Curation of datasets, assessment of their quality and completeness, and nanoSAR classification model development for metallic nanoparticles

Environmental Science: Nano

Volumn 5, Issue 8, 2018, Pages 1902-1910

  Trinh, T X ^a   Ha, My Kieu ^a   Choi, Jang Sik ^b   Byun, Hyung Gi ^b   Yoon, Tae Hyun ^a  

^a Hanyang University   (South Korea)

^b Kangwon National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; CLASSIFICATION (OF INFORMATION); DECISION TREES; LEARNING SYSTEMS; METALS; NANOSTRUCTURED MATERIALS; TOXICITY;

CLASSIFICATION MODELS; EXPERIMENTAL CONDITIONS; MACHINE LEARNING TECHNIQUES; MANUFACTURER SPECIFICATIONS; METALLIC NANOPARTICLES; PHYSICO-CHEMICAL DATA; PHYSICOCHEMICAL PROPERTY; RANDOM FOREST ALGORITHM;

DATA MINING;

ASSESSMENT METHOD; DATA MINING; DATA SET; NANOPARTICLE; NUMERICAL MODEL; TOXICITY;

EID: 85051464936     PISSN: 20518153     EISSN: 20518161     Source Type: Journal    
DOI: 10.1039/c8en00061a     Document Type: Article

References (51)

1. A. Ivask N. H. Voelcker S. A. Seabrook M. Hor J. K. Kirby M. Fenech T. P. Davis P. C. Ke DNA Melting and Genotoxicity Induced by Silver Nanoparticles and Graphene Chem. Res. Toxicol. 2015 28 1023-1035
2. W. J. Trickler S. M. Lantz R. C. Murdock A. M. Schrand B. L. Robinson G. D. Newport J. J. Schlager S. J. Oldenburg M. G. Paule W. Slikker S. M. Hussain S. F. Ali Brain microvessel endothelial cells responses to gold nanoparticles: In vitro pro-inflammatory mediators and permeability Nanotoxicology 2011 5 479-492
3. S. C. Sahu J. Zheng L. Graham L. Chen J. Ihrie J. J. Yourick R. L. Sprando Comparative cytotoxicity of nanosilver in human liver HepG2 and colon Caco2 cells in culture J. Appl. Toxicol. 2014 34 1155-1166
4. Y. Qiu Y. Liu L. Wang L. Xu R. Bai Y. Ji X. Wu Y. Zhao Y. Li C. Chen Surface chemistry and aspect ratio mediated cellular uptake of Au nanorods Biomaterials 2010 31 7606-7619
5. R. Coradeghini S. Gioria C. P. García P. Nativo F. Franchini D. Gilliland J. Ponti F. Rossi Size-dependent toxicity and cell interaction mechanisms of gold nanoparticles on mouse fibroblasts Toxicol. Lett. 2013 217 205-216
6. S. Fraga H. Faria M. E. Soares J. A. Duarte L. Soares E. Pereira C. Costa-Pereira J. P. Teixeira M. de Lourdes Bastos H. Carmo Influence of the surface coating on the cytotoxicity, genotoxicity and uptake of gold nanoparticles in human HepG2 cells J. Appl. Toxicol. 2013 33 1111-1119
7. A. K. Suresh D. A. Pelletier W. Wang J. L. Morrell-Falvey B. Gu M. J. Doktycz Cytotoxicity induced by engineered silver nanocrystallites is dependent on surface coatings and cell types Langmuir 2012 28 2727-2735
8. R. F. Hamilton S. Buckingham A. Holian The effect of size on Ag nanosphere toxicity in macrophage cell models and lung epithelial cell lines is dependent on particle dissolution Int. J. Mol. Sci. 2014 15 6815-6830
9. S. Grosse L. Evje T. Syversen Silver nanoparticle-induced cytotoxicity in rat brain endothelial cell culture Toxicol. In Vitro 2013 27 305-313
10. I. M. M. Paino V. S. Marangoni R. de C. S. de Oliveira L. M. G. Antunes V. Zucolotto Cyto and genotoxicity of gold nanoparticles in human hepatocellular carcinoma and peripheral blood mononuclear cells Toxicol. Lett. 2012 215 119-125
11. R. Foldbjerg D. A. Dang H. Autrup Cytotoxicity and genotoxicity of silver nanoparticles in the human lung cancer cell line, A549 Arch. Toxicol. 2011 85 743-750
12. A. M. Alkilany P. K. Nagaria C. R. Hexel T. J. Shaw C. J. Murphy M. D. Wyatt Cellular uptake and cytotoxicity of gold nanorods: Molecular origin of cytotoxicity and surface effects Small 2009 5 701-708
13. A. R. Gliga S. Skoglund I. Odnevall Wallinder B. Fadeel H. L. Karlsson Size-dependent cytotoxicity of silver nanoparticles in human lung cells: The role of cellular uptake, agglomeration and Ag release Part. Fibre Toxicol. 2014 11 1-17
14. T. Puzyn B. Rasulev A. Gajewicz X. Hu T. P. Dasari A. Michalkova H.-M. Hwang A. Toropov D. Leszczynska J. Leszczynski Using nano-QSAR to predict the cytotoxicity of metal oxide nanoparticles Nat. Nanotechnol. 2011 6 175-178
15. E. Oh R. Liu A. Nel K. B. Gemill M. Bilal Y. Cohen I. L. Medintz Meta-analysis of cellular toxicity for cadmium-containing quantum dots Nat. Nanotechnol. 2016 11 479-486
16. J. M. Gernand E. A. Casman A meta-analysis of carbon nanotube pulmonary toxicity studies-how physical dimensions and impurities affect the toxicity of carbon nanotubes Risk Anal. 2014 34 583-597
17. K. M. Ha X. T. Trinh J. S. Choi D. Maulina H. G. Byun T. H. Yoon Toxicity Classification of Oxide Nanomaterials: Effects of Data Gap Filling and PChem Score-based Screening Approaches Sci. Rep. 2018 8 1-11
18. J. S. Choi K. M. Ha X. T. Trinh T. H. Yoon H. G. Byun Towards a generalized toxicity prediction model for metal oxide nanomaterials using integrated data from different sources Sci. Rep. 2018 1-10
19. X. T. Trinh J. S. Choi H. Jeon H. G. Byun T. H. Yoon J. Kim Quasi-SMILES-Based Nano-Quantitative Structure-Activity Relationship Model to Predict the Cytotoxicity of Multiwalled Carbon Nanotubes to Human Lung Cells Chem. Res. Toxicol. 2018 31 183-190
20. R. Liu R. Rallo R. Weissleder C. Tassa S. Shaw Y. Cohen Nano-SAR development for bioactivity of nanoparticles with considerations of decision boundaries Small 2013 9 1842-1852
21. R. Liu R. Rallo S. George Z. Ji S. Nair A. E. Nel Y. Cohen Classification NanoSAR development for cytotoxicity of metal oxide nanoparticles Small 2011 7 1118-1126
22. R. Liu W. Jiang C. D. Walkey W. C. W. Chan Y. Cohen Prediction of nanoparticles-cell association based on corona proteins and physicochemical properties Nanoscale 2015 7 9664-9675
23. R. L. M. Robinson I. Lynch W. Peijnenburg J. Rumble F. Klaessig C. Marquardt H. Rauscher T. Puzyn R. Purian C. Åberg S. Karcher H. Vriens P. Hoet M. D. Hoover C. O. Hendren S. L. Harper How should the completeness and quality of curated nanomaterial data be evaluated? Nanoscale 2016 8 9919-9943
24. OCED, ENV/JM/MONO(2016)7, ENV/JM/MONO(2016)7, http://www.oecd.org/officialdocuments/publicdisplaydocumentpdf/?cote=ENV/JM/MONO(2016)7&doclanguage=en, (accessed 17 April 2018), 2016
25. A. Gajewicz What if the number of nanotoxicity data is too small for developing predictive Nano-QSAR models? An alternative read-across based approach for filling data gaps Nanoscale 2017 9 8435-8448
26. A. Gajewicz M. T. D. Cronin B. Rasulev J. Leszczynski T. Puzyn Novel approach for efficient predictions properties of large pool of nanomaterials based on limited set of species: Nano-read-across Nanotechnology 2014 26 015701
27. A. Gajewicz How to judge whether QSAR/read-across predictions can be trusted: a novel approach for establishing a model's applicability domain Environ. Sci.: Nano 2018 5 408-421
28. H.-J. Klimisch M. Andreae U. Tillmann A Systematic Approach for Evaluating the Quality of Experimental Toxicological and Ecotoxicological Data Regul. Toxicol. Pharmacol. 1997 25 1-5
29. L. Lubinski P. Urbaszek A. Gajewicz M. T. D. Cronin S. J. Enoch J. C. Madden D. Leszczynska J. Leszczynski T. Puzyn Evaluation criteria for the quality of published experimental data on nanomaterials and their usefulness for QSAR modelling SAR QSAR Environ. Res. 2013 24 995-1008
30. D. B. Williams and C. B.Carter, The transmission electron microscope, in Transmission electron microscopy, Springer, 1996, pp. 3-17
31. E. A. Grulke X. Wu Y. Ji E. Buhr K. Yamamoto N. W. Song A. B. Stefaniak D. Schwegler-Berry W. W. Burchett J. Lambert A. J. Stromberg Differentiating gold nanorod samples using particle size and shape distributions from transmission electron microscope images Metrologia 2018 55 254-267
32. E. A. Grulke S. B. Rice J. C. Xiong K. Yamamoto T. H. Yoon K. Thomson M. Saffaripour G. J. Smallwood J. W. Lambert A. J. Stromberg R. Macy N. J. Briot D. Qian Size and shape distributions of carbon black aggregates by transmission electron microscopy Carbon 2018 130 822-833
33. V. Svetnik A. Liaw C. Tong J. Christopher Culberson R. P. Sheridan B. P. Feuston Random Forest: A Classification and Regression Tool for Compound Classification and QSAR Modeling J. Chem. Inf. Comput. Sci. 2003 43 1947-1958
34. J. A. K. Suykens J. Vandewalle Least Squares Support Vector Machine Classifiers Neural Process. Lett. 1999 9 293-300
35. L. E. Raileanu K. Stoffel Theoretical comparison between the Gini Index and Information Gain criteria Ann. Math. Artif. Intell. 2004 41 77-93
36. J. E. Trost Statistically nonrepresentative stratified sampling: A sampling technique for qualitative studies Qual. Sociol. 1986 9 54-57
37. Y. Bengio Y. Grandvalet No Unbiased Estimator of the Variance of K-Fold Cross-Validation Yoshua J. Mach. Learn. Res. 2004 5 1089-1105
38. M. Bech D. Gyrd-Hansen Effects coding in discrete choice experiments Health. Econ. 2005 14 1079-1083
39. F. Sahigara D. Ballabio R. Todeschini V. Consonni Defining a novel k-nearest neighbours approach to assess the applicability domain of a QSAR model for reliable predictions Aust. J. Chem. 2013 5 1
40. OECD, ENV/JM/MONO(2016)2, ENV/JM/MONO(2016)2, http://www.oecd.org/officialdocuments/publicdisplaydocumentpdf/?cote=env/jm/mono(2016)2&doclanguage=en, (accessed 17 April 2018), 2016
41. T. Linsinger, G.Roebben, D.Gilliland, L.Calzolai, F.Rossi, N.Gibson and C.Klein, EUR 25404 EN, 10.2787/63490
42. J. Mast and P.-J.Temmerman, NANoREG D2.10 Protocol(s) for size-distribution analysis of primary NM particles in air, powders, and liquids, https://www.rivm.nl/dsresource?objectid=5545e510-fb1d-41d2-888f-3b7b1f55bca8, (accessed 17 April 2018)
43. K. A. Jensen, NANoREG D2.08 SOP 02 For measurement of hydrodynamic Size-Distribution and Dispersion Stability by DLS, https://www.rivm.nl/dsresource?objectid=a1b2d2b0-65e7-4404-9c86-e4680d076338, (accessed 17 April 2018)
44. M. Sokolova, N.Japkowicz and S.Szpakowicz, Beyond Accuracy, F-Score and ROC: A Family of Discriminant Measures for Performance Evaluation, in AI 2006: Advances in Artificial Intelligence, ed. A. Sattar and B. Kang, Springer Berlin Heidelberg, Berlin, Heidelberg, 2006, pp. 1015-1021
45. Y. Pan S. Neuss A. Leifert M. Fischler F. Wen U. Simon G. Schmid W. Brandau W. Jahnen-Dechent Size-dependent cytotoxicity of gold nanoparticles Small 2007 3 1941-1949
46. M. V. D. Z. Park A. M. Neigh J. P. Vermeulen L. J. J. de la Fonteyne H. W. Verharen J. J. Briedé H. van Loveren W. H. de Jong The effect of particle size on the cytotoxicity, inflammation, developmental toxicity and genotoxicity of silver nanoparticles Biomaterials 2011 32 9810-9817
47. A. Verma F. Stellacci Effect of surface properties on nanoparticle-cell interactions Small 2010 6 12-21
48. E. C. Cho J. Xie P. A. Wurm Y. Xia Understanding the role of surface charges in cellular adsorption versus internalization by selectively removing gold nanoparticles on the cell surface with a I 2/KI etchant Nano Lett. 2009 9 1080-1084
49. T. I. Netzeva A. P. Worth T. Aldenberg R. Benigni M. T. D. Cronin P. Gramatica J. S. Jaworska S. Kahn G. Klopman C. A. Marchant G. Myatt N. Nikolova-Jeliazkova G. Y. Patlewicz R. Perkins D. W. Roberts T. W. Schultz D. T. Stanton J. J. M. Van De Sandt W. Tong G. Veith C. Yang Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships ATLA, Altern. Lab. Anim. 2005 33 155-173
50. W. Tong Q. Xie H. Hong L. Shi H. Fang R. Perkins Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activity Environ. Health Perspect. 2004 112 1249-1254
51. D. W. Boukhvalov T. H. Yoon Development of Theoretical Descriptors for Cytotoxicity Evaluation of Metallic Nanoparticles Chem. Res. Toxicol. 2017 30 1549-1555