Power analysis and sample size estimation for RNA-Seq differential expression

It is crucial for researchers to optimize RNA-seq experimental designs for differential expression detection. Currently, the field lacks general methods to estimate power and sample size for RNA-Seq in complex experimental designs, under the assumption of the negative binomial distribution. We simulate RNA-Seq count data based on parameters estimated from six widely different public data sets (including cell line comparison, tissue comparison, and cancer data sets) and calculate the statistical power in paired and unpaired sample experiments. We comprehensively compare five differential expression analysis packages (DESeq, edgeR, DESeq2, sSeq, and EBSeq) and evaluate their performance by power, receiver operator characteristic (ROC) curves, and other metrics including areas under the curve (AUC), Matthews correlation coefficient (MCC), and F-measures. DESeq2 and edgeR tend to give the best performance in general. Increasing sample size or sequencing depth increases power; however, increasing sample size is more potent than sequencing depth to increase power, especially when the sequencing depth reaches 20 million reads. Long intergenic noncoding RNAs (lincRNA) yields lower power relative to the protein coding mRNAs, given their lower expression level in the same RNA-Seq experiment. On the other hand, paired-sample RNA-Seq significantly enhances the statistical power, confirming the importance of considering the multifactor experimental design. Finally, a local optimal power is achievable for a given budget constraint, and the dominant contributing factor is sample size rather than the sequencing depth. In conclusion, we provide a power analysis tool (http://www2.hawaii.edu/~lgarmire/RNASeqPowerCalculator.htm) that captures the dispersion in the data and can serve as a practical reference under the budget constraint of RNA-Seq experiments.     

Leukemic histiocytic sarcoma in a captive common squirrel monkey (Saimiri sciureus) with Saimiriine Gammaherpesvirus 2 (Rhadinovirus), Saimiri sciureus lymphocryptovirus 2 (Lymphocryptovirus) and Squirrel monkey retrovirus (β-Retrovirus) coinfection

Hematopoietic neoplasia other than lymphoma and leukemia is uncommon among non-human primates. Herein, we provide the first evidence of occurrence of leukemic histiocytic sarcoma in a captive common squirrel monkey with Saimiriine Gammaherpesvirus 2 (Rhadinovirus), Saimiri sciureus lymphocryptovirus 2 (Lymphocryptovirus), and Squirrel monkey retrovirus (β-Retrovirus) coinfection.     

Cystitis cystica and recurrent urinary tract infections in children

The pathogenesis of recurrent urinary tract infections (UTIs) in preschool children with anatomically correct urinary tract (UT) is rather obscure. In girls, the bladder wall changes of cystitis cystica (CC) may be per se responsible for UTIs recurrence. During the 20-year period, 127 preschool children (125 girls; median age: 6.1 years) with CC, in whom UT anomalies were excluded, were diagnosed. The mean duration of UTIs symptoms prior to diagnosis was 3.31 +/- 2.51 years. Cystoscopical findings were labelled as mild, moderate and severe in 22.8%, 39.4% and 37.8% of patients, respectively. Following the confirmation of CC, long-term chemoprophylaxis with sulfamethoxazole-trimethoprim/nitrofurantoin was administered. A one year UTI-free period after chemoprophylaxis discontinuation was defined as therapeutic success. With 2.5 years median duration of regular chemoprophylaxis this goal was achieved in 58 children mainly with mild/ moderate CC. Thirty children from "improved/unchanged" group taking regular prophylaxis had significant reduction of UTIs ("improved"). Only 12 children belonging to the same group taking regular prophylaxis and all children with irregular prophylaxis had approximately the same number of UTIs as before treatment ("unchanged"). The "improved/unchanged" outcomes were predominantly found in children with severe form of CC. Although urodynamic disturbances detected in more than 50% of patients in whom urodynamics was performed were not found influential on the disease outcome, they could be responsible for its development. The results of our study suggest that regular and long-lasting chemoprophylaxis remains a basis for successful treatment for majority of patients with CC, even those with severe forms. If not treated properly with chemoprophylactic agents and without fair compliance in taking drugs, the disease is prone to recurrent UTIs.     

Cytokine release and expression induced by OmpA proteins from the Gram-negative anaerobes, Porphyromonas asaccharolytica and Bacteroides fragilis

OmpA proteins from Gram-negative anaerobes Porphyromonas asaccharolytica and Bacteroides fragilis induced release and expression of IL-1alpha, tumor necrosis factor (TNF)-alpha, IFN-gamma, IL-6, and IL-10 from murine splenocytes in vitro in a dose-dependent fashion. The release of the cytokines induced by B. fragilis Bf-OmpA was at much lower levels compared with P. asaccharolytica Omp-PA; Bf-OmpA did not induce release of IL-10. Omp-PA and Bf-OmpA were able to upregulate mRNA expression of the tested cytokines. The results obtained with refolded Bf-OmpA were similar to those with native Bf-OmpA. The data presented in this research demonstrate for the first time that Omps from anaerobic bacteria can induce the release of cytokines, suggesting that Omp-PA and Bf-OmpA may play important roles in the pathogenic processes of these bacteria.     

Tropical Bacillus Strains Inoculation Enhances Maize Root Surface Area,Dry Weight,Nutrient Uptake and Grain Yield

Journal of Plant Growth Regulation - The rising demand for agricultural commodities in developing countries has put increasing pressure on land resources for higher yields, with associated growth...