GEFormerDTA: drug target affinity prediction based on transformer graph for early fusion.

Predicting the interaction affinity between drugs and target proteins is crucial for rapid and accurate drug discovery and repositioning. Therefore, more accurate prediction of DTA has become a key area of research in the field of drug discovery and drug repositioning. However, traditional experimental methods have disadvantages such as long operation cycles, high manpower requirements, and high economic costs, making it difficult to predict specific interactions between drugs and target proteins quickly and accurately. Some methods mainly use the SMILES sequence of drugs and the primary structure of proteins as inputs, ignoring the graph information such as bond encoding, degree centrality encoding, spatial encoding of drug molecule graphs, and the structural information of proteins such as secondary structure and accessible surface area. Moreover, previous methods were based on protein sequences to learn feature representations, neglecting the completeness of information. To address the completeness of drug and protein structure information, we propose a Transformer graph-based early fusion research approach for drug-target affinity prediction (GEFormerDTA). Our method reduces prediction errors caused by insufficient feature learning. Experimental results on Davis and KIBA datasets showed a better prediction of drugtarget affinity than existing affinity prediction methods.

Removal of NO in flue gas simulated by the Fe2+/Cu2+-activated double oxidant system.

⋅OHThe wet denitrification technology has a good development prospect due to its simple system and mild reaction conditions, and related research has become a hot topic in the field of flue gas purification. In this work, a novel simultaneous removal technology of NO from flue gas using Fe2+/Cu2+-catalytic H2O2/(NH4)2S2O8 system was developed for the first time. The feasibility of this new flue gas cleaning technology was explored through a series of experiments and performance analyses. The mechanism of oxidation products, free radicals and simultaneous removal of NO was revealed. The effects of the main process parameters on the removal of NO were investigated. Relevant results demonstrated that the removal efficiency of NO was elevated when the concentration of (NH4)2S2O8 or reacting temperature increased, while it was decreased after increasing the raising of Fe2+, Cu2+ and H2O2 concentrations. The main radicals were and·SO4-, using the electron spin resonance technique in the solution, and played a very important role in NO removal. The main products were carried out by ion chromatography and elemental N material accountancy, and the results showed that it was sulfate and nitrate in the solution, which provided theoretical guidance for the subsequent treatment and resource utilization of the absorption solution. The results of the study provided a theoretical basis for the industrial application of wet denitrification.

Removal of phenol from wastewater by high-gravity intensified heterogeneous catalytic ozonation with activated carbon.

In this study, the high-gravity technique is used to intensify the heterogeneous catalytic ozonation with activated carbon (AC) as the catalyst for removal of phenol from wastewater in a rotating packed bed (RPB), and the effects of high-gravity factor, inlet O3 concentration, liquid-gas ratio, and initial pH on the degradation and mineralization of phenol at room temperature are investigated. It is revealed that the degradation rate of phenol reaches 100% at 10 min and the removal rate of total organic carbon (TOC) reaches 91% at 40 min under the conditions of high-gravity factor ß = 40, inlet O3 concentration = 90 mg·L-1, liquid flow rate = 80 L·h-1, and initial pH = 11. Compared with the bubbling reactor (BR)/O3/AC and RPB/O3 systems, the mineralization rate of phenol by the RPB/O3/AC system is increased by 24.78% and 34.77%, respectively. Free radical quenching experiments are performed using tertiary butanol (TBA) and benzoquinone (BQ) as scavengers of ·OH and O2-, respectively. It is shown that the degradation and mineralization of phenol are attributed to the direct ozonation and the indirect oxidation by ·OH generated from the decomposition of O3 adsorbed on AC surface, respectively. ·OH and O2·- are also detected by electron paramagnetic resonance (EPR). Thus, it is concluded that AC-catalyzed ozonation and high-gravity technique have a synergistic effect on ·OH initiation, which in turn can significantly improve the degradation and mineralization of organic wastewater.

[Comparative analysis and research on composition of mulberry-sourced medicinal materials by fingerprint division total statistical moment method and information entropy].

The present work is to analyze the HPLC fingerprints of mulberry-sourced materials(Mori Ramulus, Mori Folium, Muri Cortex, Mori Fructus) using the fingerprint division total statistical moment method and information entropy, and to study the diffe-rences of the chemical components and the overall characteristics of the imprinting template in different parts of mulberry-sourced medicinal materials, so as to provide the basis for finding the effective substances in response to "homologous and different effect" of mulberry(Morus alba). The fingerprints of 24 batches of mulberry-related materials, such as Mori Ramulus, Mori Folium, Muri Cortex, Mori Fructus, were established, and the similarities and differences of the fingerprints were analyzed by calculating the division total statistical moment parameters and information entropy. The AUC_T, MCRT_T, VCRT_T and H values of 24 batches of mulberry-sourced materials were less than 0.05, with significant difference. Among them, all samples showed absorption peaks within 3-11, and 20-24 min, indicating that the four types had the identical or similar chemical composition in the same time period. After 34 min, none of the four types showed absorption peaks. Greater VCRT_T value of the fingerprints of the four kinds was observed at the retention time ranges of 3-4, 16-18, 25-27, and 31-32 min, indicating that the components of the four kinds were significantly different in these time periods; and VCRT_T value of the mulberry was significantly higher than that of the other three kinds of medicinal materials at the retention time windows of 3-4 and 15-17 min; the VCRT_T value of the mulberry white skin was significantly higher at the time windows of 8-10 and 28-30 min; the VCRT_T value of all four kinds was significantly higher within 21-23 min, indicating that the four herbs contain the same or similar components in the chromatogram during this period, but there may be significant differences between the content and the proportion. In addition, the information entropy of mulberry branches is the largest at 7-12, 23-27 min, and that of mulberry fruits is the largest at 2-8 min, which indicates that the components of mulberry branches and mulberry fruits respond greatly in the corresponding period of time, which is also the main peak period of their chemical components. For the chemical components and corresponding efficacy here. The results showed that there are significant differences in the components and contents of mulberry-sourced medicinal materials. The division total statistical moment and information entropy of the total amount of segments can be used to analyze the differences in the components of "homology and different effects", which could provide a more comprehensive analysis method for the determination of quality markers.

Deep neural networks for inferring binding sites of RNA-binding proteins by using distributed representations of RNA primary sequence and secondary structure.

BACKGROUND: RNA binding proteins (RBPs) play a vital role in post-transcriptional processes in all eukaryotes, such as splicing regulation, mRNA transport, and modulation of mRNA translation and decay. The identification of RBP binding sites is a crucial step in understanding the biological mechanism of post-transcriptional gene regulation. However, the determination of RBP binding sites on a large scale is a challenging task due to high cost of biochemical assays. Quite a number of studies have exploited machine learning methods to predict binding sites. Especially, deep learning is increasingly used in the bioinformatics field by virtue of its ability to learn generalized representations from DNA and protein sequences. RESULTS: In this paper, we implemented a novel deep neural network model, DeepRKE, which combines primary RNA sequence and secondary structure information to effectively predict RBP binding sites. Specifically, we used word embedding algorithm to extract features of RNA sequences and secondary structures, i.e., distributed representation of k-mers sequence rather than traditional one-hot encoding. The distributed representations are taken as input of convolutional neural networks (CNN) and bidirectional long-term short-term memory networks (BiLSTM) to identify RBP binding sites. Our results show that deepRKE outperforms existing counterpart methods on two large-scale benchmark datasets. CONCLUSIONS: Our extensive experimental results show that DeepRKE is an efficacious tool for predicting RBP binding sites. The distributed representations of RNA sequences and secondary structures can effectively detect the latent relationship and similarity between k-mers, and thus improve the predictive performance. The source code of DeepRKE is available at https://github.com/youzhiliu/DeepRKE/ .

Continuous Carbonation for Synthesis of Pseudo-Boehmite by using Cross-Flow Rotating Packed Bed through the Reaction of NaAlO2 Solution with CO2 Gas.

This research established a novel method for the preparation of pseudo-boehmite (PB) via a continuous carbonation of CO2 gas and a NaAlO2 solution in a cross-flow rotating packed bed (CF-RPB). In the CF-RPB, the NaAlO2 solution can be sheared into fine liquid filaments and droplets, and react in full contact with the CO2 gas. Effects of synthesis parameters, including the concentration of the NaAlO2 solution, the gas-liquid ratio, the rotating speed of the CF-RPB, and the final pH of the solution on the crystal structure of PB, were fully investigated. A series of characterizations, including X-ray diffraction(XRD), scanning electron microscopy(SEM), transmission electron microscopy (TEM) and Brunauer-Emmett-Teller (BET) analysis, were carried out to explain the evaluation results and to find the relationship between PB properties and the synthetic conditions. The results showed that PB with a high specific surface area (495 m2/g) and large pore volume (2.125 cc/g) can be obtained when the concentration of the NaAlO2 solution was 0.1 mol/L, the gas-liquid ratio was 3:1, the rotating speed of RPB was 600 rpm, and the final pH was around 10.5. PB obtained by this method had a higher quality compared with that using a stirred tank reactor. Moreover, the continuous carbonation can be efficiently batch-produced, which provided a new idea for an industrial application.

Removal of trace Cr(VI) from aqueous solution by porous activated carbon balls supported by nanoscale zero-valent iron composites.

In this study, porous activated carbon balls supported by nanoscale zero-valent iron composites (Fe@PACB-700) were used for the first time for the removal of trace Cr(VI) from aqueous solutions. The Fe@PACB-700 composites were prepared by a facile carbothermal reduction method and then characterized by scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS), X-ray diffraction analysis (XRD), and X-ray photoelectron spectroscopy (XPS). The results show that nZVI particles have been successfully loaded onto PACBs. Fe@PACB-700 shows an excellent Cr(VI) removal efficiency of 91.2%. The maximum adsorption capacity of Fe@PACB-700 for Cr(VI) is 22.24 mg/g, which is 4.36 times that of PACB. The residual Cr(VI) concentration is below 20 ppb with the use of 0.15 g of Fe@PACB-700, which is much lower than the allowable concentration for Cr(VI) in drinking water (0.05 mg/L). The adsorption of Cr(VI) can be well described by the Langmuir isotherm model and pseudo-second-order kinetic model. Fe@PACB-700 still has a high removal efficiency of 80% after five cycles. Thus, Fe@PACB-700 has a great potential for Cr(VI) removal from aqueous solution. Graphical abstract.

Preparation of TiO2 and Fe-TiO2 with an Impinging Stream-Rotating Packed Bed by the Precipitation Method for the Photodegradation of Gaseous Toluene.

Nano-TiO2 has always been one of the most important topics in the research of photocatalysts due to its special activity and stability. However, it has always been difficult to obtain nano-TiO2 with high dispersion, a small particle size and high photocatalytic activity. In this paper, nano-TiO2 powder was prepared by combining the high-gravity technique and direct precipitation method in an impinging stream-rotating packed bed (IS-RPB) reactor followed by Fe3+ in-situ doping. TiOSO4 and NH3·H2O solutions were cut into very small liquid microelements by high-speed rotating packing, and the mass transfer and microscopic mixing of the nucleation and growth processes of nano-TiO2 were strengthened in IS-RPB, which was beneficial to the continuous production of high quality nano-TiO2. Pure TiO2 and iron-doped nano-TiO2 (Fe-TiO2) were obtained in IS-RPB and were investigated by means of X-ray diffraction (XRD), Raman, scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), ultraviolet-visible diffuse reflectance spectroscopy (UV-vis DRS) and Brunauer-Emmett-Teller (BET) analysis, which found that pure TiO2 had a particle size of about 12.5 nm, good dispersibility and a complete anatase crystal at the rotating speed of packing of 800 rpm and calcination temperature of 500 °C. The addition of Fe3+ did not change the crystalline structure of TiO2. Iron was highly dispersed in TiO2 without the detection of aggregates and was found to exist in a positive trivalent form by XPS. With the increase of iron doping, the photoresponse range of TiO2 to visible light was broadened from 3.06 eV to 2.26 eV. The degradation efficiency of gaseous toluene by Fe-TiO2 under ultraviolet light was higher than that of pure TiO2 and commercial P25 due to Fe3+ effectively suppressing the recombination of TiO2 electrons and holes; the highest efficiency produced by 1.0% Fe-TiO2 was 95.7%.

A three-dimensional porous Co-P alloy supported on a copper foam as a new catalyst for sodium borohydride electrooxidation.

Cobalt has been extensively studied as an effective catalyst for the electrooxidation of sodium borohydride. However, there is still the problem of the low catalytic activity of cobalt catalysts. The improvement in the catalytic activity of cobalt for the electrooxidation of sodium borohydride has become a challenge. In this paper, a novel catalyst Co-P alloy was supported on a copper foam (CF) substrate by a one-step electrodeposition method. In the electrodeposition process, a Co-P/CF electrode with a three-dimensional (3D) porous structure was successfully prepared using hydrogen bubbles as a dynamic template. Through the physical characterization of Co-P/CF, it was proven that the doping of P element produced more Co clusters on the surface of the electrode, which resulted in more active sites. These characteristics were very beneficial for NaBH4 electrooxidation. The electrochemical characterization confirmed that the electrocatalytic activity of Co-P/CF for NaBH4 was better than that of Co/CF. At room temperature, for the Co-P/CF in 2.0 mol dm-3 NaOH + 0.20 mol dm-3 NaBH4 solution, the oxidation current density reached 1795 mA cm-2 at -0.20 V (vs. Ag/AgCl), which was higher than that previously reported the literature.

Highly efficient removal of heavy metal ions by carboxymethyl cellulose-immobilized Fe3O4 nanoparticles prepared via high-gravity technology.

The aim of this study is to explore facile and large-scale method for the preparation of magnetic adsorbent materials with high-efficient heavy metal removal performance. Here, based on the process intensification of high-gravity technology, the carboxymethyl cellulose-immobilized Fe3O4 nanoparticles (CMC-Fe3O4) were continuously synthesized via impinging stream-rotating packed bed. With a theoretical production rate of 2.35 kg h-1, the as-prepared CMC-Fe3O4 exhibited better adsorption capacity and faster rate for Pb(II) than those of pure Fe3O4, and the maximum adsorption capacity of Pb(II) reached up to 152.0 mg g-1. It was found that the adsorption data of Pb(II) onto CMC-Fe3O4 fit well to pseudo-second order kinetic model and Langmuir isotherm model. Moreover, the as-prepared adsorbent exhibited good reusability after five adsorption-desorption cycles. Overall, the high-gravity technology can be employed for the preparation of high-performance nano-adsorbent and has a great potential in the application of heavy metal removal.

Degradation of nitrobenzene wastewater in an acidic environment by Ti(IV)/H2O2/O3 in a rotating packed bed.

The rotating packed bed (RPB) as a continuous flow reactor performs very well in degradation of nitrobenzene wastewater. In this study, acidic nitrobenzene wastewater was degraded using ozone (O3) combined with hydrogen peroxide and titanium ions (Ti(IV)/H2O2/O3) or using only H2O2/O3 in a RPB. The degradation efficiency of nitrobenzene by Ti(IV)/H2O2/O3 is roughly 16.84% higher than that by H2O2/O3, and it reaches as high as 94.64% in 30 min at a H2O2/O3 molar ratio of 0.48. It is also found that the degradation efficiency of nitrobenzene is significantly affected by the high gravity factor, H2O2/O3 molar ratio, and Ti(IV) concentration, and it reaches a maximum at a high gravity factor of 40, a Ti(IV) concentration of 0.50 mmol/L, a pH of 4.0, a H2O2/O3 molar ratio of 0.48, a liquid flow rate of 120 L/h, and an initial nitrobenzene concentration of 1.22 mmol/L. Both direct ozonation and indirect ozonation are involved in the reaction of O3 with organic pollutants. The indirect ozonation due to the addition of different amounts of tert-butanol (·OH scavenger) in the system accounts for 84.31% of the degradation efficiency of nitrobenzene, indicating that the nitrobenzene is dominantly oxidized by ·OH generated in the RPB-Ti(IV)/H2O2/O3 process. Furthermore, the possible oxidative degradation mechanisms are also proposed to better understand the role of RPB in the removal of pollutants. Graphical abstract ᅟ.

Removal of heavy metal ions by magnetic chitosan nanoparticles prepared continuously via high-gravity reactive precipitation method.

This study aimed to provide a continuous method for the preparation of magnetic Fe3O4/Chitosan nanoparticles (Fe3O4/CS NPs) that can be applied to efficient removal of heavy metal ions from aqueous solution. Using a novel impinging stream-rotating packed bed, the continuous preparation of Fe3O4/CS NPs reached a theoretical production rate of 3.43kg/h. The as-prepared Fe3O4/CS NPs were quasi-spherical with average diameter of about 18nm and saturation magnetization of 33.5emu/g. Owing to the strong metal chelating ability of chitosan, the Fe3O4/CS NPs exhibited better adsorption capacity and faster adsorption rates for Pb(II) and Cd(II) than those of pure Fe3O4. The maximum adsorption capacities of Fe3O4/CS NPs for Pb(II) and Cd(II) were 79.24 and 36.42mgg-1, respectively. In addition, the Fe3O4/CS NPs shown excellent reusability after five adsorption-desorption cycles. All the above results provided a potential method for continuously preparing recyclable adsorbent with a wide prospect of application in wastewater treatment.

A novel electro-catalytic degradation method of phenol wastewater with Ti/IrO2-Ta2O5 anodes in high-gravity fields.

In the electro-catalytic degradation process of phenol wastewater, bubbles and mass transfer limitation will result in the decrease in wastewater degradation efficiency, a long electrolysis time and a high energy consumption. Self-made Ti/IrO2-Ta2O5 anodes and a high-gravity electro-catalytic reactor were used to improve them. The Ti/IrO2-Ta2O5 anode was prepared with a thermal decomposition method and characterized by scanning electron microscopy (SEM). Under optimum conditions, the removal efficiencies of phenol, total organic carbon (TOC) and chemical oxygen demand (COD) respectively reached 94.77%, 50.96% and 41.2% after 2 h electrolysis in the high-gravity field, which were respectively 10.93%, 16.72% and 24.84% higher than those in the normal gravity field. For about the same removal efficiencies, the electrolysis time and energy consumed in the high-gravity field were 33.3% and 15.4% lower than those consumed in the normal gravity field, respectively. The degradation pathway of phenol detected by high performance liquid chromatography (HPLC) was unchanged in the high-gravity field, but the degradation rate of phenol increased. The Ti/IrO2-Ta2O5 anode provided good stability because the removal efficiencies of phenol and TOC decreased slightly and the surface morphology of the coating was almost unchanged when it had been used in electrolysis for 11 months, about 1,200 h, in the high-gravity field. Results indicated that the phenol wastewater degradation efficiency was improved, the time was shortened, and the energy consumption was reduced in the high-gravity field.