A two step Bayesian approach for genomic prediction of breeding values

<p>Abstract</p> <p>Background</p> <p>In genomic models that assign an individual variance to each marker, the contribution of one marker to the posterior distribution of the marker variance is only one degree of freedom (df), which introduces many variance parameters with only little information per variance parameter. A better alternative could be to form clusters of markers with similar effects where markers in a cluster have a common variance. Therefore, the influence of each marker group of size <it>p </it>on the posterior distribution of the marker variances will be <it>p </it>df.</p> <p>Methods</p> <p>The simulated data from the 15^thQTL-MAS workshop were analyzed such that SNP markers were ranked based on their effects and markers with similar estimated effects were grouped together. In step 1, all markers with minor allele frequency more than 0.01 were included in a SNP-BLUP prediction model. In step 2, markers were ranked based on their estimated variance on the trait in step 1 and each 150 markers were assigned to one group with a common variance. In further analyses, subsets of 1500 and 450 markers with largest effects in step 2 were kept in the prediction model.</p> <p>Results</p> <p>Grouping markers outperformed SNP-BLUP model in terms of accuracy of predicted breeding values. However, the accuracies of predicted breeding values were lower than Bayesian methods with marker specific variances.</p> <p>Conclusions</p> <p>Grouping markers is less flexible than allowing each marker to have a specific marker variance but, by grouping, the power to estimate marker variances increases. A prior knowledge of the genetic architecture of the trait is necessary for clustering markers and appropriate prior parameterization.</p

Predicting collective behaviour at the Hajj: place, space, and the process of cooperation

Around 2 million pilgrims attend the annual Hajj to Mecca and the holy places, which are subject to dense crowding. Both architecture and psychology can be part of disaster risk reduction in relation to crowding, since both can affect the nature of collective behaviour – particularly cooperation – among pilgrims. To date, collective behaviour at the Hajj has not been systematically investigated from a psychological perspective. We examined determinants of cooperation in the Grand Mosque and plaza during the pilgrimage. A questionnaire survey of 1194 pilgrims found that the Mosque was perceived by pilgrims as one of the most crowded ritual locations. Being in the plaza (compared to the Mosque) predicted the extent of cooperation, though crowd density did not. Shared social identity with the crowd explained more of the variance than both location and density. We examined some of the process underlying cooperation. The link between shared social identity and giving support to others was stronger in the plaza than in the Mosque, and suggests the role of place and space in modulating processes of cooperation in crowds. These findings have implications for disaster risk reduction and for applications such as computer simulations of crowds in pilgrimage locations

A case report of Tuberculosis and Nocardiosis in a patient with SLE

Abstract: Nocardiosis is a rare infection that is more frequent in patients with Systemic Lupus Erythematosus and its clinical manifestations are nonspecific. While concurrent treatment by corticosteroids is an independent risk factor for nocardiosis it increases both diagnostic and management problems. This article presents a 35 years old woman who has Systemic Lupus Erythematosus. She was hospitalized due to pneumonia. The patient was determined to have tuberculosis and nocardiosis simultaneously. Keywords: Nocardiosis, Tuberculosis, Systemic lupus erythematosu

Protective effect of Hydroalcoholic Extract of Nasturtium Officinalis Against Carbon Tetrachloride-Induced Liver Damage in Rats

Abstract: Background and aim: Leaves and flowers of Nasturtium officinalis L. contain flavonoid compounds. This plant has several characteristics, such as anticancer properties, blood suger insucer and blood lipids. In the present study, the protective effect of hydroalcoholic extract of grasses in liver toxicity induced by carbon tetrachloride in Wistar rats was investigated. &nbsp; Methods: In this research, 32 male Wistar rats were randomly allocated into four equal groups of&nbsp; control (received olive Oil), positive control (received olive Oil + CCl4), and four groups as treatment 1 and 2 received olive oil intraperitoneal administration and 250, 500mg/kg body weight hydroalcoholic extract Nastartium officinals respectively. Animals were treated orally by gavage daily for 32 days. At the end of experiment, serum levels of aspartate and alanine transferase, alkaline phosphatase and total proteins were assessed. The Data was analyzed with using of one-way ANOVA, followed by Tukey's HSD tests using SPSS 21. &nbsp; Results: The mean of ALT, AST, ALP reduced and total protein increased significantly in the in the fourth group compared to the second group (P<0.05). Histological investigation demonstrated that necrosis and inflammation of liver reduced following carbon tetrachloride (CCl4)-induced hepatotoxicity. &nbsp; Conclusion: Hydroalcoholic extract of Nasturtium officinal's can protect liver cells against toxic oxidative damage caused by carbon tetrachloride. &nbsp; &nbsp

N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration

Background: Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that modulates the epithelial-to-mesenchymal transition, facilitates cell migration, and increases colorectal cancer invasion. Results: We performed multivariate analyses of data from two independent cohorts of colorectal cancer patients and show that the abundance of N-BLR is associated with tumor stage, invasion potential, and overall patient survival. Through in vitro and in vivo experiments we found that N-BLR facilitates migration primarily via crosstalk with E-cadherin and ZEB1. We showed that this crosstalk is mediated by a pyknon, a short ~20 nucleotide-long DNA motif contained in the N-BLR transcript and is targeted by members of the miR-200 family. In light of these findings, we used a microarray to investigate the expression patterns of other pyknon-containing genomic loci. We found multiple such loci that are differentially transcribed between healthy and diseased tissues in colorectal cancer and chronic lymphocytic leukemia. Moreover, we identified several new loci whose expression correlates with the colorectal cancer patients’ overall survival. Conclusions: The primate-specific N-BLR is a novel molecular contributor to the complex mechanisms that underlie metastasis in colorectal cancer and a potential novel biomarker for this disease. The presence of a functional pyknon within N-BLR and the related finding that many more pyknon-containing genomic loci in the human genome exhibit tissue-specific and disease-specific expression suggests the possibility of an alternative class of biomarkers and therapeutic targets that are primate-specifi