Application of artificial intelligence for detection of chemico-biological interactions associated with oxidative stress and DNA damage

Isothiocyanates Potentiate Tazemetostat-Induced Apoptosis by Modulating the Expression of Apoptotic Genes, Members of Polycomb Repressive Complex 2, and Levels of Tri-Methylating Lysine 27 at Histone 3 in Human Malignant Melanoma Cells

In this study, we utilized an in vitro model consisting of human malignant melanoma as well as non-tumorigenic immortalized keratinocyte cells with the aim of characterizing the therapeutic effectiveness of the clinical epigenetic drug Tazemetostat alone or in combination with various isothiocyanates. In doing so, we assessed markers of cell viability, apoptotic induction, and expression levels of key proteins capable of mediating the therapeutic response. Our data indicated, for the first time, that Tazemetostat caused a significant decrease in viability levels of malignant melanoma cells in a dose- and time-dependent manner via the induction of apoptosis, while non-malignant keratinocytes were more resistant. Moreover, combinatorial treatment protocols caused a further decrease in cell viability, together with higher apoptotic rates. In addition, a significant reduction in the Polycomb Repressive Complex 2 (PRC2) members [e.g., Enhancer of Zeste Homologue 2 (EZH2), Embryonic Ectoderm Development (EED), and suppressor of zeste 12 (SUZ12)] and tri-methylating lysine 27 at Histone 3 (H3K27me3) protein expression levels was observed, at least partially, under specific combinatorial exposure conditions. Reactivation of major apoptotic gene targets was determined at much higher levels in combinatorial treatment protocols than Tazemetostat alone, known to be involved in the induction of intrinsic and extrinsic apoptosis. Overall, we developed an optimized experimental therapeutic platform aiming to ensure the therapeutic effectiveness of Tazemetostat in malignant melanoma while at the same time minimizing toxicity against neighboring non-tumorigenic keratinocyte cells.

Gray-Level Co-occurrence Matrix Analysis of Nuclear Textural Patterns in Laryngeal Squamous Cell Carcinoma: Focus on Artificial Intelligence Methods

Gray-level co-occurrence matrix (GLCM) and discrete wavelet transform (DWT) analyses are two contemporary computational methods that can identify discrete changes in cell and tissue textural features. Previous research has indicated that these methods may be applicable in the pathology for identification and classification of various types of cancers. In this study, we present findings that squamous epithelial cells in laryngeal carcinoma, which appear morphologically intact during conventional pathohistological evaluation, have distinct nuclear GLCM and DWT features. The average values of nuclear GLCM indicators of these cells, such as angular second moment, inverse difference moment, and textural contrast, substantially differ when compared to those in noncancerous tissue. In this work, we also propose machine learning models based on random forests and support vector machine that can be successfully trained to separate the cells using GLCM and DWT quantifiers as input data. We show that, based on a limited cell sample, these models have relatively good classification accuracy and discriminatory power, which makes them suitable candidates for future development of AI-based sensors potentially applicable in laryngeal carcinoma diagnostic protocols.

Evaluating ChatGPT's Ability to Solve Higher-Order Questions on the Competency-Based Medical Education Curriculum in Medical Biochemistry

Background Healthcare-related artificial intelligence (AI) is developing. The capacity of the system to carry out sophisticated cognitive processes, such as problem-solving, decision-making, reasoning, and perceiving, is referred to as higher cognitive thinking in AI. This kind of thinking requires more than just processing facts; it also entails comprehending and working with abstract ideas, evaluating and applying data relevant to the context, and producing new insights based on prior learning and experience. ChatGPT is an artificial intelligence-based conversational software that can engage with people to answer questions and uses natural language processing models. The platform has created a worldwide buzz and keeps setting an ongoing trend in solving many complex problems in various dimensions. Nevertheless, ChatGPT's capacity to correctly respond to queries requiring higher-level thinking in medical biochemistry has not yet been investigated. So, this research aimed to evaluate ChatGPT's aptitude for responding to higher-order questions on medical biochemistry. Objective In this study, our objective was to determine whether ChatGPT can address higher-order problems related to medical biochemistry.​​​​​​ Methods​​​ This cross-sectional study was done online by conversing with the current version of ChatGPT (14 March 2023, which is presently free for registered users). It was presented with 200 medical biochemistry reasoning questions that require higher-order thinking. These questions were randomly picked from the institution's question bank and classified according to the Competency-Based Medical Education (CBME) curriculum's competency modules. The responses were collected and archived for subsequent research. Two expert biochemistry academicians examined the replies on a zero to five scale. The score's accuracy was determined by a one-sample Wilcoxon signed rank test using hypothetical values. Result The AI software answered 200 questions requiring higher-order thinking with a median score of 4.0 (Q1=3.50, Q3=4.50). Using a single sample Wilcoxon signed rank test, the result was less than the hypothetical maximum of five (p=0.001) and comparable to four (p=0.16). There was no difference in the replies to questions from different CBME modules in medical biochemistry (Kruskal-Wallis p=0.39). The inter-rater reliability of the scores scored by two biochemistry faculty members was outstanding (ICC=0.926 (95% CI: 0.814-0.971); F=19; p=0.001)​​​​​​ Conclusion The results of this research indicate that ChatGPT has the potential to be a successful tool for answering questions requiring higher-order thinking in medical biochemistry, with a median score of four out of five. However, continuous training and development with data of recent advances are essential to improve performance and make it functional for the ever-growing field of academic medical usage.

Machine learning and artificial intelligence in physiologically based pharmacokinetic modeling

Physiologically based pharmacokinetic (PBPK) models are useful tools in drug development and risk assessment of environmental chemicals. PBPK model development requires the collection of species-specific physiological, and chemical-specific absorption, distribution, metabolism, and excretion (ADME) parameters, which can be a time-consuming and expensive process. This raises a need to create computational models capable of predicting input parameter values for PBPK models, especially for new compounds. In this review, we summarize an emerging paradigm for integrating PBPK modeling with machine learning (ML) or artificial intelligence (AI)-based computational methods. This paradigm includes 3 steps (1) obtain time-concentration PK data and/or ADME parameters from publicly available databases, (2) develop ML/AI-based approaches to predict ADME parameters, and (3) incorporate the ML/AI models into PBPK models to predict PK summary statistics (eg, area under the curve and maximum plasma concentration). We also discuss a neural network architecture "neural ordinary differential equation (Neural-ODE)" that is capable of providing better predictive capabilities than other ML methods when used to directly predict time-series PK profiles. In order to support applications of ML/AI methods for PBPK model development, several challenges should be addressed (1) as more data become available, it is important to expand the training set by including the structural diversity of compounds to improve the prediction accuracy of ML/AI models; (2) due to the black box nature of many ML models, lack of sufficient interpretability is a limitation; (3) Neural-ODE has great potential to be used to generate time-series PK profiles for new compounds with limited ADME information, but its application remains to be explored. Despite existing challenges, ML/AI approaches will continue to facilitate the efficient development of robust PBPK models for a large number of chemicals.

Artificial neural networks in contemporary toxicology research

Artificial neural networks (ANNs) have a huge potential in toxicology research. They may be used to predict toxicity of various chemical compounds or classify the compounds based on their toxic effects. Today, numerous ANN models have been developed, some of which may be used to detect and possibly explain complex chemico-biological interactions. Fully connected multilayer perceptrons may in some circumstances have high classification accuracy and discriminatory power in separating damaged from intact cells after exposure to a toxic substance. Regularized and not fully connected convolutional neural networks can detect and identify discrete changes in patterns of two-dimensional data associated with toxicity. Bayesian neural networks with weight marginalization sometimes may have better prediction performance when compared to traditional approaches. With the further development of artificial intelligence, it is expected that ANNs will in the future become important parts of various accurate and affordable biosensors for detection of various toxic substances and evaluation of their biochemical properties. In this concise review article, we discuss the recent research focused on the scientific value of ANNs in evaluation and prediction of toxicity of chemical compounds.

Bioactive limonoids from Carapa guianensis seeds oil and the sustainable use of its by-products

Carapa guianensis (Andiroba, Meliaceae) is considered a multipurpose tree. In Brazil, Indigenous people have used it as insect repellent and in the treatment of various diseases. Most biological activities and popular uses are attributed to limonoids, which are highly oxygenated tetranortriterpenoids. More than 300 limonoids have been described in Meliaceae family. Limonoids from Andiroba oil have shown high anti-inflammatory and anti-allergic activities in vivo, by inhibiting platelet activating factors and many inflammatory mediators such as IL-5, IL-1β and TNF-α. It also reduced T lymphocytes, eosinophils and mast cells. In corroboration with the wide popular use of Andiroba oil, no significant cytotoxicity or genotoxicity in vivo was reported. This oil promotes apoptosis in a gastric cancer cell line (ACP02) at high concentrations, without showing mutagenic effects, and is suggested to increase the body's nonspecific resistance and adaptive capacity to stressors, exhibit some antioxidant activity, and protect against oxidative DNA damages. Recently, new methodologies of toxicological assays have been applied. They include in chemico, in vitro, in silico and ex vivo procedures, and take place to substitute the use of laboratory animals. Andiroba by-products have been used in sustainable oil production processes and as fertilizers and soil conditioners, raw material for soap production, biodegradable surfactants and an alternative natural source of biodegradable polymer in order to reduce environmental impacts. This review reinforces the relevance of Andiroba and highlights its ability to add value to its by-products and to minimize possible risks to the health of the Amazonian population.

Machine learning and artificial intelligence in toxicological sciences

Machine learning and artificial intelligence approaches have revolutionized multiple disciplines, including toxicology. This review summarizes representative recent applications of machine learning and artificial intelligence approaches in different areas of toxicology, including physiologically based pharmacokinetic (PBPK) modeling, quantitative structure-activity relationship modeling for toxicity prediction, adverse outcome pathway analysis, high-throughput screening, toxicogenomics, big data and toxicological databases. By leveraging machine learning and artificial intelligence approaches, now it is possible to develop PBPK models for hundreds of chemicals efficiently, to create in silico models to predict toxicity for a large number of chemicals with similar accuracies compared to in vivo animal experiments, and to analyze a large amount of different types of data (toxicogenomics, high-content image data, etc.) to generate new insights into toxicity mechanisms rapidly, which was impossible by manual approaches in the past. To continue advancing the field of toxicological sciences, several challenges should be considered: (1) not all machine learning models are equally useful for a particular type of toxicology data, and thus it is important to test different methods to determine the optimal approach; (2) current toxicity prediction is mainly on bioactivity classification (yes/no), so additional studies are needed to predict the intensity of effect or dose-response relationship; (3) as more data become available, it is crucial to perform rigorous data quality check and develop infrastructure to store, share, analyze, evaluate, and manage big data; and (4) it is important to convert machine learning models to user-friendly interfaces to facilitate their applications by both computational and bench scientists.

Artificial intelligence approaches to the biochemistry of oxidative stress: Current state of the art

Artificial intelligence (AI) and machine learning models are today frequently used for classification and prediction of various biochemical processes and phenomena. In recent years, numerous research efforts have been focused on developing such models for assessment, categorization, and prediction of oxidative stress. Supervised machine learning can successfully automate the process of evaluation and quantification of oxidative damage in biological samples, as well as extract useful data from the abundance of experimental results. In this concise review, we cover the possible applications of neural networks, decision trees and regression analysis as three common strategies in machine learning. We also review recent works on the various weaknesses and limitations of artificial intelligence in biochemistry and related scientific areas. Finally, we discuss future innovative approaches on the ways how AI can contribute to the automation of oxidative stress measurement and diagnosis of diseases associated with oxidative damage.

Gray-Level Co-occurrence Matrix Analysis for the Detection of Discrete, Ethanol-Induced, Structural Changes in Cell Nuclei: An Artificial Intelligence Approach

Gray-level co-occurrence matrix (GLCM) analysis is a contemporary and innovative computational method for the assessment of textural patterns, applicable in almost any area of microscopy. The aim of our research was to perform the GLCM analysis of cell nuclei in Saccharomyces cerevisiae yeast cells after the induction of sublethal cell damage with ethyl alcohol, and to evaluate the performance of various machine learning (ML) models regarding their ability to separate damaged from intact cells. For each cell nucleus, five GLCM parameters were calculated: angular second moment, inverse difference moment, GLCM contrast, GLCM correlation, and textural variance. Based on the obtained GLCM data, we applied three ML approaches: neural network, random trees, and binomial logistic regression. Statistically significant differences in GLCM features were observed between treated and untreated cells. The multilayer perceptron neural network had the highest classification accuracy. The model also showed a relatively high level of sensitivity and specificity, as well as an excellent discriminatory power in the separation of treated from untreated cells. To the best of our knowledge, this is the first study to demonstrate that it is possible to create a relatively sensitive GLCM-based ML model for the detection of alcohol-induced damage in Saccharomyces cerevisiae cell nuclei.

Association between Chromatin Structural Organization of Peripheral Blood Neutrophils and Self-Perceived Mental Stress: Gray-Level Co-occurrence Matrix Analysis

Methods based on the evaluation of textural patterns in microscopy, such as the “gray-level co-occurrence matrix” (GLCM) analysis are modern and innovative computer and mathematical algorithms that can be used to quantify subtle structural changes in cells and their organelles. Potential application of GLCM method in the fields of psychophysiology and psychiatry to this date has not been systematically investigated. The main objective of our study was to test the existence and strength of the association between chromatin structural organization of peripheral blood neutrophils and levels of self-perceived mental stress. The research was done on a sample of 100 healthy student athletes, and the Depression, Anxiety, and Stress Scales (DASS-21) were used for the estimation of psychological distress. Chromatin textural homogeneity and uniformity were negatively correlated (p < 0.01) with mental distress and had relatively good discriminatory power in differentiating participants with normal and elevated stress levels. As an addition, we propose the creation of a machine learning model based on binomial logistic regression that uses these and other GLCM features to predict stress elevation. To the best of our knowledge, these results are one of the first to establish the link between neutrophil chromatin structural organization quantified by the GLCM method and indicators of normal psychological functioning.