A review on heterogeneous solid catalysts and related catalytic mechanisms for epoxidation of olefins with H2O2

The epoxidation reaction using heterogeneous solid catalysts with H2O2 as oxidants are environmentally friendly routes to produce extensively useful epoxides which are traditionally obtained from capital-intensive or environmentally polluted processes. In this paper, various types of solid catalysts for the epoxidation of olefins with H2O2 as oxidants are reviewed. The efficient catalysts reported include microporous and mesoporous molecular sieves, layered-type materials, inorganic oxides, supported catalysts, zeolite encapsulated metal complexes, polyoxometalates, and supported organometallic catalysts. The proposed reaction mechanisms over different solid catalysts are summarized. The problems and perspectives to further efficiently improve the catalytic performances of the concerned heterogeneous catalysts for epoxidation reaction are remarked

Regulation of progesterone receptor signaling by BRCA1 in mammary cancer

Inherited mutations of the BRCA1 gene (chromosome 17q21), a tumor suppressor, lead to an increased risk of breast cancer, ovarian cancer, and several other hormone-responsive tumor types. Over the last ten years, BRCA1 has been found to play major roles in DNA damage signaling, repair, and cell cycle checkpoints. In addition, unfolding evidence suggests that BRCA1 functions as a co-regulator for steroid hormone receptors and modulates steroid hormone action. In this paper, we will briefly review this evidence and present a model to address the role of the progesterone and estrogen receptors in BRCA1 mutant mammary carcinogenesis. Finally, we will consider some of the clinical implications of this model

Signal-BNF: A Bayesian Network Fusing Approach to Predict Signal Peptides

A signal peptide is a short peptide chain that directs the transport of a protein and has become the crucial vehicle in finding new drugs or reprogramming cells for gene therapy. As the avalanche of new protein sequences generated in the postgenomic era, the challenge of identifying new signal sequences has become even more urgent and critical in biomedical engineering. In this paper, we propose a novel predictor called Signal-BNF to predict the N-terminal signal peptide as well as its cleavage site based on Bayesian reasoning network. Signal-BNF is formed by fusing the results of different Bayesian classifiers which used different feature datasets as its input through weighted voting system. Experiment results show that Signal-BNF is superior to the popular online predictors such as Signal-3L and PrediSi. Signal-BNF is featured by high prediction accuracy that may serve as a useful tool for further investigating many unclear details regarding the molecular mechanism of the zip code protein-sorting system in cells

StackEPI: identification of cell line-specific enhancer–promoter interactions based on stacking ensemble learning

Abstract Background Understanding the regulatory role of enhancer–promoter interactions (EPIs) on specific gene expression in cells contributes to the understanding of gene regulation, cell differentiation, etc., and its identification has been a challenging task. On the one hand, using traditional wet experimental methods to identify EPIs often means a lot of human labor and time costs. On the other hand, although the currently proposed computational methods have good recognition effects, they generally require a long training time. Results In this study, we studied the EPIs of six human cell lines and designed a cell line-specific EPIs prediction method based on a stacking ensemble learning strategy, which has better prediction performance and faster training speed, called StackEPI. Specifically, by combining different encoding schemes and machine learning methods, our prediction method can extract the cell line-specific effective information of enhancer and promoter gene sequences comprehensively and in many directions, and make accurate recognition of cell line-specific EPIs. Ultimately, the source code to implement StackEPI and experimental data involved in the experiment are available at https://github.com/20032303092/StackEPI.git . Conclusions The comparison results show that our model can deliver better performance on the problem of identifying cell line-specific EPIs and outperform other state-of-the-art models. In addition, our model also has a more efficient computation speed

DeepASDPred: a CNN-LSTM-based deep learning method for Autism spectrum disorders risk RNA identification

Abstract Background Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders characterized by difficulty communicating with society and others, behavioral difficulties, and a brain that processes information differently than normal. Genetics has a strong impact on ASD associated with early onset and distinctive signs. Currently, all known ASD risk genes are able to encode proteins, and some de novo mutations disrupting protein-coding genes have been demonstrated to cause ASD. Next-generation sequencing technology enables high-throughput identification of ASD risk RNAs. However, these efforts are time-consuming and expensive, so an efficient computational model for ASD risk gene prediction is necessary. Results In this study, we propose DeepASDPerd, a predictor for ASD risk RNA based on deep learning. Firstly, we use K-mer to feature encode the RNA transcript sequences, and then fuse them with corresponding gene expression values to construct a feature matrix. After combining chi-square test and logistic regression to select the best feature subset, we input them into a binary classification prediction model constructed by convolutional neural network and long short-term memory for training and classification. The results of the tenfold cross-validation proved our method outperformed the state-of-the-art methods. Dataset and source code are available at https://github.com/Onebear-X/DeepASDPred is freely available. Conclusions Our experimental results show that DeepASDPred has outstanding performance in identifying ASD risk RNA genes

iterb-PPse: Identification of transcriptional terminators in bacterial by incorporating nucleotide properties into PseKNC.

Terminator is a DNA sequence that gives the RNA polymerase the transcriptional termination signal. Identifying terminators correctly can optimize the genome annotation, more importantly, it has considerable application value in disease diagnosis and therapies. However, accurate prediction methods are deficient and in urgent need. Therefore, we proposed a prediction method "iterb-PPse" for terminators by incorporating 47 nucleotide properties into PseKNC-Ⅰ and PseKNC-Ⅱ and utilizing Extreme Gradient Boosting to predict terminators based on Escherichia coli and Bacillus subtilis. Combing with the preceding methods, we employed three new feature extraction methods K-pwm, Base-content, Nucleotidepro to formulate raw samples. The two-step method was applied to select features. When identifying terminators based on optimized features, we compared five single models as well as 16 ensemble models. As a result, the accuracy of our method on benchmark dataset achieved 99.88%, higher than the existing state-of-the-art predictor iTerm-PseKNC in 100 times five-fold cross-validation test. Its prediction accuracy for two independent datasets reached 94.24% and 99.45% respectively. For the convenience of users, we developed a software on the basis of "iterb-PPse" with the same name. The open software and source code of "iterb-PPse" are available at https://github.com/Sarahyouzi/iterb-PPse

I2DS: Interpretable Intrusion Detection System Using Autoencoder and Additive Tree

Intrusion detection system (IDS), the second security gate behind the firewall, can monitor the network without affecting the network performance and ensure the system security from the internal maximum. Many researches have applied traditional machine learning models, deep learning models, or hybrid models to IDS to improve detection effect. However, according to Predicted accuracy, Descriptive accuracy, and Relevancy (PDR) framework, most of detection models based on model-based interpretability lack good detection performance. To solve the problem, in this paper, we have proposed a novel intrusion detection system model based on model-based interpretability, called Interpretable Intrusion Detection System (I2DS). We firstly combine normal and attack samples reconstructed by AutoEncoder (AE) with training samples to highlight the normal and attack features, so that the classifier has a gorgeous effect. Then, Additive Tree (AddTree) is used as a binary classifier, which can provide excellent predictive performance in the combined dataset while maintaining good model-based interpretability. In the experiment, UNSW-NB15 dataset is used to evaluate our proposed model. For detection performance, I2DS achieves a detection accuracy of 99.95%, which is better than most of state-of-the-art intrusion detection methods. Moreover, I2DS maintains higher simulatability and captures the decision rules easily

IHCP: interpretable hepatitis C prediction system based on black-box machine learning models

Abstract Background Hepatitis C is a prevalent disease that poses a high risk to the human liver. Early diagnosis of hepatitis C is crucial for treatment and prognosis. Therefore, developing an effective medical decision system is essential. In recent years, many computational methods have been proposed to identify hepatitis C patients. Although existing hepatitis prediction models have achieved good results in terms of accuracy, most of them are black-box models and cannot gain the trust of doctors and patients in clinical practice. As a result, this study aims to use various Machine Learning (ML) models to predict whether a patient has hepatitis C, while also using explainable models to elucidate the prediction process of the ML models, thus making the prediction process more transparent. Result We conducted a study on the prediction of hepatitis C based on serological testing and provided comprehensive explanations for the prediction process. Throughout the experiment, we modeled the benchmark dataset, and evaluated model performance using fivefold cross-validation and independent testing experiments. After evaluating three types of black-box machine learning models, Random Forest (RF), Support Vector Machine (SVM), and AdaBoost, we adopted Bayesian-optimized RF as the classification algorithm. In terms of model interpretation, in addition to using common SHapley Additive exPlanations (SHAP) to provide global explanations for the model, we also utilized the Local Interpretable Model-Agnostic Explanations with stability (LIME_stabilitly) to provide local explanations for the model. Conclusion Both the fivefold cross-validation and independent testing show that our proposed method significantly outperforms the state-of-the-art method. IHCP maintains excellent model interpretability while obtaining excellent predictive performance. This helps uncover potential predictive patterns of the model and enables clinicians to better understand the model's decision-making process