Gabriel B. M. Camara

COVID-19, the illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus belonging to the Coronaviridade family, a single-strand positive-sense RNA genome, has been spreading around the world and has been declared a pandemic by the World Health Organization. On 17 January 2022, there were more than 329 million cases, with more than 5.5 million deaths. Although COVID-19 has a low mortality rate, its high capacities for contamination, spread, and mutation worry the authorities, especially after the emergence of the Omicron variant, which has a high transmission capacity and can more easily contaminate even vaccinated people. Such outbreaks require elucidation of the taxonomic classification and origin of the virus (SARS-CoV-2) from the genomic sequence for strategic planning, containment, and treatment of the disease. Thus, this work proposes a high-accuracy technique to classify viruses and other organisms from a genome sequence using a deep learning convolutional neural network (CNN). Unlike the other literature, the proposed approach does not limit the length of the genome sequence. The results show that the novel proposal accurately distinguishes SARS-CoV-2 from the sequences of other viruses. The results were obtained from 1557 instances of SARS-CoV-2 from the National Center for Biotechnology Information (NCBI) and 14,684 different viruses from the Virus-Host DB. As a CNN has several changeable parameters, the tests were performed with forty-eight different architectures; the best of these had an accuracy of 91.94 ± 2.62% in classifying viruses into their realms correctly, in addition to 100% accuracy in classifying SARS-CoV-2 into its respective realm, Riboviria. For the subsequent classifications (family, genera, and subgenus), this accuracy increased, which shows that the proposed architecture may be viable in the classification of the virus that causes COVID-19.

Nano-hybrid systems are products of interactions between organic and inorganic materials designed and planned to develop drug delivery platforms that can be self-assembled. Poloxamine, commercially available as Tetronic^®, is formed by blocks of copolymers consisting of poly (ethylene oxide) (PEO) and poly (propylene oxide) (PPO) units arranged in a four-armed star shape. Structurally, Tetronics are similar to Pluronics^®, with an additional feature as they are also pH-dependent due to their central ethylenediamine unit. Laponite is a synthetic clay arranged in the form of discs with a diameter of approximately 25 nm and a thickness of 1 nm. Both compounds are biocompatible and considered as candidates for the formation of carrier systems. The objective is to explore associations between a Tetronic (T1304) and LAP (Laponite) at concentrations of 1–20% (w/w) and 0–3% (w/w), respectively. Response surface methodology (RMS) and two types of machine learning (multilayer perceptron (MLP) and support vector machine (SVM)) were used to evaluate the physical behavior of the systems and the β-Lapachone (β-Lap) solubility in the systems. β-Lap (model drug with low solubility in water) has antiviral, antiparasitic, antitumor, and anti-inflammatory properties. The results show an adequate machine learning approach to predict the physical behavior of nanocarrier systems with and without the presence of LAP. Additionally, the analysis performed with SVM showed better results (R² > 0.97) in terms of data adjustment in the evaluation of β-Lap solubility. Furthermore, this work presents a new methodology for classifying phase behavior using ML. The new methodology allows the creation of a phase behavior surface for different concentrations of T1304 and LAP at different pHs and temperatures. The machine learning strategies used were excellent in assisting in the optimized development of new nano-hybrid platforms.

Since December 2019, the world has been intensely affected by the COVID-19 pandemic, caused by the SARS-CoV-2 virus, first identified in Wuhan, China. In the case of a novel virus identification, the early elucidation of taxonomic classification and origin of the virus genomic sequence is essential for strategic planning, containment, and treatments. Deep learning techniques have been successfully used in many viral classification problems associated with viral infections diagnosis, metagenomics, phylogenetic, and analysis. This work proposes to generate an efficient viral genome classifier for the SARS-CoV-2 virus using the deep neural network (DNN) based on stacked sparse autoencoder (SSAE) technique. We performed four different experiments to provide different levels of taxonomic classification of the SARS-CoV-2 virus. The confusion matrix presented the validation and test sets and the ROC curve for the validation set. In all experiments, the SSAE technique provided great performance results. In this work, we explored the utilization of image representations of the complete genome sequences as the SSAE input to provide a viral classification of the SARS-CoV-2. For that, a dataset based on k -mers image representation, with k = 6, was applied. The results indicated the applicability of using this deep learning technique in genome classification problems.

Nano-hybrid formulations combine organic and inorganic materials in self-assembled platforms for drug delivery. Laponite is a synthetic clay, biocompatible, and a guest of compounds. Poloxamines are amphiphilic four-armed compounds and have pH-sensitive and thermosensitive properties. The association of Laponite and Poloxamine can be used to improve attachment to drugs and to increase the solubility of β-Lapachone (β-Lap). β-Lap has antiviral, antiparasitic, antitumor, and anti-inflammatory properties. However, the low water solubility of β-Lap limits its clinical and medical applications. All samples were prepared by mixing Tetronic 1304 and LAP in a range of 1–20% (w/w) and 0–3% (w/w), respectively. The β-Lap solubility was analyzed by UV-vis spectrophotometry, and physical behavior was evaluated across a range of temperatures. The analysis of data consisted of response surface methodology (RMS), and two kinds of machine learning (ML): multilayer perceptron (MLP) and support vector machine (SVM). The ML techniques, generated from a training process based on experimental data, obtained the best correlation coefficient adjustment for drug solubility and adequate physical classifications of the systems. The SVM method presented the best fit results of β-Lap solubilization. In silico tools promoted fine-tuning, and near-experimental data show β-Lap solubility and classification of physical behavior to be an excellent strategy for use in developing new nano-hybrid platforms.