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Chapagain A, Abuoliem D, Cho IH. Enabling Fast AI-Driven Inverse Design of a Multifunctional Nanosurface by Parallel Evolution Strategies. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 15:27. [PMID: 39791786 PMCID: PMC11722515 DOI: 10.3390/nano15010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 12/24/2024] [Accepted: 12/26/2024] [Indexed: 01/12/2025]
Abstract
Multifunctional nanosurfaces receive growing attention due to their versatile properties. Capillary force lithography (CFL) has emerged as a simple and economical method for fabricating these surfaces. In recent works, the authors proposed to leverage the evolution strategies (ES) to modify nanosurface characteristics with CFL to achieve specific functionalities such as frictional, optical, and bactericidal properties. For artificial intelligence (AI)-driven inverse design, earlier research integrates basic multiphysics principles such as dynamic viscosity, air diffusivity, surface tension, and electric potential with backward deep learning (DL) on the framework of ES. As a successful alternative to reinforcement learning, ES performed well for the AI-driven inverse design. However, the computational limitations of ES pose a critical technical challenge to achieving fast and efficient design. This paper addresses the challenges by proposing a parallel-computing-based ES (named parallel ES). The parallel ES demonstrated the desired speed and scalability, accelerating the AI-driven inverse design of multifunctional nanopatterned surfaces. Detailed parallel ES algorithms and cost models are presented, showing its potential as a promising tool for advancing AI-driven nanomanufacturing.
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Affiliation(s)
| | | | - In Ho Cho
- Department of Civil, Construction, and Environmental Engineering, Iowa State University, Ames, IA 50011, USA; (A.C.); (D.A.)
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2
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Furxhi I, Perucca M, Koivisto AJ, Bengalli R, Mantecca P, Nicosia A, Burrueco-Subirà D, Vázquez-Campos S, Lahive E, Blosi M, de Ipiña JL, Oliveira J, Carriere M, Vineis C, Costa A. A roadmap towards safe and sustainable by design nanotechnology: Implementation for nano-silver-based antimicrobial textile coatings production by ASINA project. Comput Struct Biotechnol J 2024; 25:127-142. [PMID: 39040658 PMCID: PMC11262112 DOI: 10.1016/j.csbj.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/24/2024] Open
Abstract
This report demonstrates a case study within the ASINA project, aimed at instantiating a roadmap with quantitative metrics for Safe(r) and (more) Sustainable by Design (SSbD) options. We begin with a description of ASINA's methodology across the product lifecycle, outlining the quantitative elements within: Physical-Chemical Features (PCFs), Key Decision Factors (KDFs), and Key Performance Indicators (KPIs). Subsequently, we delve in a proposed decision support tool for implementing the SSbD objectives across various dimensions-functionality, cost, environment, and human health safety-within a broader European context. We then provide an overview of the technical processes involved, including design rationales, experimental procedures, and tools/models developed within ASINA in delivering nano-silver-based antimicrobial textile coatings. The result is pragmatic, actionable metrics intended to be estimated and assessed in future SSbD applications and to be adopted in a common SSbD roadmap aligned with the EU's Green Deal objectives. The methodological approach is transparently and thoroughly described to inform similar projects through the integration of KPIs into SSbD and foster data-driven decision-making. Specific results and project data are beyond this work's scope, which is to demonstrate the ASINA roadmap and thus foster SSbD-oriented innovation in nanotechnology.
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Affiliation(s)
- Irini Furxhi
- CNR-ISSMC Istituto di Scienza e Tecnologia dei Materiali Ceramici, Via Granarolo, 64, 48018 Faenza, RA, Italy
| | - Massimo Perucca
- Project HUB360, C.so Laghi 22, 10051 Avigliana, Turin, Italy
| | - Antti Joonas Koivisto
- APM Air Pollution Management, Mattilanmäki 38, FI-33610 Tampere, Finland
- INAR Institute for Atmospheric and Earth System Research, University of Helsinki, PL 64, UHEL, FI-00014 Helsinki, Finland
- ARCHE Consulting, Liefkensstraat 35D, Wondelgem B-9032, Belgium
| | - Rossella Bengalli
- POLARIS Research Center, Dept. of Earth and Environmental Sciences, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Paride Mantecca
- POLARIS Research Center, Dept. of Earth and Environmental Sciences, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Alessia Nicosia
- CNR-ISAC Institute of Atmospheric Sciences and Climate, Via Gobetti 101, 40129 Bologna, Italy
| | | | | | - Elma Lahive
- Centre for Ecology & Hydrology (UKCEH), England, United Kingdom
| | - Magda Blosi
- CNR-ISSMC Istituto di Scienza e Tecnologia dei Materiali Ceramici, Via Granarolo, 64, 48018 Faenza, RA, Italy
| | - Jesús Lopez de Ipiña
- TECNALIA Research and Innovation - Basque Research and Technology Alliance (BRTA), Parque Tecnológico de Alava, Leonardo Da Vinci 11, 01510 Miñano, Spain
| | - Juliana Oliveira
- CeNTI - Centre of Nanotechnology and Smart Materials, Rua Fernando Mesquita 2785, 4760-034 Vila Nova de Famalicão, Portugal
| | - Marie Carriere
- CEA, CNRS, Univ. Grenoble Alpes, Grenoble INP, IRIG, SYMMES, Grenoble 38000, France
| | - Claudia Vineis
- CNR-STIIMA Istituto di Sistemi e Tecnologie Industriali Intelligenti per il Manifatturiero Avanzato, Italy
| | - Anna Costa
- CNR-ISSMC Istituto di Scienza e Tecnologia dei Materiali Ceramici, Via Granarolo, 64, 48018 Faenza, RA, Italy
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3
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Furxhi I, Faccani L, Zanoni I, Brigliadori A, Vespignani M, Costa AL. Design rules applied to silver nanoparticles synthesis: A practical example of machine learning application. Comput Struct Biotechnol J 2024; 25:20-33. [PMID: 38444982 PMCID: PMC10914561 DOI: 10.1016/j.csbj.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
The synthesis of silver nanoparticles with controlled physicochemical properties is essential for governing their intended functionalities and safety profiles. However, synthesis process involves multiple parameters that could influence the resulting properties. This challenge could be addressed with the development of predictive models that forecast endpoints based on key synthesis parameters. In this study, we manually extracted synthesis-related data from the literature and leveraged various machine learning algorithms. Data extraction included parameters such as reactant concentrations, experimental conditions, as well as physicochemical properties. The antibacterial efficiencies and toxicological profiles of the synthesized nanoparticles were also extracted. In a second step, based on data completeness, we employed regression algorithms to establish relationships between synthesis parameters and desired endpoints and to build predictive models. The models for core size and antibacterial efficiency were trained and validated using a cross-validation approach. Finally, the features' impact was evaluated via Shapley values to provide insights into the contribution of features to the predictions. Factors such as synthesis duration, scale of synthesis and the choice of capping agents emerged as the most significant predictors. This study demonstrated the potential of machine learning to aid in the rational design of synthesis process and paves the way for the safe-by-design principles development by providing insights into the optimization of the synthesis process to achieve the desired properties. Finally, this study provides a valuable dataset compiled from literature sources with significant time and effort from multiple researchers. Access to such datasets notably aids computational advances in the field of nanotechnology.
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Affiliation(s)
- Irini Furxhi
- CNR-ISSMC (Former ISTEC), National Research Council of Italy-Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy
- Transgero Limited, Limerick, Ireland
| | - Lara Faccani
- CNR-ISSMC (Former ISTEC), National Research Council of Italy-Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy
| | - Ilaria Zanoni
- CNR-ISSMC (Former ISTEC), National Research Council of Italy-Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy
| | - Andrea Brigliadori
- CNR-ISSMC (Former ISTEC), National Research Council of Italy-Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy
| | - Maurizio Vespignani
- CNR-ISSMC (Former ISTEC), National Research Council of Italy-Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy
| | - Anna Luisa Costa
- CNR-ISSMC (Former ISTEC), National Research Council of Italy-Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy
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4
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Fan Y, Sun N, Lv S, Jiang H, Zhang Z, Wang J, Xie Y, Yue X, Hu B, Ju B, Yu P. Prediction of developmental toxic effects of fine particulate matter (PM 2.5) water-soluble components via machine learning through observation of PM 2.5 from diverse urban areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174027. [PMID: 38906297 DOI: 10.1016/j.scitotenv.2024.174027] [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: 03/25/2024] [Revised: 06/09/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
Abstract
The global health implications of fine particulate matter (PM2.5) underscore the imperative need for research into its toxicity and chemical composition. In this study, zebrafish embryos exposed to the water-soluble components of PM2.5 from two cities (Harbin and Hangzhou) with differences in air quality, underwent microscopic examination to identify primary target organs. The Harbin PM2.5 induced dose-dependent organ malformation in zebrafish, indicating a higher level of toxicity than that of the Hangzhou sample. Harbin PM2.5 led to severe deformities such as pericardial edema and a high mortality rate, while the Hangzhou sample exhibited hepatotoxicity, causing delayed yolk sac absorption. The experimental determination of PM2.5 constituents was followed by the application of four algorithms for predictive toxicological assessment. The random forest algorithm correctly predicted each of the effect classes and showed the best performance, suggesting that zebrafish malformation rates were strongly correlated with water-soluble components of PM2.5. Feature selection identified the water-soluble ions F- and Cl- and metallic elements Al, K, Mn, and Be as potential key components affecting zebrafish development. This study provides new insights into the developmental toxicity of PM2.5 and offers a new approach for predicting and exploring the health effects of PM2.5.
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Affiliation(s)
- Yang Fan
- Department of Medical Oncology of the Second Affiliated Hospital, Department of Toxicology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Nannan Sun
- Hangzhou SanOmics AI Co., Ltd, Hangzhou 311103, China
| | - Shenchong Lv
- Department of Medical Oncology of the Second Affiliated Hospital, Department of Toxicology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Hui Jiang
- Department of Medical Oncology of the Second Affiliated Hospital, Department of Toxicology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ziqing Zhang
- Department of Medical Oncology of the Second Affiliated Hospital, Department of Toxicology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Junjie Wang
- Department of Medical Oncology of the Second Affiliated Hospital, Department of Toxicology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yiyi Xie
- Department of Medical Oncology of the Second Affiliated Hospital, Department of Toxicology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaomin Yue
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Baolan Hu
- College of Environmental Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Bin Ju
- Hangzhou SanOmics AI Co., Ltd, Hangzhou 311103, China.
| | - Peilin Yu
- Department of Medical Oncology of the Second Affiliated Hospital, Department of Toxicology, Zhejiang University School of Medicine, Hangzhou 310058, China.
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5
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Balraadjsing S, J G M Peijnenburg W, Vijver MG. Building species trait-specific nano-QSARs: Model stacking, navigating model uncertainties and limitations, and the effect of dataset size. ENVIRONMENT INTERNATIONAL 2024; 188:108764. [PMID: 38788418 DOI: 10.1016/j.envint.2024.108764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
A strong need exists for broadly applicable nano-QSARs, capable of predicting toxicological outcomes towards untested species and nanomaterials, under different environmental conditions. Existing nano-QSARs are generally limited to only a few species but the inclusion of species characteristics into models can aid in making them applicable to multiple species, even when toxicity data is not available for biological species. Species traits were used to create classification- and regression machine learning models to predict acute toxicity towards aquatic species for metallic nanomaterials. Afterwards, the individual classification- and regression models were stacked into a meta-model to improve performance. Additionally, the uncertainty and limitations of the models were assessed in detail (beyond the OECD principles) and it was investigated whether models would benefit from the addition of more data. Results showed a significant improvement in model performance following model stacking. Investigation of model uncertainties and limitations highlighted the discrepancy between the applicability domain and accuracy of predictions. Data points outside of the assessed chemical space did not have higher likelihoods of generating inadequate predictions or vice versa. It is therefore concluded that the applicability domain does not give complete insight into the uncertainty of predictions and instead the generation of prediction intervals can help in this regard. Furthermore, results indicated that an increase of the dataset size did not improve model performance. This implies that larger dataset sizes may not necessarily improve model performance while in turn also meaning that large datasets are not necessarily required for prediction of acute toxicity with nano-QSARs.
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Affiliation(s)
- Surendra Balraadjsing
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA Leiden, the Netherlands.
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA Leiden, the Netherlands; Centre for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), PO Box 1, 3720 BA Bilthoven, the Netherlands
| | - Martina G Vijver
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA Leiden, the Netherlands
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6
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Irmak SE, Ozdemir GD, Ozdemir MA, Ercan UK. Machine learning-aided evaluation of oxidative strength of cold atmospheric plasma-treated water. Biomed Phys Eng Express 2024; 10:045016. [PMID: 38697029 DOI: 10.1088/2057-1976/ad464f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 05/04/2024]
Abstract
Plasma medicine is gaining attraction in the medical field, particularly the use of cold atmospheric plasma (CAP) in biomedicine. The chemistry of the plasma is complex, and the reactive oxygen species (ROS) within it are the basis for the biological effect of CAP on the target. Understanding how the oxidative power of ROS responds to diverse plasma parameters is vital for standardizing the effective application of CAP. The proven applicability of machine learning (ML) in the field of medicine is encouraging, as it can also be applied in the field of plasma medicine to correlate the oxidative strength of plasma-treated water (PTW) according to different parameters. In this study, plasma-treated water was mixed with potassium iodide-starch reagent for color formation that could be linked to the oxidative capacity of PTW. Corresponding images were captured resulting from the exposure of the color-forming agent to water treated with plasma for different time points. Several ML models were trained to distinguish the color changes sourced by the oxidative strength of ROS. The AdaBoost Classifier (ABC) algorithm demonstrated better performance among the classification models used by extracting color-based features from the images. Our results, with a test accuracy of 63.5%, might carry a potential for future standardization in the field of plasma medicine with an automated system that can be created to interpret the oxidative properties of ROS in different plasma treatment parameters via ML.
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Affiliation(s)
- Seyma Ecem Irmak
- Department of Biomedical Engineering, Graduate School of Natural and Applied Sciences, Izmir Katip Celebi University, 35620 Cigli, Izmir, Turkey
| | - Gizem Dilara Ozdemir
- Department of Biomedical Engineering, Graduate School of Natural and Applied Sciences, Izmir Katip Celebi University, 35620 Cigli, Izmir, Turkey
- Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, 35620 Cigli, Izmir, Turkey
| | - Mehmet Akif Ozdemir
- Department of Biomedical Engineering, Graduate School of Natural and Applied Sciences, Izmir Katip Celebi University, 35620 Cigli, Izmir, Turkey
- Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, 35620 Cigli, Izmir, Turkey
| | - Utku Kürşat Ercan
- Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, 35620 Cigli, Izmir, Turkey
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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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8
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Wu Y, Liu P, Mehrjou B, Chu PK. Interdisciplinary-Inspired Smart Antibacterial Materials and Their Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2305940. [PMID: 37469232 DOI: 10.1002/adma.202305940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023]
Abstract
The discovery of antibiotics has saved millions of lives, but the emergence of antibiotic-resistant bacteria has become another problem in modern medicine. To avoid or reduce the overuse of antibiotics in antibacterial treatments, stimuli-responsive materials, pathogen-targeting nanoparticles, immunogenic nano-toxoids, and biomimetic materials are being developed to make sterilization better and smarter than conventional therapies. The common goal of smart antibacterial materials (SAMs) is to increase the antibiotic efficacy or function via an antibacterial mechanism different from that of antibiotics in order to increase the antibacterial and biological properties while reducing the risk of drug resistance. The research and development of SAMs are increasingly interdisciplinary because new designs require the knowledge of different fields and input/collaboration from scientists in different fields. A good understanding of energy conversion in materials, physiological characteristics in cells and bacteria, and bactericidal structures and components in nature are expected to promote the development of SAMs. In this review, the importance of multidisciplinary insights for SAMs is emphasized, and the latest advances in SAMs are categorized and discussed according to the pertinent disciplines including materials science, physiology, and biomimicry.
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Affiliation(s)
- Yuzheng Wu
- Department of Physics, Department of Materials Science and Engineering and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Pei Liu
- Department of Physics, Department of Materials Science and Engineering and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Babak Mehrjou
- Department of Physics, Department of Materials Science and Engineering and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Paul K Chu
- Department of Physics, Department of Materials Science and Engineering and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
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9
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Ficiarà E, Stura I, Vernone A, Silvagno F, Cavalli R, Guiot C. Iron Overload in Brain: Transport Mismatches, Microbleeding Events, and How Nanochelating Therapies May Counteract Their Effects. Int J Mol Sci 2024; 25:2337. [PMID: 38397013 PMCID: PMC10889007 DOI: 10.3390/ijms25042337] [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: 01/11/2024] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Iron overload in many brain regions is a common feature of aging and most neurodegenerative diseases. In this review, the causes, mechanisms, mathematical models, and possible therapies are summarized. Indeed, physiological and pathological conditions can be investigated using compartmental models mimicking iron trafficking across the blood-brain barrier and the Cerebrospinal Fluid-Brain exchange membranes located in the choroid plexus. In silico models can investigate the alteration of iron homeostasis and simulate iron concentration in the brain environment, as well as the effects of intracerebral iron chelation, determining potential doses and timing to recover the physiological state. Novel formulations of non-toxic nanovectors with chelating capacity are already tested in organotypic brain models and could be available to move from in silico to in vivo experiments.
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Affiliation(s)
- Eleonora Ficiarà
- School of Pharmacy, University of Camerino, 62032 Camerino, MC, Italy;
| | - Ilaria Stura
- Department of Neurosciences, Università degli Studi di Torino, 10125 Torino, TO, Italy; (A.V.); (C.G.)
| | - Annamaria Vernone
- Department of Neurosciences, Università degli Studi di Torino, 10125 Torino, TO, Italy; (A.V.); (C.G.)
| | - Francesca Silvagno
- Department of Oncology, Università degli Studi di Torino, 10126 Torino, TO, Italy;
| | - Roberta Cavalli
- Department of Drug Science and Technology, Università degli Studi di Torino, 10125 Torino, TO, Italy;
| | - Caterina Guiot
- Department of Neurosciences, Università degli Studi di Torino, 10125 Torino, TO, Italy; (A.V.); (C.G.)
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10
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Olcay B, Ozdemir GD, Ozdemir MA, Ercan UK, Guren O, Karaman O. Prediction of the synergistic effect of antimicrobial peptides and antimicrobial agents via supervised machine learning. BMC Biomed Eng 2024; 6:1. [PMID: 38233957 DOI: 10.1186/s42490-024-00075-z] [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: 03/24/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Infectious diseases not only cause severe health problems but also burden the healthcare system. Therefore, the effective treatment of those diseases is crucial. Both conventional approaches, such as antimicrobial agents, and novel approaches, like antimicrobial peptides (AMPs), are used to treat infections. However, due to the drawbacks of current approaches, new solutions are still being investigated. One recent approach is the use of AMPs and antimicrobial agents in combination, but determining synergism is with a huge variety of AMPs time-consuming and requires multiple experimental studies. Machine learning (ML) algorithms are widely used to predict biological outcomes, particularly in the field of AMPs, but no previous research reported on predicting the synergistic effects of AMPs and antimicrobial agents. RESULTS Several supervised ML models were implemented to accurately predict the synergistic effect of AMPs and antimicrobial agents. The results demonstrated that the hyperparameter-optimized Light Gradient Boosted Machine Classifier (oLGBMC) yielded the best test accuracy of 76.92% for predicting the synergistic effect. Besides, the feature importance analysis reveals that the target microbial species, the minimum inhibitory concentrations (MICs) of the AMP and the antimicrobial agents, and the used antimicrobial agent were the most important features for the prediction of synergistic effect, which aligns with recent experimental studies in the literature. CONCLUSION This study reveals that ML algorithms can predict the synergistic activity of two different antimicrobial agents without the need for complex and time-consuming experimental procedures. The implications support that the ML models may not only reduce the experimental cost but also provide validation of experimental procedures.
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Affiliation(s)
- Basak Olcay
- Department of Biomedical Engineering, Graduate School of Natural and Applied Sciences, Izmir Katip Celebi University, Izmir, Turkey
| | - Gizem D Ozdemir
- Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, Izmir, Turkey
| | - Mehmet A Ozdemir
- Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, Izmir, Turkey.
| | - Utku K Ercan
- Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, Izmir, Turkey
| | - Onan Guren
- Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, Izmir, Turkey
| | - Ozan Karaman
- Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, Izmir, Turkey
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11
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Zhou Y, Wang Y, Peijnenburg W, Vijver MG, Balraadjsing S, Fan W. Using Machine Learning to Predict Adverse Effects of Metallic Nanomaterials to Various Aquatic Organisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17786-17795. [PMID: 36730792 DOI: 10.1021/acs.est.2c07039] [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] [Indexed: 06/18/2023]
Abstract
The wide production and use of metallic nanomaterials (MNMs) leads to increased emissions into the aquatic environments and induces high potential risks. Experimentally evaluating the (eco)toxicity of MNMs is time-consuming and expensive due to the multiple environmental factors, the complexity of material properties, and the species diversity. Machine learning (ML) models provide an option to deal with heterogeneous data sets and complex relationships. The present study established an in silico model based on a machine learning properties-environmental conditions-multi species-toxicity prediction model (ML-PEMST) that can be applied to predict the toxicity of different MNMs toward multiple aquatic species. Feature importance and interaction analysis based on the random forest method indicated that exposure duration, illumination, primary size, and hydrodynamic diameter were the main factors affecting the ecotoxicity of MNMs to a variety of aquatic organisms. Illumination was demonstrated to have the most interaction with the other features. Moreover, incorporating additional detailed information on the ecological traits of the test species will allow us to further optimize and improve the predictive performance of the model. This study provides a new approach for ecotoxicity predictions for organisms in the aquatic environment and will help us to further explore exposure pathways and the risk assessment of MNMs.
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Affiliation(s)
- Yunchi Zhou
- School of Space and Environment, Beihang University, Beijing100191, China
| | - Ying Wang
- School of Space and Environment, Beihang University, Beijing100191, China
| | - Willie Peijnenburg
- Institute of Environmental Science (CML), Leiden University, Leiden2300, RA, The Netherlands
- Center for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), Bilthoven3720, BA, The Netherlands
| | - Martina G Vijver
- Institute of Environmental Science (CML), Leiden University, Leiden2300, RA, The Netherlands
| | - Surendra Balraadjsing
- Institute of Environmental Science (CML), Leiden University, Leiden2300, RA, The Netherlands
| | - Wenhong Fan
- School of Space and Environment, Beihang University, Beijing100191, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing100191, China
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12
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Yalezo N, Musee N. Meta-analysis of engineered nanoparticles dynamic aggregation in freshwater-like systems using machine learning techniques. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 337:117739. [PMID: 36934506 DOI: 10.1016/j.jenvman.2023.117739] [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: 12/18/2022] [Revised: 02/17/2023] [Accepted: 03/12/2023] [Indexed: 06/18/2023]
Abstract
Predictive algorithms for exposure characterization of engineered nanoparticles (ENPs) in the ecosystems are essential to improve the development of robust nano-safety frameworks. Here, machine learning (ML) techniques were utilised for data mining and prediction of the dynamic aggregation transformation process in aqueous environments using case studies of nZnO and nTiO2. Supervised ML models using input variables of natural organic matter, ionic strength, size, and ENPs concentration showed poor prediction performance based on statistical metric values of root mean square error (RMSE), mean absolute error (MAE), coefficient of determination (R2), and Nash-Sutcliffe efficiency (NSE) for both types of ENP. On the contrary, algorithms developed using model input parameters of zeta potential, pH, and time had good generalisation and high prediction accuracy. Among the five developed ML algorithms, random forest regression, support vector regression, and artificial neural network generated good prediction accuracy for both data sets. Therefore, the use of ML can be valuable in the development of robust nano-safety frameworks to optimise societal benefits, and for proactive long-term ecological protection.
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Affiliation(s)
- Ntsikelelo Yalezo
- Emerging Contaminants Ecological and Risk Assessment (ECERA) Group, Department of Chemical Engineering, University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa
| | - Ndeke Musee
- Emerging Contaminants Ecological and Risk Assessment (ECERA) Group, Department of Chemical Engineering, University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa.
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13
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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: 2] [Impact Index Per Article: 1.0] [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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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: 16] [Impact Index Per Article: 8.0] [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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Priyadarshini R, Abdullah AS, Karthikeyan KV, Vinoth M, Martin B, Geerthik S, Wilfred F, Alyami NM, Sundaram RS. Utilization of Bioinorganic Nanodrugs and Nanomaterials for the Control of Infectious Diseases Using Deep Learning. BIOMED RESEARCH INTERNATIONAL 2023; 2023:7464159. [PMID: 37124928 PMCID: PMC10147522 DOI: 10.1155/2023/7464159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/27/2022] [Accepted: 01/18/2023] [Indexed: 05/02/2023]
Abstract
As one of the main causes of morbidity and mortality, viral infections have a major impact on the well-being and economics of every nation in the globe. The ability to predictably diagnose viral infections improves the provision of good healthcare as well as the control and prevention of these conditions. Nanomaterials have gained widespread usage in the medical industry recently due to the rapid advancement of nanotechnology and their exceptional chemical and physical qualities, such as their small size and synthesized surface properties. The utilization of nanoparticles for illness detection, surveillance, control, preventive, and therapy, such as the treatment of bacterial infections, is referred to as nanomedicine. Nanomedicine is a comprehensive discipline that is founded on the usage of nanotechnology for clinical objectives. Nanoparticles, which have a nanoscale dimension and exhibit highly controllable optical and physical characteristics as well as the ability to bind to a large variety of chemicals, are among the most popular nanomaterials in nanomedicine. A deep learning framework of autoencoder for categorization study on viral infections is built based on actual hospital patient history of viral infections from August 2015 to August 2020. The information comprises of 10,950 cases, comprising outpatients and inpatients, encompassing the infectious diseases. Of such 10,950 instances, training set made up 70% or 7665 instances, and testing data made up 30% or 3285 instances. The data processing was done using the presented recurrent neural network-artificial bee colony (RNN-ABC) method. Sparse data densifying processes are done through the autoencoder to enhance the system learning outcome. The suggested autoencoder system was also evaluated to other widely used models, including support vector machine, logistic regression, random forest, and Naïve Bayes. In comparison to other approaches, the study's findings demonstrate how well the suggested autoencoder model can predict viral diseases. The methods used for this research can aid in removing reported lags in current monitoring systems, hence reducing society's expenses.
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Affiliation(s)
- R. Priyadarshini
- School of Computer Science and Engineering, Vellore Institute of Technology, Chennai, Tamil Nadu, India
| | - A. Sheik Abdullah
- School of Computer Science and Engineering, Vellore Institute of Technology, Chennai, Tamil Nadu, India
| | - K. V. Karthikeyan
- Department of Electronics and Communication Engineering, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamil Nadu, India
| | - M. Vinoth
- Department of Electronics and Communication Engineering, K. Ramakrishnan College of Engineering, Trichy, 621112 Tamil Nadu, India
| | - Betty Martin
- Department of Electronics and Communication Engineering, SASTRA Deemed to be University, Thirumalaisamuthiram, Thanjavur, 613401 Tamil Nadu, India
| | - S. Geerthik
- Department of Information Technology, Agni College of Technology, Chennai, 600130 Tamil Nadu, India
| | - Florin Wilfred
- Department of Electrical, Electronics and Communication Engineering, St. Joseph College of Engineering and Technology, St. Joseph University in Tanzania, Dar es Salaam, Tanzania
| | - Nour M. Alyami
- Department of Zoology, C. Abdul Hakeem College of Engineering, Vellore, 632509 Tamil Nadu, India
| | - R. S. Sundaram
- Department of Health Sciences, University of Texas, Austin, TX, USA
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16
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Furxhi I, Bengalli R, Motta G, Mantecca P, Kose O, Carriere M, Haq EU, O’Mahony C, Blosi M, Gardini D, Costa A. Data-Driven Quantitative Intrinsic Hazard Criteria for Nanoproduct Development in a Safe-by-Design Paradigm: A Case Study of Silver Nanoforms. ACS APPLIED NANO MATERIALS 2023; 6:3948-3962. [PMID: 36938492 PMCID: PMC10012170 DOI: 10.1021/acsanm.3c00173] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The current European (EU) policies, that is, the Green Deal, envisage safe and sustainable practices for chemicals, which include nanoforms (NFs), at the earliest stages of innovation. A theoretically safe and sustainable by design (SSbD) framework has been established from EU collaborative efforts toward the definition of quantitative criteria in each SSbD dimension, namely, the human and environmental safety dimension and the environmental, social, and economic sustainability dimensions. In this study, we target the safety dimension, and we demonstrate the journey toward quantitative intrinsic hazard criteria derived from findable, accessible, interoperable, and reusable data. Data were curated and merged for the development of new approach methodologies, that is, quantitative structure-activity relationship models based on regression and classification machine learning algorithms, with the intent to predict a hazard class. The models utilize system (i.e., hydrodynamic size and polydispersity index) and non-system (i.e., elemental composition and core size)-dependent nanoscale features in combination with biological in vitro attributes and experimental conditions for various silver NFs, functional antimicrobial textiles, and cosmetics applications. In a second step, interpretable rules (criteria) followed by a certainty factor were obtained by exploiting a Bayesian network structure crafted by expert reasoning. The probabilistic model shows a predictive capability of ≈78% (average accuracy across all hazard classes). In this work, we show how we shifted from the conceptualization of the SSbD framework toward the realistic implementation with pragmatic instances. This study reveals (i) quantitative intrinsic hazard criteria to be considered in the safety aspects during synthesis stage, (ii) the challenges within, and (iii) the future directions for the generation and distillation of such criteria that can feed SSbD paradigms. Specifically, the criteria can guide material engineers to synthesize NFs that are inherently safer from alternative nanoformulations, at the earliest stages of innovation, while the models enable a fast and cost-efficient in silico toxicological screening of previously synthesized and hypothetical scenarios of yet-to-be synthesized NFs.
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Affiliation(s)
- Irini Furxhi
- Transgero
Ltd, Limerick V42V384, Ireland
- Department
of Accounting and Finance, Kemmy Business School, University of Limerick, Limerick V94T9PX, Ireland
| | - Rossella Bengalli
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza
della Scienza 1, Milano 20126, Italy
| | - Giulia Motta
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza
della Scienza 1, Milano 20126, Italy
| | - Paride Mantecca
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza
della Scienza 1, Milano 20126, Italy
| | - Ozge Kose
- Univ.
Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SYMMES, Grenoble 38000, France
| | - Marie Carriere
- Univ.
Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SYMMES, Grenoble 38000, France
| | - Ehtsham Ul Haq
- Department
of Physics, and Bernal Institute, University
of Limerick, Limerick V94TC9PX, Ireland
| | - Charlie O’Mahony
- Department
of Physics, and Bernal Institute, University
of Limerick, Limerick V94TC9PX, Ireland
| | - Magda Blosi
- Istituto
di Scienza e Tecnologia dei Materiali Ceramici (CNR-ISTEC), Via Granarolo, 64, Faenza 48018, Ravenna, Italy
| | - Davide Gardini
- Istituto
di Scienza e Tecnologia dei Materiali Ceramici (CNR-ISTEC), Via Granarolo, 64, Faenza 48018, Ravenna, Italy
| | - Anna Costa
- Istituto
di Scienza e Tecnologia dei Materiali Ceramici (CNR-ISTEC), Via Granarolo, 64, Faenza 48018, Ravenna, Italy
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17
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Photo-Antibacterial Activity of Two-Dimensional (2D)-Based Hybrid Materials: Effective Treatment Strategy for Controlling Bacterial Infection. Antibiotics (Basel) 2023; 12:antibiotics12020398. [PMID: 36830308 PMCID: PMC9952232 DOI: 10.3390/antibiotics12020398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Bacterial contamination in water bodies is a severe scourge that affects human health and causes mortality and morbidity. Researchers continue to develop next-generation materials for controlling bacterial infections from water. Photo-antibacterial activity continues to gain the interest of researchers due to its adequate, rapid, and antibiotic-free process. Photo-antibacterial materials do not have any side effects and have a minimal chance of developing bacterial resistance due to their rapid efficacy. Photocatalytic two-dimensional nanomaterials (2D-NMs) have great potential for the control of bacterial infection due to their exceptional properties, such as high surface area, tunable band gap, specific structure, and tunable surface functional groups. Moreover, the optical and electric properties of 2D-NMs might be tuned by creating heterojunctions or by the doping of metals/carbon/polymers, subsequently enhancing their photo-antibacterial ability. This review article focuses on the synthesis of 2D-NM-based hybrid materials, the effect of dopants in 2D-NMs, and their photo-antibacterial application. We also discuss how we could improve photo-antibacterials by using different strategies and the role of artificial intelligence (AI) in the photocatalyst and in the degradation of pollutants. Finally, we discuss was of improving the photo-antibacterial activity of 2D-NMs, the toxicity mechanism, and their challenges.
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18
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Mirzaei M, Furxhi I, Murphy F, Mullins M. Employing Supervised Algorithms for the Prediction of Nanomaterial's Antioxidant Efficiency. Int J Mol Sci 2023; 24:ijms24032792. [PMID: 36769135 PMCID: PMC9918003 DOI: 10.3390/ijms24032792] [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: 12/15/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Reactive oxygen species (ROS) are compounds that readily transform into free radicals. Excessive exposure to ROS depletes antioxidant enzymes that protect cells, leading to oxidative stress and cellular damage. Nanomaterials (NMs) exhibit free radical scavenging efficiency representing a potential solution for oxidative stress-induced disorders. This study aims to demonstrate the application of machine learning (ML) algorithms for predicting the antioxidant efficiency of NMs. We manually compiled a comprehensive dataset based on a literature review of 62 in vitro studies. We extracted NMs' physico-chemical (P-chem) properties, the NMs' synthesis technique and various experimental conditions as input features to predict the antioxidant efficiency measured by a 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. Following data pre-processing, various regression models were trained and validated. The random forest model showed the highest predictive performance reaching an R2 = 0.83. The attribute importance analysis revealed that the NM's type, core-size and dosage are the most important attributes influencing the prediction. Our findings corroborate with those of the prior research landscape regarding the importance of P-chem characteristics. This study expands the application of ML in the nano-domain beyond safety-related outcomes by capturing the functional performance. Accordingly, this study has two objectives: (1) to develop a model to forecast the antioxidant efficiency of NMs to complement conventional in vitro assays and (2) to underline the lack of a comprehensive database and the scarcity of relevant data and/or data management practices in the nanotechnology field, especially with regards to functionality assessments.
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Affiliation(s)
- Mahsa Mirzaei
- Department of Accounting and Finance, Kemmy Business School, University of Limerick, V94PH93 Limerick, Ireland
| | - Irini Furxhi
- Department of Accounting and Finance, Kemmy Business School, University of Limerick, V94PH93 Limerick, Ireland
- Transgero Limited, Newcastle West, V42V384 Limerick, Ireland
- Correspondence: ; Tel.: +353-85-106-9771
| | - Finbarr Murphy
- Department of Accounting and Finance, Kemmy Business School, University of Limerick, V94PH93 Limerick, Ireland
| | - Martin Mullins
- Department of Accounting and Finance, Kemmy Business School, University of Limerick, V94PH93 Limerick, Ireland
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19
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Chen X, Lv H. Intelligent control of nanoparticle synthesis on microfluidic chips with machine learning. NPG ASIA MATERIALS 2022; 14:69. [DOI: 10.1038/s41427-022-00416-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 01/12/2025]
Abstract
AbstractNanoparticles play irreplaceable roles in optoelectronic sensing, medical therapy, material science, and chemistry due to their unique properties. There are many synthetic pathways used for the preparation of nanoparticles, and different synthetic pathways can produce nanoparticles with different properties. Therefore, it is crucial to control the properties of nanoparticles precisely to impart the desired functions. In general, the properties of nanoparticles are influenced by their sizes and morphologies. Current technology for the preparation of nanoparticles on microfluidic chips requires repeated experimental debugging and significant resources to synthesize nanoparticles with precisely the desired properties. Machine learning-assisted synthesis of nanoparticles is a sensible choice for addressing this challenge. In this paper, we review many recent studies on syntheses of nanoparticles assisted by machine learning. Moreover, we describe the working steps of machine learning, the main algorithms, and the main ways to obtain datasets. Finally, we discuss the current problems of this research and provide an outlook.
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20
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The Application of Artificial Intelligence in Magnetic Hyperthermia Based Research. FUTURE INTERNET 2022. [DOI: 10.3390/fi14120356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The development of nanomedicine involves complex nanomaterial research involving magnetic nanomaterials and their use in magnetic hyperthermia. The selection of the optimal treatment strategies is time-consuming, expensive, unpredictable, and not consistently effective. Delivering personalized therapy that obtains maximal efficiency and minimal side effects is highly important. Thus, Artificial Intelligence (AI) based algorithms provide the opportunity to overcome these crucial issues. In this paper, we briefly overview the significance of the combination of AI-based methods, particularly the Machine Learning (ML) technique, with magnetic hyperthermia. We considered recent publications, reports, protocols, and review papers from Scopus and Web of Science Core Collection databases, considering the PRISMA-S review methodology on applying magnetic nanocarriers in magnetic hyperthermia. An algorithmic performance comparison in terms of their types and accuracy, data availability taking into account their amount, types, and quality was also carried out. Literature shows AI support of these studies from the physicochemical evaluation of nanocarriers, drug development and release, resistance prediction, dosing optimization, the combination of drug selection, pharmacokinetic profile characterization, and outcome prediction to the heat generation estimation. The papers reviewed here clearly illustrate that AI-based solutions can be considered as an effective supporting tool in drug delivery, including optimization and behavior of nanocarriers, both in vitro and in vivo, as well as the delivery process. Moreover, the direction of future research, including the prediction of optimal experiments and data curation initiatives has been indicated.
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21
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Balraadjsing S, Peijnenburg WJGM, Vijver MG. Exploring the potential of in silico machine learning tools for the prediction of acute Daphnia magna nanotoxicity. CHEMOSPHERE 2022; 307:135930. [PMID: 35961453 DOI: 10.1016/j.chemosphere.2022.135930] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 07/19/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Engineered nanomaterials (ENMs) are ubiquitous nowadays, finding their application in different fields of technology and various consumer products. Virtually any chemical can be manipulated at the nano-scale to display unique characteristics which makes them appealing over larger sized materials. As the production and development of ENMs have increased considerably over time, so too have concerns regarding their adverse effects and environmental impacts. It is unfeasible to assess the risks associated with every single ENM through in vivo or in vitro experiments. As an alternative, in silico methods can be employed to evaluate ENMs. To perform such an evaluation, we collected data from databases and literature to create classification models based on machine learning algorithms in accordance with the principles laid out by the OECD for the creation of QSARs. The aim was to investigate the performance of various machine learning algorithms towards predicting a well-defined in vivo toxicity endpoint (Daphnia magna immobilization) and also to identify which features are important drivers of D. magna in vivo nanotoxicity. Results indicated highly comparable model performance between all algorithms and predictive performance exceeding ∼0.7 for all evaluated metrics (e.g. accuracy, sensitivity, specificity, balanced accuracy, Matthews correlation coefficient, area under the receiver operator characteristic curve). The random forest, artificial neural network, and k-nearest neighbor models displayed the best performance but this was only marginally better compared to the other models. Furthermore, the variable importance analysis indicated that molecular descriptors and physicochemical properties were generally important within most models, while features related to the exposure conditions produced slightly conflicting results. Lastly, results also indicate that reliable and robust machine learning models can be generated for in vivo endpoints with smaller datasets.
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Affiliation(s)
- Surendra Balraadjsing
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands.
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands; Centre for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), PO Box 1, 3720 BA, Bilthoven, the Netherlands
| | - Martina G Vijver
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
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22
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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: 4.7] [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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23
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Xue K, Wang F, Suwardi A, Han MY, Teo P, Wang P, Wang S, Ye E, Li Z, Loh XJ. Biomaterials by design: Harnessing data for future development. Mater Today Bio 2021; 12:100165. [PMID: 34877520 PMCID: PMC8628044 DOI: 10.1016/j.mtbio.2021.100165] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 01/18/2023] Open
Abstract
Biomaterials is an interdisciplinary field of research to achieve desired biological responses from new materials, regardless of material type. There have been many exciting innovations in this discipline, but commercialization suffers from a lengthy discovery to product pipeline, with many failures along the way. Success can be greatly accelerated by harnessing machine learning techniques to comb through large amounts of data. There are many potential benefits of moving from an unstructured empirical approach to a development strategy that is entrenched in data. Here, we discuss the recent work on the use of machine learning in the discovery and design of biomaterials, including new polymeric, metallic, ceramics, and nanomaterials, and how machine learning can interface with emerging use cases of 3D printing. We discuss the steps for closer integration of machine learning to make this exciting possibility a reality.
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Affiliation(s)
| | | | | | | | | | | | | | - Enyi Ye
- Institute of Materials Research and Engineering, A∗STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
| | - Zibiao Li
- Institute of Materials Research and Engineering, A∗STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
| | - Xian Jun Loh
- Institute of Materials Research and Engineering, A∗STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
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