Breast cancer (BC) is a heterogeneous disease where genomic alterations, protein expression deregulation, signaling pathway alterations, hormone disruption, ethnicity and environmental determinants are involved. Due to the complexity of BC, the prediction of proteins involved in this disease is a trending topic in drug design. This work is proposing accurate prediction classifier for BC proteins using six sets of protein sequence descriptors and 13 machine-learning methods. After using a univariate feature selection for the mix of five descriptor families, the best classifier was obtained using multilayer perceptron method (artificial neural network) and 300 features. The performance of the model is demonstrated by the area under the receiver operating characteristics (AUROC) of 0.980 ± 0.0037, and accuracy of 0.936 ± 0.0056 (3-fold cross-validation). Regarding the prediction of 4,504 cancer-associated proteins using this model, the best ranked cancer immunotherapy proteins related to BC were RPS27, SUPT4H1, CLPSL2, POLR2K, RPL38, AKT3, CDK3, RPS20, RASL11A and UBTD1; the best ranked metastasis driver proteins related to BC were S100A9, DDA1, TXN, PRNP, RPS27, S100A14, S100A7, MAPK1, AGR3 and NDUFA13; and the best ranked RNA-binding proteins related to BC were S100A9, TXN, RPS27L, RPS27, RPS27A, RPL38, MRPL54, PPAN, RPS20 and CSRP1. This powerful model predicts several BC-related proteins that should be deeply studied to find new biomarkers and better therapeutic targets. Scripts can be downloaded athttps://github.com/muntisa/neural-networks-for-breast-cancer-proteins.

This study evaluated the antioxidative effects of magnolol based on the mouse model induced by Enterotoxigenic Escherichia coli (E. coli, ETEC). All experimental mice were equally treated with ETEC suspensions (3.45×109 CFU/ml) after oral administration of magnolol for 7 days at the dose of 0, 100, 300 and 500 mg/kg Body Weight (BW), respectively. The oxidative metabolites and antioxidases for each sample (organism of mouse) were determined: Malondialdehyde (MDA), Nitric Oxide (NO), Glutathione (GSH), Myeloperoxidase (MPO), Catalase (CAT), Superoxide Dismutase (SOD), and Glutathione Peroxidase (GPx). In addition, we also determined the corresponding mRNA expressions of CAT, SOD and GPx as well as the Total Antioxidant Capacity (T-AOC). The experiment was completed with a theoretical study that predicts a series of 79 ChEMBL activities of magnolol with 47 proteins in 18 organisms using a Quantitative Structure- Activity Relationship (QSAR) classifier based on the Moving Averages (MAs) of Rcpi descriptors in three types of experimental conditions (biological activity with specific units, protein target and organisms). Six Machine Learning methods from Weka software were tested and the best QSAR classification model was provided by Random Forest with True Positive Rate (TPR) of 0.701 and Area under Receiver Operating Characteristic (AUROC) of 0.790 (test subset, 10-fold crossvalidation). The model is predicting if the new ChEMBL activities are greater or lower than the average values for the magnolol targets in different organisms.

Colorectal cancer is one of the most frequent types of cancer in the world and generates important social impact. The understanding of the specific metabolism of this disease and the transformations of the specific drugs will allow finding effective prevention, diagnosis and treatment of the colorectal cancer. All the terms that describe the drug metabolism contribute to the construction of ontology in order to help scientists to link the correlated information and to find the most useful data about this topic. The molecular components involved in this metabolism are included in complex network such as metabolic pathways in order to describe all the molecular interactions in the colorectal cancer. The graphical method of processing biological information such as graphs and complex networks leads to the numerical characterization of the colorectal cancer drug metabolic network by using invariant values named topological indices. Thus, this method can help scientists to study the most important elements in the metabolic pathways and the dynamics of the networks during mutations, denaturation or evolution for any type of disease. This review presents the last studies regarding ontology and complex networks of the colorectal cancer drug metabolism and a basic topology characterization of the drug metabolic process subontology from the Gene Ontology.

Physicians in the Intensive Care Unit (ICU) are specially trained to deal constantly with very large and complex quantities of clinical data and make quick decisions as they face complications. However, the amount of information generated and the way the data are presented may overload the cognitive skills of even experienced professionals and lead to inaccurate or erroneous actions that put patients’ lives at risk. In this paper, we present the design, development, and validation of iOSC3, an ontology-based system for intelligent supervision and treatment of critical patients with acute cardiac disorders. The system analyzes the patient’s condition and provides a recommendation about the treatment that should be administered to achieve the fastest possible recovery. If the recommendation is accepted by the doctor, the system automatically modifies the quantity of drugs that are being delivered to the patient. The knowledge base is constituted by an OWL ontology and a set of SWRL rules that represent the expert’s knowledge. iOSC3 has been developed in collaboration with experts from the Cardiac Intensive Care Unit (CICU) of the Meixoeiro Hospital, one of the most significant hospitals in the northwest region of Spain.