SEEI: spherical evolution with feedback mechanism for identifying epistatic interactions.

BACKGROUND: Detecting epistatic interactions (EIs) involves the exploration of associations among single nucleotide polymorphisms (SNPs) and complex diseases, which is an important task in genome-wide association studies. The EI detection problem is dependent on epistasis models and corresponding optimization methods. Although various models and methods have been proposed to detect EIs, identifying EIs efficiently and accurately is still a challenge. RESULTS: Here, we propose a linear mixed statistical epistasis model (LMSE) and a spherical evolution approach with a feedback mechanism (named SEEI). The LMSE model expands the existing single epistasis models such as LR-Score, K2-Score, Mutual information, and Gini index. The SEEI includes an adaptive spherical search strategy and population updating strategy, which ensures that the algorithm is not easily trapped in local optima. We analyzed the performances of 8 random disease models, 12 disease models with marginal effects, 30 disease models without marginal effects, and 10 high-order disease models. The 60 simulated disease models and a real breast cancer dataset were used to evaluate eight algorithms (SEEI, EACO, EpiACO, FDHEIW, MP-HS-DHSI, NHSA-DHSC, SNPHarvester, CSE). Three evaluation criteria (pow1, pow2, pow3), a T-test, and a Friedman test were used to compare the performances of these algorithms. The results show that the SEEI algorithm (order 1, averages ranks = 13.125) outperformed the other algorithms in detecting EIs. CONCLUSIONS: Here, we propose an LMSE model and an evolutionary computing method (SEEI) to solve the optimization problem of the LMSE model. The proposed method performed better than the other seven algorithms tested in its ability to identify EIs in genome-wide association datasets. We identified new SNP-SNP combinations in the real breast cancer dataset and verified the results. Our findings provide new insights for the diagnosis and treatment of breast cancer. AVAILABILITY AND IMPLEMENTATION: https://github.com/scutdy/SSO/blob/master/SEEI.zip .

Integrated analysis of the DNA methylome and RNA transcriptome during the development of skeletal muscle in Duroc pigs.

BACKGROUND: Skeletal muscle development plays a crucial role in yield and quality of pork; however, this process is influenced by various factors. In this study, we employed whole-genome bisulfite sequencing (WGBS) and transcriptome sequencing to comprehensively investigate the longissimus dorsi muscle (LDM), aiming to identify key genes that impact the growth and development of Duroc pigs with different average daily gains (ADGs). RESULTS: Eight pigs were selected and divided into two groups based on ADGs: H (774.89 g) group and L (658.77 g) group. Each pair of the H and L groups were half-siblings. The results of methylation sequencing revealed 2631 differentially methylated genes (DMGs) involved in metabolic processes, signalling, insulin secretion, and other biological activities. Furthermore, a joint analysis was conducted on these DMGs and the differentially expressed genes (DEGs) obtained from transcriptome sequencing of the same individual. This analysis identified 316 differentially methylated and differentially expressed genes (DMEGs), including 18 DMEGs in promoter regions and 294 DMEGs in gene body regions. Finally, LPAR1 and MEF2C were selected as candidate genes associated with muscle development. Bisulfite sequencing PCR (BSP) and quantitative real-time PCR (qRT-PCR) revealed that the promoter region of LPAR1 exhibited significantly lower methylation levels (P < 0.05) and greater expression levels (P < 0.05) in the H group than in the L group. Additionally, hypermethylation was observed in the gene body region of MEF2C, as was a low expression level, in the H group (P < 0.05). CONCLUSIONS: These results suggest that the differences in the ADGs of Duroc pigs fed the same diet may be influenced by the methylation levels and expression levels of genes related to skeletal muscle development.

Correlation analysis between the in vivo bioavailability and in vitro bioaccessibility of nitro PAHs in soil: Application of simplified FOREhST in vitro methods based on the Chinese pharmacopoeia.

In this study, the relative bioavailability (RBA) of nitrated polycyclic aromatic hydrocarbons (NPAHs) in soil samples (n = 30) was assessed using an in vivo mouse model. Based on the correlation between the bioaccessibility data obtained from the Tenax improved traditional Fed ORganic Estimation human Simulation Test (FOREhST) in vitro method (TITF) and the bioavailability data obtained from in vivo experiments, the TITF method was further optimized and simplified by referring to the "Pharmacopoeia of the People's Republic of China: Volume IV, 2020" to adjust the formulation and parameters of the gastrointestinal fluid (GIF) in order to establish a simpler and lower cost in vitro method for the determination of the bioaccessibilities of NPAHs. The dose-accumulation relationship of the in vivo experiment showed that the linear dose-response was better in adipose tissue (R2 = 0.77-0.93), and the accumulation of NPAHs in adipose tissue was higher than that in kidney or liver tissue. Depending on the mouse adipose model, the NPAHs-RBA ranged from 1.88 % to 73.92 %, and a strongly significant negative relationship (R2 = 0.94, p < 0.05) was found between the NPAHs-RBA and Log Kow. The simplified experiment of the TITF showed that the composition of the GIF medium had a significant effect on the bioaccessibilities of NPAHs. The NPAH bioaccessibilities measured by the Tenax improved simplified FOREhST method (TISF) (9.0-36.5 %) were higher than that of the traditional FOREhST method (6.8-22.8 %) but significantly lower than that of the TITF method (16.8-55.2 %). With an increase in the bile concentration in the GIF (from 6 to 10 g/L), the bioaccessibilities of NPAHs increased from 9.0 to 36.5 % to 12.9-42.4 %. The accuracies of the four in vitro methods for predicting the bioavailabilities of NPAHs was in the following order: Tenax improved simplified FOREhST method with increased bile concentration (TITF-IB) (R2 = 0.54-0.87) ≈ TITF (R2 = 0.55-0.85) > TISF (R2 = 0.41-0.77) > FOREhST (R2 = 0.02-0.68). These results indicated that the simple in vitro method could also effectively predict the bioavailabilities of NPAHs.

Bioaccessibility and bioavailability of NPAHs in soils using in vitro-in vivo assays: Comparison of laboratory and outdoor environmental aging effect.

Aging process is one of the most important factors that markedly reduces bioaccessibility and bioavailability (bioac-bioav) of organic contaminants. However, only few data on comparison of the effects of laboratory artificial aging (LAA) and outdoor environmental aging (OEA) processes on nitrated polycyclic aromatic hydrocarbons (NPAHs) bioac-bioav are available. In the current study, oral bioac-bioav of NPAHs in LAA and OEA soils (aging time intervals: 0, 45, 90, 120 and 150 d) were measured by in vitro traditional Fed ORganic Estimation human Simulation Test (FOREhST) and Tenax improved FOREhST (TI-FOREhST) methods, and in vivo mouse model. Tenax significantly increased the bioaccessibility of NPAHs in freshly spiked and aging soils from 0.3-40.9 % to 15.6-95.3 %, and 0.3-40.9 % to 1.0-84.5 %, respectively. Aging significantly reduced the NPAHs bioaccessibility (from 36.5 % to 10.7 %, and 12.1 % to 5.1 % as measured by FOREhST and TI-FOREhST, respectively) and bioavailability (from 27.7 % to 9.9 %, as measured by mouse model). The changes in bioac-bioav were mainly observed within the first 120 d of aging. The statistical analyses of NPAHs bioac-bioav showed no significant difference (p > 0.05) among the aging time intervals in LAA and OEA soils, which demonstrated that the LAA can relatively represent the OEA. Determination of TOC content in LAA and OEA soil can intuitively reflect whether the difference of NPAHs bioac-bioav between two aging treatment groups is significant. The mean bioaccessibility of NPAHs in soil measured by TI-FOREhST (mean 20.6 %) is closer to the bioavailability measured by mouse model (mean 19.4 %), indicating that Tenax improved in vitro method is more reliable than traditional methods, to predict the bioavailability of NPAHs.

[Characterizing the interaction between roxarsone and humic acid by fluorescence quenching experiment].

In this study, the methods of fluorescence spectroscopy and fluorescence quenching titration technique were used to identify the interactions between humic acid (HA) and roxarsone (ROX). Effects of HA concentration, pH and temperature on the bonding strength between HA and ROX were investigated. The results showed that the four fluorescence peaks (E(x)/E(m) = 300 nm/480 nm, 370 nm/480 nm, 420 nm/500 nm, 460 nm/520 nm, marked as peak A, B, C, D respectively) of HA could be quenched by ROX. The extent of decreases in fluorescence intensities of different peaks was different and followed the order of C > B > A > D. The common logarithm of association constants (lg K) between peak A and ROX increased slightly with the increase of HA concentration and were much larger than the bimolecular quenching constant of O2. It was confirmed that the carboxyl groups and the carboxide groups of HA were quenched statically by ROX. The lg K values fluctuated between 3.55 L x mol(-1) and 3.98 L x mol(-1) when pH ranged from 5.00 to 9.00, and the maximum value occurred at pH 6.00. It might be resulted from the fact that pH could change the formation of ROX and conformation of phenolic hydroxyl groups and carboxyl groups in HA. The lg K values decreased and fluctuated between 2.65 L x mol(-1) and 3.89 L x mol(-1) with temperature ranging from 25.0 degrees C to 55.0 degrees C, which further confirmed the static quenching interaction between HA and ROX. Transient-fluorescence spectrum analyses and liner model simulations revealed that single static quenching was the main mechanism between ROX and the functional groups of fluorescence peak A, B, D in HA, and combined dynamic and static quenching was the main mechanism between ROX and the functional groups of peak C in HA.

[Degradation of oxytetracycline with ozonation in acetic acid solvent].

Use acetic acid as the media of ozone degradation of oxytetracycline (OTC), and effects of the initial dosing ratio of ozone/OTC, ozone flow, free radical scavenger, metal ions on the removal rate of OTC were investigated respectively. The results showed that acetic acid had a high ozone stability and solubility. OTC had a high removal rate and degradation rate in acetic acid solution. With the increase of OTC dosage, the removal rate of OTC decreased in acetic acid. Removal rate of OTC was increased distinctly when ozone flow increased properly. It was also observed that free radical scavenger had a significantly negative effect on OTC ozonation degradation in acetic acid. Furthermore the main reactions of OTC ozone oxidation were direct oxidation and indirect oxidation in acetic acid. When Fe3+ and Co2+ were existent in acetic acid, the degradation of OTC was inhibited significantly.

[Influence of EPS on silicate corrosion inhibition for copper pipe in soft water].

The effects of sodium alginate on silicate corrosion inhibition for copper pipe in simulated soft water were investigated. The results showed that more soluble copper release was occurred when low concentration sodium alginate was in presence. The 1 a aged copper pipe released more soluble copper than the 3 a and 10 a aged copper pipe. The sequence of concentration of soluble copper release was c 1 a > c 3 a, > c 10 a. However, compared to the low concentration sodium alginate, soluble copper released from the 1 a aged copper pipe increased, and the 3 a and 10 a aged copper pipe were inverse when high level sodium alginate was in presence. These phenomena showed that the effect of silicate corrosion inhibition decreased when extracellular polymer substances was dissolved in soft water. Under the conditions of pH 7.5 and sodium alginate 16 mg/L, soluble copper release tend was gradually increase-decrease-gradually run-up which due to the absorption of sodium alginate on the surface of copper surface and the complex interaction between sodium alginate, silicate and copper ions. When the initial pH value was low, compared to the system of no sodium alginate, the soluble copper release distinctly increased in the presence of sodium alginate. The amount of soluble copper released from 1 a copper pipe is higher than that from 3 a and 10 a aged copper pipe, which due to the different components of copper corrosion by-products on the surface of different aged copper pipes and the different solubility of different corrosion by-products.

Quantitative structure retention relationship studies for predicting relative retention times of chlorinated phenols on gas chromatography.

A new method of quantitative structure-retention relationship (QSRR) studies was reported for predicting gas chromatography (GC) relative retention times (RRTs) of chlorinated phenols (CPs) using a DB-5 column. Chemical descriptors were calculated from the molecular structure of CPs and related to their gas chromatographic RRTs by using multiple linear regression analysis. The proposed model had a multiple square correlation coefficient R2 = 0.970, standard error SE = 0.0472, and significant level P = 0.0000. The QSRR model also reveals that the gas chromatographic relative retention times of CPs are associated with physicochemical property interactions with the stationary phase, and influenced by the number of chlorine and oxygen in the CP mOlecules.