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Berrington de González A, Masten SA, Bhatti P, Fortner RT, Peters S, Santonen T, Yakubovskaya MG, Barouki R, Barros SBM, Barupal D, Beane Freeman LE, Calaf GM, Dillner J, El Rhazi K, Fritschi L, Fukushima S, Godderis L, Kogevinas M, Lachenmeier DW, Mandrioli D, Muchengeti MM, Niemeier RT, Pappas JJ, Pi J, Purdue MP, Riboli E, Rodríguez T, Schlünssen V, Benbrahim-Tallaa L, de Conti A, Facchin C, Pasqual E, Wedekind R, Ahmadi A, Chittiboyina S, Herceg Z, Kulasingam S, Lauby-Secretan B, MacLehose R, Sanaa M, Schüz J, Suonio E, Zavadil J, Mattock H, Madia F, Schubauer-Berigan MK. Advisory Group recommendations on priorities for the IARC Monographs. Lancet Oncol 2024; 25:546-548. [PMID: 38621402 DOI: 10.1016/s1470-2045(24)00208-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Affiliation(s)
| | - Scott A Masten
- International Agency for Research on Cancer, Lyon, France
| | - Parveen Bhatti
- International Agency for Research on Cancer, Lyon, France
| | | | - Susan Peters
- International Agency for Research on Cancer, Lyon, France
| | - Tiina Santonen
- International Agency for Research on Cancer, Lyon, France
| | | | - Robert Barouki
- International Agency for Research on Cancer, Lyon, France
| | | | - Dinesh Barupal
- International Agency for Research on Cancer, Lyon, France
| | | | - Gloria M Calaf
- International Agency for Research on Cancer, Lyon, France
| | - Joakim Dillner
- International Agency for Research on Cancer, Lyon, France
| | | | - Lin Fritschi
- International Agency for Research on Cancer, Lyon, France
| | | | - Lode Godderis
- International Agency for Research on Cancer, Lyon, France
| | | | | | | | | | | | - Jane J Pappas
- International Agency for Research on Cancer, Lyon, France
| | - Jingbo Pi
- International Agency for Research on Cancer, Lyon, France
| | - Mark P Purdue
- International Agency for Research on Cancer, Lyon, France
| | - Elio Riboli
- International Agency for Research on Cancer, Lyon, France
| | | | | | | | - Aline de Conti
- International Agency for Research on Cancer, Lyon, France
| | | | - Elisa Pasqual
- International Agency for Research on Cancer, Lyon, France
| | | | - Ayat Ahmadi
- International Agency for Research on Cancer, Lyon, France
| | | | - Zdenko Herceg
- International Agency for Research on Cancer, Lyon, France
| | | | | | | | - Moez Sanaa
- International Agency for Research on Cancer, Lyon, France
| | - Joachim Schüz
- International Agency for Research on Cancer, Lyon, France
| | - Eero Suonio
- International Agency for Research on Cancer, Lyon, France
| | - Jiri Zavadil
- International Agency for Research on Cancer, Lyon, France
| | - Heidi Mattock
- International Agency for Research on Cancer, Lyon, France
| | - Federica Madia
- International Agency for Research on Cancer, Lyon, France
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2
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Habiballah S, Heath LS, Reisfeld B. A deep-learning approach for identifying prospective chemical hazards. Toxicology 2024; 501:153708. [PMID: 38104655 DOI: 10.1016/j.tox.2023.153708] [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: 10/18/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
With the aim of helping to set safe exposure limits for the general population, various techniques have been implemented to conduct risk assessments for chemicals and other environmental stressors; however, none of these tools facilitate the identification of completely new chemicals that are likely hazardous and elicit an adverse biological effect. Here, we detail a novel in silico, deep-learning framework that is designed to systematically generate structures for new chemical compounds that are predicted to be chemical hazards. To assess the utility of the framework, we applied the tool to four endpoints related to environmental toxicants and their impacts on human and animal health: (i) toxicity to honeybees, (ii) immunotoxicity, (iii) endocrine disruption via ER-α antagonism, and (iv) mutagenicity. In addition, we characterized the predicted potency of these compounds and examined their structural relationship to existing chemicals of concern. As part of the array of emerging new approach methodologies (NAMs), we anticipate that such a framework will be a significant asset to risk assessors and other environmental scientists when planning and forecasting. Though not in the scope of the present study, we expect that the methodology detailed here could also be useful in the de novo design of more environmentally-friendly industrial chemicals.
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Affiliation(s)
- Sohaib Habiballah
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1370, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061-0106, USA
| | - Brad Reisfeld
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1370, USA; Colorado School of Public Health, Colorado State University, Fort Collins, CO 80523-1612, USA.
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3
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Turner MC, Cogliano V, Guyton K, Madia F, Straif K, Ward EM, Schubauer-Berigan MK. Research Recommendations for Selected IARC-Classified Agents: Impact and Lessons Learned. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:105001. [PMID: 37902675 PMCID: PMC10615125 DOI: 10.1289/ehp12547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/31/2023]
Abstract
BACKGROUND The International Agency for Research on Cancer (IARC) Monographs program assembles expert working groups who publish a critical review and evaluation of data on agents of interest. These comprehensive reviews provide a unique opportunity to identify research needs to address classification uncertainties. A multidisciplinary expert review and workshop held in 2009 identified research gaps and needs for 20 priority occupational chemicals, metals, dusts, and physical agents, with the goal of stimulating advances in epidemiological studies of cancer and carcinogen mechanisms. Overarching issues were also described. OBJECTIVES In this commentary we review the current status of the evidence for the 20 priority agents identified in 2009. We examine whether identified Research Recommendations for each agent were addressed and their potential impact on resolving classification uncertainties. METHODS We reviewed the IARC classifications of each of the 20 priority agents and identified major new epidemiological and human mechanistic studies published since the last evaluation. Information sources were either the published Monograph for agents that have been reevaluated or, for agents not yet reevaluated, Advisory Group reports and literature searches. Findings are described in view of recent methodological developments in Monographs evidence evaluation processes. DISCUSSION The majority of the 20 priority agents were reevaluated by IARC since 2009. The overall carcinogen classifications of 9 agents advanced, and new cancer sites with either "sufficient" or "limited" evidence of carcinogenicity were also identified for 9 agents. Examination of published findings revealed whether evidence gaps and Research Recommendations have been addressed and highlighted remaining uncertainties. During the past decade, new research addressed a range of the 2009 recommendations and supported updated classifications for priority agents. This supports future efforts to systematically apply findings of Monograph reviews to identify research gaps and priorities relevant to evaluation criteria established in the updated IARC Monograph Preamble. https://doi.org/10.1289/EHP12547.
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Affiliation(s)
- Michelle C. Turner
- Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Vincent Cogliano
- California Environmental Protection Agency Office of Environmental Health Hazard Assessment, Oakland, California, USA
| | - Kathryn Guyton
- National Academies of Sciences, Engineering, and Medicine, Washington, District of Columbia, USA
| | - Federica Madia
- International Agency for Research on Cancer, Lyon, France
| | - Kurt Straif
- Barcelona Institute for Global Health, Barcelona, Spain
- Boston College, Massachusetts, USA
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4
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Borghoff SJ, Cohen SS, Jiang X, Lea IA, Klaren WD, Chappell GA, Britt JK, Rivera BN, Choski NY, Wikoff DS. Updated systematic assessment of human, animal and mechanistic evidence demonstrates lack of human carcinogenicity with consumption of aspartame. Food Chem Toxicol 2023; 172:113549. [PMID: 36493943 DOI: 10.1016/j.fct.2022.113549] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
Aspartame has been studied extensively and evaluated for its safety in foods and beverages yet concerns for its potential carcinogenicity have persisted, driven primarily by animal studies conducted at the Ramazzini Institute (RI). To address this controversy, an updated systematic review of available human, animal, and mechanistic data was conducted leveraging critical assessment tools to consider the quality and reliability of data. The evidence base includes 12 animal studies and >40 epidemiological studies reviewed by the World Health Organization which collectively demonstrate a lack of carcinogenic effect. Assessment of >1360 mechanistic endpoints, including many guideline-based genotoxicity studies, demonstrate a lack of activity associated with endpoints grouped to key characteristics of carcinogens. Other non-specific mechanistic data (e.g., mixed findings of oxidative stress across study models, tissues, and species) do not provide evidence of a biologically plausible carcinogenic pathway associated with aspartame. Taken together, available evidence supports that aspartame consumption is not carcinogenic in humans and that the inconsistent findings of the RI studies may be explained by flaws in study design and conduct (despite additional analyses to address study limitations), as acknowledged by authoritative bodies.
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Affiliation(s)
| | - Sarah S Cohen
- EpidStrategies, A Division of ToxStrategies, RTP, NC, USA
| | - Xiaohui Jiang
- EpidStrategies, A Division of ToxStrategies, RTP, NC, USA
| | - Isabel A Lea
- ToxStrategies, Inc., Research Triangle Park, NC, USA
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Zhang X, Felter SP, Api AM, Joshi K, Selechnik D. A Cautionary tale for using read-across for cancer hazard classification: Case study of isoeugenol and methyl eugenol. Regul Toxicol Pharmacol 2022; 136:105280. [DOI: 10.1016/j.yrtph.2022.105280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/16/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
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A Narrative Literature Review of Natural Language Processing Applied to the Occupational Exposome. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19148544. [PMID: 35886395 PMCID: PMC9316260 DOI: 10.3390/ijerph19148544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023]
Abstract
The evolution of the Exposome concept revolutionised the research in exposure assessment and epidemiology by introducing the need for a more holistic approach on the exploration of the relationship between the environment and disease. At the same time, further and more dramatic changes have also occurred on the working environment, adding to the already existing dynamic nature of it. Natural Language Processing (NLP) refers to a collection of methods for identifying, reading, extracting and untimely transforming large collections of language. In this work, we aim to give an overview of how NLP has successfully been applied thus far in Exposome research. Methods: We conduct a literature search on PubMed, Scopus and Web of Science for scientific articles published between 2011 and 2021. We use both quantitative and qualitative methods to screen papers and provide insights into the inclusion and exclusion criteria. We outline our approach for article selection and provide an overview of our findings. This is followed by a more detailed insight into selected articles. Results: Overall, 6420 articles were screened for the suitability of this review, where we review 37 articles in depth. Finally, we discuss future avenues of research and outline challenges in existing work. Conclusions: Our results show that (i) there has been an increase in articles published that focus on applying NLP to exposure and epidemiology research, (ii) most work uses existing NLP tools and (iii) traditional machine learning is the most popular approach.
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Barupal DK, Mahajan P, Fakouri-Baygi S, Wright RO, Arora M, Teitelbaum SL. CCDB: A database for exploring inter-chemical correlations in metabolomics and exposomics datasets. ENVIRONMENT INTERNATIONAL 2022; 164:107240. [PMID: 35461097 PMCID: PMC9195052 DOI: 10.1016/j.envint.2022.107240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 05/18/2023]
Abstract
Inter-chemical correlations in metabolomics and exposomics datasets provide valuable information for studying relationships among chemicals reported for human specimens. With an increase in the number of compounds for these datasets, a network graph analysis and visualization of the correlation structure is difficult to interpret. We have developed the Chemical Correlation Database (CCDB), as a systematic catalogue of inter-chemical correlation in publicly available metabolomics and exposomics studies. The database has been provided via an online interface to create single compound-centric views. We have demonstrated various applications of the database to explore: 1) the chemicals from a chemical class such as Per- and Polyfluoroalkyl Substances (PFAS), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), phthalates and tobacco smoke related metabolites; 2) xenobiotic metabolites such as caffeine and acetaminophen; 3) endogenous metabolites (acyl-carnitines); and 4) unannotated peaks for PFAS. The database has a rich collection of 35 human studies, including the National Health and Nutrition Examination Survey (NHANES) and high-quality untargeted metabolomics datasets. CCDB is supported by a simple, interactive and user-friendly web-interface to retrieve and visualize the inter-chemical correlation data. The CCDB has the potential to be a key computational resource in metabolomics and exposomics facilitating the expansion of our understanding about biological and chemical relationships among metabolites and chemical exposures in the human body. The database is available at www.ccdb.idsl.me site.
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Affiliation(s)
- Dinesh Kumar Barupal
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA.
| | - Priyanka Mahajan
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Sadjad Fakouri-Baygi
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Robert O Wright
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Manish Arora
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Susan L Teitelbaum
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
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Scholten B, Simón LG, Krishnan S, Vermeulen R, Pronk A, Gyori BM, Bachman JA, Vlaanderen J, Stierum R. Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:37002. [PMID: 35238605 PMCID: PMC8893280 DOI: 10.1289/ehp9112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 12/23/2021] [Accepted: 02/15/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Mechanistic data is increasingly used in hazard identification of chemicals. However, the volume of data is large, challenging the efficient identification and clustering of relevant data. OBJECTIVES We investigated whether evidence identification for hazard assessment can become more efficient and informed through an automated approach that combines machine reading of publications with network visualization tools. METHODS We chose 13 chemicals that were evaluated by the International Agency for Research on Cancer (IARC) Monographs program incorporating the key characteristics of carcinogens (KCCs) approach. Using established literature search terms for KCCs, we retrieved and analyzed literature using Integrated Network and Dynamical Reasoning Assembler (INDRA). INDRA combines large-scale literature processing with pathway databases and extracts relationships between biomolecules, bioprocesses, and chemicals into statements (e.g., "benzene activates DNA damage"). These statements were subsequently assembled into networks and compared with the KCC evaluation by the IARC, to evaluate the informativeness of our approach. RESULTS We found, in general, larger networks for those chemicals which the IARC has evaluated the evidence to be strong for KCC induction. Larger networks were not directly linked to publication count, given that we retrieved small networks for several chemicals with little support for KCC activation according to the IARC, despite the significant volume of literature for these specific chemicals. In addition, interpreting networks for genotoxicity and DNA repair showed concordance with the IARC KCC evaluation. DISCUSSION Our method is an automated approach to condense mechanistic literature into searchable and interpretable networks based on an a priori ontology. The approach is no replacement of expert evaluation but, instead, provides an informed structure for experts to quickly identify which statements are made in which papers and how these could connect. We focused on the KCCs because these are supported by well-described search terms. The method needs to be tested in other frameworks as well to demonstrate its generalizability. https://doi.org/10.1289/EHP9112.
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Affiliation(s)
- Bernice Scholten
- Research Group Risk Analysis for Products in Development, The Netherlands Organisation for applied scientific research, Utrecht, Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Laura Guerrero Simón
- Research Group Risk Analysis for Products in Development, The Netherlands Organisation for applied scientific research, Utrecht, Netherlands
| | - Shaji Krishnan
- Research Group Risk Analysis for Products in Development, The Netherlands Organisation for applied scientific research, Utrecht, Netherlands
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Anjoeka Pronk
- Research Group Risk Analysis for Products in Development, The Netherlands Organisation for applied scientific research, Utrecht, Netherlands
| | - Benjamin M. Gyori
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - John A. Bachman
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jelle Vlaanderen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Rob Stierum
- Research Group Risk Analysis for Products in Development, The Netherlands Organisation for applied scientific research, Utrecht, Netherlands
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9
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Margarit DH, González NS, Romanelli LM, Fendrik AJ, Scagliotti AF, Reale MV. An integrative model of cancer cell differentiation with immunotherapy . Phys Biol 2021; 18. [PMID: 34633296 DOI: 10.1088/1478-3975/ac2e72] [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: 05/24/2021] [Accepted: 10/11/2021] [Indexed: 11/11/2022]
Abstract
In order to improve cancer treatments, cancer cell differentiation and immunotherapy are the subjects of several studies in different branches of interdisciplinary sciences. In this work, we develop a new population model that integrates other complementary ones, thus emphasizing the relationship between cancer cells at different differentiation stages and the main immune system cells. For this new system, specific ranges were found where transdifferentiation of differentiated cancer cells can occur. In addition, a specific therapy against cancer stem cells was analysed by simulating cytotoxic cell vaccines. In reference to the latter, the different combinations of parameters that optimize it were studied.
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Affiliation(s)
- David H Margarit
- Instituto de Ciencias, Universidad Nacional de General Sarmiento (UNGS), J M Gutiérrez 1150, Los Polvorines (B1613), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Nadia S González
- Instituto de Ciencias, Universidad Nacional de General Sarmiento (UNGS), J M Gutiérrez 1150, Los Polvorines (B1613), Buenos Aires, Argentina
| | - Lilia M Romanelli
- Instituto de Ciencias, Universidad Nacional de General Sarmiento (UNGS), J M Gutiérrez 1150, Los Polvorines (B1613), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Alejandro J Fendrik
- Instituto de Ciencias, Universidad Nacional de General Sarmiento (UNGS), J M Gutiérrez 1150, Los Polvorines (B1613), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Ariel F Scagliotti
- Instituto de Ciencias, Universidad Nacional de General Sarmiento (UNGS), J M Gutiérrez 1150, Los Polvorines (B1613), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Marcela V Reale
- Instituto de Ciencias, Universidad Nacional de General Sarmiento (UNGS), J M Gutiérrez 1150, Los Polvorines (B1613), Buenos Aires, Argentina.,Departamento de Ingeniería e Investigaciones Tecnológicas, Universidad Nacional de La Matanza (UNLaM), Florencio Varela 1903, San Justo (B1754), Buenos Aires, Argentina
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