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Jang WJ, Lee S, Jeong CH. Uncovering transcriptomic biomarkers for enhanced diagnosis of methamphetamine use disorder: a comprehensive review. Front Psychiatry 2024; 14:1302994. [PMID: 38260797 PMCID: PMC10800441 DOI: 10.3389/fpsyt.2023.1302994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Methamphetamine use disorder (MUD) is a chronic relapsing disorder characterized by compulsive Methamphetamine (MA) use despite its detrimental effects on physical, psychological, and social well-being. The development of MUD is a complex process that involves the interplay of genetic, epigenetic, and environmental factors. The treatment of MUD remains a significant challenge, with no FDA-approved pharmacotherapies currently available. Current diagnostic criteria for MUD rely primarily on self-reporting and behavioral assessments, which have inherent limitations owing to their subjective nature. This lack of objective biomarkers and unidimensional approaches may not fully capture the unique features and consequences of MA addiction. Methods We performed a literature search for this review using the Boolean search in the PubMed database. Results This review explores existing technologies for identifying transcriptomic biomarkers for MUD diagnosis. We examined non-invasive tissues and scrutinized transcriptomic biomarkers relevant to MUD. Additionally, we investigated transcriptomic biomarkers identified for diagnosing, predicting, and monitoring MUD in non-invasive tissues. Discussion Developing and validating non-invasive MUD biomarkers could address these limitations, foster more precise and reliable diagnostic approaches, and ultimately enhance the quality of care for individuals with MA addiction.
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Affiliation(s)
| | | | - Chul-Ho Jeong
- College of Pharmacy, Keimyung University, Daegu, Republic of Korea
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Phat NK, Tien NTN, Anh NK, Yen NTH, Lee YA, Trinh HKT, Le KM, Ahn S, Cho YS, Park S, Kim DH, Long NP, Shin JG. Alterations of lipid-related genes during anti-tuberculosis treatment: insights into host immune responses and potential transcriptional biomarkers. Front Immunol 2023; 14:1210372. [PMID: 38022579 PMCID: PMC10644770 DOI: 10.3389/fimmu.2023.1210372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Background The optimal diagnosis and treatment of tuberculosis (TB) are challenging due to underdiagnosis and inadequate treatment monitoring. Lipid-related genes are crucial components of the host immune response in TB. However, their dynamic expression and potential usefulness for monitoring response to anti-TB treatment are unclear. Methodology In the present study, we used a targeted, knowledge-based approach to investigate the expression of lipid-related genes during anti-TB treatment and their potential use as biomarkers of treatment response. Results and discussion The expression levels of 10 genes (ARPC5, ACSL4, PLD4, LIPA, CHMP2B, RAB5A, GABARAPL2, PLA2G4A, MBOAT2, and MBOAT1) were significantly altered during standard anti-TB treatment. We evaluated the potential usefulness of this 10-lipid-gene signature for TB diagnosis and treatment monitoring in various clinical scenarios across multiple populations. We also compared this signature with other transcriptomic signatures. The 10-lipid-gene signature could distinguish patients with TB from those with latent tuberculosis infection and non-TB controls (area under the receiver operating characteristic curve > 0.7 for most cases); it could also be useful for monitoring response to anti-TB treatment. Although the performance of the new signature was not better than that of previous signatures (i.e., RISK6, Sambarey10, Long10), our results suggest the usefulness of metabolism-centric biomarkers. Conclusions Lipid-related genes play significant roles in TB pathophysiology and host immune responses. Furthermore, transcriptomic signatures related to the immune response and lipid-related gene may be useful for TB diagnosis and treatment monitoring.
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Affiliation(s)
- Nguyen Ky Phat
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Tran Nam Tien
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Ky Anh
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Thi Hai Yen
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Yoon Ah Lee
- School of Mathematics, Statistics and Data Science, Sungshin Women's University, Seoul, Republic of Korea
| | - Hoang Kim Tu Trinh
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh, Ho Chi Minh, Vietnam
| | - Kieu-Minh Le
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh, Ho Chi Minh, Vietnam
| | - Sangzin Ahn
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Yong-Soon Cho
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Seongoh Park
- School of Mathematics, Statistics and Data Science, Sungshin Women's University, Seoul, Republic of Korea
- Data Science Center, Sungshin Women's University, Seoul, Republic of Korea
| | - Dong Hyun Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Jae-Gook Shin
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
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Abstract
Psoriasis is a chronic disease that is caused by multiple factors and is identified by itchiness, unpleasant, red, or white scaly patches on the skin, particularly on regularly chafed body regions such as the lateral areas of the limbs. Reports suggest that globally around 2%-3% of the population suffers from psoriasis. In this review, we have discussed the clinical classification of psoriasis and also the ideal characteristics of the biomarkers. An overview regarding the discovery of the biomarker and method for validating the study has been discussed. A growing body of research suggests a link to certain other systemic symptoms such as cardiovascular disorder, metabolic syndrome, and few other comorbidities such as hypertension and nonalcoholic fatty liver disease. Natural killer (NK) cells are lymphocyte cells that concentrate on the destruction of virally infected and malignant cells; these tend to produce a wide range of inflammatory cytokines, some of which are associated with the etiology of psoriasis. Detailed information on the molecular pathogenesis of psoriasis in which interleukin (IL)-17, IL-23, tumor necrosis factor-α (TNF-α), and CCL20 play a very significant role in the development of psoriasis. In this review, we have discussed an overview of the recent state of the biomarkers available for the diagnosis and treatment of psoriasis by emphasizing on the available biomarkers such as epigenomic, transcriptomic, glycomic, and metabolomic. The most recent advancements in molecular-targeted therapy utilizing biologics and oral systemic therapy (methotrexate, apremilast) enable to adequately treat the most serious psoriatic symptoms and also the studies have validated the efficacy of biologic therapy such as TNF-α antagonist (infliximab, adalimumab), IL-23 antagonist (guselkumab, risankizumab), and IL-17 antagonist (secukinumab, ixekizumab). Finally, an overview about the technological opportunities as well as various challenges has been discussed.
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Affiliation(s)
- Deblina Dan
- Department of Pharmaceutics, Amity Institute of Pharmacy, Lucknow, Amity University Uttar Pradesh, Noida, India
| | - Nimisha Srivastava
- Department of Pharmaceutics, Amity Institute of Pharmacy, Lucknow, Amity University Uttar Pradesh, Noida, India
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Chen R, Lin YT, Fornace AJ, Li HH. A high-throughput and highly automated genotoxicity screening assay. ALTEX 2021; 39:71-81. [PMID: 34585733 DOI: 10.14573/altex.2102121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 09/20/2021] [Indexed: 11/23/2022]
Abstract
The increasing number of compounds under development and chemicals in commerce that require safety assessments pose a serious challenge for regulatory agencies worldwide. In vitro screening using toxicogenomic biomarkers has been proposed as a first-tier screen in chemical assessments and has been endorsed internationally. We previously developed, evaluated, and validated an in vitro transcriptomic biomarker responsive to DNA-damage-inducing (DDI) agents, namely TGx-DDI, for genotoxicity testing in human cells, and demonstrated the feasibility of using TGx-DDI in a medium-throughput, cell-based genotoxicity testing system by implementing this biomarker with the Nanostring nCounter system. In this current study, we took the advantage of Nanostring nCounter Plexset technology to develop a highly automated, multiplexed, and high-throughput genotoxicity testing assay, designated as the TGx-DDI Plexset assay, which can increase the screening efficiency by eight-fold compared to standard nCounter technology while decreasing the hands-on time. We demonstrated the high-throughput capability of this assay by eliminating concentration determination and RNA extraction steps without compromising the specificity and sensitivity of TGx-DDI. Thus, we propose that this simple, highly automated, multiplexed high-throughput pipeline can be widely used in chemical screening and assessment.
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Affiliation(s)
- Renxiang Chen
- Department of Oncology, and Department of Biochemistry, Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA.,Amelia Technologies LLC, Rockville, MD, USA.,Current address: RNAimmune Inc., Gaithersburg, MD, USA
| | - Yun-Tien Lin
- Department of Oncology, and Department of Biochemistry, Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Albert J Fornace
- Department of Oncology, and Department of Biochemistry, Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Heng-Hong Li
- Department of Oncology, and Department of Biochemistry, Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
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Liu Q, Wang Y, Duan M, Fan Y, Pan X, Liu S, Yu Q, Huang L, Zhou F. Females and Males Show Differences in Early-Stage Transcriptomic Biomarkers of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. Diagnostics (Basel) 2021; 11:347. [PMID: 33669819 DOI: 10.3390/diagnostics11020347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/25/2022] Open
Abstract
The incidence and mortality rates of lung cancers are different between females and males. Therefore, sex information should be an important part of how to train and optimize a diagnostic model. However, most of the existing studies do not fully utilize this information. This study carried out a comparative investigation between sex-specific models and sex-independent models. Three feature selection algorithms and five classifiers were utilized to evaluate the contribution of the sex information to the detection of early-stage lung cancers. Both lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) showed that the sex-specific models outperformed the sex-independent detection of early-stage lung cancers. The Venn plots suggested that females and males shared only a few transcriptomic biomarkers of early-stage lung cancers. Our experimental data suggested that sex information should be included in optimizing disease diagnosis models.
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Unger L, Abril C, Gerber V, Jagannathan V, Koch C, Hamza E. Diagnostic potential of three serum microRNAs as biomarkers for equine sarcoid disease in horses and donkeys. J Vet Intern Med 2021; 35:610-619. [PMID: 33415768 PMCID: PMC7848377 DOI: 10.1111/jvim.16027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are potential biomarkers for equine sarcoids (ES). OBJECTIVES To assess eca-miR-331, eca-miR-100, and eca-miR-1 as serum biomarkers for ES disease. ANIMALS Sixty-eight ES cases (56 horses, 12 donkeys), 69 tumor-free controls (60 horses, 9 donkeys), and 20 horses with other skin tumors. METHODS For this case-control study, expression of serum eca-miR-331, eca-miR-100, and eca-miR-1 in ES-affected equids was compared to tumor-free age-, sex-, and breed-matched control horses and donkeys with other skin tumors using reverse transcription quantitative PCR (polymerase chain reaction) for relative miRNA quantification. Biological, preanalytical, and clinical variable influences on miRNA expression were examined. Receiver operator characteristic (ROC) curve analyses were used to determine differences in miRNA expression between groups. RESULTS The expression of eca-miR-100 was affected by age (P = .003) and expression of eca-miR-100 and eca-miR-1 were affected by hemolysis (both P < .001). Eca-miR-331 was unaffected by biological variation, hemolysis, ES type, and disease severity. Eca-miR-331 concentrations were higher in ES-affected compared to tumor-free controls (P = .002). The ROC curve analysis indicated an area under the curve of 0.65 (P = .002) with a sensitivity of 60%, specificity of 71%, and positive and negative likelihood ratios of 2.1 and 0.56, respectively, to diagnose ES. Eca-miR-331 expression did not discriminate between horses with ES and other skin tumors. Expression of eca-miR-100 and eca-miR-1 was not different between groups. CONCLUSIONS AND CLINICAL IMPORTANCE Serum eca-miR-331 expression is neither sensitive nor specific enough as a single ES biomarker. If combined with other miRNAs, it may be helpful for ES diagnosis.
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Affiliation(s)
- Lucia Unger
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
| | - Carlos Abril
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
| | - Vinzenz Gerber
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Christoph Koch
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
| | - Eman Hamza
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
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Cho E, Buick JK, Williams A, Chen R, Li H, Corton JC, Fornace AJ, Aubrecht J, Yauk CL. Assessment of the performance of the TGx-DDI biomarker to detect DNA damage-inducing agents using quantitative RT-PCR in TK6 cells. Environ Mol Mutagen 2019; 60:122-133. [PMID: 30488505 PMCID: PMC6588084 DOI: 10.1002/em.22257] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/03/2018] [Accepted: 10/04/2018] [Indexed: 05/05/2023]
Abstract
Gene expression biomarkers are now available for application in the identification of genotoxic hazards. The TGx-DDI transcriptomic biomarker can accurately distinguish DNA damage-inducing (DDI) from non-DDI exposures based on changes in the expression of 64 biomarker genes. The 64 genes were previously derived from whole transcriptome DNA microarray profiles of 28 reference agents (14 DDI and 14 non-DDI) after 4 h treatments of TK6 human lymphoblastoid cells. To broaden the applicability of TGx-DDI, we tested the biomarker using quantitative RT-PCR (qPCR), which is accessible to most molecular biology laboratories. First, we selectively profiled the expression of the 64 biomarker genes using TaqMan qPCR assays in 96-well arrays after exposing TK6 cells to the 28 reference agents for 4 h. To evaluate the classification capability of the qPCR profiles, we used the reference qPCR signature to classify 24 external validation chemicals using two different methods-a combination of three statistical analyses and an alternative, the Running Fisher test. The qPCR results for the reference set were comparable to the original microarray biomarker; 27 of the 28 reference agents (96%) were accurately classified. Moreover, the two classification approaches supported the conservation of TGx-DDI classification capability using qPCR; the combination of the two approaches accurately classified 21 of the 24 external validation chemicals, demonstrating 100% sensitivity, 81% specificity, and 91% balanced accuracy. This study demonstrates that qPCR can be used when applying the TGx-DDI biomarker and will improve the accessibility of TGx-DDI for genotoxicity screening. Environ. Mol. Mutagen. 60: 122-133, 2019. © 2018 Her Majesty the Queen in Right of Canada Environmental and Molecular Mutagenesis.
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Affiliation(s)
- Eunnara Cho
- Environmental Health Science and Research BureauHealth CanadaOttawaOntarioCanada
- Department of BiologyCarleton UniversityOttawaOntarioCanada
| | - Julie K. Buick
- Environmental Health Science and Research BureauHealth CanadaOttawaOntarioCanada
| | - Andrew Williams
- Environmental Health Science and Research BureauHealth CanadaOttawaOntarioCanada
| | - Renxiang Chen
- Department of Oncology, Lombardi Comprehensive Cancer CenterGeorgetown University Medical CenterWashingtonDistrict of Columbia
| | - Heng‐Hong Li
- Department of Oncology, Lombardi Comprehensive Cancer CenterGeorgetown University Medical CenterWashingtonDistrict of Columbia
- Department of Biochemistry and Molecular and Cellular BiologyGeorgetown University Medical CenterWashingtonDistrict of Columbia
| | | | - Albert J. Fornace
- Department of Oncology, Lombardi Comprehensive Cancer CenterGeorgetown University Medical CenterWashingtonDistrict of Columbia
- Department of Biochemistry and Molecular and Cellular BiologyGeorgetown University Medical CenterWashingtonDistrict of Columbia
| | - Jiri Aubrecht
- Takeda Pharmaceuticals USA Inc.CambridgeMassachusetts
| | - Carole L. Yauk
- Environmental Health Science and Research BureauHealth CanadaOttawaOntarioCanada
- Department of BiologyCarleton UniversityOttawaOntarioCanada
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Li HH, Chen R, Hyduke DR, Williams A, Frötschl R, Ellinger-Ziegelbauer H, O'Lone R, Yauk CL, Aubrecht J, Fornace AJ Jr. Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs. Proc Natl Acad Sci U S A 2017; 114:E10881-9. [PMID: 29203651 DOI: 10.1073/pnas.1714109114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Standard in vitro assays to assess genotoxicity frequently generate positive results that are subsequently found to be irrelevant for in vivo carcinogenesis and human cancer risk assessment. Currently used follow-up methods, such as animal testing, are expensive and time-consuming, and the development of approaches enabling more accurate mechanism-based risk assessment is essential. We developed an in vitro transcriptomic biomarker-based approach that provides a robust biomarker reflecting stress-signaling responses. The biomarker correctly identifies the vast majority of irrelevant genotoxicity results from in vitro chromosome damage assays. TGx-DDI, a multigene biomarker for DNA damage-inducing agents, is the first biomarker that not only shows convincing interlaboratory and intralaboratory reproducibility, but also performs accurately in a system suitable for high-throughput screening. Interpretation of positive genotoxicity findings using the current in vitro testing battery is a major challenge to industry and regulatory agencies. These tests, especially mammalian cell assays, have high sensitivity but suffer from low specificity, leading to high rates of irrelevant positive findings (i.e., positive results in vitro that are not relevant to human cancer hazard). We developed an in vitro transcriptomic biomarker-based approach that provides biological relevance to positive genotoxicity assay data, particularly for in vitro chromosome damage assays, and propose its application for assessing the relevance of the in vitro positive results to carcinogenic hazard. The transcriptomic biomarker TGx-DDI (previously known as TGx-28.65) readily distinguishes DNA damage-inducing (DDI) agents from non-DDI agents. In this study, we demonstrated the ability of the biomarker to classify 45 test agents across a broad set of chemical classes as DDI or non-DDI. Furthermore, we assessed the biomarker’s utility in derisking known irrelevant positive agents and evaluated its performance across analytical platforms. We correctly classified 90% (9 of 10) of chemicals with irrelevant positive findings in in vitro chromosome damage assays as negative. We developed a standardized experimental and analytical protocol for our transcriptomics biomarker, as well as an enhanced application of TGx-DDI for high-throughput cell-based genotoxicity testing using nCounter technology. This biomarker can be integrated in genetic hazard assessment as a follow-up to positive chromosome damage findings. In addition, we propose how it might be used in chemical screening and assessment. This approach offers an opportunity to significantly improve risk assessment and reduce cost.
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