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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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Guo W, Archer J, Moore M, Shojaee S, Zou W, Ge W, Benjamin L, Adeuya A, Fairchild R, Hong H. Software-Assisted Pattern Recognition of Persistent Organic Pollutants in Contaminated Human and Animal Food. Molecules 2021; 26:molecules26030685. [PMID: 33525602 PMCID: PMC7865765 DOI: 10.3390/molecules26030685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 11/28/2022] Open
Abstract
Persistent Organic Pollutants (POPs) are a serious food safety concern due to their persistence and toxic effects. To promote food safety and protect human health, it is important to understand the sources of POPs and how to minimize human exposure to these contaminants. The POPs Program within the U.S. Food and Drug Administration (FDA), manually evaluates congener patterns of POPs-contaminated samples and sometimes compares the finding to other previously analyzed samples with similar patterns. This manual comparison is time consuming and solely depends on human expertise. To improve the efficiency of this evaluation, we developed software to assist in identifying potential sources of POPs contamination by detecting similarities between the congener patterns of a contaminated sample and potential environmental source samples. Similarity scores were computed and used to rank potential source samples. The software has been tested on a diverse set of incurred samples by comparing results from the software with those from human experts. We demonstrated that the software provides results consistent with human expert observation. This software also provided the advantage of reliably evaluating an increased sample lot which increased overall efficiency.
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Affiliation(s)
- Wenjing Guo
- National Center for Toxicological Research, U.S. Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA; (W.G.); (W.Z.); (W.G.)
| | - Jeffrey Archer
- Office of Regulatory Affairs, Office of Regulatory Science, Arkansas Laboratory, U.S. Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA; (J.A.); (M.M.); (S.S.); (R.F.)
| | - Morgan Moore
- Office of Regulatory Affairs, Office of Regulatory Science, Arkansas Laboratory, U.S. Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA; (J.A.); (M.M.); (S.S.); (R.F.)
| | - Sina Shojaee
- Office of Regulatory Affairs, Office of Regulatory Science, Arkansas Laboratory, U.S. Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA; (J.A.); (M.M.); (S.S.); (R.F.)
| | - Wen Zou
- National Center for Toxicological Research, U.S. Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA; (W.G.); (W.Z.); (W.G.)
| | - Weigong Ge
- National Center for Toxicological Research, U.S. Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA; (W.G.); (W.Z.); (W.G.)
| | - Linda Benjamin
- Center for Veterinary Medicine, U.S. Food & Drug Administration, 7500 Standish Place, Rockville, MD 20855, USA;
| | - Anthony Adeuya
- Center for Food Safety and Applied Nutrition, U.S. Food & Drug Administration, 5001 Campus Dr, College Park, MD 20740, USA;
| | - Russell Fairchild
- Office of Regulatory Affairs, Office of Regulatory Science, Arkansas Laboratory, U.S. Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA; (J.A.); (M.M.); (S.S.); (R.F.)
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA; (W.G.); (W.Z.); (W.G.)
- Correspondence: ; Tel.: +1-(870)-543-7296
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O'Shea K, Misra BB. Software tools, databases and resources in metabolomics: updates from 2018 to 2019. Metabolomics 2020; 16:36. [PMID: 32146531 DOI: 10.1007/s11306-020-01657-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/01/2020] [Indexed: 12/24/2022]
Abstract
Metabolomics has evolved as a discipline from a discovery and functional genomics tool, and is now a cornerstone in the era of big data-driven precision medicine. Sample preparation strategies and analytical technologies have seen enormous growth, and keeping pace with data analytics is challenging, to say the least. This review introduces and briefly presents around 100 metabolomics software resources, tools, databases, and other utilities that have surfaced or have improved in 2019. Table 1 provides the computational dependencies of the tools, categorizes the resources based on utility and ease of use, and provides hyperlinks to webpages where the tools can be downloaded or used. This review intends to keep the community of metabolomics researchers up to date with all the software tools, resources, and databases developed in 2019, in one place.
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Affiliation(s)
- Keiron O'Shea
- Institute of Biological, Environmental, and Rural Studies, Aberystwyth University, Ceredigion, Wales, SY23 3DA, UK
| | - Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA.
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Guo W, Pan B, Sakkiah S, Yavas G, Ge W, Zou W, Tong W, Hong H. Persistent Organic Pollutants in Food: Contamination Sources, Health Effects and Detection Methods. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E4361. [PMID: 31717330 PMCID: PMC6888492 DOI: 10.3390/ijerph16224361] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/30/2019] [Accepted: 11/05/2019] [Indexed: 12/20/2022]
Abstract
Persistent organic pollutants (POPs) present in foods have been a major concern for food safety due to their persistence and toxic effects. To ensure food safety and protect human health from POPs, it is critical to achieve a better understanding of POP pathways into food and develop strategies to reduce human exposure. POPs could present in food in the raw stages, transferred from the environment or artificially introduced during food preparation steps. Exposure to these pollutants may cause various health problems such as endocrine disruption, cardiovascular diseases, cancers, diabetes, birth defects, and dysfunctional immune and reproductive systems. This review describes potential sources of POP food contamination, analytical approaches to measure POP levels in food and efforts to control food contamination with POPs.
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Affiliation(s)
| | | | | | | | | | | | | | - Huixiao Hong
- U.S. Food & Drug Administration, National Center for Toxicological Research, 3900 NCTR Road, Jefferson, AR 72079, USA; (W.G.); (B.P.); (S.S.); (G.Y.); (W.G.); (W.Z.); (W.T.)
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