrace, allows for charging considerably higher prices than non-aromatic landraces. Thus, breeding this profitable trait has become a priority for Malaysian rice breeding. Despite many studies on aroma genetics, ambiguities considering its genetic basis remain. It has been observed that identifying quantitative trait loci (QTLs) based on anchor markers, particularly candidate genes controlling a trait of interest, can increase the power of QTL detection. Hence, this study aimed to locate QTLs that influence natural variations in rice scent using microsatellites and candidate gene-based sequence polymorphisms. For this purpose, an F2 mapping population including 189 individual plants was developed by MRQ74 crosses with 'MR84', a non-scented Malaysian accession. Additionally, qualitative and quantitative approaches were applied to obtain a phenotype data framework. Consequently, we identified two QTLs on chromosomes 4 and 8. These QTLs explained from 3.2% to 39.3% of the total fragrance phenotypic variance. In addition, we could resolve linkage group 8 by adding six gene-based primers in the interval harboring the most robust QTL. Hence, we could locate a putative fgr allele in the QTL found on chromosome 8 in the interval RM223-SCU015RM (1.63cM). The identified QTLs represent an important step toward recognition of the rice flavor genetic control mechanism. In addition, this identification will likely accelerate the progress of the use of molecular markers for gene isolation, gene-based cloning, and marker-assisted selection breeding programs aimed at improving rice cultivars.
    Matched MeSH terms: Bayes Theorem
  13. Alpay F, Zare Y, Kamalludin MH, Huang X, Shi X, Shook GE, et al.
    PLoS One, 2014;9(12):e111704.
    PMID: 25473852 DOI: 10.1371/journal.pone.0111704
    Paratuberculosis, or Johne's disease, is a chronic, granulomatous, gastrointestinal tract disease of cattle and other ruminants caused by the bacterium Mycobacterium avium, subspecies paratuberculosis (MAP). Control of Johne's disease is based on programs of testing and culling animals positive for infection with MAP while concurrently modifying management to reduce the likelihood of infection. The current study is motivated by the hypothesis that genetic variation in host susceptibility to MAP infection can be dissected and quantifiable associations with genetic markers identified. For this purpose, a case-control, genome-wide association study was conducted using US Holstein cattle phenotyped for MAP infection using a serum ELISA and/or fecal culture test. Cases included cows positive for either serum ELISA, fecal culture or both. Controls consisted of animals negative for the serum ELISA test or both serum ELISA and fecal culture when both were available. Controls were matched by herd and proximal birth date with cases. A total of 856 cows (451 cases and 405 controls) were used in initial discovery analyses, and an additional 263 cows (159 cases and 104 controls) from the same herds were used as a validation data set. Data were analyzed in a single marker analysis controlling for relatedness of individuals (GRAMMAR-GC) and also in a Bayesian analysis in which multiple marker effects were estimated simultaneously (GenSel). For the latter, effects of non-overlapping 1 Mb marker windows across the genome were estimated. Results from the two discovery analyses were generally concordant; however, discovery results were generally not well supported in analysis of the validation data set. A combined analysis of discovery and validation data sets provided strongest support for SNPs and 1 Mb windows on chromosomes 1, 2, 6, 7, 17 and 29.
    Matched MeSH terms: Bayes Theorem
  14. Masuda S, Tani N, Ueno S, Lee SL, Muhammad N, Kondo T, et al.
    PLoS One, 2013;8(12):e82039.
    PMID: 24391712 DOI: 10.1371/journal.pone.0082039
    Pollinator syndrome is one of the most important determinants regulating pollen dispersal in tropical tree species. It has been widely accepted that the reproduction of tropical forest species, especially dipterocarps that rely on insects with weak flight for their pollination, is positively density-dependent. However differences in pollinator syndrome should affect pollen dispersal patterns and, consequently, influence genetic diversity via the mating process. We examined the pollen dispersal pattern and mating system of Shorea maxwelliana, the flowers of which are larger than those of Shorea species belonging to section Mutica which are thought to be pollinated by thrips (weak flyers). A Bayesian mating model based on the paternity of seeds collected from mother trees during sporadic and mass flowering events revealed that the estimated pollen dispersal kernel and average pollen dispersal distance were similar for both flowering events. This evidence suggests that the putative pollinators - small beetles and weevils - effectively contribute to pollen dispersal and help to maintain a high outcrossing rate even during sporadic flowering events. However, the reduction in pollen donors during a sporadic event results in a reduction in effective pollen donors, which should lead to lower genetic diversity in the next generation derived from seeds produced during such an event. Although sporadic flowering has been considered less effective for outcrossing in Shorea species that depend on thrips for their pollination, effective pollen dispersal by the small beetles and weevils ensures outcrossing during periods of low flowering tree density, as occurs in a sporadic flowering event.
    Matched MeSH terms: Bayes Theorem
  15. Syed-Shabthar SM, Rosli MK, Mohd-Zin NA, Romaino SM, Fazly-Ann ZA, Mahani MC, et al.
    Mol Biol Rep, 2013 Aug;40(8):5165-76.
    PMID: 23686165 DOI: 10.1007/s11033-013-2619-y
    Bali cattle is a domestic cattle breed that can be found in Malaysia. It is a domestic cattle that was purely derived from a domestication event in Banteng (Bos javanicus) around 3,500 BC in Indonesia. This research was conducted to portray the phylogenetic relationships of the Bali cattle with other cattle species in Malaysia based on maternal and paternal lineage. We analyzed the cytochrome c oxidase I (COI) mitochondrial gene and SRY of Y chromosome obtained from five species of the Bos genus (B. javanicus, Bos gaurus, Bos indicus, Bos taurus, and Bos grunniens). The water buffalo (Bubalus bubalis) was used as an outgroup. The phylogenetic relationships were observed by employing several algorithms: Neighbor-Joining (PAUP version 4.0), Maximum parsimony (PAUP version 4.0) and Bayesian inference (MrBayes 3.1). Results from the maternal data showed that the Bali cattle formed a monophyletic clade, and together with the B. gaurus clade formed a wild cattle clade. Results were supported by high bootstrap and posterior probability values together with genetic distance data. For the paternal lineage, the sequence variation is low (with parsimony informative characters: 2/660) resulting an unresolved Neighbor-Joining tree. However, Bali cattle and other domestic cattle appear in two monophyletic clades distinct from yak, gaur and selembu. This study expresses the potential of the COI gene in portraying the phylogenetic relationships between several Bos species which is important for conservation efforts especially in decision making since cattle is highly bred and hybrid breeds are often formed. Genetic conservation for this high quality beef cattle breed is important by maintaining its genetic characters to prevent extinction or even decreased the genetic quality.
    Matched MeSH terms: Bayes Theorem
  16. Nazri A, Lio P
    PLoS One, 2012;7(1):e28713.
    PMID: 22253694 DOI: 10.1371/journal.pone.0028713
    The output of state-of-the-art reverse-engineering methods for biological networks is often based on the fitting of a mathematical model to the data. Typically, different datasets do not give single consistent network predictions but rather an ensemble of inconsistent networks inferred under the same reverse-engineering method that are only consistent with the specific experimentally measured data. Here, we focus on an alternative approach for combining the information contained within such an ensemble of inconsistent gene networks called meta-analysis, to make more accurate predictions and to estimate the reliability of these predictions. We review two existing meta-analysis approaches; the Fisher transformation combined coefficient test (FTCCT) and Fisher's inverse combined probability test (FICPT); and compare their performance with five well-known methods, ARACNe, Context Likelihood or Relatedness network (CLR), Maximum Relevance Minimum Redundancy (MRNET), Relevance Network (RN) and Bayesian Network (BN). We conducted in-depth numerical ensemble simulations and demonstrated for biological expression data that the meta-analysis approaches consistently outperformed the best gene regulatory network inference (GRNI) methods in the literature. Furthermore, the meta-analysis approaches have a low computational complexity. We conclude that the meta-analysis approaches are a powerful tool for integrating different datasets to give more accurate and reliable predictions for biological networks.
    Matched MeSH terms: Bayes Theorem
  17. 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: Bayes Theorem
  18. Kaur H, Ahmad M, Scaria V
    Interdiscip Sci, 2016 Mar;8(1):95-101.
    PMID: 26298582 DOI: 10.1007/s12539-015-0273-x
    There is emergence of multidrug-resistant Salmonella enterica serotype typhi in pandemic proportions throughout the world, and therefore, there is a necessity to speed up the discovery of novel molecules having different modes of action and also less influenced by the resistance formation that would be used as drug for the treatment of salmonellosis particularly typhoid fever. The PhoP regulon is well studied and has now been shown to be a critical regulator of number of gene expressions which are required for intracellular survival of S. enterica and pathophysiology of disease like typhoid. The evident roles of two-component PhoP-/PhoQ-regulated products in salmonella virulence have motivated attempts to target them therapeutically. Although the discovery process of biologically active compounds for the treatment of typhoid relies on hit-finding procedure, using high-throughput screening technology alone is very expensive, as well as time consuming when performed on large scales. With the recent advancement in combinatorial chemistry and contemporary technique for compounds synthesis, there are more and more compounds available which give ample growth of diverse compound library, but the time and endeavor required to screen these unfocused massive and diverse library have been slightly reduced in the past years. Hence, there is demand to improve the high-quality hits and success rate for high-throughput screening that required focused and biased compound library toward the particular target. Therefore, we still need an advantageous and expedient method to prioritize the molecules that will be utilized for biological screens, which saves time and is also inexpensive. In this concept, in silico methods like machine learning are widely applicable technique used to build computational model for high-throughput virtual screens to prioritize molecules for advance study. Furthermore, in computational analysis, we extended our study to identify the common enriched structural entities among the biologically active compound toward finding out the privileged scaffold.
    Matched MeSH terms: Bayes Theorem
  19. Ng KT, Oong XY, Pang YK, Hanafi NS, Kamarulzaman A, Tee KK
    Emerg Microbes Infect, 2015 Aug;4(8):e47.
    PMID: 26421270 DOI: 10.1038/emi.2015.47
    Matched MeSH terms: Bayes Theorem
  20. Lo Presti A, Cella E, Giovanetti M, Lai A, Angeletti S, Zehender G, et al.
    J Med Virol, 2016 Mar;88(3):380-8.
    PMID: 26252523 DOI: 10.1002/jmv.24345
    Nipah virus, member of the Paramyxoviridae family, is classified as a Biosafety Level-4 agent and category C priority pathogen. Nipah virus disease is endemic in south Asia and outbreaks have been reported in Malaysia, Singapore, India, and Bangladesh. Bats of the genus Pteropus appear to be the natural reservoir of this virus. The aim of this study was to investigate the genetic diversity of Nipah virus, to estimate the date of origin and the spread of the infection. The mean value of Nipah virus N gene evolutionary rate, was 6.5 × 10(-4) substitution/site/year (95% HPD: 2.3 × 10(-4)-1.18 × 10(-3)). The time-scaled phylogenetic analysis showed that the root of the tree originated in 1947 (95% HPD: 1888-1988) as the virus entered in south eastern Asiatic regions. The segregation of sequences in two main clades (I and II) indicating that Nipah virus had two different introductions: one in 1995 (95% HPD: 1985-2002) which correspond to clade I, and the other in 1985 (95% HPD: 1971-1996) which correspond to clade II. The phylogeographic reconstruction indicated that the epidemic followed two different routes spreading to the other locations. The trade of infected pigs may have played a role in the spread of the virus. Bats of the Pteropus genus, that are able to travel to long distances, may have contributed to the spread of the infection. Negatively selected sites, statistically supported, could reflect the stability of the viral N protein.
    Matched MeSH terms: Bayes Theorem
Filters
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links