Search Results (12)

Organophosphorus pesticides (OPs) have become one of the most widely used pesticides in Chinese agriculture; however, methods to identify potential restrictions on OPs molecules are lacking. Therefore, this study retrieved the OPs restriction list and constructed eight multi-class, multi-category machine learning models for OPs restrictions. Among these, the random forest (RF) model demonstrated excellent predictive performance, as it was successfully validated and applied. Potential environmental transformation products of OPs were obtained using EAWAG-BBD software, while toxicity indicators for the parent OPs and their transformation products were predicted with ADMETlab 3.0 software. This study found that unrestricted OPs, such as phorate, parathion, and chlorpyrifos, exhibited a high probability of toxicity. Additionally, the environmental transformation products of OPs posed similar comprehensive toxicity risks as the parent compounds. A special attention list for OPs was created based on the toxicity risks of unrestricted parent OPs and their transformation products, using standard deviation classification. Phorate and parathion were identified as OPs requiring special attention. This paper aims to provide an effective method for identifying the potential restriction levels of OPs and to propose an evaluation system that comprehensively considers the health risk, thereby supporting the improvement and optimization of management and usage strategies for OPs. Full article

Predicting the toxicity of nanoparticles plays an important role in biomedical nanotechnologies, in particular in the creation of new drugs. Safety analysis of nanoparticles can identify potentially harmful effects on living organisms and the environment. Advanced machine learning models are used to predict the toxicity of nanoparticles in a nutrient solution. In this article, we performed a comparative analysis of the current state of research in the field of nanoparticle toxicity analysis using machine learning methods; we trained a regression model for predicting the quantitative toxicity of nanoparticles depending on their concentration in the nutrient solution at a fixed point in time with the achieved metrics values of MSE = 2.19 and RMSE = 1.48; we trained a multi-class classification model for predicting the toxicity class of nanoparticles depending on their concentration in the nutrient solution at a fixed point in time with the achieved metrics values of Accuracy = 0.9756, Recall = 0.9623, F1-Score = 0.9640, and Log Loss = 0.1855. As a result of the analysis, we concluded the good predictive ability of the trained models. The optimal dosages for the nanoparticles under study were determined as follows: ZnO = 9.5 × 10⁻⁵ mg/mL; Fe₃O₄ = 0.1 mg/mL; SiO₂ = 1 mg/mL. The most significant features of predictive models are the diameter of the nanoparticle and the nanoparticle concentration in the nutrient solution. Full article

Optimization of land management and agricultural practices require precise classification of soil properties. This study presents a method to fine-tune deep neural network (DNN) hyperparameters for multiclass classification of soil properties using genetic algorithms (GAs) with knowledge-based generation of hyperparameters. The focus is on classifying soil attributes, including nutrient availability (0.78 ± 0.11), nutrient retention capacity (0.86 ± 0.05), rooting conditions (0.85 ± 0.07), oxygen availability to roots (0.84 ± 0.05), excess salts (0.96 ± 0.02), toxicity (0.96 ± 0.01), and soil workability (0.84 ± 0.09), with these accuracies representing the results from classification with variations from cross-validation. A dataset from the USA, which includes land-use distribution, aspect distribution, slope distribution, and climate data for each plot, is utilized. A GA is applied to explore a wide range of hyperparameters, such as the number of layers, neurons per layer, activation functions, optimizers, learning rates, and loss functions. Additionally, ensemble methods such as random forest and gradient boosting machines were employed, demonstrating comparable accuracy to the DNN approach. This research contributes to the advancement of precision agriculture by providing a robust machine learning (ML) framework for accurate soil property classification. By enabling more informed and efficient land management decisions, it promotes sustainable agricultural practices that optimize resource use and enhance soil health for long-term ecological balance. Full article

Among the various compounds regarded as emerging contaminants (ECs), pharmaceuticals and personal care products (PPCPs) are of particular concern. Their continuous release into the environment has a negative global impact on human life. This review summarizes the sources, occurrence, persistence, consequences of exposure, and toxicity of PPCPs, and evaluates the various analytical methods used in the identification and quantification of PPCPs in a variety of solid and liquid environmental matrices. The current techniques of choice for the analysis of PPCPs are state-of-the-art liquid chromatography coupled to mass spectrometry (LC-MS) or tandem mass spectrometry (LC-MS²). However, the complexity of the environmental matrices and the trace levels of micropollutants necessitate the use of advanced sample treatments before these instrumental analyses. Solid-phase extraction (SPE) with different sorbents is now the predominant method used for the extraction of PPCPs from environmental samples. This review also addresses the ongoing analytical method challenges, including sample clean-up and matrix effects, focusing on the occurrence, sample preparation, and analytical methods presently available for the determination of environmental residues of PPCPs. Continuous development of innovative analytical methods is essential for overcoming existing limitations and ensuring the consistency and diversity of analytical methods used in investigations of environmental multi-class compounds. Full article

Environmental chemicals, such as PFAS, exist as mixtures and are frequently encountered at varying concentrations, which can lead to serious health effects, such as cancer. Therefore, understanding the dose-dependent toxicity of chemical mixtures is essential for health risk assessment. However, comprehensive methods to assess toxicity and identify the mechanisms of these harmful mixtures are currently absent. In this study, the dose-dependent toxicity assessments of chemical mixtures are performed in three methodologically distinct phases. In the first phase, we evaluated our machine-learning method (AI-HNN) and pathophysiology method (CPTM) for predicting toxicity. In the second phase, we integrated AI-HNN and CPTM to establish a comprehensive new approach method (NAM) framework called AI-CPTM that is targeted at refining prediction accuracy and providing a comprehensive understanding of toxicity mechanisms. The third phase involved experimental validations of the AI-CPTM predictions. Initially, we developed binary, multiclass classification, and regression models to predict binary, categorical toxicity, and toxic potencies using nearly a thousand experimental mixtures. This empirical dataset was expanded with assumption-based virtual mixtures, compensating for the lack of experimental data and broadening the scope of the dataset. For comparison, we also developed machine-learning models based on RF, Bagging, AdaBoost, SVR, GB, KR, DT, KN, and Consensus methods. The AI-HNN achieved overall accuracies of over 80%, with the AUC exceeding 90%. In the final phase, we demonstrated the superior performance and predictive capability of AI-CPTM, including for PFAS mixtures and their interaction effects, through rigorous literature and statistical validations, along with experimental dose-response zebrafish-embryo toxicity assays. Overall, the AI-CPTM approach significantly improves upon the limitations of standalone AI models, showing extensive enhancements in identifying toxic chemicals and mixtures and their mechanisms. This study is the first to develop a hybrid NAM that integrates AI with a pathophysiology method to comprehensively predict chemical-mixture toxicity, carcinogenicity, and mechanisms. Full article

This study addresses the challenge of assessing the carcinogenic potential of hazardous chemical mixtures, such as per- and polyfluorinated substances (PFASs), which are known to contribute significantly to cancer development. Here, we propose a novel framework called HNN_MixCancer that utilizes a hybrid neural network (HNN) integrated into a machine-learning framework. This framework incorporates a mathematical model to simulate chemical mixtures, enabling the creation of classification models for binary (carcinogenic or noncarcinogenic) and multiclass classification (categorical carcinogenicity) and regression (carcinogenic potency). Through extensive experimentation, we demonstrate that our HNN model outperforms other methodologies, including random forest, bootstrap aggregating, adaptive boosting, support vector regressor, gradient boosting, kernel ridge, decision tree with AdaBoost, and KNeighbors, achieving a superior accuracy of 92.7% in binary classification. To address the limited availability of experimental data and enrich the training data, we generate an assumption-based virtual library of chemical mixtures using a known carcinogenic and noncarcinogenic single chemical for all the classification models. Remarkably, in this case, all methods achieve accuracies exceeding 98% for binary classification. In external validation tests, our HNN method achieves the highest accuracy of 80.5%. Furthermore, in multiclass classification, the HNN demonstrates an overall accuracy of 96.3%, outperforming RF, Bagging, and AdaBoost, which achieved 91.4%, 91.7%, and 80.2%, respectively. In regression models, HNN, RF, SVR, GB, KR, DT with AdaBoost, and KN achieved average R² values of 0.96, 0.90, 0.77, 0.94, 0.96, 0.96, and 0.97, respectively, showcasing their effectiveness in predicting the concentration at which a chemical mixture becomes carcinogenic. Our method exhibits exceptional predictive power in prioritizing carcinogenic chemical mixtures, even when relying on assumption-based mixtures. This capability is particularly valuable for toxicology studies that lack experimental data on the carcinogenicity and toxicity of chemical mixtures. To our knowledge, this study introduces the first method for predicting the carcinogenic potential of chemical mixtures. The HNN_MixCancer framework offers a novel alternative for dose-dependent carcinogen prediction. Ongoing efforts involve implementing the HNN method to predict mixture toxicity and expanding the application of HNN_MixCancer to include multiple mixtures such as PFAS mixtures and co-occurring chemicals. Full article

Humans are exposed to thousands of chemicals, including environmental chemicals. Unfortunately, little is known about their potential toxicity, as determining the toxicity remains challenging due to the substantial resources required to assess a chemical in vivo. Here, we present a novel hybrid neural network (HNN) deep learning method, called HNN-Tox, to predict chemical toxicity at different doses. To develop a hybrid HNN-Tox method, we combined two neural network frameworks, the Convolutional Neural Network (CNN) and the multilayer perceptron (MLP)-type feed-forward neural network (FFNN). Combining the CNN and FCNN in the field of environmental chemical toxicity prediction is a novel approach. We developed several binary and multiclass classification models to assess dose-range chemical toxicity that is trained based on thousands of chemicals with known toxicity. The performance of the HNN-Tox was compared with other machine-learning methods, including Random Forest (RF), Bootstrap Aggregation (Bagging), and Adaptive Boosting (AdaBoost). We also analyzed the model performance dependency on varying features, descriptors, dataset size, route of exposure, and toxic dose. The HNN-Tox model, trained on 59,373 chemicals annotated with known LD50 and routes of exposure, maintained its predictive ability with an accuracy of 84.9% and 84.1%, even after reducing the descriptor size from 318 to 51, and the area under the ROC curve (AUC) was 0.89 and 0.88, respectively. Further, we validated the HNN-Tox with several external toxic chemical datasets on a large scale. The HNN-Tox performed optimally or better than the other machine-learning methods for diverse chemicals. This study is the first to report a large-scale prediction of dose-range chemical toxicity with varying features. The HNN-Tox has broad applicability in predicting toxicity for diverse chemicals and could serve as an alternative methodology approach to animal-based toxicity assessment. Full article

Radiotherapy is one of the main treatments for localized head and neck (HN) cancer. To design a personalized treatment with reduced radio-induced toxicity, accurate delineation of organs at risk (OAR) is a crucial step. Manual delineation is time- and labor-consuming, as well as observer-dependent. Deep learning (DL) based segmentation has proven to overcome some of these limitations, but requires large databases of homogeneously contoured image sets for robust training. However, these are not easily obtained from the standard clinical protocols as the OARs delineated may vary depending on the patient’s tumor site and specific treatment plan. This results in incomplete or partially labeled data. This paper presents a solution to train a robust DL-based automated segmentation tool exploiting a clinical partially labeled dataset. We propose a two-step workflow for OAR segmentation: first, we developed longitudinal OAR-specific 3D segmentation models for pseudo-contour generation, completing the missing contours for some patients; with all OAR available, we trained a multi-class 3D convolutional neural network (nnU-Net) for final OAR segmentation. Results obtained in 44 independent datasets showed superior performance of the proposed methodology for the segmentation of fifteen OARs, with an average Dice score coefficient and surface Dice similarity coefficient of 80.59% and 88.74%. We demonstrated that the model can be straightforwardly integrated into the clinical workflow for standard and adaptive radiotherapy. Full article

Cyanotoxins are toxic metabolites produced by most cyanobacteria. In recent years, the occurrence of cyanobacterial blooms in aquatic ecosystems has temporally and spatially increased because of nutrient oversupply caused by human and also by climatic changes. This increase has a negative impact on water quality, ecosystem integrity, and human health. Cyanotoxins constitute a group of compounds with diverse physicochemical properties and their presence in drinkable, fishable, and recreational water is the main health-damaging cause. They are also able to bioaccumulate in plants and vegetables irrigated with contaminated water. Research on the development of suitable analytical methods is needed to establish early-warning strategies for the improved protectionof humans and ecosystems health. Liquid chromatography coupled with mass spectrometry (LC-MS) has been the preferred option for the control of these compounds, mainly using reverse-phase mode or hydrophilic interaction liquid chromatography (HILIC) in order to separate multiclass cyanotoxins of varying polarity, which cannot be handled by the commonly used reverse phase columns. In this work, we propose the use of capillary electrophoresis (CE) coupled with tandem mass spectrometry using triple quadrupole and positive electrospray ionization (CE-(ESI)-MS/MS) to determine a mixture of cyanotoxins with different polarity. CE is an advantageous alternative to LC given its short analysis times, high resolution, low sample and reagent volumes, and the use of silica capillaries and buffers as separation media, resulting in lower cost and low environmental impact. Moreover, CE allows the analysis of molecules hardly affordable by LC, such as polar and very similar compounds (e.g., isomers). The method is designed for the simultaneous determination of eight cyanotoxins belonging to three different classes: cyclic peptides (microcystin-LR, microcystin-RR, and nodularin), alkaloids (cylindrospermopsin, anatoxin-a), and three non-protein amino acids isomers (β-methylamino-L-alanine, 2,4-diaminobutyric acid, and N-(2-aminoethyl) glycine). Separation was achieved using an acidic background electrolyte (BGE) consisting in 2 M of formic acid (FA) and 20% acetonitrile in water. The proper separation and resolution of the three non-protein amino acid isomers was one of the main challenges of the method. This was overcome by applying a voltage of 30 kV in a 90 cm length capillary at 20 °C. Parameters affecting MS detection and the sheath–liquid interface were also studied. Finally, the fixed values were: a sheath gas flow rate of 5 L/min at 195 °C; sheath–liquid consists of MeOH/H2O/FA (50:49.95:0.05 v/v/v), a flow rate of 15 μL/min; and a nozzle voltage of 2000 V; N₂ dry gas rate of 11 L/min at 150 °C; a nebulizer pressure of 10 psi; and a capillary voltage of 2000 V. Online pre-concentration approaches were tested in order to achieve higher sensitivity, obtaining a enrichment factor of 4 with a mixed technique of pH-junction and Field Amplied Sample Stacking (FASS). Full article

Molecules with pleasant odors, unacceptable odors, and even serious toxicity are closely related to human social life. It is impractical to identify the odors of molecules in large quantities (particularly hazardous odors) using experimental methods. Computer-aided methods have currently attracted increasing attention for the prediction of molecular odors. Here, through models based on multilayer perceptron (MLP) and physicochemical descriptors (MLP-Des), MLP and molecular fingerprint, and convolutional neural network (CNN), we conduct the two-class prediction of odor/no odor, fruity/no odor, floral/no odor, and woody/no odor, and the multi-class prediction of fruity/flowery/woody/no odor on our newly refined molecular odor datasets. We show that three kinds of predictors can robustly predict molecular odors. The MLP-Des model not only exhibits the best prediction results (the AUC values are 0.99 and 0.86 for the two- and multi-classification models, respectively) but can also well reflect the characteristics of the structure–odor relationship of molecules. The CNN model takes 2D molecular images as input and can automatically extract the structural features related to molecular odors. The proposed models are of great help for the prediction of molecular odorants, understanding the underlying relationship between chemical structure and odor perception, and the discovery of new odorous and/or hazardous molecules. Full article

Machine learning classification algorithms are widely used for the prediction and classification of the different properties of molecules such as toxicity or biological activity. The prediction of toxic vs. non-toxic molecules is important due to testing on living animals, which has ethical and cost drawbacks as well. The quality of classification models can be determined with several performance parameters. which often give conflicting results. In this study, we performed a multi-level comparison with the use of different performance metrics and machine learning classification methods. Well-established and standardized protocols for the machine learning tasks were used in each case. The comparison was applied to three datasets (acute and aquatic toxicities) and the robust, yet sensitive, sum of ranking differences (SRD) and analysis of variance (ANOVA) were applied for evaluation. The effect of dataset composition (balanced vs. imbalanced) and 2-class vs. multiclass classification scenarios was also studied. Most of the performance metrics are sensitive to dataset composition, especially in 2-class classification problems. The optimal machine learning algorithm also depends significantly on the composition of the dataset. Full article

P-glycoprotein (P-gp) is a transmembrane protein that actively transports a wide variety of chemically diverse compounds out of the cell. It is highly associated with the ADMET (absorption, distribution, metabolism, excretion and toxicity) properties of drugs/drug candidates and contributes to decreasing toxicity by eliminating compounds from cells, thereby preventing intracellular accumulation. Therefore, in the drug discovery and toxicological assessment process it is advisable to pay attention to whether a compound under development could be transported by P-gp or not. In this study, an in silico multiclass classification model capable of predicting the probability of a compound to interact with P-gp was developed using a counter-propagation artificial neural network (CP ANN) based on a set of 2D molecular descriptors, as well as an extensive dataset of 2512 compounds (1178 P-gp inhibitors, 477 P-gp substrates and 857 P-gp non-active compounds). The model provided a good classification performance, producing non error rate (NER) values of 0.93 for the training set and 0.85 for the test set, while the average precision (AvPr) was 0.93 for the training set and 0.87 for the test set. An external validation set of 385 compounds was used to challenge the model’s performance. On the external validation set the NER and AvPr values were 0.70 for both indices. We believe that this in silico classifier could be effectively used as a reliable virtual screening tool for identifying potential P-gp ligands. Full article