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Xiao X, Trinh TX, Gerelkhuu Z, Ha E, Yoon TH. Automated machine learning in nanotoxicity assessment: A comparative study of predictive model performance. Comput Struct Biotechnol J 2024; 25:9-19. [PMID: 38414794 PMCID: PMC10899003 DOI: 10.1016/j.csbj.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/29/2024] Open
Abstract
Computational modeling has earned significant interest as an alternative to animal testing of toxicity assessment. However, the process of selecting an appropriate algorithm and fine-tuning hyperparameters for the developing of optimized models takes considerable time, expertise, and an intensive search. The recent emergence of automated machine learning (autoML) approaches, available as user-friendly platforms, has proven beneficial for individuals with limited knowledge in ML-based predictive model development. These autoML platforms automate crucial steps in model development, including data preprocessing, algorithm selection, and hyperparameter tuning. In this study, we used seven previously published and publicly available datasets for oxides and metals to develop nanotoxicity prediction models. AutoML platforms, namely Vertex AI, Azure, and Dataiku, were employed and performance measures such as accuracy, F1 score, precision, and recall for these autoML-based models were then compared with those of conventional ML-based models. The results demonstrated clearly that the autoML platforms produced more reliable nanotoxicity prediction models, outperforming those built with conventional ML algorithms. While none of the three autoML platforms significantly outperformed the others, distinctions exist among them in terms of the available options for choosing technical features throughout the model development steps. This allows users to select an autoML platform that aligns with their knowledge of predictive model development and its technical features. Additionally, prediction models constructed from datasets with better data quality displayed, enhanced performance than those built from datasets with lower data quality, indicating that future studies with high-quality datasets can further improve the performance of those autoML-based prediction models.
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Affiliation(s)
- Xiao Xiao
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, the Republic of Korea
| | - Tung X Trinh
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, the Republic of Korea
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, the Republic of Korea
| | - Zayakhuu Gerelkhuu
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, the Republic of Korea
- Yoon Idea Lab. Co. Ltd, Seoul 04763, the Republic of Korea
| | - Eunyong Ha
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, the Republic of Korea
| | - Tae Hyun Yoon
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, the Republic of Korea
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, the Republic of Korea
- Yoon Idea Lab. Co. Ltd, Seoul 04763, the Republic of Korea
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2
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Fan L, Shen Y, Lou D, Gu N. Progress in the Computer-Aided Analysis in Multiple Aspects of Nanocatalysis Research. Adv Healthc Mater 2024:e2401576. [PMID: 38936401 DOI: 10.1002/adhm.202401576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/08/2024] [Indexed: 06/29/2024]
Abstract
Making the utmost of the differences and advantages of multiple disciplines, interdisciplinary integration breaks the science boundaries and accelerates the progress in mutual quests. As an organic connection of material science, enzymology, and biomedicine, nanozyme-related research is further supported by computer technology, which injects in new vitality, and contributes to in-depth understanding, unprecedented insights, and broadened application possibilities. Utilizing computer-aided first-principles method, high-speed and high-throughput mathematic, physic, and chemic models are introduced to perform atomic-level kinetic analysis for nanocatalytic reaction process, and theoretically illustrate the underlying nanozymetic mechanism and structure-function relationship. On this basis, nanozymes with desirable properties can be designed and demand-oriented synthesized without repeated trial-and-error experiments. Besides that, computational analysis and device also play an indispensable role in nanozyme-based detecting methods to realize automatic readouts with improved accuracy and reproducibility. Here, this work focuses on the crossing of nanocatalysis research and computational technology, to inspire the research in computer-aided analysis in nanozyme field to a greater extent.
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Affiliation(s)
- Lin Fan
- Medical School of Nanjing University, Nanjing, 210093, P. R. China
- School of Integrated Circuit Science and Engineering (Industry-Education Integration School), Nanjing University of Posts and Telecommunications, Nanjing, 210023, P. R. China
| | - Yilei Shen
- School of Integrated Circuit Science and Engineering (Industry-Education Integration School), Nanjing University of Posts and Telecommunications, Nanjing, 210023, P. R. China
| | - Doudou Lou
- Nanjing Institute for Food and Drug Control, Nanjing, 211198, P. R. China
| | - Ning Gu
- Medical School of Nanjing University, Nanjing, 210093, P. R. China
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Ammar A, Evelo C, Willighagen E. FAIR assessment of nanosafety data reusability with community standards. Sci Data 2024; 11:503. [PMID: 38755173 PMCID: PMC11099147 DOI: 10.1038/s41597-024-03324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
Nanomaterials hold great promise for improving our society, and it is crucial to understand their effects on biological systems in order to enhance their properties and ensure their safety. However, the lack of consistency in experimental reporting, the absence of universally accepted machine-readable metadata standards, and the challenge of combining such standards hamper the reusability of previously produced data for risk assessment. Fortunately, the research community has responded to these challenges by developing minimum reporting standards that address several of these issues. By converting twelve published minimum reporting standards into a machine-readable representation using FAIR maturity indicators, we have created a machine-friendly approach to annotate and assess datasets' reusability according to those standards. Furthermore, our NanoSafety Data Reusability Assessment (NSDRA) framework includes a metadata generator web application that can be integrated into experimental data management, and a new web application that can summarize the reusability of nanosafety datasets for one or more subsets of maturity indicators, tailored to specific computational risk assessment use cases. This approach enhances the transparency, communication, and reusability of experimental data and metadata. With this improved FAIR approach, we can facilitate the reuse of nanosafety research for exploration, toxicity prediction, and regulation, thereby advancing the field and benefiting society as a whole.
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Affiliation(s)
- Ammar Ammar
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
| | - Chris Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
| | - Egon Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
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Zhao Q, Zheng Y, Qiu Y, Yu Y, Huang M, Wu Y, Chen X, Huang Y, Cui S, Zhuang S. Graph Convolutional Network-Enhanced Model for Screening Persistent, Mobile, and Toxic and Very Persistent and Very Mobile Substances. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6149-6157. [PMID: 38556993 DOI: 10.1021/acs.est.4c01201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The global management for persistent, mobile, and toxic (PMT) and very persistent and very mobile (vPvM) substances has been further strengthened with the rapid increase of emerging contaminants. The development of a ready-to-use and publicly available tool for the high-throughput screening of PMT/vPvM substances is thus urgently needed. However, the current model building with the coupling of conventional algorithms, small-scale data set, and simplistic features hinders the development of a robust model for screening PMT/vPvM with wide application domains. Here, we construct a graph convolutional network (GCN)-enhanced model with feature fusion of a molecular graph and molecular descriptors to effectively utilize the significant correlation between critical descriptors and PMT/vPvM substances. The model is built with 213,084 substances following the latest PMT classification criteria. The application domains of the GCN-enhanced model assessed by kernel density estimation demonstrate the high suitability for high-throughput screening PMT/vPvM substances with both a high accuracy rate (86.6%) and a low false-negative rate (6.8%). An online server named PMT/vPvM profiler is further developed with a user-friendly web interface (http://www.pmt.zj.cn/). Our study facilitates a more efficient evaluation of PMT/vPvM substances with a globally accessible screening platform.
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Affiliation(s)
- Qiming Zhao
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yuting Zheng
- Solid Waste and Chemicals Management Center, Ministry of Ecology and Environment of the People's Republic of China, Beijing 100029, China
| | - Yu Qiu
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yang Yu
- Solid Waste and Chemicals Management Center, Ministry of Ecology and Environment of the People's Republic of China, Beijing 100029, China
| | - Meiling Huang
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yiqu Wu
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xiyu Chen
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yizhou Huang
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shixuan Cui
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shulin Zhuang
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
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5
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Nandipati M, Fatoki O, Desai S. Bridging Nanomanufacturing and Artificial Intelligence-A Comprehensive Review. MATERIALS (BASEL, SWITZERLAND) 2024; 17:1621. [PMID: 38612135 PMCID: PMC11012965 DOI: 10.3390/ma17071621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/05/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024]
Abstract
Nanomanufacturing and digital manufacturing (DM) are defining the forefront of the fourth industrial revolution-Industry 4.0-as enabling technologies for the processing of materials spanning several length scales. This review delineates the evolution of nanomaterials and nanomanufacturing in the digital age for applications in medicine, robotics, sensory technology, semiconductors, and consumer electronics. The incorporation of artificial intelligence (AI) tools to explore nanomaterial synthesis, optimize nanomanufacturing processes, and aid high-fidelity nanoscale characterization is discussed. This paper elaborates on different machine-learning and deep-learning algorithms for analyzing nanoscale images, designing nanomaterials, and nano quality assurance. The challenges associated with the application of machine- and deep-learning models to achieve robust and accurate predictions are outlined. The prospects of incorporating sophisticated AI algorithms such as reinforced learning, explainable artificial intelligence (XAI), big data analytics for material synthesis, manufacturing process innovation, and nanosystem integration are discussed.
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Affiliation(s)
- Mutha Nandipati
- Department of Industrial and Systems Engineering, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA; (M.N.); (O.F.)
| | - Olukayode Fatoki
- Department of Industrial and Systems Engineering, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA; (M.N.); (O.F.)
| | - Salil Desai
- Department of Industrial and Systems Engineering, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA; (M.N.); (O.F.)
- Center of Excellence in Product Design and Advanced Manufacturing, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA
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6
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Mortensen HM, Beach B, Slaughter W, Senn J, Williams A, Boyes W. Translating nanoEHS data using EPA NaKnowBase and the resource description framework. F1000Res 2024; 13:169. [PMID: 38800073 PMCID: PMC11128042 DOI: 10.12688/f1000research.141056.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 05/29/2024] Open
Abstract
Background The U.S. Federal Government has supported the generation of extensive amounts of nanomaterials and related nano Environmental Health and Safety (nanoEHS) data, there is a need to make these data available to stakeholders. With recent efforts, a need for improved interoperability, translation, and sustainability of Federal nanoEHS data in the United States has been realized. The NaKnowBase (NKB) is a relational database containing experimental results generated by the EPA Office of Research and Development (ORD) regarding the actions of engineered nanomaterials on environmental and biological systems. Through the interaction of the National Nanotechnology Initiative's Nanotechnology Environmental Health Implications (NEHI) Working Group, and the Database and Informatics Interest Group (DIIG), a U.S. Federal nanoEHS Consortium has been formed. Methods The primary goal of this consortium is to establish a "common language" for nanoEHS data that aligns with FAIR data standards. A second goal is to overcome nomenclature issues inherent to nanomaterials data, ultimately allowing data sharing and interoperability across the diverse U.S. Federal nanoEHS data compendium, but also in keeping a level of consistency that will allow interoperability with U.S. and European partners. The most recent version of the EPA NaKnowBase (NKB) has been implemented for semantic integration. Computational code has been developed to use each NKB record as input, modify and filter table data, and subsequently output each modified record to a Research Description Framework (RDF). To improve the accuracy and efficiency of this process the EPA has created the OntoSearcher tool. This tool partially automates the ontology mapping process, thereby reducing onerous manual curation. Conclusions Here we describe the efforts of the US EPA in promoting FAIR data standards for Federal nanoEHS data through semantic integration, as well as in the development of NAMs (computational tools) to facilitate these improvements for nanoEHS data at the Federal partner level.
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Affiliation(s)
- Holly M. Mortensen
- ORD-CPHEA, US Environmental Protection agency, Research Triangle Park, NC, 27711, USA
| | - Bradley Beach
- Appointee at the Office of Research and Development, US Environmental Protection Agency, Oak Ridge Institute for Science and Education (ORISE), Research Triangle Park, NC, 27711, USA
| | - Weston Slaughter
- Appointee at the Office of Research and Development, US Environmental Protection Agency, Oak Ridge Institute for Science and Education (ORISE), Research Triangle Park, NC, 27711, USA
- Department of Biology, Duke University, Durham, NC, USA
| | - Jonathan Senn
- Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
- Metabolon, Inc. Precision Metabolomics, Durham, NC, USA
| | - Antony Williams
- ORD-CCTE, US Environmental Protection Agency, RTP, NC, 27711, USA
| | - William Boyes
- ORD-CPHEA, US Environmental Protection agency, Research Triangle Park, NC, 27711, USA
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7
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Huang-Zhu CA, Sheavly JK, Chew AK, Patel SJ, Van Lehn RC. Ligand Lipophilicity Determines Molecular Mechanisms of Nanoparticle Adsorption to Lipid Bilayers. ACS NANO 2024; 18:6424-6437. [PMID: 38354368 DOI: 10.1021/acsnano.3c11854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The interactions of ligand-functionalized nanoparticles with the cell membrane affect cellular uptake, cytotoxicity, and related behaviors, but relating these interactions to ligand properties remains challenging. In this work, we perform coarse-grained molecular dynamics simulations to study how the adsorption of ligand-functionalized cationic gold nanoparticles (NPs) to a single-component lipid bilayer (as a model cell membrane) is influenced by ligand end group lipophilicity. A set of 2 nm diameter NPs, each coated with a monolayer of organic ligands that differ only in their end groups, was simulated to mimic NPs recently studied experimentally. Metadynamics calculations were performed to determine key features of the free energy landscape for adsorption as a function of the distance of the NP from the bilayer and the number of NP-lipid contacts. These simulations revealed that NP adsorption is thermodynamically favorable for all NPs due to the extraction of lipids from the bilayer and into the NP monolayer. To resolve ligand-dependent differences in adsorption behavior, string method calculations were performed to compute minimum free energy pathways for adsorption. These calculations revealed a surprising nonmonotonic dependence of the free energy barrier for adsorption on ligand end group lipophilicity. Large free energy barriers are predicted for the least lipophilic end groups because favorable NP-lipid contacts are initiated only through the unfavorable protrusion of lipid tail groups out of the bilayer. The smallest free energy barriers are predicted for end groups of intermediate lipophilicity which promote NP-lipid contacts by intercalating within the bilayer. Unexpectedly, large free energy barriers are also predicted for the most lipophilic end groups which remain sequestered within the ligand monolayer rather than intercalating within the bilayer. These trends are broadly in agreement with past experimental measurements and reveal how subtle variations in ligand lipophilicity dictate adsorption mechanisms and associated kinetics by influencing the interplay of lipid-ligand interactions.
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Affiliation(s)
- Carlos A Huang-Zhu
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jonathan K Sheavly
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Alex K Chew
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samarthaben J Patel
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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8
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Wang L, Quine S, Frickenstein AN, Lee M, Yang W, Sheth VM, Bourlon MD, He Y, Lyu S, Garcia-Contreras L, Zhao YD, Wilhelm S. Exploring and Analyzing the Systemic Delivery Barriers for Nanoparticles. ADVANCED FUNCTIONAL MATERIALS 2024; 34:2308446. [PMID: 38828467 PMCID: PMC11142462 DOI: 10.1002/adfm.202308446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Indexed: 06/05/2024]
Abstract
Most nanomedicines require efficient in vivo delivery to elicit diagnostic and therapeutic effects. However, en route to their intended tissues, systemically administered nanoparticles often encounter delivery barriers. To describe these barriers, we propose the term "nanoparticle blood removal pathways" (NBRP), which summarizes the interactions between nanoparticles and the body's various cell-dependent and cell-independent blood clearance mechanisms. We reviewed nanoparticle design and biological modulation strategies to mitigate nanoparticle-NBRP interactions. As these interactions affect nanoparticle delivery, we studied the preclinical literature from 2011-2021 and analyzed nanoparticle blood circulation and organ biodistribution data. Our findings revealed that nanoparticle surface chemistry affected the in vivo behavior more than other nanoparticle design parameters. Combinatory biological-PEG surface modification improved the blood area under the curve by ~418%, with a decrease in liver accumulation of up to 47%. A greater understanding of nanoparticle-NBRP interactions and associated delivery trends will provide new nanoparticle design and biological modulation strategies for safer, more effective, and more efficient nanomedicines.
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Affiliation(s)
- Lin Wang
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Skyler Quine
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Alex N. Frickenstein
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Michael Lee
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Wen Yang
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Vinit M. Sheth
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Margaret D. Bourlon
- College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73117, USA
| | - Yuxin He
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Shanxin Lyu
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Lucila Garcia-Contreras
- College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73117, USA
| | - Yan D. Zhao
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73012, USA
- Stephenson Cancer Center, Oklahoma City, Oklahoma, 73104, USA
| | - Stefan Wilhelm
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
- Stephenson Cancer Center, Oklahoma City, Oklahoma, 73104, USA
- Institute for Biomedical Engineering, Science, and Technology (IBEST), Norman, Oklahoma, 73019, USA
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Chen H, Xie J, Huang C, Liang Y, Zhang Y, Zhao X, Ling Y, Wang L, Zheng Q, Yang X. Database and review of disinfection by-products since 1974: Constituent elements, molecular weights, and structures. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132792. [PMID: 37856956 DOI: 10.1016/j.jhazmat.2023.132792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 10/21/2023]
Abstract
Since trihalomethanes were discovered in 1974, disinfection by-products (DBPs) in drinking water have attracted extensive attention. In 2011, more than 600 known DBPs were compiled; however, newly reported DBPs have not been integrated. The rapid development of mass spectrometry has led to a significant increase in the number of DBPs, therefore, there is a need to develop a database of all DBPs and their properties. Herein, a database including 6310 DBPs (651 confirmed, 1478 identified and 4142 proposed) reported between 1974 and 2022 was constructed and made available for public use at https://dbps.com.cn/main. This database can be a tool in screening new DBPs, comprehensively reviewing, and developing predictive models. In this paper, to demonstrate the functions of the database and provide useful information for this area, the origin of the collected DBPs was presented, and some basic information, including elemental composition, molecular weight, functional groups, and carbon frameworks, were comparatively analyzed. The results showed that the proportion of DBPs verified by standard compounds and frequently detected in real water is less than 7.0%, and most of DBPs remained to be identified. Approximately 88% of DBPs contain halogens, and brominated -DBPs occupied a similar ratio to chlorinated -DBPs in real water. Acids were the main functional groups of DBPs, aliphatic and aromatic compounds are the two major carbon frameworks, and the molecular weights of most DBPs ranged from 200 to 400 Da. In addition, 4142 proposed DBPs as obtained using high-resolution mass spectrometry, were characterized based on the modified van Krevelen diagram and adjusted indexes with halogens. Most of the proposed DBPs featured lignin and tannin structures, and phenolic/highly unsaturated DBPs account for the majority.
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Affiliation(s)
- Hechao Chen
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, China
| | - Jidao Xie
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430078, China
| | | | - Yining Liang
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, China
| | - Yulin Zhang
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, China
| | - Xiaoyan Zhao
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, China
| | - Yuhua Ling
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, China
| | - Lei Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qi Zheng
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, China
| | - Xiaoqiu Yang
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, China.
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10
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Tang W, Zhang X, Hong H, Chen J, Zhao Q, Wu F. Computational Nanotoxicology Models for Environmental Risk Assessment of Engineered Nanomaterials. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:155. [PMID: 38251120 PMCID: PMC10819018 DOI: 10.3390/nano14020155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/08/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
Abstract
Although engineered nanomaterials (ENMs) have tremendous potential to generate technological benefits in numerous sectors, uncertainty on the risks of ENMs for human health and the environment may impede the advancement of novel materials. Traditionally, the risks of ENMs can be evaluated by experimental methods such as environmental field monitoring and animal-based toxicity testing. However, it is time-consuming, expensive, and impractical to evaluate the risk of the increasingly large number of ENMs with the experimental methods. On the contrary, with the advancement of artificial intelligence and machine learning, in silico methods have recently received more attention in the risk assessment of ENMs. This review discusses the key progress of computational nanotoxicology models for assessing the risks of ENMs, including material flow analysis models, multimedia environmental models, physiologically based toxicokinetics models, quantitative nanostructure-activity relationships, and meta-analysis. Several challenges are identified and a perspective is provided regarding how the challenges can be addressed.
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Affiliation(s)
- Weihao Tang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xuejiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Qing Zhao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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11
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Cui S, Gao Y, Huang Y, Shen L, Zhao Q, Pan Y, Zhuang S. Advances and applications of machine learning and deep learning in environmental ecology and health. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 335:122358. [PMID: 37567408 DOI: 10.1016/j.envpol.2023.122358] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Machine learning (ML) and deep learning (DL) possess excellent advantages in data analysis (e.g., feature extraction, clustering, classification, regression, image recognition and prediction) and risk assessment and management in environmental ecology and health (EEH). Considering the rapid growth and increasing complexity of data in EEH, it is of significance to summarize recent advances and applications of ML and DL in EEH. This review summarized the basic processes and fundamental algorithms of the ML and DL modeling, and indicated the urgent needs of ML and DL in EEH. Recent research hotspots such as environmental ecology and restoration, environmental fate of new pollutants, chemical exposures and risks, chemical hazard identification and control were highlighted. Various applications of ML and DL in EEH demonstrate their versatility and technological revolution, and present some challenges. The perspective of ML and DL in EEH were further outlined to promote the innovative analysis and cultivation of the ML-driven research paradigm.
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Affiliation(s)
- Shixuan Cui
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Yuchen Gao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yizhou Huang
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Lilai Shen
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qiming Zhao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yaru Pan
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shulin Zhuang
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China.
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12
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Furxhi I, Willighagen E, Evelo C, Costa A, Gardini D, Ammar A. A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability. NANOIMPACT 2023; 31:100475. [PMID: 37423508 DOI: 10.1016/j.impact.2023.100475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
INTRODUCTION The current effort towards the digital transformation across multiple scientific domains requires data that is Findable, Accessible, Interoperable and Reusable (FAIR). In addition to the FAIR data, what is required for the application of computational tools, such as Quantitative Structure Activity Relationships (QSARs), is a sufficient data volume and the ability to merge sources into homogeneous digital assets. In the nanosafety domain there is a lack of FAIR available metadata. METHODOLOGY To address this challenge, we utilized 34 datasets from the nanosafety domain by exploiting the NanoSafety Data Reusability Assessment (NSDRA) framework, which allowed the annotation and assessment of dataset's reusability. From the framework's application results, eight datasets targeting the same endpoint (i.e. numerical cellular viability) were selected, processed and merged to test several hypothesis including universal versus nanogroup-specific QSAR models (metal oxide and nanotubes), and regression versus classification Machine Learning (ML) algorithms. RESULTS Universal regression and classification QSARs reached an 0.86 R2 and 0.92 accuracy, respectively, for the test set. Nanogroup-specific regression models reached 0.88 R2 for nanotubes test set followed by metal oxide (0.78). Nanogroup-specific classification models reached 0.99 accuracy for nanotubes test set, followed by metal oxide (0.91). Feature importance revealed different patterns depending on the dataset with common influential features including core size, exposure conditions and toxicological assay. Even in the case where the available experimental knowledge was merged, the models still failed to correctly predict the outputs of an unseen dataset, revealing the cumbersome conundrum of scientific reproducibility in realistic applications of QSAR for nanosafety. To harness the full potential of computational tools and ensure their long-term applications, embracing FAIR data practices is imperative in driving the development of responsible QSAR models. CONCLUSIONS This study reveals that the digitalization of nanosafety knowledge in a reproducible manner has a long way towards its successful pragmatic implementation. The workflow carried out in the study shows a promising approach to increase the FAIRness across all the elements of computational studies, from dataset's annotation, selection, merging to FAIR modeling reporting. This has significant implications for future research as it provides an example of how to utilize and report different tools available in the nanosafety knowledge system, while increasing the transparency of the results. One of the main benefits of this workflow is that it promotes data sharing and reuse, which is essential for advancing scientific knowledge by making data and metadata FAIR compliant. In addition, the increased transparency and reproducibility of the results can enhance the trustworthiness of the computational findings.
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Affiliation(s)
- Irini Furxhi
- Transgero Limited, Cullinagh, Newcastle West, Co. Limerick, Ireland; Dept. of Accounting and Finance, Kemmy Business School, University of Limerick, V94PH93, Ireland.
| | - Egon Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, the Netherlands.
| | - Chris Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, the Netherlands.
| | - Anna Costa
- National Research Council, Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy.
| | - Davide Gardini
- National Research Council, Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy.
| | - Ammar Ammar
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, the Netherlands.
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He Y, Liu G, Hu S, Wang X, Jia J, Zhou H, Yan X. Implementing comprehensive machine learning models of multispecies toxicity assessment to improve regulation of organic compounds. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131942. [PMID: 37390684 DOI: 10.1016/j.jhazmat.2023.131942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/12/2023] [Accepted: 06/24/2023] [Indexed: 07/02/2023]
Abstract
Machine learning has made significant progress in assessing the risk associated with hazardous chemicals. However, most models were constructed by randomly selecting one algorithm and one toxicity endpoint towards single species, which may cause biased regulation of chemicals. In the present study, we implemented comprehensive prediction models involving multiple advanced machine learning and end-to-end deep learning to assess the aquatic toxicity of chemicals. The generated optimal models accurately unravel the quantitative structure-toxicity relationships, with the correlation coefficients of all training sets from 0.59 to 0.81 and of the test sets from 0.56 to 0.83. For each chemical, its ecological risk was determined from the toxicity information towards multiple species. The results also revealed the toxicity mechanism of chemicals was species sensitivity, and the high-level organisms were faced with more serious side effects from hazardous substances. The proposed approach was finally applied to screen over 16,000 compounds and identify high-risk chemicals. We believe that the current approach can provide a useful tool for predicting the toxicity of diverse organic chemicals and help regulatory authorities make more reasonable decisions.
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Affiliation(s)
- Ying He
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Guohong Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Agriculture and Biological Sciences, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Song Hu
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Xiaohong Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jianbo Jia
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Hongyu Zhou
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Xiliang Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Agriculture and Biological Sciences, Qiannan Normal University for Nationalities, Duyun 558000, China.
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14
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Yan X, Yue T, Winkler DA, Yin Y, Zhu H, Jiang G, Yan B. Converting Nanotoxicity Data to Information Using Artificial Intelligence and Simulation. Chem Rev 2023. [PMID: 37262026 DOI: 10.1021/acs.chemrev.3c00070] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Decades of nanotoxicology research have generated extensive and diverse data sets. However, data is not equal to information. The question is how to extract critical information buried in vast data streams. Here we show that artificial intelligence (AI) and molecular simulation play key roles in transforming nanotoxicity data into critical information, i.e., constructing the quantitative nanostructure (physicochemical properties)-toxicity relationships, and elucidating the toxicity-related molecular mechanisms. For AI and molecular simulation to realize their full impacts in this mission, several obstacles must be overcome. These include the paucity of high-quality nanomaterials (NMs) and standardized nanotoxicity data, the lack of model-friendly databases, the scarcity of specific and universal nanodescriptors, and the inability to simulate NMs at realistic spatial and temporal scales. This review provides a comprehensive and representative, but not exhaustive, summary of the current capability gaps and tools required to fill these formidable gaps. Specifically, we discuss the applications of AI and molecular simulation, which can address the large-scale data challenge for nanotoxicology research. The need for model-friendly nanotoxicity databases, powerful nanodescriptors, new modeling approaches, molecular mechanism analysis, and design of the next-generation NMs are also critically discussed. Finally, we provide a perspective on future trends and challenges.
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Affiliation(s)
- Xiliang Yan
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Tongtao Yue
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Institute of Coastal Environmental Pollution Control, Ocean University of China, Qingdao 266100, China
| | - David A Winkler
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- School of Pharmacy, University of Nottingham, Nottingham NG7 2QL, U.K
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Yongguang Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hao Zhu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Bing Yan
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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15
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Scott-Fordsmand JJ, Amorim MJB. Using Machine Learning to make nanomaterials sustainable. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160303. [PMID: 36410486 DOI: 10.1016/j.scitotenv.2022.160303] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/06/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Sustainable development is a key challenge for contemporary human societies; failure to achieve sustainability could threaten human survival. In this review article, we illustrate how Machine Learning (ML) could support more sustainable development, covering the basics of data gathering through each step of the Environmental Risk Assessment (ERA). The literature provides several examples showing how ML can be employed in most steps of a typical ERA.A key observation is that there are currently no clear guidance for using such autonomous technologies in ERAs or which standards/checks are required. Steering thus seems to be the most important task for supporting the use of ML in the ERA of nano- and smart-materials. Resources should be devoted to developing a strategy for implementing ML in ERA with a strong emphasis on data foundations, methodologies, and the related sensitivities/uncertainties. We should recognise historical errors and biases (e.g., in data) to avoid embedding them during ML programming.
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Affiliation(s)
| | - Mónica J B Amorim
- Department of Biology & CESAM, University of Aveiro, 3810-193 Aveiro, Portugal.
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16
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Liu G, Yan X, Li C, Hu S, Yan J, Yan B. Unraveling the joint toxicity of transition-metal dichalcogenides and per- and polyfluoroalkyl substances in aqueous mediums by experimentation, machine learning and molecular dynamics. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130303. [PMID: 36345062 DOI: 10.1016/j.jhazmat.2022.130303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/18/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
The environmental fate of transition-metal dichalcogenides (TMDCs) may be further complicated by interacting with existing pollutants, especially per- and polyfluoroalkyl substances (PFAS). However, due to their sheer volume, it is impossible to explore all possible interactions by simply utilizing experimental methods. Herein, we used two model TMDC nanosheets, molybdenum disulfide (MoS2) and tungsten disulfide (WS2), and seven PFAS to explore their interactions and subsequent impacts on model cell lines and zebrafish. Utilizing experimental methods and machine learning approaches, we showed that TMDCs-PFAS interactions can pose unique challenges due to their interaction-specific toxicity niches towards cell lines. Further in vivo experiments, together with molecular dynamics simulation, suggested that TMDCs-PFAS interactions in aqueous environments significantly increased their bioaccumulation in zebrafish towards different target organs, mostly due to the differences in loading PFAS. Such enhanced bioaccumulation increased the oxidative stress in zebrafish liver and intestine, as demonstrated by the increased reactive oxygen species (ROS) level and other enzyme activities, which eventually led to obvious histopathological alterations in the liver and intestine. Our study highlights the importance of exploring interactions between emerging and existing contaminants with state-of-art techniques in aqueous environments and its significance in safeguarding aquatic environment health.
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Affiliation(s)
- Guohong Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Agriculture and Biological Sciences, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Xiliang Yan
- School of Agriculture and Biological Sciences, Qiannan Normal University for Nationalities, Duyun 558000, China.
| | - Chengjun Li
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Agriculture and Biological Sciences, Qiannan Normal University for Nationalities, Duyun 558000, China.
| | - Song Hu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Jiachen Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Bing Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China.
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17
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Wang T, Russo DP, Bitounis D, Demokritou P, Jia X, Huang H, Zhu H. Integrating structure annotation and machine learning approaches to develop graphene toxicity models. CARBON 2023; 204:484-494. [PMID: 36845527 PMCID: PMC9957041 DOI: 10.1016/j.carbon.2022.12.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Modern nanotechnology provides efficient and cost-effective nanomaterials (NMs). The increasing usage of NMs arises great concerns regarding nanotoxicity in humans. Traditional animal testing of nanotoxicity is expensive and time-consuming. Modeling studies using machine learning (ML) approaches are promising alternatives to direct evaluation of nanotoxicity based on nanostructure features. However, NMs, including two-dimensional nanomaterials (2DNMs) such as graphenes, have complex structures making them difficult to annotate and quantify the nanostructures for modeling purposes. To address this issue, we constructed a virtual graphenes library using nanostructure annotation techniques. The irregular graphene structures were generated by modifying virtual nanosheets. The nanostructures were digitalized from the annotated graphenes. Based on the annotated nanostructures, geometrical nanodescriptors were computed using Delaunay tessellation approach for ML modeling. The partial least square regression (PLSR) models for the graphenes were built and validated using a leave-one-out cross-validation (LOOCV) procedure. The resulted models showed good predictivity in four toxicity-related endpoints with the coefficient of determination (R2) ranging from 0.558 to 0.822. This study provides a novel nanostructure annotation strategy that can be applied to generate high-quality nanodescriptors for ML model developments, which can be widely applied to nanoinformatics studies of graphenes and other NMs.
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Affiliation(s)
- Tong Wang
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA
| | - Daniel P. Russo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA
| | - Dimitrios Bitounis
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA 02115, USA
- Nanoscience and Advanced Materials Center, Environmental Occupational Health Sciences Institute, School of Public Health, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA 02115, USA
- Nanoscience and Advanced Materials Center, Environmental Occupational Health Sciences Institute, School of Public Health, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Xuelian Jia
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA
| | - Heng Huang
- Department of Electrical and Computer Engineering, Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Boulevard, Pittsburgh, Pennsylvania, USA
| | - Hao Zhu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA
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18
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Toropova AP, Toropov AA, Fjodorova N. In Silico Simulation of Impacts of Metal Nano-Oxides on Cell Viability in THP-1 Cells Based on the Correlation Weights of the Fragments of Molecular Structures and Codes of Experimental Conditions Represented by Means of Quasi-SMILES. Int J Mol Sci 2023; 24:ijms24032058. [PMID: 36768396 PMCID: PMC9917241 DOI: 10.3390/ijms24032058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
A simulation of the effect of metal nano-oxides at various concentrations (25, 50, 100, and 200 milligrams per millilitre) on cell viability in THP-1 cells (%) based on data on the molecular structure of the oxide and its concentration is proposed. We used a simplified molecular input-line entry system (SMILES) to represent the molecular structure. So-called quasi-SMILES extends usual SMILES with special codes for experimental conditions (concentration). The approach based on building up models using quasi-SMILES is self-consistent, i.e., the predictive potential of the model group obtained by random splits into training and validation sets is stable. The Monte Carlo method was used as a basis for building up the above groups of models. The CORAL software was applied to building the Monte Carlo calculations. The average determination coefficient for the five different validation sets was R2 = 0.806 ± 0.061.
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Affiliation(s)
- Alla P. Toropova
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri, 2, 20156 Milano, Italy
- Correspondence: ; Tel.: +39-02-3901-4595
| | - Andrey A. Toropov
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri, 2, 20156 Milano, Italy
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Yang RX, McCandler CA, Andriuc O, Siron M, Woods-Robinson R, Horton MK, Persson KA. Big Data in a Nano World: A Review on Computational, Data-Driven Design of Nanomaterials Structures, Properties, and Synthesis. ACS NANO 2022; 16:19873-19891. [PMID: 36378904 PMCID: PMC9798871 DOI: 10.1021/acsnano.2c08411] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/08/2022] [Indexed: 05/30/2023]
Abstract
The recent rise of computational, data-driven research has significant potential to accelerate materials discovery. Automated workflows and materials databases are being rapidly developed, contributing to high-throughput data of bulk materials that are growing in quantity and complexity, allowing for correlation between structural-chemical features and functional properties. In contrast, computational data-driven approaches are still relatively rare for nanomaterials discovery due to the rapid scaling of computational cost for finite systems. However, the distinct behaviors at the nanoscale as compared to the parent bulk materials and the vast tunability space with respect to dimensionality and morphology motivate the development of data sets for nanometric materials. In this review, we discuss the recent progress in data-driven research in two aspects: functional materials design and guided synthesis, including commonly used metrics and approaches for designing materials properties and predicting synthesis routes. More importantly, we discuss the distinct behaviors of materials as a result of nanosizing and the implications for data-driven research. Finally, we share our perspectives on future directions for extending the current data-driven research into the nano realm.
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Affiliation(s)
- Ruo Xi Yang
- Materials
Science Division, Lawrence Berkeley National
Laboratory, Berkeley, California94720, United States
| | - Caitlin A. McCandler
- Materials
Science Division, Lawrence Berkeley National
Laboratory, Berkeley, California94720, United States
- Department
of Materials Science and Engineering, University
of California, Berkeley, California94720, United States
| | - Oxana Andriuc
- Department
of Chemistry, University of California, Berkeley, California94720, United States
- Liquid
Sunlight Alliance and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Martin Siron
- Materials
Science Division, Lawrence Berkeley National
Laboratory, Berkeley, California94720, United States
- Department
of Materials Science and Engineering, University
of California, Berkeley, California94720, United States
| | - Rachel Woods-Robinson
- Materials
Science Division, Lawrence Berkeley National
Laboratory, Berkeley, California94720, United States
| | - Matthew K. Horton
- Materials
Science Division, Lawrence Berkeley National
Laboratory, Berkeley, California94720, United States
- Department
of Materials Science and Engineering, University
of California, Berkeley, California94720, United States
| | - Kristin A. Persson
- Department
of Materials Science and Engineering, University
of California, Berkeley, California94720, United States
- Molecular
Foundry, Energy Sciences Area, Lawrence
Berkeley National Laboratory, Berkeley, California94720, United States
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20
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Ke W, Crist RM, Clogston JD, Stern ST, Dobrovolskaia MA, Grodzinski P, Jensen MA. Trends and patterns in cancer nanotechnology research: A survey of NCI's caNanoLab and nanotechnology characterization laboratory. Adv Drug Deliv Rev 2022; 191:114591. [PMID: 36332724 PMCID: PMC9712232 DOI: 10.1016/j.addr.2022.114591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022]
Abstract
Cancer nanotechnologies possess immense potential as therapeutic and diagnostic treatment modalities and have undergone significant and rapid advancement in recent years. With this emergence, the complexities of data standards in the field are on the rise. Data sharing and reanalysis is essential to more fully utilize this complex, interdisciplinary information to answer research questions, promote the technologies, optimize use of funding, and maximize the return on scientific investments. In order to support this, various data-sharing portals and repositories have been developed which not only provide searchable nanomaterial characterization data, but also provide access to standardized protocols for synthesis and characterization of nanomaterials as well as cutting-edge publications. The National Cancer Institute's (NCI) caNanoLab is a dedicated repository for all aspects pertaining to cancer-related nanotechnology data. The searchable database provides a unique opportunity for data mining and the use of artificial intelligence and machine learning, which aims to be an essential arm of future research studies, potentially speeding the design and optimization of next-generation therapies. It also provides an opportunity to track the latest trends and patterns in nanomedicine research. This manuscript provides the first look at such trends extracted from caNanoLab and compares these to similar metrics from the NCI's Nanotechnology Characterization Laboratory, a laboratory providing preclinical characterization of cancer nanotechnologies to researchers around the globe. Together, these analyses provide insight into the emerging interests of the research community and rise of promising nanoparticle technologies.
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Affiliation(s)
- Weina Ke
- Bioinformatics and Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, United States
| | - Rachael M Crist
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, United States
| | - Jeffrey D Clogston
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, United States
| | - Stephan T Stern
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, United States
| | - Piotr Grodzinski
- Nanodelivery Systems and Devices Branch, Cancer Imaging Program, National Cancer Institute, Rockville, MD, United States
| | - Mark A Jensen
- Bioinformatics and Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, United States.
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21
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Li J, Yue L, Zhao Q, Cao X, Tang W, Chen F, Wang C, Wang Z. Prediction models on biomass and yield of rice affected by metal (oxide) nanoparticles using nano-specific descriptors. NANOIMPACT 2022; 28:100429. [PMID: 36130713 DOI: 10.1016/j.impact.2022.100429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
The use of in silico tools to investigate the interactions between metal (oxide) nanoparticles (NPs) and plant biological responses is preferred because it allows us to understand molecular mechanisms and improve prediction efficiency by saving time, labor, and cost. In this study, four models (C5.0 decision tree, discriminant function analysis, random forest, and stepwise multiple linear regression analysis) were applied to predict the effect of NPs on rice biomass and yield. Nano-specific descriptors (size-dependent molecular descriptors and image-based descriptors) were introduced to estimate the behavior of NPs in plants to appropriately represent the wide space of NPs. The results showed that size-dependent molecular descriptors (e.g., E-state and connectivity indices) and image-based descriptors (e.g., extension, area, and minimum ferret diameter) were associated with the behavior of NPs in rice. The performance of the constructed models was within acceptable ranges (correlation coefficient ranged from 0.752 to 0.847 for biomass and from 0.803 to 0.905 for yield, while the accuracy ranged from 64% to 77% for biomass and 81% to 89% for yield). The developed model can be used to quickly and efficiently evaluate the impact of NPs under a wide range of experimental conditions and sufficient training data.
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Affiliation(s)
- Jing Li
- Institute of Environmental Processotes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Le Yue
- Institute of Environmental Processotes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qing Zhao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Xuesong Cao
- Institute of Environmental Processotes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Weihao Tang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Feiran Chen
- Institute of Environmental Processotes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processotes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Zhenyu Wang
- Institute of Environmental Processotes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
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22
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Junnuthula V, Kolimi P, Nyavanandi D, Sampathi S, Vora LK, Dyawanapelly S. Polymeric Micelles for Breast Cancer Therapy: Recent Updates, Clinical Translation and Regulatory Considerations. Pharmaceutics 2022; 14:pharmaceutics14091860. [PMID: 36145608 PMCID: PMC9501124 DOI: 10.3390/pharmaceutics14091860] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/15/2022] [Accepted: 09/01/2022] [Indexed: 12/13/2022] Open
Abstract
With the growing burden of cancer, parallel advancements in anticancer nanotechnological solutions have been witnessed. Among the different types of cancers, breast cancer accounts for approximately 25% and leads to 15% of deaths. Nanomedicine and its allied fields of material science have revolutionized the science of medicine in the 21st century. Novel treatments have paved the way for improved drug delivery systems that have better efficacy and reduced adverse effects. A variety of nanoformulations using lipids, polymers, inorganic, and peptide-based nanomedicines with various functionalities are being synthesized. Thus, elaborate knowledge of these intelligent nanomedicines for highly promising drug delivery systems is of prime importance. Polymeric micelles (PMs) are generally easy to prepare with good solubilization properties; hence, they appear to be an attractive alternative over the other nanosystems. Although an overall perspective of PM systems has been presented in recent reviews, a brief discussion has been provided on PMs for breast cancer. This review provides a discussion of the state-of-the-art PMs together with the most recent advances in this field. Furthermore, special emphasis is placed on regulatory guidelines, clinical translation potential, and future aspects of the use of PMs in breast cancer treatment. The recent developments in micelle formulations look promising, with regulatory guidelines that are now more clearly defined; hence, we anticipate early clinical translation in the near future.
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Affiliation(s)
- Vijayabhaskarreddy Junnuthula
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00790 Helsinki, Finland
- Correspondence: (V.J.); (S.D.)
| | - Praveen Kolimi
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, Oxford, MS 38677, USA
| | - Dinesh Nyavanandi
- Pharmaceutical Development Services, Thermo Fisher Scientific, Cincinnati, OH 45237, USA
| | - Sunitha Sampathi
- GITAM School of Pharmacy, GITAM Deemed to be University, Hyderabad 502329, India
| | | | - Sathish Dyawanapelly
- Department of Pharmaceutical Science and Technology, Institute of Chemical Technology, Mumbai 400019, India
- Correspondence: (V.J.); (S.D.)
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23
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Wyrzykowska E, Mikolajczyk A, Lynch I, Jeliazkova N, Kochev N, Sarimveis H, Doganis P, Karatzas P, Afantitis A, Melagraki G, Serra A, Greco D, Subbotina J, Lobaskin V, Bañares MA, Valsami-Jones E, Jagiello K, Puzyn T. Representing and describing nanomaterials in predictive nanoinformatics. NATURE NANOTECHNOLOGY 2022; 17:924-932. [PMID: 35982314 DOI: 10.1038/s41565-022-01173-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Engineered nanomaterials (ENMs) enable new and enhanced products and devices in which matter can be controlled at a near-atomic scale (in the range of 1 to 100 nm). However, the unique nanoscale properties that make ENMs attractive may result in as yet poorly known risks to human health and the environment. Thus, new ENMs should be designed in line with the idea of safe-and-sustainable-by-design (SSbD). The biological activity of ENMs is closely related to their physicochemical characteristics, changes in these characteristics may therefore cause changes in the ENMs activity. In this sense, a set of physicochemical characteristics (for example, chemical composition, crystal structure, size, shape, surface structure) creates a unique 'representation' of a given ENM. The usability of these characteristics or nanomaterial descriptors (nanodescriptors) in nanoinformatics methods such as quantitative structure-activity/property relationship (QSAR/QSPR) models, provides exciting opportunities to optimize ENMs at the design stage by improving their functionality and minimizing unforeseen health/environmental hazards. A computational screening of possible versions of novel ENMs would return optimal nanostructures and manage ('design out') hazardous features at the earliest possible manufacturing step. Safe adoption of ENMs on a vast scale will depend on the successful integration of the entire bulk of nanodescriptors extracted experimentally with data from theoretical and computational models. This Review discusses directions for developing appropriate nanomaterial representations and related nanodescriptors to enhance the reliability of computational modelling utilized in designing safer and more sustainable ENMs.
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Affiliation(s)
| | - Alicja Mikolajczyk
- QSAR Lab Ltd, Gdańsk, Poland
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | | | - Nikolay Kochev
- Ideaconsult Ltd, Sofia, Bulgaria
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, Zografou, Athens, Greece
| | - Philip Doganis
- School of Chemical Engineering, National Technical University of Athens, Zografou, Athens, Greece
| | - Pantelis Karatzas
- School of Chemical Engineering, National Technical University of Athens, Zografou, Athens, Greece
| | | | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, Vari, Greece
| | - Angela Serra
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Dario Greco
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Julia Subbotina
- School of Physics, University College Dublin, Belfield, Dublin, Ireland
| | - Vladimir Lobaskin
- School of Physics, University College Dublin, Belfield, Dublin, Ireland
| | - Miguel A Bañares
- Instituto de Catálisis y Petroleoquimica, ICP CSIC, Madrid, Spain
| | - Eugenia Valsami-Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Karolina Jagiello
- QSAR Lab Ltd, Gdańsk, Poland
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Tomasz Puzyn
- QSAR Lab Ltd, Gdańsk, Poland.
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.
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24
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Konstantopoulos G, Koumoulos EP, Charitidis CA. Digital Innovation Enabled Nanomaterial Manufacturing; Machine Learning Strategies and Green Perspectives. NANOMATERIALS 2022; 12:nano12152646. [PMID: 35957077 PMCID: PMC9370746 DOI: 10.3390/nano12152646] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 02/05/2023]
Abstract
Machine learning has been an emerging scientific field serving the modern multidisciplinary needs in the Materials Science and Manufacturing sector. The taxonomy and mapping of nanomaterial properties based on data analytics is going to ensure safe and green manufacturing with consciousness raised on effective resource management. The utilization of predictive modelling tools empowered with artificial intelligence (AI) has proposed novel paths in materials discovery and optimization, while it can further stimulate the cutting-edge and data-driven design of a tailored behavioral profile of nanomaterials to serve the special needs of application environments. The previous knowledge of the physics and mathematical representation of material behaviors, as well as the utilization of already generated testing data, received specific attention by scientists. However, the exploration of available information is not always manageable, and machine intelligence can efficiently (computational resources, time) meet this challenge via high-throughput multidimensional search exploration capabilities. Moreover, the modelling of bio-chemical interactions with the environment and living organisms has been demonstrated to connect chemical structure with acute or tolerable effects upon exposure. Thus, in this review, a summary of recent computational developments is provided with the aim to cover excelling research and present challenges towards unbiased, decentralized, and data-driven decision-making, in relation to increased impact in the field of advanced nanomaterials manufacturing and nanoinformatics, and to indicate the steps required to realize rapid, safe, and circular-by-design nanomaterials.
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Affiliation(s)
- Georgios Konstantopoulos
- RNANO Lab—Research Unit of Advanced, Composite, Nano Materials & Nanotechnology, School of Chemical Engineering, National Technical University of Athens, GR15773 Athens, Greece; (G.K.); (C.A.C.)
| | - Elias P. Koumoulos
- Innovation in Research & Engineering Solutions (IRES), Boulevard Edmond Machtens 79/22, 1080 Brussels, Belgium
- Correspondence:
| | - Costas A. Charitidis
- RNANO Lab—Research Unit of Advanced, Composite, Nano Materials & Nanotechnology, School of Chemical Engineering, National Technical University of Athens, GR15773 Athens, Greece; (G.K.); (C.A.C.)
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25
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Abstract
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.
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Affiliation(s)
- Zhoumeng Lin
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, 32610, USA.,Center for Environmental and Human Toxicology, University of Florida, FL, 32608, USA
| | - Wei-Chun Chou
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, 32610, USA.,Center for Environmental and Human Toxicology, University of Florida, FL, 32608, USA
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26
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Yu F, Hu X. Machine learning may accelerate the recognition and control of microplastic pollution: Future prospects. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128730. [PMID: 35338937 DOI: 10.1016/j.jhazmat.2022.128730] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Microplastics (MPs, sizes <5 mm) have been found to be widely distributed in various environments, such as marine, freshwater, terrestrial and atmospheric systems. Machine learning provides a potential solution for evaluating the ecological risks of MPs based on big data. Compared with traditional models, data-driven machine learning can accelerate the realization of the control of hazardous MPs and reduce the impact of MPs at both local and global scales. However, there are some urgent issues that should be resolved. For example, lack of MP databases and incomparable literatures causing the current MP data cannot fully support big data research. Therefore, it is imperative to formulate a set of standard and universal MP collection and testing protocols. For machine learning, predictions of large-scale MP distribution and the corresponding environmental risks remain lacking. To accelerate studies of MPs in the future, the methods and theories achieved for other particle pollutants, such as nanomaterials and aerosols, can be referenced. Beyond predication alone, the improvement of causality and interpretability of machine learning deserves attention in the studies of MP risks. Overall, this perspective paper provides insights for the development of machine learning methods in research on the environmental risks of MPs.
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Affiliation(s)
- Fubo Yu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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27
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Hu S, Liu G, Zhang J, Yan J, Zhou H, Yan X. Linking electron ionization mass spectra of organic chemicals to toxicity endpoints through machine learning and experimentation. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128558. [PMID: 35228074 DOI: 10.1016/j.jhazmat.2022.128558] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Quantitative structure-activity relationship (QSAR) modeling has been widely used to predict the potential harm of chemicals, in which the prediction heavily relies on the accurate annotation of chemical structures. However, it is difficult to determine the accurate structure of an unknown compound in many cases, such as in complex water environments. Here, we solved the above problem by linking electron ionization mass spectra (EI-MS) of organic chemicals to toxicity endpoints through various machine learning methods. The proposed method was verified by predicting 50% growth inhibition of Tetrahymena pyriformis (T. pyriformis) and liver toxicity. The optimal model performance obtained an R2 > 0.7 or balanced accuracy > 0.72 for both the training set and test set. External experimentation further verified the application potential of our proposed method in the toxicity prediction of unknown chemicals. Feature importance analysis allowed us to identify critical spectral features that were responsible for chemical-induced toxicity. Our approach has the potential for toxicity prediction in such fields that it is difficult to determine accurate chemical structures.
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Affiliation(s)
- Song Hu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Guohong Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jin Zhang
- School of Public Health, Guizhou Medical University, Guiyang 550025, China
| | - Jiachen Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Hongyu Zhou
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xiliang Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
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28
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Zhou X, Jin W, Sun H, Li C, Jia J. Perturbation of autophagy: An intrinsic toxicity mechanism of nanoparticles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153629. [PMID: 35131247 DOI: 10.1016/j.scitotenv.2022.153629] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/11/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Nanoparticles (NPs) have been widely used for various purposes due to their unique physicochemical properties. Such widespread applications greatly increase the possibility of human exposure to NPs in various ways. Once entering the human body, NPs may interfere with cellular homeostasis and thus affect the physiological system. As a result, it is necessary to evaluate the potential disturbance of NPs to multiple cell functions, including autophagy. Autophagy is an important cell function to maintain cellular homeostasis, and minimizing the disturbance caused by NP exposures to autophagy is critical to nanosafety. Herein, we summarized the recent research progress in nanotoxicity with particular focuses on the perturbation of NPs to cell autophagy. The basic processes of autophagy and complex relationships between autophagy and major human diseases were further discussed to emphasize the importance of keeping autophagy under control. Moreover, the most recent advances on perturbation of different types of NPs to autophagy were also reviewed. Last but not least, we also discussed major research challenges and potential coping strategies and proposed a safe-by-design strategy towards safer applications of NPs.
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Affiliation(s)
- Xiaofei Zhou
- College of Science & Technology, Hebei Agricultural University, Huanghua 061100, China
| | - Weitao Jin
- College of Science & Technology, Hebei Agricultural University, Huanghua 061100, China
| | - Hainan Sun
- Shandong Vocational College of Light Industry, Zibo 255300, China
| | - Chengjun Li
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Jianbo Jia
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
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29
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Toropova AP, Toropov AA. Nanomaterials: Quasi-SMILES as a flexible basis for regulation and environmental risk assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153747. [PMID: 35149067 DOI: 10.1016/j.scitotenv.2022.153747] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Basic principles and problems of the systematization of data on nanomaterials are discussed. The eclectic character of nanomaterials is defined as the key difference between nanomaterials and traditional substances. The quasi-SMILES technique is described and discussed. The possible role of the approach is bridging between experimentalists and developers of models for endpoints related to nanomaterials. The use of models on the possible impact of nanomaterials on the environment and human health has been collected and compared. The new criteria of the predictive potential for the above models are discussed. The advantage of the statistical criteria sensitive simultaneously to both the correlation coefficient and the root mean square error noted. The rejection of the border between the effect of the biochemical reality of substances at a molecular level and the effect of experiment conditions at the macro level gives the possibility to develop models that are epistemologically more reliable in the comparison with traditional models based exclusively on the molecular structure-biological activity interdependence (without taking into account experimental conditions). Models of the physicochemical and biochemical behaviour of nanomaterials are necessary in order to develop and apply new industrial achievements, everyday comfort species, medicine, cosmetics, and foods without negative effects on ecology and human health. The CORAL (abbreviation CORrelation And Logic) software provides the user with the possibility to build up nano-QSAR models as a mathematical function of so-called correlation weights of fragments of quasi-SMILES. These models are built up via the Monte Carlo method. Apparently, the quasi-SMILES is a universal representation of nano-reality since there is no limitation to choose the list of eclectic data able to have an impact on nano-phenomena. This paradigm is a convenient language to the conversation of experimentalists and developers of models for nano-phenomena.
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Affiliation(s)
- Alla P Toropova
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy.
| | - Andrey A Toropov
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
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30
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Text-mined dataset of gold nanoparticle synthesis procedures, morphologies, and size entities. Sci Data 2022; 9:234. [PMID: 35618761 PMCID: PMC9135747 DOI: 10.1038/s41597-022-01321-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/08/2022] [Indexed: 12/13/2022] Open
Abstract
Gold nanoparticles are highly desired for a range of technological applications due to their tunable properties, which are dictated by the size and shape of the constituent particles. Many heuristic methods for controlling the morphological characteristics of gold nanoparticles are well known. However, the underlying mechanisms controlling their size and shape remain poorly understood, partly due to the immense range of possible combinations of synthesis parameters. Data-driven methods can offer insight to help guide understanding of these underlying mechanisms, so long as sufficient synthesis data are available. To facilitate data mining in this direction, we have constructed and made publicly available a dataset of codified gold nanoparticle synthesis protocols and outcomes extracted directly from the nanoparticle materials science literature using natural language processing and text-mining techniques. This dataset contains 5,154 data records, each representing a single gold nanoparticle synthesis article, filtered from a database of 4,973,165 publications. Each record contains codified synthesis protocols and extracted morphological information from a total of 7,608 experimental and 12,519 characterization paragraphs. Measurement(s) | gold nanoparticle morphology • gold nanoparticle size • gold nanoparticle synthesis data | Technology Type(s) | natural language processing |
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31
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Chew AK, Pedersen JA, Van Lehn RC. Predicting the Physicochemical Properties and Biological Activities of Monolayer-Protected Gold Nanoparticles Using Simulation-Derived Descriptors. ACS NANO 2022; 16:6282-6292. [PMID: 35289596 DOI: 10.1021/acsnano.2c00301] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gold nanoparticles are versatile materials for biological applications because their properties can be modulated by assembling ligands on their surface to form monolayers. However, the physicochemical properties and behaviors of monolayer-protected nanoparticles in biological environments are difficult to anticipate because they emerge from the interplay of ligand-ligand and ligand-solvent interactions that cannot be readily inferred from ligand chemical structure alone. In this work, we demonstrate that quantitative nanostructure-activity relationship (QNAR) models can employ descriptors calculated from molecular dynamics simulations to predict nanoparticle properties and cellular uptake. We performed atomistic molecular dynamics simulations of 154 monolayer-protected gold nanoparticles and calculated a small library of simulation-derived descriptors that capture nanoparticle structural and chemical properties in aqueous solution. We then parametrized QNAR models using interpretable regression algorithms to predict experimental measurements of nanoparticle octanol-water partition coefficients, zeta potentials, and cellular uptake obtained from a curated database. These models reveal that simulation-derived descriptors can accurately predict experimental trends and provide physical insight into what descriptors are most important for obtaining desired nanoparticle properties or behaviors in biological environments. Finally, we demonstrate model generalizability by predicting cell uptake trends for 12 nanoparticles not included in the original data set. These results demonstrate that QNAR models parametrized with simulation-derived descriptors are accurate, generalizable computational tools that could be used to guide the design of monolayer-protected gold nanoparticles for biological applications without laborious trial-and-error experimentation.
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Affiliation(s)
- Alex K Chew
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joel A Pedersen
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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32
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Forest V. Experimental and Computational Nanotoxicology-Complementary Approaches for Nanomaterial Hazard Assessment. NANOMATERIALS 2022; 12:nano12081346. [PMID: 35458054 PMCID: PMC9031966 DOI: 10.3390/nano12081346] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 12/25/2022]
Abstract
The growing development and applications of nanomaterials lead to an increasing release of these materials in the environment. The adverse effects they may elicit on ecosystems or human health are not always fully characterized. Such potential toxicity must be carefully assessed with the underlying mechanisms elucidated. To that purpose, different approaches can be used. First, experimental toxicology consisting of conducting in vitro or in vivo experiments (including clinical studies) can be used to evaluate the nanomaterial hazard. It can rely on variable models (more or less complex), allowing the investigation of different biological endpoints. The respective advantages and limitations of in vitro and in vivo models are discussed as well as some issues associated with experimental nanotoxicology. Perspectives of future developments in the field are also proposed. Second, computational nanotoxicology, i.e., in silico approaches, can be used to predict nanomaterial toxicity. In this context, we describe the general principles, advantages, and limitations especially of quantitative structure–activity relationship (QSAR) models and grouping/read-across approaches. The aim of this review is to provide an overview of these different approaches based on examples and highlight their complementarity.
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Affiliation(s)
- Valérie Forest
- Mines Saint-Etienne, Univ Lyon, Univ Jean Monnet, Etablissement Français du Sang, INSERM, U1059 Sainbiose, Centre CIS, F-42023 Saint-Etienne, France
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33
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Lin Z, Chou WC, Cheng YH, He C, Monteiro-Riviere NA, Riviere JE. Predicting Nanoparticle Delivery to Tumors Using Machine Learning and Artificial Intelligence Approaches. Int J Nanomedicine 2022; 17:1365-1379. [PMID: 35360005 PMCID: PMC8961007 DOI: 10.2147/ijn.s344208] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/10/2022] [Indexed: 12/12/2022] Open
Abstract
Background Low delivery efficiency of nanoparticles (NPs) to the tumor is a critical barrier in the field of cancer nanomedicine. Strategies on how to improve NP tumor delivery efficiency remain to be determined. Methods This study analyzed the roles of NP physicochemical properties, tumor models, and cancer types in NP tumor delivery efficiency using multiple machine learning and artificial intelligence methods, using data from a recently published Nano-Tumor Database that contains 376 datasets generated from a physiologically based pharmacokinetic (PBPK) model. Results The deep neural network model adequately predicted the delivery efficiency of different NPs to different tumors and it outperformed all other machine learning methods; including random forest, support vector machine, linear regression, and bagged model methods. The adjusted determination coefficients (R2) in the full training dataset were 0.92, 0.77, 0.77 and 0.76 for the maximum delivery efficiency (DEmax), delivery efficiency at 24 h (DE24), at 168 h (DE168), and at the last sampling time (DETlast). The corresponding R2 values in the test dataset were 0.70, 0.46, 0.33 and 0.63, respectively. Also, this study showed that cancer type was an important determinant for the deep neural network model in predicting the tumor delivery efficiency across all endpoints (19-29%). Among all physicochemical properties, the Zeta potential and core material played a greater role than other properties, such as the type, shape, and targeting strategy. Conclusion This study provides a quantitative model to improve the design of cancer nanomedicine with greater tumor delivery efficiency. These results help to improve our understanding of the causes of low NP tumor delivery efficiency. This study demonstrates the feasibility of integrating artificial intelligence with PBPK modeling approaches to study cancer nanomedicine.
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Affiliation(s)
- Zhoumeng Lin
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, USA
- Institute of Computational Comparative Medicine, Kansas State University, Manhattan, KS, USA
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Wei-Chun Chou
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, USA
- Institute of Computational Comparative Medicine, Kansas State University, Manhattan, KS, USA
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yi-Hsien Cheng
- Institute of Computational Comparative Medicine, Kansas State University, Manhattan, KS, USA
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Chunla He
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Nancy A Monteiro-Riviere
- Nanotechnology Innovation Center of Kansas State, Kansas State University, Manhattan, KS, USA
- Center for Chemical Toxicology Research and Pharmacokinetics, North Carolina State University, Raleigh, NC, USA
| | - Jim E Riviere
- Center for Chemical Toxicology Research and Pharmacokinetics, North Carolina State University, Raleigh, NC, USA
- 1Data Consortium, Kansas State University, Olathe, KS, USA
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Li J, Chen C, Xia T. Understanding Nanomaterial-Liver Interactions to Facilitate the Development of Safer Nanoapplications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2106456. [PMID: 35029313 PMCID: PMC9040585 DOI: 10.1002/adma.202106456] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/23/2021] [Indexed: 05/02/2023]
Abstract
Nanomaterials (NMs) are widely used in commercial and medical products, such as cosmetics, vaccines, and drug carriers. Exposure to NMs via various routes such as dermal, inhalation, and ingestion has been shown to gain access to the systemic circulation, resulting in the accumulation of NMs in the liver. The unique organ structures and blood flow features facilitate the liver sequestration of NMs, which may cause adverse effects in the liver. Currently, most in vivo studies are focused on NMs accumulation at the organ level and evaluation of the gross changes in liver structure and functions, however, cell-type-specific uptake and responses, as well as the molecular mechanisms at cellular levels leading to effects at organ levels are lagging. Herein, the authors systematically review diverse interactions of NMs with the liver, specifically on major liver cell types including Kupffer cells (KCs), liver sinusoidal endothelial cells (LSECs), hepatic stellate cells (HSCs), and hepatocytes as well as the detailed molecular mechanisms involved. In addition, the knowledge gained on nano-liver interactions that can facilitate the development of safer nanoproducts and nanomedicine is also reviewed.
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Affiliation(s)
- Jiulong Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
| | - Tian Xia
- Center of Environmental Implications of Nanotechnology (UC CEIN), California NanoSystems Institute, Division of NanoMedicine, Department of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
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Gianti E, Percec S. Machine Learning at the Interface of Polymer Science and Biology: How Far Can We Go? Biomacromolecules 2022; 23:576-591. [PMID: 35133143 DOI: 10.1021/acs.biomac.1c01436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This Perspective outlines recent progress and future directions for using machine learning (ML), a data-driven method, to address critical questions in the design, synthesis, processing, and characterization of biomacromolecules. The achievement of these tasks requires the navigation of vast and complex chemical and biological spaces, difficult to accomplish with reasonable speed. Using modern algorithms and supercomputers, quantum physics methods are able to examine systems containing a few hundred interacting species and determine the probability of finding them in a particular region of phase space, thereby anticipating their properties. Likewise, modern approaches in chemistry and biomolecular simulation, supported by high performance computing, have culminated in producing data sets of escalating size and intrinsically high complexity. Hence, using ML to extract relevant information from these fields is of paramount importance to advance our understanding of chemical and biomolecular systems. At the heart of ML approaches lie statistical algorithms, which by evaluating a portion of a given data set, identify, learn, and manipulate the underlying rules that govern the whole data set. The assembly of a quality model to represent the data followed by the predictions and elimination of error sources are the key steps in ML. In addition to a growing infrastructure of ML tools to address complex problems, an increasing number of aspects related to our understanding of the fundamental properties of biomacromolecules are exposed to ML. These fields, including those residing at the interface of polymer science and biology (i.e., structure determination, de novo design, folding, and dynamics), strive to adopt and take advantage of the transformative power offered by approaches in the ML domain, which clearly has the potential of accelerating research in the field of biomacromolecules.
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Affiliation(s)
- Eleonora Gianti
- Institute for Computational Molecular Science (ICMS), Temple University, Philadelphia, Pennsylvania 19122, United States.,Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Simona Percec
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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Choi YK, Kern NR, Kim S, Kanhaiya K, Afshar Y, Jeon SH, Jo S, Brooks BR, Lee J, Tadmor EB, Heinz H, Im W. CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems. J Chem Theory Comput 2022; 18:479-493. [PMID: 34871001 PMCID: PMC8752518 DOI: 10.1021/acs.jctc.1c00996] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular modeling and simulation are invaluable tools for nanoscience that predict mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide molecular-level insight into underlying mechanisms. However, building nanomaterial-containing systems remains challenging due to the lack of reliable and integrated cyberinfrastructures. Here we present Nanomaterial Modeler in CHARMM-GUI, a web-based cyberinfrastructure that provides an automated process to generate various nanomaterial models, associated topologies, and configuration files to perform state-of-the-art molecular dynamics simulations using most simulation packages. The nanomaterial models are based on the interface force field, one of the most reliable force fields (FFs). The transferability of nanomaterial models among the simulation programs was assessed by single-point energy calculations, which yielded 0.01% relative absolute energy differences for various surface models and equilibrium nanoparticle shapes. Three widely used Lennard-Jones (LJ) cutoff methods are employed to evaluate the compatibility of nanomaterial models with respect to conventional biomolecular FFs: simple truncation at r = 12 Å (12 cutoff), force-based switching over 10 to 12 Å (10-12 fsw), and LJ particle mesh Ewald with no cutoff (LJPME). The FF parameters with these LJ cutoff methods are extensively validated by reproducing structural, interfacial, and mechanical properties. We find that the computed density and surface energies are in good agreement with reported experimental results, although the simulation results increase in the following order: 10-12 fsw <12 cutoff < LJPME. Nanomaterials in which LJ interactions are a major component show relatively higher deviations (up to 4% in density and 8% in surface energy differences) compared with the experiment. Nanomaterial Modeler's capability is also demonstrated by generating complex systems of nanomaterial-biomolecule and nanomaterial-polymer interfaces with a combination of existing CHARMM-GUI modules. We hope that Nanomaterial Modeler can be used to carry out innovative nanomaterial modeling and simulations to acquire insight into the structure, dynamics, and underlying mechanisms of complex nanomaterial-containing systems.
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Affiliation(s)
- Yeol Kyo Choi
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Nathan R. Kern
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Seonghan Kim
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Krishan Kanhaiya
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80301, USA
| | - Yaser Afshar
- Department of Aerospace Engineering and Mechanics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sun Hee Jeon
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Sunhwan Jo
- Leadership Computing Facility, Argonne National Laboratory, 9700 Cass Ave, Argonne, IL 60439, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jumin Lee
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Ellad B. Tadmor
- Department of Aerospace Engineering and Mechanics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80301, USA
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
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Poppleton E, Mallya A, Dey S, Joseph J, Šulc P. Nanobase.org: a repository for DNA and RNA nanostructures. Nucleic Acids Res 2022; 50:D246-D252. [PMID: 34747480 PMCID: PMC8728195 DOI: 10.1093/nar/gkab1000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
We introduce a new online database of nucleic acid nanostructures for the field of DNA and RNA nanotechnology. The database implements an upload interface, searching and database browsing. Each deposited nanostructures includes an image of the nanostructure, design file, an optional 3D view, and additional metadata such as experimental data, protocol or literature reference. The database accepts nanostructures in any preferred format used by the uploader for the nanostructure design. We further provide a set of conversion tools that encourage design file conversion into common formats (oxDNA and PDB) that can be used for setting up simulations, interactive editing or 3D visualization. The aim of the repository is to provide to the DNA/RNA nanotechnology community a resource for sharing their designs for further reuse in other systems and also to function as an archive of the designs that have been achieved in the field so far. Nanobase.org is available at https://nanobase.org/.
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Affiliation(s)
- Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Aatmik Mallya
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Swarup Dey
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- Wyss Institute, Harvard University, Boston, MA 02115, USA
| | - Joel Joseph
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
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Furxhi I. Health and environmental safety of nanomaterials: O Data, Where Art Thou? NANOIMPACT 2022; 25:100378. [PMID: 35559884 DOI: 10.1016/j.impact.2021.100378] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 06/15/2023]
Abstract
Nanotechnology keeps drawing attention due to the great tunable properties of nanomaterials in comparison to their bulk conventional materials. The growth of nanotechnology in combination with the digitization era has led to an increased need of safety related data. In addition to safety, new data-driven paradigms on safe and sustainable by design materials are stressing the necessity of data even more. Data is a fundamental asset to the scientific community in studying and analysing the entire life-cycle of nanomaterials. Unfortunately, data exist in a scattered fashion, in different sources and formats. To our knowledge, there is no study focusing on aspects of actual data-structure knowledge that exists in literature and databases. The purpose of this review research is to transparently and comprehensively, display to the nanoscience community the datasets readily available for machine learning purposes making it convenient and more efficient for the next users such as modellers or data curators to retrieve information. We systematically recorded the features and descriptors available in the datasets and provide synopsised information on their ranges, forms and metrics in the supplementary material.
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Affiliation(s)
- Irini Furxhi
- Transgero Limited, Cullinagh, Newcastle West, Co. Limerick, Ireland; Dept. of Accounting and Finance, Kemmy Business School, University of Limerick, V94PH93, Ireland.
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Zhou T, Sun C. Effect of physical manipulation pulmonary rehabilitation on lung cancer patients after thoracoscopic lobectomy. Thorac Cancer 2021; 13:308-315. [PMID: 34882313 PMCID: PMC8807280 DOI: 10.1111/1759-7714.14225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 11/27/2022] Open
Abstract
Background To introduce a new postoperative pulmonary rehabilitation program named physical manipulation pulmonary rehabilitation (PMPR) and to explore the effect of perioperative management, including PMPR, on patients with non‐small cell lung cancer (NSCLC) after thoracoscopic lobectomy. Methods A randomized controlled trial was conducted between April and June 2021 at the Department of Thoracic Surgery, Beijing Hospital. Adult patients with NSCLC who had undergone thoracoscopic lobectomy were allocated to the treatment and control groups using a random number table. The treatment group received both conventional pulmonary rehabilitation (CVPR) and 14 days of PMPR after surgery; the control group patients received CVPR only. PMPR included relaxing and exercising the intercostal muscles, thoracic costal joint and abdominal breathing muscles. Pulmonary function tests and the 6‐min walk test were conducted preoperatively and 7, 14, 21 and 28 days postoperatively. The postoperative length of hospital stay, chest tube retention time and postoperative pulmonary complications were recorded. The baseline data, pulmonary function parameters and prognosis were compared with t‐ and chi‐square tests between the two groups. Results A total of 86 patients were enrolled, and 44 patients were allocated to the treatment group. There were no significant differences in the baseline data for age, sex, body mass index, basic disease, surgical plan or preoperative pulmonary function between the two groups (all p > 0.05). The peak expiratory flow of patients in the treatment group was higher than that of those in the control group 21 days after surgery (316 ± 95 vs. 272 ± 103 l/min, respectively, p = 0.043), and forced expiratory volume in the first second on day 28 after surgery was greater than that in the control group (2.1 ± 0.2 vs. 1.9 ± 0.3 L, respectively, p < 0.001). There were no significant differences in forced vital capacity or 6‐min walk test scores (both p > 0.05). There were no significant differences in the incidences of pneumonia and atelectasis between the two groups (both p > 0.05). The postoperative length of hospital stay (3.3 ± 1.3 vs. 3.9 ± 1.5 days, p = 0.043) and chest tube retention time (66 ± 30 vs. 81 ± 35 h, p = 0.036) in the treatment group were shorter than those in the control group. Conclusions We determined that PMPR could improve early lung function in patients with NSCLC after thoracoscopic lobectomy, and that chest tube retention time and length of hospital stay were shortened.
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Affiliation(s)
- Ting Zhou
- Thoracic surgery Department, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Chao Sun
- Nursing Department, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
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Yan J, Yan X, Hu S, Zhu H, Yan B. Comprehensive Interrogation on Acetylcholinesterase Inhibition by Ionic Liquids Using Machine Learning and Molecular Modeling. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14720-14731. [PMID: 34636548 DOI: 10.1021/acs.est.1c02960] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Quantitative structure-activity relationship (QSAR) modeling can be used to predict the toxicity of ionic liquids (ILs), but most QSAR models have been constructed by arbitrarily selecting one machine learning method and ignored the overall interactions between ILs and biological systems, such as proteins. In order to obtain more reliable and interpretable QSAR models and reveal the related molecular mechanism, we performed a systematic analysis of acetylcholinesterase (AChE) inhibition by 153 ILs using machine learning and molecular modeling. Our results showed that more reliable and stable QSAR models (R2 > 0.85 for both cross-validation and external validation) were obtained by combining the results from multiple machine learning approaches. In addition, molecular docking results revealed that the cations and organic anions of ILs bound to specific amino acid residues of AChE through noncovalent interactions such as π interactions and hydrogen bonds. The calculation results of binding free energy showed that an electrostatic interaction (ΔEele < -285 kJ/mol) was the main driving force for the binding of ILs to AChE. The overall findings from this investigation demonstrate that a systematic approach is much more convincing. Future research in this direction will help design the next generation of biosafe ILs.
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Affiliation(s)
- Jiachen Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, People's Republic of China
| | - Xiliang Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, People's Republic of China
| | - Song Hu
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, People's Republic of China
| | - Hao Zhu
- The Rutgers Center for Computational and Integrative Biology, Camden, New Jersey 08102, United States
| | - Bing Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, People's Republic of China
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, People's Republic of China
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Prasad M, Kumar R, Buragohain L, Kumari A, Ghosh M. Organoid Technology: A Reliable Developmental Biology Tool for Organ-Specific Nanotoxicity Evaluation. Front Cell Dev Biol 2021; 9:696668. [PMID: 34631696 PMCID: PMC8495170 DOI: 10.3389/fcell.2021.696668] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/13/2021] [Indexed: 12/14/2022] Open
Abstract
Engineered nanomaterials are bestowed with certain inherent physicochemical properties unlike their parent materials, rendering them suitable for the multifaceted needs of state-of-the-art biomedical, and pharmaceutical applications. The log-phase development of nano-science along with improved "bench to beside" conversion carries an enhanced probability of human exposure with numerous nanoparticles. Thus, toxicity assessment of these novel nanoscale materials holds a key to ensuring the safety aspects or else the global biome will certainly face a debacle. The toxicity may span from health hazards due to direct exposure to indirect means through food chain contamination or environmental pollution, even causing genotoxicity. Multiple ways of nanotoxicity evaluation include several in vitro and in vivo methods, with in vitro methods occupying the bulk of the "experimental space." The underlying reason may be multiple, but ethical constraints in in vivo animal experiments are a significant one. Two-dimensional (2D) monoculture is undoubtedly the most exploited in vitro method providing advantages in terms of cost-effectiveness, high throughput, and reproducibility. However, it often fails to mimic a tissue or organ which possesses a defined three-dimensional structure (3D) along with intercellular communication machinery. Instead, microtissues such as spheroids or organoids having a precise 3D architecture and proximate in vivo tissue-like behavior can provide a more realistic evaluation than 2D monocultures. Recent developments in microfluidics and bioreactor-based organoid synthesis have eased the difficulties to prosper nano-toxicological analysis in organoid models surpassing the obstacle of ethical issues. The present review will enlighten applications of organoids in nanotoxicological evaluation, their advantages, and prospects toward securing commonplace nano-interventions.
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Affiliation(s)
- Minakshi Prasad
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Rajesh Kumar
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Lukumoni Buragohain
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | | | - Mayukh Ghosh
- Department of Veterinary Physiology and Biochemistry, RGSC, Banaras Hindu University, Varanasi, India
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Yu H, Zhao Z, Cheng F. Predicting and investigating cytotoxicity of nanoparticles by translucent machine learning. CHEMOSPHERE 2021; 276:130164. [PMID: 33725618 DOI: 10.1016/j.chemosphere.2021.130164] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/25/2021] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
Safety concerns of engineered nanoparticles (ENPs) hamper their applications and commercialization in many potential fields. Machine learning has been proved as a great tool to understand the complex ENP-organism-environment relationship. However, good-performance machine learning models usually exist as black boxes, which may be difficult to build trust and whose ways of expressing knowledge rarely directly map to forms familiar to scientists. Here, we present an approach for uncovering causal structure in nanotoxicity datasets by mutual-validated and model-agnostic interpretation methods. Model predictions can be explained from feature importance, feature effects, and feature interactions. The utility of this approach is demonstrated through two case studies, the cytotoxicity of cadmium-containing quantum dots and metal oxide nanoparticles. Further, these case studies indicate the efficacy and impacts at two scales: (i) model interpretation, where the most relevant features for correlating cytotoxicity are identified and their influence on model predictions and interactions with other features are then explained, and (ii) model validation, where the difference among interpretation results of different methods (or the difference between interpretation results and well-known toxicity mechanisms) may reflect some inherent problems in the used dataset (or the developed models). Our approach of integrating machine learning models and interpretation methods provides a roadmap for predicting the toxicity of ENPs in a translucent way.
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Affiliation(s)
- Hengjie Yu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, PR China
| | - Zhilin Zhao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, PR China
| | - Fang Cheng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, PR China.
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Ji Z, Guo W, Sakkiah S, Liu J, Patterson TA, Hong H. Nanomaterial Databases: Data Sources for Promoting Design and Risk Assessment of Nanomaterials. NANOMATERIALS 2021; 11:nano11061599. [PMID: 34207026 PMCID: PMC8234318 DOI: 10.3390/nano11061599] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/19/2022]
Abstract
Nanomaterials have drawn increasing attention due to their tunable and enhanced physicochemical and biological performance compared to their conventional bulk materials. Owing to the rapid expansion of the nano-industry, large amounts of data regarding the synthesis, physicochemical properties, and bioactivities of nanomaterials have been generated. These data are a great asset to the scientific community. However, the data are on diverse aspects of nanomaterials and in different sources and formats. To help utilize these data, various databases on specific information of nanomaterials such as physicochemical characterization, biomedicine, and nano-safety have been developed and made available online. Understanding the structure, function, and available data in these databases is needed for scientists to select appropriate databases and retrieve specific information for research on nanomaterials. However, to our knowledge, there is no study to systematically compare these databases to facilitate their utilization in the field of nanomaterials. Therefore, we reviewed and compared eight widely used databases of nanomaterials, aiming to provide the nanoscience community with valuable information about the specific content and function of these databases. We also discuss the pros and cons of these databases, thus enabling more efficient and convenient utilization.
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Plata DL, Janković NZ. Achieving sustainable nanomaterial design though strategic cultivation of big data. NATURE NANOTECHNOLOGY 2021; 16:612-614. [PMID: 33986513 DOI: 10.1038/s41565-021-00902-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Desirée L Plata
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Nina Z Janković
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
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Yu H, Luo D, Dai L, Cheng F. In silico nanosafety assessment tools and their ecosystem-level integration prospect. NANOSCALE 2021; 13:8722-8739. [PMID: 33960351 DOI: 10.1039/d1nr00115a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Engineered nanomaterials (ENMs) have tremendous potential in many fields, but their applications and commercialization are difficult to widely implement due to their safety concerns. Recently, in silico nanosafety assessment has become an important and necessary tool to realize the safer-by-design strategy of ENMs and at the same time to reduce animal tests and exposure experiments. Here, in silico nanosafety assessment tools are classified into three categories according to their methodologies and objectives, including (i) data-driven prediction for acute toxicity, (ii) fate modeling for environmental pollution, and (iii) nano-biological interaction modeling for long-term biological effects. Released ENMs may cross environmental boundaries and undergo a variety of transformations in biological and environmental media. Therefore, the potential impacts of ENMs must be assessed from a multimedia perspective and with integrated approaches considering environmental and biological effects. Ecosystems with biodiversity and an abiotic environment may be used as an excellent integration platform to assess the community- and ecosystem-level nanosafety. In this review, the advances and challenges of in silico nanosafety assessment tools are carefully discussed. Furthermore, their integration at the ecosystem level may provide more comprehensive and reliable nanosafety assessment by establishing a site-specific interactive system among ENMs, abiotic environment, and biological communities.
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Affiliation(s)
- Hengjie Yu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Limin Dai
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
| | - Fang Cheng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
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Huang HJ, Lee YH, Hsu YH, Liao CT, Lin YF, Chiu HW. Current Strategies in Assessment of Nanotoxicity: Alternatives to In Vivo Animal Testing. Int J Mol Sci 2021; 22:4216. [PMID: 33921715 PMCID: PMC8073679 DOI: 10.3390/ijms22084216] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/01/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
Millions of experimental animals are widely used in the assessment of toxicological or biological effects of manufactured nanomaterials in medical technology. However, the animal consciousness has increased and become an issue for debate in recent years. Currently, the principle of the 3Rs (i.e., reduction, refinement, and replacement) is applied to ensure the more ethical application of humane animal research. In order to avoid unethical procedures, the strategy of alternatives to animal testing has been employed to overcome the drawbacks of animal experiments. This article provides current alternative strategies to replace or reduce the use of experimental animals in the assessment of nanotoxicity. The currently available alternative methods include in vitro and in silico approaches, which can be used as cost-effective approaches to meet the principle of the 3Rs. These methods are regarded as non-animal approaches and have been implemented in many countries for scientific purposes. The in vitro experiments related to nanotoxicity assays involve cell culture testing and tissue engineering, while the in silico methods refer to prediction using molecular docking, molecular dynamics simulations, and quantitative structure-activity relationship (QSAR) modeling. The commonly used novel cell-based methods and computational approaches have the potential to help minimize the use of experimental animals for nanomaterial toxicity assessments.
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Affiliation(s)
- Hung-Jin Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
| | - Yu-Hsuan Lee
- Department of Cosmeceutics, China Medical University, Taichung 406040, Taiwan;
| | - Yung-Ho Hsu
- Division of Nephrology, Department of Internal Medicine, Hsin Kuo Min Hospital, Taipei Medical University, Taoyuan City 320001, Taiwan;
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei 11031, Taiwan
| | - Chia-Te Liao
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei 11031, Taiwan
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Yuh-Feng Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei 11031, Taiwan
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Hui-Wen Chiu
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei 11031, Taiwan
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
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Llewellyn SV, Niemeijer M, Nymark P, Moné MJ, van de Water B, Conway GE, Jenkins GJS, Doak SH. In Vitro Three-Dimensional Liver Models for Nanomaterial DNA Damage Assessment. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006055. [PMID: 33448117 DOI: 10.1002/smll.202006055] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Whilst the liver possesses the ability to repair and restore sections of damaged tissue following acute injury, prolonged exposure to engineered nanomaterials (ENM) may induce repetitive injury leading to chronic liver disease. Screening ENM cytotoxicity using 3D liver models has recently been performed, but a significant challenge has been the application of such in vitro models for evaluating ENM associated genotoxicity; a vital component of regulatory human health risk assessment. This review considers the benefits, limitations, and adaptations of specific in vitro approaches to assess DNA damage in the liver, whilst identifying critical advancements required to support a multitude of biochemical endpoints, focusing on nano(geno)toxicology (e.g., secondary genotoxicity, DNA damage, and repair following prolonged or repeated exposures).
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Affiliation(s)
- Samantha V Llewellyn
- In vitro Toxicology Group, Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, Swansea, Wales, SA2 8PP, UK
| | - Marije Niemeijer
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Penny Nymark
- Division of Toxicology, Misvik Biology, Karjakatu 35 B, Turku, FI-20520, Finland
- Institute of Environmental Medicine, Karolinska Institute, Nobels väg 13, Stockholm, 17 177, Sweden
| | - Martijn J Moné
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Gillian E Conway
- In vitro Toxicology Group, Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, Swansea, Wales, SA2 8PP, UK
| | - Gareth J S Jenkins
- In vitro Toxicology Group, Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, Swansea, Wales, SA2 8PP, UK
| | - Shareen H Doak
- In vitro Toxicology Group, Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, Swansea, Wales, SA2 8PP, UK
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An J, Chua CK, Mironov V. Application of Machine Learning in 3D Bioprinting: Focus on Development of Big Data and Digital Twin. Int J Bioprint 2021; 7:342. [PMID: 33585718 PMCID: PMC7875058 DOI: 10.18063/ijb.v7i1.342] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
The application of machine learning (ML) in bioprinting has attracted considerable attention recently. Many have focused on the benefits and potential of ML, but a clear overview of how ML shapes the future of three-dimensional (3D) bioprinting is still lacking. Here, it is proposed that two missing links, Big Data and Digital Twin, are the key to articulate the vision of future 3D bioprinting. Creating training databases from Big Data curation and building digital twins of human organs with cellular resolution and properties are the most important and urgent challenges. With these missing links, it is envisioned that future 3D bioprinting will become more digital and in silico, and eventually strike a balance between virtual and physical experiments toward the most efficient utilization of bioprinting resources. Furthermore, the virtual component of bioprinting and biofabrication, namely, digital bioprinting, will become a new growth point for digital industry and information technology in future.
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Affiliation(s)
- Jia An
- Singapore Centre for 3D Printing, School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Chee Kai Chua
- Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372
| | - Vladimir Mironov
- 3D Bioprinting Solutions, 68/2 Kashirskoe Highway, Moscow, Russian Federation 115409
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Marciniak L, Nowak M, Trojanowska A, Tylkowski B, Jastrzab R. The Effect of pH on the Size of Silver Nanoparticles Obtained in the Reduction Reaction with Citric and Malic Acids. MATERIALS 2020; 13:ma13235444. [PMID: 33260479 PMCID: PMC7730334 DOI: 10.3390/ma13235444] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 11/24/2022]
Abstract
In colloidal methods, the morphology of nanoparticles (size and shape) as well as their stability can be controlled by changing the concentration of the substrate, stabilizer, adding inorganic salts, changing the reducer/substrate molar ratio, and changing the pH and reaction time. The synthesis of silver nanoparticles was carried out according to the modified Lee and Meisel method in a wide pH range (from 2.0 to 11.0) using citric acid and malic acid, without adding any additives or stabilizers. Keeping the same reaction conditions as the concentration of acid and silver ions, temperature, and heating time, it was possible to determine the relationship between the reaction pH, the type of acid, and the size of the silver nanoparticles formed. Obtained colloids were analyzed by UV-Vis spectroscopy and investigated by means of Transmission Electron Microscope (TEM). The study showed that the colloids reduced with citric acid and malic acid are stable over time for a minimum of seven weeks. We observed that reactions occurred for citric acid from pH 6.0 to 11.0 and for malic acid from pH 7.0 to 11.0. The average size of the quasi-spherical nanoparticles changed with pH due to the increase of reaction rate.
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Affiliation(s)
- Lukasz Marciniak
- Faculty of Chemistry, Adam Mickiewicz University, 61-614 Poznan, Poland; (L.M.); (M.N.)
| | - Martyna Nowak
- Faculty of Chemistry, Adam Mickiewicz University, 61-614 Poznan, Poland; (L.M.); (M.N.)
| | - Anna Trojanowska
- Centre Tecnològic de Catalunya, Chemical Technologies Unit, Eurecat, 43007 Tarragona, Spain; (A.T.); (B.T.)
| | - Bartosz Tylkowski
- Centre Tecnològic de Catalunya, Chemical Technologies Unit, Eurecat, 43007 Tarragona, Spain; (A.T.); (B.T.)
| | - Renata Jastrzab
- Faculty of Chemistry, Adam Mickiewicz University, 61-614 Poznan, Poland; (L.M.); (M.N.)
- Correspondence: ; Tel.: +48-6‐9328‐8787
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50
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Russo DP, Yan X, Shende S, Huang H, Yan B, Zhu H. Virtual Molecular Projections and Convolutional Neural Networks for the End-to-End Modeling of Nanoparticle Activities and Properties. Anal Chem 2020; 92:13971-13979. [PMID: 32970421 DOI: 10.1021/acs.analchem.0c02878] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Digitalizing complex nanostructures into data structures suitable for machine learning modeling without losing nanostructure information has been a major challenge. Deep learning frameworks, particularly convolutional neural networks (CNNs), are especially adept at handling multidimensional and complex inputs. In this study, CNNs were applied for the modeling of nanoparticle activities exclusively from nanostructures. The nanostructures were represented by virtual molecular projections, a multidimensional digitalization of nanostructures, and used as input data to train CNNs. To this end, 77 nanoparticles with various activities and/or physicochemical property results were used for modeling. The resulting CNN model predictions show high correlations with the experimental results. An analysis of a trained CNN quantitatively showed that neurons were able to recognize distinct nanostructure features critical to activities and physicochemical properties. This "end-to-end" deep learning approach is well suited to digitalize complex nanostructures for data-driven machine learning modeling and can be broadly applied to rationally design nanoparticles with desired activities.
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Affiliation(s)
- Daniel P Russo
- Center for Computational and Integrative Biology, Rutgers University, 201 S Broadway, Camden, New Jersey 08103, United States
| | - Xiliang Yan
- Center for Computational and Integrative Biology, Rutgers University, 201 S Broadway, Camden, New Jersey 08103, United States.,Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Sunil Shende
- Center for Computational and Integrative Biology, Rutgers University, 201 S Broadway, Camden, New Jersey 08103, United States.,Department of Computer Science, Rutgers University, 227 Penn Street, Camden, New Jersey 08102, United States
| | | | - Bing Yan
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.,School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Hao Zhu
- Center for Computational and Integrative Biology, Rutgers University, 201 S Broadway, Camden, New Jersey 08103, United States.,Department of Chemistry, Rutgers University, 315 Penn Street, Camden, New Jersey 08102, United States
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