Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives

By reproducing differential expression analysis simulation results presented by Li et al , we identified a caveat in the data generation process. Data not truly generated under the null hypothesis led to incorrect comparisons of benchmark methods. We provide corrected simulation results that demonstrate the good performance of dearseq and argue against the superiority of the Wilcoxon rank-sum test as suggested by Li et al . Please see related Research article with DOI 10.1186/s13059-022-02648-4

Optimization of cristal violet adsorption by calcium silicate waste material

In this study, calcium silicate waste material was used as adsorbent of crystal violet in batch mode. The calcium silicate was synthesised from fluosilicic acid (FSA), which is a by-product of phosphoric acid manufacture. The obtained calcium silicate was characterised by X-ray fluorescence spectroscopy. The response surfaces, through the Box-Behnken model were used to model and optimize various adsorption parameters namely, the initial concentration of CV (A: 10–100 mg/L), the contact time (B: 5–50 min), the dose of adsorbent (C: 1–5 g/L) and the pH (D: 3–10). The removal efficiency of CV (97.86%), after statistical analysis, was obtained under the following optimal conditions: an adsorbent dose of 3.349 g/L, an initial CV concentration of 58 mg/L, a pH of 6.87 and a contact time of 30.49 min. The study of the four factors effects highlighted a positive effect on the removal of crystal violet. The interactions between adsorption time (B) and pH (D) and between adsorbent dose (C) and pH (D) were significantly important. However, an intermediate situation was noticed in the case of the interaction between adsorbent dose (C) and crystal violet concentration (A), where the lines cannot be considered parallel but do not cross each other in the analysed area either. The analysis of the residues showed that they are normally distributed and fluctuate in a random pattern. The adsorption kinetics were well described by the pseudo second order model and the equilibrium data were in agreement with the Langmuir isotherm model with a maximum adsorption capacity of 277.78 mg/g

Modelling and Optimizing the Removal of Methylene Blue by a Mixture of Titaniferous Sand and Attapulgite Using Complete Factorial Design

This paper focuses on the removal of methylene blue by adsorption using a mixture of titaniferous sand and attapulgite. The different adsorbents were characterized by X-ray fluorescence spectroscopy and their different parameters such as pH, zero charge potential, and specific surface area were determined. The experiments performed were optimized and modeled by a full 2-level and 4-factor design. The four factors are the ratio of titaniferous sand and attapulgite, the concentration of methylene blue, pH, and time. These vary from 4 to 19, 20 to 100 mg/L, 2 to 9, and 30 to 150 min respectively. The study of the effects of the different factors showed that the effect of methylene blue concentration and pH significantly influence the adsorption capacity and removal efficiency of the dye. The optimum parameters (adsorbent ratio, adsorbate concentration, pH and time) obtained for the adsorption capacity through the desirability function are: 19, 100mg/L, 9 and 150min. Those obtained for the yield are: 4, 100mg/L, 9, 150min. The pseudo second order adsorption kinetics gave an equilibrium adsorption capacity qe (calculated) = 7.6863 mg/g which is almost equal to that obtained experimentally qe (exp) = 7.3562 mg/g. This shows that the pseudo second order kinetic model is the adequate mathematical model to describe the methylene blue adsorption phenomenon on the mixture of titaniferous sand and attapulgite. The thermodynamic study showed that the methylene blue adsorption reaction is exothermic, non-spontaneous, and the degree of disorder of the particles at the adsorbing surface decreases