SIGRN: Inferring Gene Regulatory Network with Soft Introspective Variational Autoencoders.

Gene regulatory networks (GRNs) exhibit the complex regulatory relationships among genes, which are essential for understanding developmental biology and uncovering the fundamental aspects of various biological phenomena. It is an effective and economical way to infer GRNs from single-cell RNA sequencing (scRNA-seq) with computational methods. Recent researches have been done on the problem by using variational autoencoder (VAE) and structural equation model (SEM).

Identification of cancer driver genes based on dynamic incentive model.

Cancer is a complex genomic mutation disease, and identifying cancer driver genes promotes the development of targeted drugs and personalized therapies. The current computational method takes less consideration of the relationship among features and the effect of noise in protein-protein interaction(PPI) data, resulting in a low recognition rate. In this paper, we propose a cancer driver genes identification method based on dynamic incentive model, DIM.

Identification of cancer driver genes based on hierarchical weak consensus model.

Unlabelled: Cancer is a complex gene mutation disease that derives from the accumulation of mutations during somatic cell evolution. With the advent of high-throughput technology, a large amount of omics data has been generated, and how to find cancer-related driver genes from a large number of omics data is a challenge. In the early stage, the researchers developed many frequency-based driver genes identification methods, but they could not identify driver genes with low mutation rates well.

Essential proteins discovery based on dominance relationship and neighborhood similarity centrality.

Essential proteins play a vital role in development and reproduction of cells. The identification of essential proteins helps to understand the basic survival of cells. Due to time-consuming, costly and inefficient with biological experimental methods for discovering essential proteins, computational methods have gained increasing attention.

Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP.

Background: Although gene expression data play significant roles in biological and medical studies, their applications are hampered due to the difficulty and high expenses of gathering them through biological experiments. It is an urgent problem to generate high quality gene expression data with computational methods. WGAN-GP, a generative adversarial network-based method, has been successfully applied in augmenting gene expression data.

Identifying driver pathways based on a parameter-free model and a partheno-genetic algorithm.

Background: Tremendous amounts of omics data accumulated have made it possible to identify cancer driver pathways through computational methods, which is believed to be able to offer critical information in such downstream research as ascertaining cancer pathogenesis, developing anti-cancer drugs, and so on. It is a challenging problem to identify cancer driver pathways by integrating multiple omics data.

Results: In this study, a parameter-free identification model SMCMN, incorporating both pathway features and gene associations in Protein-Protein Interaction (PPI) network, is proposed.

Robust electrolysis system divided by bipolar electrode and non-conductive membrane for energy-efficient calcium hardness removal.

In this study, an energy-efficient divided bipolar electrolysis system was developed for water softening, where two PTFE membranes were used as the separating materials and a bipolar electrode was employed to enhance the HO-splitting reactions. As compared with other two operation modes, the optimum calcium harness removal efficiencies of 85% and 57% could be reached in the induction cathode effluent and terminal effluent, respectively, at 8 mA cm in the mode A. Increasing the current density from 5 to 20 mA cm evidently promoted the removal of calcium hardness from 33% to 65% in the terminal effluent and the CaCO precipitation rate from 743 to 1462 gCaCO h m with the increased energy consumption from 0.

Differentiating the reaction mechanism of three-dimensionally electrocatalytic system packed with different particle electrodes: Electro-oxidation versus electro-fenton.

Recently, there are still some controversial mechanisms of the 3D electrocatalytic oxidation system, which would probably confound its industrial application. From the conventional viewpoint, the TiO material may be the desired particle electrodes in the 3D system since its high oxygen evolution potential favors the production of OH via HO splitting reaction at the anode side of TiO particle electrodes. In fact, the incorporation of TiO particles showed phenol degradation of 88% and COD removal of 51% within 120 min, under the optimum conditions at energy consumption of 0.

Investigation on the adverse impacts of electrochemically produced ClO on assessing the treatment performance of dimensionally stable anode (DSA) for Cl-containing wastewater.

The presence of chloride ions can facilitate the COD removal efficiency due to the involvement of active chlorine species in the electro-oxidation process, but few attentions have been paid to the negative effect of the electro-generated oxychlorides on electro-oxidation performance. In this study, the effects of oxychlorides were investigated as functions of current density and phenol concentration using DSA anodes in terms of the evaluation of the COD removal performance and the biological toxicity. The results show that oxychlorides formed in the electro-oxidation system could result in the over-evaluation of the COD removal performance.

Identification of cancer-related module in protein-protein interaction network based on gene prioritization.

With the rapid development of deep sequencing technologies, a large amount of high-throughput data has been available for studying the carcinogenic mechanism at the molecular level. It has been widely accepted that the development and progression of cancer are regulated by modules/pathways rather than individual genes. The investigation of identifying cancer-related active modules has received an extensive attention.

miR-205-3p Functions as a Tumor Suppressor in Ovarian Carcinoma.

Ovarian cancer (OC) represents the most lethal form of gynaecologic cancers in developed countries. To develop a better therapeutic against OC, characterizing new classes of molecular regulators such as microRNAs (miRNAs) involved in OC tumorigenesis becomes immensely important. We used human OC cell lines to study the expression pattern of miRNA-205-3p.

Natural selection and genetic diversity of domain I of Plasmodium falciparum apical membrane antigen-1 on Bioko Island.

Background: Plasmodium falciparum apical membrane antigen-1 (PfAMA-1) is a promising candidate antigen for a blood-stage malaria vaccine. However, antigenic variation and diversity of PfAMA-1 are still major problems to design a universal malaria vaccine based on this antigen, especially against domain I (DI). Detail understanding of the PfAMA-1 gene polymorphism can provide useful information on this potential vaccine component.

MiR-144-3p: a novel tumor suppressor targeting MAPK6 in cervical cancer.

Cervical cancer is the third most common gynecologic cancer in the world. Exploration of the molecular mechanism underlying cervical cancer pathogenesis will provide new insights into the development of novel therapies. In this study, we were aimed to characterize a novel miRNA in cervical cancer tumorigenesis.

Identifying mutated driver pathways in cancer by integrating multi-omics data.

Since the driver pathway in cancer plays a crucial role in the formation and progression of cancer, it is very imperative to identify driver pathways, which will offer important information for precision medicine or personalized medicine. In this paper, an improved maximum weight submatrix problem model is proposed by integrating such three kinds of omics data as somatic mutations, copy number variations, and gene expressions. The model tries to adjust coverage and mutual exclusivity with the average weight of genes in a pathway, and simultaneously considers the correlation among genes, so that the pathway having high coverage but moderate mutual exclusivity can be identified.

A fast and accurate enumeration-based algorithm for haplotyping a triploid individual.

Background: Haplotype assembly, reconstructing haplotypes from sequence data, is one of the major computational problems in bioinformatics. Most of the current methodologies for haplotype assembly are designed for diploid individuals. In recent years, genomes having more than two sets of homologous chromosomes have attracted many research groups that are interested in the genomics of disease, phylogenetics, botany and evolution.

The purification and characterization of a novel alkali-stable pectate lyase produced by Bacillus subtilis PB1.

Pectinase is an important kind of enzyme with many industrial applications, among which pectinases produced by bacteria were scarce compared with fungal sources. In this study, a novel bacterium which produced extracellular pectinase was firstly isolated from flue-cured tobacco leaves and identified as Bacillus subtilis PB1 according to its 16S rRNA gene. The pectinolytic enzyme was purified by ammonium sulfate precipitation, ion-exchange and gel filtration chromatography, after which molecular weight was determined as 43.

Improvement of simultaneous determination of neutral monosaccharides and uronic acids by gas chromatography.

Although pre-column derivatization with n-propylamine and acetic anhydride combined with the gas chromatograph was a useful method for the analysis of monosaccharide composition, failure often occurs because of lack of detail information on the mechanism as well as the operating key point in derivatization process. In this study, the key points in the derivatization (lactonization time, the amount of n-propylamine and acetic anhydride) were investigated and optimized to improve the method. Under the optimal conditions, the derivatives of seven neutral monosaccharides and two uronic acids were simultaneouly obtained, after which they were well separated and detected by GC.

Predicting essential proteins based on subcellular localization, orthology and PPI networks.

Background: Essential proteins play an indispensable role in the cellular survival and development. There have been a series of biological experimental methods for finding essential proteins; however they are time-consuming, expensive and inefficient. In order to overcome the shortcomings of biological experimental methods, many computational methods have been proposed to predict essential proteins.

Purification and characterization of a novel bacteriocin produced by Lactobacillus crustorum MN047 isolated from koumiss from Xinjiang, China.

The growing emergence of antibiotic-resistant bacteria in the food industry needs to be controlled with effective antimicrobials. In this study, bacteriocin MN047 A (BMA) was found to have antibacterial activity against multidrug-resistant bacteria. It was produced by Lactobacillus crustorum MN047, which was first isolated from koumiss, a traditional fermented dairy product from Xinjiang Autonomous Region, China.

TG-MS analysis and kinetic study for thermal decomposition of six representative components of municipal solid waste under steam atmosphere.

Thermal decomposition of six representative components of municipal solid waste (MSW, including lignin, printing paper, cotton, rubber, polyvinyl chloride (PVC) and cabbage) was investigated by thermogravimetric-mass spectroscopy (TG-MS) under steam atmosphere. Compared with TG and derivative thermogravimetric (DTG) curves under N2 atmosphere, thermal decomposition of MSW components under steam atmosphere was divided into pyrolysis and gasification stages. In the pyrolysis stage, the shapes of TG and DTG curves under steam atmosphere were almost the same with those under N2 atmosphere.

Haplotyping a single triploid individual based on genetic algorithm.

The minimum error correction model is an important combinatorial model for haplotyping a single individual. In this article, triploid individual haplotype reconstruction problem is studied by using the model. A genetic algorithm based method GTIHR is presented for reconstructing the triploid individual haplotype.

Corn stalks char from fast pyrolysis as precursor material for preparation of activated carbon in fluidized bed reactor.

Corn stalks char from fast pyrolysis was activated by physical and chemical activation process in a fluidized bed reactor. The structure and morphology of the carbons were characterized by N2 adsorption and SEM. Effects of activation time and activation agents on the structure of activation carbon were investigated.

Multi-Gaussian-DAEM-reaction model for thermal decompositions of cellulose, hemicellulose and lignin: comparison of N₂ and CO₂ atmosphere.

Thermal decompositions of three components of biomass (cellulose, hemicellulose and lignin) were studied using nonisothermal thermogravimetric analysis (TGA) under both oxidative and inert atmospheres at a heating rate of 10 K min(-1). The multi-Gaussian-distributed activation energy model (DAEM)-reaction model was first developed to describe thermal decomposition behaviors of three components. Results showed that the presence of CO₂ enhanced the thermal decompositions of three components in high temperature range, but made little difference in low temperature range.

TG/FTIR analysis on co-pyrolysis behavior of PE, PVC and PS.

The pyrolysis and co-pyrolysis behaviors of polyethylene (PE), polystyrene (PS) and polyvinyl chloride (PVC) under N2 atmosphere were analyzed by Thermal gravimetric/Fourier transform infrared (TG/FTIR). The volatile products were analyzed to investigate the interaction of the plastic blends during the thermal decomposition process. The TGA results showed that the thermal stability increased followed by PVC, PS and PE.

Gasification kinetic analysis of the three pseudocomponents of biomass-cellulose, semicellulose and lignin.

The gasification kinetic analysis of the three pseudocomponents (hemicellulose, cellulose and lignin) of biomass decomposition in the agent of CO2 were investigated. The Multi-peaks method was used to fit the Gaussian distribution model of DTG curves. The Friedman method was used to estimate the effective Eα, and the master plot method was used for the determination of the kinetic model.