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Dasgupta S, Sharapova T, Mahalingaiah PK, Chorley BN, Shoieb A, Tsuji T, Dos Santos AAC, Chari R, Ebrahimi A, Dalmas Wilk DA, Pettit S, Bawa B, Vaughan E, van Vleet TR, Mitchell CA, Yuen PST. Urinary MicroRNA biomarkers of nephrotoxicity in Macaca fascicularis. Regul Toxicol Pharmacol 2024; 151:105668. [PMID: 38936797 DOI: 10.1016/j.yrtph.2024.105668] [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: 01/08/2024] [Revised: 06/10/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
Drug-induced kidney injury (DIKI) refers to kidney damage resulting from the administration of medications. The aim of this project was to identify reliable urinary microRNA (miRNAs) biomarkers that can be used as potential predictors of DIKI before disease diagnosis. This study quantified a panel of six miRNAs (miRs-210-3p, 423-5p, 143-3p, 130b-3p, 486-5p, 193a-3p) across multiple time points using urinary samples from a previous investigation evaluating effects of a nephrotoxicant in cynomolgus monkeys. Exosome-associated miRNA exhibited distinctive trends when compared to miRNAs quantified in whole urine, which may reflect a different urinary excretion mechanism of miRNAs than those released passively into the urine. Although further research and mechanistic studies are required to elucidate how these miRNAs regulate signaling in disease pathways, we present, for the first time, data that several miRNAs displayed strong correlations with histopathology scores, thus indicating their potential use as biomarkers to predict the development of DIKI in preclinical studies and clinical trials. Also, these findings can potentially be translated into other non-clinical species or human for the detection of DIKI.
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Affiliation(s)
- Subham Dasgupta
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | | | | | - Brian N Chorley
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | | | - Takayuki Tsuji
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alef A C Dos Santos
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rohit Chari
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Syril Pettit
- Health and Environmental Sciences Institute, Washington, DC, USA
| | | | | | | | | | - Peter S T Yuen
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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2
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Corton JC, Hill T, Sutherland JJ, Stevens JL, Rooney J. A Set of Six Gene Expression Biomarkers Identify Rat Liver Tumorigens in Short-term Assays. Toxicol Sci 2020; 177:11-26. [PMID: 32603430 PMCID: PMC8026143 DOI: 10.1093/toxsci/kfaa101] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Chemical-induced liver cancer occurs in rodents through well-characterized adverse outcome pathways. We hypothesized that measurement of the 6 most common molecular initiating events (MIEs) in liver cancer adverse outcome pathways in short-term assays using only gene expression will allow early identification of chemicals and their associated doses that are likely to be tumorigenic in the liver in 2-year bioassays. We tested this hypothesis using transcript data from a rat liver microarray compendium consisting of 2013 comparisons of 146 chemicals administered at doses with previously established effects on rat liver tumor induction. Five MIEs were measured using previously characterized gene expression biomarkers composed of gene sets predictive for genotoxicity and activation of 1 or more xenobiotic receptors (aryl hydrocarbon receptor, constitutive activated receptor, estrogen receptor, and peroxisome proliferator-activated receptor α). Because chronic injury can be important in tumorigenesis, we also developed a biomarker for cytotoxicity that had a 96% balanced accuracy. Characterization of the genes in each biomarker set using the unsupervised TXG-MAP network model demonstrated that the genes were associated with distinct functional coexpression modules. Using the Toxicological Priority Index to rank chemicals based on their ability to activate the MIEs showed that chemicals administered at tumorigenic doses clearly gave the highest ranked scores. Balanced accuracies using thresholds derived from either TG-GATES or DrugMatrix data sets to predict tumorigenicity in independent sets of chemicals were up to 93%. These results show that a MIE-directed approach using only gene expression biomarkers could be used in short-term assays to identify chemicals and their doses that cause tumors.
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Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
| | - Thomas Hill
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
- Oak Ridge Institute for Science and Education (ORISE)
| | | | - James L Stevens
- Indiana Biosciences Research Institute, Indianapolis, Indiana
- Paradox Found LLC, Apex, North Carolina
| | - John Rooney
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
- Oak Ridge Institute for Science and Education (ORISE)
- Integrated Lab Services, Research Triangle Park, NC 27560
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Corton JC, Witt KL, Yauk CL. Identification of p53 Activators in a Human Microarray Compendium. Chem Res Toxicol 2019; 32:1748-1759. [PMID: 31397557 DOI: 10.1021/acs.chemrestox.9b00052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biomarkers predictive of molecular and toxicological effects are needed to interpret emerging high-throughput transcriptomic data streams. The previously characterized 63 gene TGx-DDI biomarker that includes 20 genes known to be regulated by p53 was previously shown to accurately predict DNA damage in chemically treated cells. We comprehensively evaluated whether the molecular basis of the DDI predictions was based on a p53-dependent response. The biomarker was compared to microarray data in a compendium derived from human cells using the Running Fisher test, a nonparametric correlation test. Using the biomarker, we identified conditions that led to p53 activation, including exposure to the chemical nutlin-3 which disrupts interactions between p53 and the negative regulator MDM2 or by knockdown of MDM2. The expression of most of the genes in the biomarker (75%) were found to depend on p53 activation status based on gene behavior after TP53 overexpression or knockdown. The biomarker identified DDI chemicals that were strong inducers of p53 in wild-type cells; these p53 responses were decreased or abolished in cells after p53 knockdown by siRNAs. Using the biomarker, we screened ∼1950 chemicals in ∼9800 human cell line chemical vs control comparisons and identified ∼100 chemicals that caused p53 activation. Among the positive chemicals were many that are known to activate p53 through direct and indirect DNA damaging mechanisms. These results contribute to the evidence that the TGx-DDI biomarker is useful for identifying chemicals that cause DDI and activate p53.
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Affiliation(s)
- J Christopher Corton
- Integrated Systems Toxicology Division, NHEERL , United States Environmental Protection Agency , Research Triangle Park, Durham , North Carolina 27711 , United States
| | - Kristine L Witt
- Division of the National Toxicology Program , National Institute of Environmental Health Sciences , Research Triangle Park, Durham , North Carolina 27709 , United States
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada , Ottawa , Ontario K1A 0K9 , Canada
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Gi M, Fujioka M, Yamano S, Kakehashi A, Oishi Y, Okuno T, Yukimatsu N, Yamaguchi T, Tago Y, Kitano M, Hayashi SM, Wanibuchi H. Chronic dietary toxicity and carcinogenicity studies of dammar resin in F344 rats. Arch Toxicol 2018; 92:3565-3583. [PMID: 30251054 DOI: 10.1007/s00204-018-2316-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/19/2018] [Indexed: 01/09/2023]
Abstract
Dammar resin is a natural food additive and flavoring substance present in many foods and drinks. The present study evaluates the chronic toxicity and carcinogenicity of dietary dammar resin in F344 rats. Dietary concentrations in the 52-week chronic toxicity study were 0, 0.03, 0.125, 0.5, or 2%. The major treatment-related deleterious effects were body weight suppression, increased relative liver weight, and low hemoglobin levels in males and females. Foci of cellular alteration in the liver were observed in the male 2% group, but not in any other group. The no-observed-adverse-effect level for chronic toxicity was 0.125% for males (200.4 mg/kg b.w./day) and females (241.9 mg/kg b.w./day). Dietary concentrations in the 104-week carcinogenicity study were 0, 0.03, 0.5, or 2%. Dammar resin induced hemorrhagic diathesis in males and females, possibly via the inhibition of extrinsic and intrinsic coagulation pathways. Incidences of hepatocellular adenomas and carcinomas were significantly increased in the male 2% group, but not in any other group. In the 4-week subacute toxicity study, the livers of male rat-fed diet-containing 2% dammar resin had increased levels of protein oxidation and increased the expression of two anti-apoptotic and seven cytochrome P450 (CYP) genes. There was also an increased tendency of oxidative DNA damage. These findings demonstrate that dammar resin is hepatocarcinogenic in male F344 rats and underlines the roles of inhibition of apoptosis, induction of CYP enzymes, and oxidative stress in dammar resin-induced hepatocarcinogenesis.
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Affiliation(s)
- Min Gi
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
| | - Masaki Fujioka
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
| | - Shotaro Yamano
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
- Japan Bioassay Research Center, Japan Organization of Occupational Health and Safety, Hadano, 257-0015, Kanagawa, Japan
| | - Anna Kakehashi
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
| | - Yuji Oishi
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
| | - Takahiro Okuno
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
| | - Nao Yukimatsu
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
| | - Takashi Yamaguchi
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
| | - Yoshiyuki Tago
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
| | - Mistuaki Kitano
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
| | - Shim-Mo Hayashi
- Global Scientific and Regulatory Affairs, San-Ei Gen F.F.I., Inc., 1-1-11 Sanwa-cho, Toyonaka, 561-8588, Osaka, Japan
| | - Hideki Wanibuchi
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan.
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Identification of consensus biomarkers for predicting non-genotoxic hepatocarcinogens. Sci Rep 2017; 7:41176. [PMID: 28117354 PMCID: PMC5259716 DOI: 10.1038/srep41176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/16/2016] [Indexed: 12/31/2022] Open
Abstract
The assessment of non-genotoxic hepatocarcinogens (NGHCs) is currently relying on two-year rodent bioassays. Toxicogenomics biomarkers provide a potential alternative method for the prioritization of NGHCs that could be useful for risk assessment. However, previous studies using inconsistently classified chemicals as the training set and a single microarray dataset concluded no consensus biomarkers. In this study, 4 consensus biomarkers of A2m, Ca3, Cxcl1, and Cyp8b1 were identified from four large-scale microarray datasets of the one-day single maximum tolerated dose and a large set of chemicals without inconsistent classifications. Machine learning techniques were subsequently applied to develop prediction models for NGHCs. The final bagging decision tree models were constructed with an average AUC performance of 0.803 for an independent test. A set of 16 chemicals with controversial classifications were reclassified according to the consensus biomarkers. The developed prediction models and identified consensus biomarkers are expected to be potential alternative methods for prioritization of NGHCs for further experimental validation.
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Yauk CL, Buick JK, Williams A, Swartz CD, Recio L, Li H, Fornace AJ, Thomson EM, Aubrecht J. Application of the TGx-28.65 transcriptomic biomarker to classify genotoxic and non-genotoxic chemicals in human TK6 cells in the presence of rat liver S9. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:243-60. [PMID: 26946220 PMCID: PMC5021161 DOI: 10.1002/em.22004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 05/05/2023]
Abstract
In vitro transcriptional signatures that predict toxicities can facilitate chemical screening. We previously developed a transcriptomic biomarker (known as TGx-28.65) for classifying agents as genotoxic (DNA damaging) and non-genotoxic in human lymphoblastoid TK6 cells. Because TK6 cells do not express cytochrome P450s, we confirmed accurate classification by the biomarker in cells co-exposed to 1% 5,6 benzoflavone/phenobarbital-induced rat liver S9 for metabolic activation. However, chemicals may require different types of S9 for activation. Here we investigated the response of TK6 cells to higher percentages of Aroclor-, benzoflavone/phenobarbital-, or ethanol-induced rat liver S9 to expand TGx-28.65 biomarker applicability. Transcriptional profiles were derived 3 to 4 hr following a 4 hr co-exposure of TK6 cells to test chemicals and S9. Preliminary studies established that 10% Aroclor- and 5% ethanol-induced S9 alone did not induce the TGx-28.65 biomarker genes. Seven genotoxic and two non-genotoxic chemicals (and concurrent solvent and positive controls) were then tested with one of the S9s (selected based on cell survival and micronucleus induction). Relative survival and micronucleus frequency was assessed by flow cytometry in cells 20 hr post-exposure. Genotoxic/non-genotoxic chemicals were accurately classified using the different S9s. One technical replicate of cells co-treated with dexamethasone and 10% Aroclor-induced S9 was falsely classified as genotoxic, suggesting caution in using high S9 concentrations. Even low concentrations of genotoxic chemicals (those not causing cytotoxicity) were correctly classified, demonstrating that TGx-28.65 is a sensitive biomarker of genotoxicity. A meta-analysis of datasets from 13 chemicals supports that different S9s can be used in TK6 cells, without impairing classification using the TGx-28.65 biomarker.
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Affiliation(s)
- Carole L. Yauk
- Environmental Health Science and Research Bureau, Health CanadaOttawaOntarioCanada
| | - Julie K. Buick
- Environmental Health Science and Research Bureau, Health CanadaOttawaOntarioCanada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health CanadaOttawaOntarioCanada
| | - Carol D. Swartz
- Integrated Laboratory Systems IncResearch Triangle ParkNorth Carolina
| | - Leslie Recio
- Integrated Laboratory Systems IncResearch Triangle ParkNorth Carolina
| | - Heng‐Hong Li
- Department of Biochemistry and Molecular and Cellular BiologyGeorgetown University Medical CenterWashingtonDistrict of Columbia
- Department of OncologyGeorgetown University Medical CenterWashingtonDistrict of Columbia
| | - Albert J. Fornace
- Department of Biochemistry and Molecular and Cellular BiologyGeorgetown University Medical CenterWashingtonDistrict of Columbia
- Department of OncologyGeorgetown University Medical CenterWashingtonDistrict of Columbia
| | - Errol M. Thomson
- Environmental Health Science and Research Bureau, Health CanadaOttawaOntarioCanada
| | - Jiri Aubrecht
- Drug Safety Research and Development, Pfizer IncGrotonConnecticut
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8
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Igarashi Y, Nakatsu N, Yamashita T, Ono A, Ohno Y, Urushidani T, Yamada H. Open TG-GATEs: a large-scale toxicogenomics database. Nucleic Acids Res 2014; 43:D921-7. [PMID: 25313160 PMCID: PMC4384023 DOI: 10.1093/nar/gku955] [Citation(s) in RCA: 265] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Toxicogenomics focuses on assessing the safety of compounds using gene expression profiles. Gene expression signatures from large toxicogenomics databases are expected to perform better than small databases in identifying biomarkers for the prediction and evaluation of drug safety based on a compound's toxicological mechanisms in animal target organs. Over the past 10 years, the Japanese Toxicogenomics Project consortium (TGP) has been developing a large-scale toxicogenomics database consisting of data from 170 compounds (mostly drugs) with the aim of improving and enhancing drug safety assessment. Most of the data generated by the project (e.g. gene expression, pathology, lot number) are freely available to the public via Open TG-GATEs (Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System). Here, we provide a comprehensive overview of the database, including both gene expression data and metadata, with a description of experimental conditions and procedures used to generate the database. Open TG-GATEs is available from https://toxico.nibiohn.go.jp/english/index.html.
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Affiliation(s)
- Yoshinobu Igarashi
- Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan
| | - Noriyuki Nakatsu
- Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan
| | - Tomoya Yamashita
- Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan Hitachi, Ltd. Information & Telecommunication Systems Company, Government & Public Corporation Information Systems Division, Tokyo 136-8832, Japan
| | - Atsushi Ono
- National Institute of Health and Sciences, Tokyo 158-0098, Japan
| | - Yasuo Ohno
- National Institute of Health and Sciences, Tokyo 158-0098, Japan
| | - Tetsuro Urushidani
- Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan Department of Pathophysiology, Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kyoto 610-0332, Japan
| | - Hiroshi Yamada
- Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan
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A novel toxicogenomics-based approach to categorize (non-)genotoxic carcinogens. Arch Toxicol 2014; 89:2413-27. [DOI: 10.1007/s00204-014-1368-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/04/2014] [Indexed: 10/24/2022]
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Wink S, Hiemstra S, Huppelschoten S, Danen E, Niemeijer M, Hendriks G, Vrieling H, Herpers B, van de Water B. Quantitative high content imaging of cellular adaptive stress response pathways in toxicity for chemical safety assessment. Chem Res Toxicol 2014; 27:338-55. [PMID: 24450961 DOI: 10.1021/tx4004038] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over the past decade, major leaps forward have been made on the mechanistic understanding and identification of adaptive stress response landscapes underlying toxic insult using transcriptomics approaches. However, for predictive purposes of adverse outcome several major limitations in these approaches exist. First, the limited number of samples that can be analyzed reduces the in depth analysis of concentration-time course relationships for toxic stress responses. Second these transcriptomics analysis have been based on the whole cell population, thereby inevitably preventing single cell analysis. Third, transcriptomics is based on the transcript level, totally ignoring (post)translational regulation. We believe these limitations are circumvented with the application of high content analysis of relevant toxicant-induced adaptive stress signaling pathways using bacterial artificial chromosome (BAC) green fluorescent protein (GFP) reporter cell-based assays. The goal is to establish a platform that incorporates all adaptive stress pathways that are relevant for toxicity, with a focus on drug-induced liver injury. In addition, cellular stress responses typically follow cell perturbations at the subcellular organelle level. Therefore, we complement our reporter line panel with reporters for specific organelle morphometry and function. Here, we review the approaches of high content imaging of cellular adaptive stress responses to chemicals and the application in the mechanistic understanding and prediction of chemical toxicity at a systems toxicology level.
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Affiliation(s)
- Steven Wink
- Division of Toxicology, Leiden Academic Centre for Drug Research (LACDR), Leiden University , The Netherlands
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The Past, Present, and Future of Chemical Risk Assessment. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2014. [DOI: 10.1007/978-1-4939-0521-8_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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