Article
Multidisciplinary Sciences
Yuan Mei, Kaijun Wu
Summary: This paper constructs a complete framework for compound selection, including feature selection, relationship mapping, and multi-objective optimization problem solving. It proposes a feature selection method based on unsupervised spectral clustering to select more comprehensive features, uses the CatBoost algorithm for relationship mapping, and improves the AGE-MOEA algorithm for multi-objective optimization, achieving better prediction and search performance.
SCIENTIFIC REPORTS
(2022)
Article
Environmental Sciences
Linda Bertato, Nicola Chirico, Ester Papa
Summary: This study developed linear and non-linear regression QSAR models to predict the bioaccumulation potential of substances in aquatic organisms, as well as linear and non-linear classification models to assess bioaccumulation capability. These models demonstrated good predictive accuracy and met regulatory requirements.
Article
Environmental Sciences
Jia-Yun Xu, Kun Wang, Shu-Hui Men, Yang Yang, Quan Zhou, Zhen-Guang Yan
Summary: Bioconcentration factor (BCF) is an important parameter for developing human health ambient water quality criteria (HHAWQC) for chemical pollutants. Traditional experimental methods are time-consuming and expensive, thus modeling approaches for predicting BCF have gained attention. However, previous models can only predict BCF for a single category of substance and species, limiting their applications. In this study, a QSAR-QSIIR model incorporating optimized molecular and bioactivity descriptors was constructed using the MLP machine learning algorithm, significantly improving BCF prediction accuracy.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Marine & Freshwater Biology
Hannah Mahoney, Jenna Cantin, Yuwei Xie, Markus Brinkmann, John P. Giesy
Summary: This study aimed to characterize the effects of PFECHS using in vitro systems, such as rainbow trout liver cells and lymphocytes. The results showed that exposure to PFECHS caused minor acute toxic effects and had a low bioconcentration factor. However, PFECHS was observed to affect mitochondrial membrane and key molecular receptors related to oxidative stress.
AQUATIC TOXICOLOGY
(2023)
Review
Environmental Sciences
Yanyan Zhang, Joann K. Whalen, Sebastien Sauve
Summary: Microcystins are highly phytotoxic to durum wheat, corn, white mustard, and garden cress, while leafy vegetables may bioconcentrate more microcystins in their edible parts. Human health risks from ingesting microcystins may be greater for leafy vegetables, but further research is needed to confirm bioconcentration levels in realistic environments.
ENVIRONMENTAL POLLUTION
(2021)
Article
Chemistry, Multidisciplinary
Sushil Kumar, Gergo Ignacz, Gyorgy Szekely
Summary: This study explores the use of green solvents to synthesize COFs, evaluating crystallinity and porosity to assess quality and identifying gamma-butyrolactone, para-cymene, and PolarClean as excellent green solvents. For the first time, the researchers successfully predicted the surface area and crystallinity of COFs using quantitative structure-property relationships and machine learning approaches.
Article
Chemistry, Medicinal
Robert P. Sheridan, J. Chris Culberson, Elizabeth Joshi, Matthew Tudor, Prabha Karnachi
Summary: This article examines the predictivity of quantitative structure-activity relationship (QSAR) models for different versions over a period of 10 years and provides insights into the application of these models in chemical design and synthesis. However, unexpected behavior and unclear explanations were found, which may be related to activity cliffs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Food Science & Technology
Valentina Andreea Petre, Florentina Laura Chiriac, Irina Eugenia Lucaciu, Iuliana Paun, Florinela Pirvu, Vasile Ion Iancu, Laura Novac, Stefania Gheorghe
Summary: The bioaccumulation and biotransformation of perfluorooctanoic acid (PFOA) in carp were evaluated in this study. PFOA and its metabolites were found in various organs of the fish, with the highest concentrations detected in the gallbladder, kidneys, brain, liver, and gonads. This study highlights the importance of monitoring and risk assessment of new synthetic chemicals in aquatic resources.
Article
Computer Science, Artificial Intelligence
Andrea Mastropietro, Giuseppe Pasculli, Juergen Bajorath
Summary: In drug design, graph neural networks (GNNs) are used to predict compound potency by analyzing graph representations of protein-ligand interactions. The study reveals that GNNs are influenced by ligand memorization during learning and certain GNN architectures prioritize interaction information for predicting high affinities. While GNNs do not comprehensively account for protein-ligand interactions and physical reality, they provide a helpful balance between ligand memorization and learning of interaction patterns.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Multidisciplinary Sciences
Tiago Janela, Juergen Bajorath
Summary: Compound potency predictions play a crucial role in drug discovery, but benchmark calculations have inherent limitations. Machine learning methods and simple controls show similar performance, with narrow error margins. Intermediate potency compounds have a significant impact on potency predictions, regardless of learning, and can be accurately predicted.
SCIENTIFIC REPORTS
(2023)
Article
Marine & Freshwater Biology
So Shinya, Fumiya Nishibe, Yared Beyene Yohannes, Mayumi Ishizuka, Shouta M. Nakayama, Yoshinori Ikenaka
Summary: Pesticide exposure, especially neonicotinoid insecticides (NNIs), is a major factor contributing to the decline of amphibian populations worldwide. However, the metabolism, distribution, and neurotoxicity of NNIs in amphibians remain poorly understood. This study exposed Western clawed frogs to clothianidin (CLT) and found that the highest concentrations of CLT were detected in the skin, indicating high risk of skin absorption. Frogs also showed higher CLT metabolic ability compared to zebrafish. Additionally, NNI residues were detected in wild frogs, soil, and water in agricultural areas of Japan, suggesting the potential toxicity of NNIs to amphibians.
AQUATIC TOXICOLOGY
(2023)
Article
Environmental Sciences
Wenzhu Wu, Jing Xu, Yezhi Dou, Jia Yu, Deyang Kong, Lixiang Zhou
Summary: This study aims to understand the bioaccumulation of pyraoxystrobin in fish. The measured bioconcentration factors (BCFs) and clearance rates were compared to estimated values from prediction models, showing close agreement.
Article
Pharmacology & Pharmacy
Cheng Peng, Shanqi Zhou, Yinjie Zhang, Hongchang Zhang, Wei Zhang, Siyuan Ling, Shuangqing Hu
Summary: In this study, the accumulation and elimination of nonylphenol (NP) in zebrafish were investigated. The results showed that the LC50 values of NP in zebrafish ranged from 474 to 238 μg/L. The depuration stage followed a first-order kinetic model, with a decreased depuration rate constant (K-2) with higher NP concentration. The half-life (t(1/2)) of NP was shorter in the trunk compared to the whole fish, indicating faster elimination from the trunk by preferential transfer and rapid diffusion in reverse. The bioconcentration factors (BCFSS) suggested that muscle tissue was the major site of NP storage.
Article
Environmental Sciences
Antonietta Siciliano, Marco Guida, Sara Serafini, Maria Micillo, Emilia Galdiero, Simona Carfagna, Giovanna Salbitani, Franca Tommasi, Giusy Lofrano, Edith Guadalupe Padilla Suarez, Isidora Gjata, Antonios Apostolos Brouziotis, Marco Trifuoggi, Renato Liguori, Marco Race, Massimiliano Fabbricino, Giovanni Libralato
Summary: The study focused on the impact of rare earth elements La and Ce on microalgae and found that low concentrations of La and Ce may be slightly toxic to microalgae, with the potential for bioaccumulation and transfer along the food web.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Environmental Sciences
Laura J. Carter, James M. Armitage, Bryan W. Brooks, John W. Nichols, Stefan Trapp
Summary: The extent of bioaccumulation of chemicals in aquatic and terrestrial organisms is crucial for protecting public health and the environment. Existing mathematical models can describe the accumulation of neutral organic chemicals and weak acids/bases, but lack mechanistic insights for ionizable pharmaceuticals and personal care products (PPCPs). Targeted experiments are needed to address partitioning and sorption behaviors, membrane permeability, influence of salts and complexes, biotransformation, and modeling gaps and risk profiles of ionizable PPCPs.
ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Cosimo Toma, Alberto Manganaro, Giuseppa Raitano, Marco Marzo, Domenico Gadaleta, Diego Baderna, Alessandra Roncaglioni, Nynke Kramer, Emilio Benfenati
Summary: This study developed classification and regression models for inhalation and oral slope factors, which showed good accuracy and R^2 values. These models may assist regulatory authorities in decision-making and weighing evidence in chemical safety assessments.
Correction
Environmental Sciences
Kamel Mansouri, Agnes Karmaus, Jeremy Fitzpatrick, Grace Patlewicz, Prachi Pradeep, Domenico Alberga, Nathalie Alepee, Timothy E. H. Allen, Dave Allen, Vinicius M. Alves, Carolina H. Andrade, Tyler R. Auernhammer, Davide Ballabio, Shannon Bell, Emilio Benfenati, Sudin Bhattacharya, Joyce V. Bastos, Stephen Boyd, J. B. Brown, Stephen J. Capuzzi, Yaroslav Chushak, Heather Ciallella, Alex M. Clark, Viviana Consonni, Pankaj R. Daga, Sean Ekins, Sherif Farag, Maxim Fedorov, Denis Fourches, Domenico Gadaleta, Feng Gao, Jeffery M. Gearhart, Garett Goh, Jonathan M. Goodman, Francesca Grisoni, Christopher M. Grulke, Thomas Hartung, Matthew Hirn, Pavel Karpov, Alexandru Korotcov, Giovanna J. Lavado, Michael Lawless, Xinhao Li, Thomas Luechtefeld, Filippo Lunghini, Giuseppe F. Mangiatordi, Gilles Marcou, Dan Marsh, Todd Martin, Andrea Mauri, Eugene N. Muratov, Glenn J. Myatt, Dac-Trung Nguyen, Orazio Nicolotti, Reine Note, Paritosh Pande, Amanda K. Parks, Tyler Peryea, Ahsan Polash, Robert Rallo, Alessandra Roncaglioni, Craig Rowlands, Patricia Ruiz, Daniel Russo, Ahmed Sayed, Risa Sayre, Timothy Sheils, Charles Siegel, Arthur C. Silva, Anton Simeonov, Sergey Sosnin, Noel Southall, Judy Strickland, Yun Tang, Brian Teppen, Igor V. Tetko, Dennis Thomas, Valery Tkachenko, Roberto Todeschini, Cosimo Toma, Ignacio Tripodi, Daniela Trisciuzzi, Alexander Tropsha, Alexandre Varnek, Kristijan Vukovic, Zhongyu Wang, Liguo Wang, Katrina M. Waters, Andrew J. Wedlake, Sanjeeva J. Wijeyesakere, Dan Wilson, Zijun Xiao, Hongbin Yang, Gergely Zahoranszky-Kohalmi, Alexey V. Zakharov, Fagen F. Zhang, Zhen Zhang, Tongan Zhao, Hao Zhu, Kimberley M. Zorn, Warren Casey, Nicole C. Kleinstreuer
ENVIRONMENTAL HEALTH PERSPECTIVES
(2021)
Article
Environmental Sciences
Jonathan M. Dilger, Todd M. Martin, Benjamin P. Wilkins, Brian C. Bohrer, Kelly M. Thoreson, Patrick W. Fedick
Summary: Green pyrotechnics aim to remove environmental pollutants and health hazards, but often overlook the formation of chemical products during exothermic reactions. Through pyrolysis-gas chromatography-mass spectrometry, new side product derivatives with lower toxicities were identified in a lab-scale pyrotechnic red smoke composition. Machine learning models predicted high toxicities for common military pyrotechnic dyes and their chlorinated side products, indicating a need to revise green pyrotechnic engineering objectives.
Correction
Environmental Sciences
Kamel Mansouri, Agnes L. Karmaus, Jeremy Fitzpatrick, Grace Patlewicz, Prachi Pradeep, Domenico Alberga, Nathalie Alepee, Timothy E. H. Allen, Dave Allen, Vinicius M. Alves, Carolina H. Andrade, Tyler R. Auernhammer, Davide Ballabio, Shannon Bell, Emilio Benfenati, Sudin Bhattacharya, Joyce V. Bastos, Stephen Boyd, J. B. Brown, Stephen J. Capuzzi, Yaroslav Chushak, Heather Ciallella, Alex M. Clark, Viviana Consonni, Pankaj R. Daga, Sean Ekins, Sherif Farag, Maxim Fedorov, Denis Fourches, Domenico Gadaleta, Feng Gao, Jeffery M. Gearhart, Garett Goh, Jonathan M. Goodman, Francesca Grisoni, Christopher M. Grulke, Thomas Hartung, Matthew Hirn, Pavel Karpov, Alexandru Korotcov, Giovanna J. Lavado, Michael Lawless, Xinhao Li, Thomas Luechtefeld, Filippo Lunghini, Giuseppe F. Mangiatordi, Gilles Marcou, Dan Marsh, Todd Martin, Andrea Mauri, Eugene N. Muratov, Glenn J. Myatt, Dac-Trung Nguyen, Orazio Nicolotti, Reine Note, Paritosh Pande, Amanda K. Parks, Tyler Peryea, Ahsan H. Polash, Robert Rallo, Alessandra Roncaglioni, Craig Rowlands, Patricia Ruiz, Daniel P. Russo, Ahmed Sayed, Risa Sayre, Timothy Sheils, Charles Siegel, Arthur C. Silva, Anton Simeonov, Sergey Sosnin, Noel Southall, Judy Strickland, Yun Tang, Brian Teppen, Igor V. Tetko, Dennis Thomas, Valery Tkachenko, Roberto Todeschini, Cosimo Toma, Ignacio Tripodi, Daniela Trisciuzzi, Alexander Tropsha, Alexandre Varnek, Kristijan Vukovic, Zhongyu Wang, Liguo Wang, Katrina M. Waters, Andrew J. Wedlake, Sanjeeva J. Wijeyesakere, Dan Wilson, Zijun Xiao, Hongbin Yang, Gergely Zahoranszky-Kohalmi, Alexey V. Zakharov, Fagen F. Zhang, Zhen Zhang, Tongan Zhao, Hao Zhu, Kimberley M. Zorn, Warren Casey, Nicole C. Kleinstreuer
ENVIRONMENTAL HEALTH PERSPECTIVES
(2021)
Article
Biochemistry & Molecular Biology
Cosimo Toma, Claudia I. Cappelli, Alberto Manganaro, Anna Lombardo, Juergen Arning, Emilio Benfenati
Summary: This study developed predictive models for acute and chronic toxicities in Raphidocelis subcapitata, Daphnia magna, and fish, with the random forest machine learning approach yielding the best results. The models showed good statistical quality for all endpoints, and are freely available for use as individual models in the VEGA platform and for prioritization in JANUS software.
Review
Engineering, Environmental
Chelsea Berg, Brian Crone, Brian Gullett, Mark Higuchi, Max J. Krause, Paul M. Lemieux, Todd Martin, Erin P. Shields, Ed Struble, Eben Thoma, Andrew Whitehill
Summary: This paper examines four novel, non-combustion technologies or applications for the treatment of persistent per- and polyfluoroalkyl substances (PFAS) wastes. These technologies are introduced to the reader along with their current state of development and areas for further development. This information will be useful for developers, policy makers, and facility managers that are facing increasing issues with disposal of PFAS wastes.
JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION
(2022)
Article
Toxicology
Grace Patlewicz, Jeffry L. Dean, Catherine F. Gibbons, Richard S. Judson, Nagalakshmi Keshava, Leora Vegosen, Todd M. Martin, Prachi Pradeep, Anita Simha, Sarah H. Warren, Maureen R. Gwinn, David M. Demarini
Summary: The Toxic Substances Control Act requires risk-based evaluations of existing chemicals, and a tiered approach was developed to screen potential candidates based on genotoxicity and carcinogenicity information. The approach utilized a large database of carcinogenicity and genotoxicity data to make overall outcome determinations, showing promise in identifying potential candidates for prioritization from a genotoxicity and carcinogenicity perspective.
COMPUTATIONAL TOXICOLOGY
(2021)
Article
Chemistry, Physical
Paul Harten, Todd Martin, Daniel Chang, Douglas Young
Summary: This article presents a method that combines different types of impacts caused by solvents into a comprehensive environmental index, allowing for the comparison of solvents based on their cumulative impact on the environment. Using the software tool PARIS III, potential replacements with similar activities but lower environmental indexes can be found, reducing the overall environmental impact of harmful solvents.
JOURNAL OF SOLUTION CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Edoardo Luca Vigano, Erika Colombo, Giuseppa Raitano, Alberto Manganaro, Alessio Sommovigo, Jean Lou C. M. Dorne, Emilio Benfenati
Summary: This study developed a new open-access software called VERA, which assesses the similarity between chemicals using structural alerts, pre-defined molecular groups, and structural similarity. VERA can accurately identify botanicals associated with carcinogenicity and provide clusters of similar substances.
Article
Chemistry, Medicinal
Charles N. Lowe, Nathaniel Charest, Christian Ramsland, Daniel T. Chang, Todd M. Martin, Antony J. Williams
Summary: The careful assembly, training, and validation of QSAR/QSPR models are crucial as data sets become larger and machine learning tools become more accessible. Regulatory agencies like the US EPA need to scrutinize all aspects of these models for environmental assessment purposes. This study applies the OECD's principles to a water solubility model using random forest regression, achieving comparable performance to previous models.
CHEMICAL RESEARCH IN TOXICOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Alberto Danieli, Erika Colombo, Giuseppa Raitano, Anna Lombardo, Alessandra Roncaglioni, Alberto Manganaro, Alessio Sommovigo, Edoardo Carnesecchi, Jean-Lou C. M. Dorne, Emilio Benfenati
Summary: A thorough assessment of in silico models and their applicability domain is crucial for utilizing new approach methodologies (NAMs) in chemical risk assessment and building users' confidence. The VEGA tool is examined in this study to evaluate the applicability domain of in silico models, demonstrating its efficiency in identifying less accurate predictions for various toxicological endpoints. The tool evaluates chemical structures and related features, providing valuable insights for both regression models and classifiers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Mohamed Ateia, Jean Van Buren, William Barrett, Todd Martin, Gerard G. Back
Summary: One type of firefighting foam, AFFF, contains PFAS, which has raised concerns about its environmental and health impacts. In response, there has been a surge in research on fluorine-free alternatives, and a new military specification for fluorine-free foam was released in January 2023. This paper critically analyzes the current state of fluorine-free options, exploring the challenges and opportunities in terms of performance, cost, and regulations. The evaluation shows that the transition to fluorine-free replacements is complex and requires careful consideration of trade-offs, but it provides valuable insights for future research and enhancing the safety and sustainability of fire suppression systems.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Environmental Sciences
Kamel Mansouri, Agnes L. Karmaus, Jeremy Fitzpatrick, Grace Patlewicz, Prachi Pradeep, Domenico Alberga, Nathalie Alepee, Timothy E. H. Allen, Dave Allen, Vinicius M. Alves, Carolina H. Andrade, Tyler R. Auernhammer, Davide Ballabio, Shannon Bell, Emilio Benfenati, Sudin Bhattacharya, Joyce Bastos, Stephen Boyd, J. B. Brown, Stephen J. Capuzzi, Yaroslav Chushak, Heather Ciallella, Alex M. Clark, Viviana Consonni, Pankaj R. Daga, Sean Ekins, Sherif Farag, Maxim Fedorov, Denis Fourches, Domenico Gadaleta, Feng Gao, Jeffery M. Gearhart, Garett Goh, Jonathan M. Goodman, Francesca Grisoni, Christopher M. Grulke, Thomas Hartung, Matthew Hirn, Pavel Karpov, Alexandru Korotcov, Giovanna J. Lavado, Michael Lawless, Xinhao Li, Thomas Luechtefeld, Filippo Lunghini, Giuseppe F. Mangiatordi, Gilles Marcou, Dan Marsh, Todd Martin, Andrea Mauri, Eugene N. Muratov, Glenn J. Myatt, Dac-Trung Nguyen, Orazio Nicolotti, Reine Note, Paritosh Pande, Amanda K. Parks, Tyler Peryea, Ahsan H. Polash, Robert Rallo, Alessandra Roncaglioni, Craig Rowlands, Patricia Ruiz, Daniel P. Russo, Ahmed Sayed, Risa Sayre, Timothy Sheils, Charles Siegel, Arthur C. Silva, Anton Simeonov, Sergey Sosnin, Noel Southall, Judy Strickland, Yun Tang, Brian Teppen, Igor Tetko, Dennis Thomas, Valery Tkachenko, Roberto Todeschini, Cosimo Toma, Ignacio Tripodi, Daniela Trisciuzzi, Alexander Tropsha, Alexandre Varnek, Kristijan Vukovic, Zhongyu Wang, Liguo Wang, Katrina M. Waters, Andrew J. Wedlake, Sanjeeva J. Wijeyesakere, Dan Wilson, Zijun Xiao, Hongbin Yang, Gergely Zahoranszky-Kohalmi, Alexey Zakharov, Fagen F. Zhang, Zhen Zhang, Tongan Zhao, Hao Zhu, Kimberley M. Zorn, Warren Casey, Nicole C. Kleinstreuer
Summary: The international collaboration in developing in silico models for predicting acute oral toxicity, resulting in the CATMoS, has demonstrated high performance in terms of accuracy and robustness. This modeling suite is being evaluated by regulatory agencies as a potential replacement for in vivo rat acute oral toxicity studies.
ENVIRONMENTAL HEALTH PERSPECTIVES
(2021)
Article
Medicine, Research & Experimental
Gianluca Selvestrel, Federica Robino, Diego Baderna, Serena Manganelli, David Asturiol, Alberto Manganaro, Matteo Zanotti Russo, Giovanna Lavado, Cosimo Toma, Alessandra Roncaglioni, Emilio Benfenati
Summary: The software is a new, free tool for safety assessment of cosmetic products, allowing users to evaluate the toxicological properties of cosmetic ingredients while considering regulatory frameworks and risks to consumers. It provides assessment of various toxicological properties and calculates safety margins using experimental values or predictions.
ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION
(2021)
