1
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Valko M, Leibfritz D, Moncol J, Cronin MTD, Mazur M, Telser J. Free radicals and antioxidants in normal physiological functions and human disease. Int J Biochem Cell Biol 2006; 39:44-84. [PMID: 16978905 DOI: 10.1016/j.biocel.2006.07.001] [Citation(s) in RCA: 8858] [Impact Index Per Article: 466.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 05/27/2006] [Accepted: 07/05/2006] [Indexed: 11/19/2022]
Abstract
Reactive oxygen species (ROS) and reactive nitrogen species (RNS, e.g. nitric oxide, NO(*)) are well recognised for playing a dual role as both deleterious and beneficial species. ROS and RNS are normally generated by tightly regulated enzymes, such as NO synthase (NOS) and NAD(P)H oxidase isoforms, respectively. Overproduction of ROS (arising either from mitochondrial electron-transport chain or excessive stimulation of NAD(P)H) results in oxidative stress, a deleterious process that can be an important mediator of damage to cell structures, including lipids and membranes, proteins, and DNA. In contrast, beneficial effects of ROS/RNS (e.g. superoxide radical and nitric oxide) occur at low/moderate concentrations and involve physiological roles in cellular responses to noxia, as for example in defence against infectious agents, in the function of a number of cellular signalling pathways, and the induction of a mitogenic response. Ironically, various ROS-mediated actions in fact protect cells against ROS-induced oxidative stress and re-establish or maintain "redox balance" termed also "redox homeostasis". The "two-faced" character of ROS is clearly substantiated. For example, a growing body of evidence shows that ROS within cells act as secondary messengers in intracellular signalling cascades which induce and maintain the oncogenic phenotype of cancer cells, however, ROS can also induce cellular senescence and apoptosis and can therefore function as anti-tumourigenic species. This review will describe the: (i) chemistry and biochemistry of ROS/RNS and sources of free radical generation; (ii) damage to DNA, to proteins, and to lipids by free radicals; (iii) role of antioxidants (e.g. glutathione) in the maintenance of cellular "redox homeostasis"; (iv) overview of ROS-induced signaling pathways; (v) role of ROS in redox regulation of normal physiological functions, as well as (vi) role of ROS in pathophysiological implications of altered redox regulation (human diseases and ageing). Attention is focussed on the ROS/RNS-linked pathogenesis of cancer, cardiovascular disease, atherosclerosis, hypertension, ischemia/reperfusion injury, diabetes mellitus, neurodegenerative diseases (Alzheimer's disease and Parkinson's disease), rheumatoid arthritis, and ageing. Topics of current debate are also reviewed such as the question whether excessive formation of free radicals is a primary cause or a downstream consequence of tissue injury.
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8858 |
2
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Abstract
Metal-induced toxicity and carcinogenicity, with an emphasis on the generation and role of reactive oxygen and nitrogen species, is reviewed. Metal-mediated formation of free radicals causes various modifications to DNA bases, enhanced lipid peroxidation, and altered calcium and sulfhydryl homeostasis. Lipid peroxides, formed by the attack of radicals on polyunsaturated fatty acid residues of phospholipids, can further react with redox metals finally producing mutagenic and carcinogenic malondialdehyde, 4-hydroxynonenal and other exocyclic DNA adducts (etheno and/or propano adducts). Whilst iron (Fe), copper (Cu), chromium (Cr), vanadium (V) and cobalt (Co) undergo redox-cycling reactions, for a second group of metals, mercury (Hg), cadmium (Cd) and nickel (Ni), the primary route for their toxicity is depletion of glutathione and bonding to sulfhydryl groups of proteins. Arsenic (As) is thought to bind directly to critical thiols, however, other mechanisms, involving formation of hydrogen peroxide under physiological conditions, have been proposed. The unifying factor in determining toxicity and carcinogenicity for all these metals is the generation of reactive oxygen and nitrogen species. Common mechanisms involving the Fenton reaction, generation of the superoxide radical and the hydroxyl radical appear to be involved for iron, copper, chromium, vanadium and cobalt primarily associated with mitochondria, microsomes and peroxisomes. However, a recent discovery that the upper limit of "free pools" of copper is far less than a single atom per cell casts serious doubt on the in vivo role of copper in Fenton-like generation of free radicals. Nitric oxide (NO) seems to be involved in arsenite-induced DNA damage and pyrimidine excision inhibition. Various studies have confirmed that metals activate signalling pathways and the carcinogenic effect of metals has been related to activation of mainly redox-sensitive transcription factors, involving NF-kappaB, AP-1 and p53. Antioxidants (both enzymatic and non-enzymatic) provide protection against deleterious metal-mediated free radical attacks. Vitamin E and melatonin can prevent the majority of metal-mediated (iron, copper, cadmium) damage both in vitro systems and in metal-loaded animals. Toxicity studies involving chromium have shown that the protective effect of vitamin E against lipid peroxidation may be associated rather with the level of non-enzymatic antioxidants than the activity of enzymatic antioxidants. However, a very recent epidemiological study has shown that a daily intake of vitamin E of more than 400 IU increases the risk of death and should be avoided. While previous studies have proposed a deleterious pro-oxidant effect of vitamin C (ascorbate) in the presence of iron (or copper), recent results have shown that even in the presence of redox-active iron (or copper) and hydrogen peroxide, ascorbate acts as an antioxidant that prevents lipid peroxidation and does not promote protein oxidation in humans in vitro. Experimental results have also shown a link between vanadium and oxidative stress in the etiology of diabetes. The impact of zinc (Zn) on the immune system, the ability of zinc to act as an antioxidant in order to reduce oxidative stress and the neuroprotective and neurodegenerative role of zinc (and copper) in the etiology of Alzheimer's disease is also discussed. This review summarizes recent findings in the metal-induced formation of free radicals and the role of oxidative stress in the carcinogenicity and toxicity of metals.
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Review |
20 |
3236 |
3
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Cherkasov A, Muratov EN, Fourches D, Varnek A, Baskin II, Cronin M, Dearden J, Gramatica P, Martin YC, Todeschini R, Consonni V, Kuz'min VE, Cramer R, Benigni R, Yang C, Rathman J, Terfloth L, Gasteiger J, Richard A, Tropsha A. QSAR modeling: where have you been? Where are you going to? J Med Chem 2014; 57:4977-5010. [PMID: 24351051 PMCID: PMC4074254 DOI: 10.1021/jm4004285] [Citation(s) in RCA: 1124] [Impact Index Per Article: 102.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Quantitative structure-activity relationship modeling is one of the major computational tools employed in medicinal chemistry. However, throughout its entire history it has drawn both praise and criticism concerning its reliability, limitations, successes, and failures. In this paper, we discuss (i) the development and evolution of QSAR; (ii) the current trends, unsolved problems, and pressing challenges; and (iii) several novel and emerging applications of QSAR modeling. Throughout this discussion, we provide guidelines for QSAR development, validation, and application, which are summarized in best practices for building rigorously validated and externally predictive QSAR models. We hope that this Perspective will help communications between computational and experimental chemists toward collaborative development and use of QSAR models. We also believe that the guidelines presented here will help journal editors and reviewers apply more stringent scientific standards to manuscripts reporting new QSAR studies, as well as encourage the use of high quality, validated QSARs for regulatory decision making.
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Historical Article |
11 |
1124 |
4
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Eriksson L, Jaworska J, Worth AP, Cronin MTD, McDowell RM, Gramatica P. Methods for reliability and uncertainty assessment and for applicability evaluations of classification- and regression-based QSARs. ENVIRONMENTAL HEALTH PERSPECTIVES 2003; 111:1361-75. [PMID: 12896860 PMCID: PMC1241620 DOI: 10.1289/ehp.5758] [Citation(s) in RCA: 860] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This article provides an overview of methods for reliability assessment of quantitative structure-activity relationship (QSAR) models in the context of regulatory acceptance of human health and environmental QSARs. Useful diagnostic tools and data analytical approaches are highlighted and exemplified. Particular emphasis is given to the question of how to define the applicability borders of a QSAR and how to estimate parameter and prediction uncertainty. The article ends with a discussion regarding QSAR acceptability criteria. This discussion contains a list of recommended acceptability criteria, and we give reference values for important QSAR performance statistics. Finally, we emphasize that rigorous and independent validation of QSARs is an essential step toward their regulatory acceptance and implementation.
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Review |
22 |
860 |
5
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Netzeva TI, Worth A, Aldenberg T, Benigni R, Cronin MTD, Gramatica P, Jaworska JS, Kahn S, Klopman G, Marchant CA, Myatt G, Nikolova-Jeliazkova N, Patlewicz GY, Perkins R, Roberts D, Schultz T, Stanton DW, van de Sandt JJM, Tong W, Veith G, Yang C. Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships. The report and recommendations of ECVAM Workshop 52. Altern Lab Anim 2005; 33:155-73. [PMID: 16180989 DOI: 10.1177/026119290503300209] [Citation(s) in RCA: 446] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Multicenter Study |
20 |
446 |
6
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Adler S, Basketter D, Creton S, Pelkonen O, van Benthem J, Zuang V, Andersen KE, Angers-Loustau A, Aptula A, Bal-Price A, Benfenati E, Bernauer U, Bessems J, Bois FY, Boobis A, Brandon E, Bremer S, Broschard T, Casati S, Coecke S, Corvi R, Cronin M, Daston G, Dekant W, Felter S, Grignard E, Gundert-Remy U, Heinonen T, Kimber I, Kleinjans J, Komulainen H, Kreiling R, Kreysa J, Leite SB, Loizou G, Maxwell G, Mazzatorta P, Munn S, Pfuhler S, Phrakonkham P, Piersma A, Poth A, Prieto P, Repetto G, Rogiers V, Schoeters G, Schwarz M, Serafimova R, Tähti H, Testai E, van Delft J, van Loveren H, Vinken M, Worth A, Zaldivar JM. Alternative (non-animal) methods for cosmetics testing: current status and future prospects-2010. Arch Toxicol 2011; 85:367-485. [PMID: 21533817 DOI: 10.1007/s00204-011-0693-2] [Citation(s) in RCA: 371] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 03/03/2011] [Indexed: 01/09/2023]
Abstract
The 7th amendment to the EU Cosmetics Directive prohibits to put animal-tested cosmetics on the market in Europe after 2013. In that context, the European Commission invited stakeholder bodies (industry, non-governmental organisations, EU Member States, and the Commission's Scientific Committee on Consumer Safety) to identify scientific experts in five toxicological areas, i.e. toxicokinetics, repeated dose toxicity, carcinogenicity, skin sensitisation, and reproductive toxicity for which the Directive foresees that the 2013 deadline could be further extended in case alternative and validated methods would not be available in time. The selected experts were asked to analyse the status and prospects of alternative methods and to provide a scientifically sound estimate of the time necessary to achieve full replacement of animal testing. In summary, the experts confirmed that it will take at least another 7-9 years for the replacement of the current in vivo animal tests used for the safety assessment of cosmetic ingredients for skin sensitisation. However, the experts were also of the opinion that alternative methods may be able to give hazard information, i.e. to differentiate between sensitisers and non-sensitisers, ahead of 2017. This would, however, not provide the complete picture of what is a safe exposure because the relative potency of a sensitiser would not be known. For toxicokinetics, the timeframe was 5-7 years to develop the models still lacking to predict lung absorption and renal/biliary excretion, and even longer to integrate the methods to fully replace the animal toxicokinetic models. For the systemic toxicological endpoints of repeated dose toxicity, carcinogenicity and reproductive toxicity, the time horizon for full replacement could not be estimated.
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Review |
14 |
371 |
7
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Dearden JC, Cronin MTD, Kaiser KLE. How not to develop a quantitative structure-activity or structure-property relationship (QSAR/QSPR). SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2009; 20:241-66. [PMID: 19544191 DOI: 10.1080/10629360902949567] [Citation(s) in RCA: 295] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Although thousands of quantitative structure-activity and structure-property relationships (QSARs/QSPRs) have been published, as well as numerous papers on the correct procedures for QSAR/QSPR analysis, many analyses are still carried out incorrectly, or in a less than satisfactory manner. We have identified 21 types of error that continue to be perpetrated in the QSAR/QSPR literature, and each of these is discussed, with examples (including some of our own). Where appropriate, we make recommendations for avoiding errors and for improving and enhancing QSAR/QSPR analyses.
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Review |
16 |
295 |
8
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Gupta P, Mellors J, Kingsley L, Riddler S, Singh MK, Schreiber S, Cronin M, Rinaldo CR. High viral load in semen of human immunodeficiency virus type 1-infected men at all stages of disease and its reduction by therapy with protease and nonnucleoside reverse transcriptase inhibitors. J Virol 1997; 71:6271-5. [PMID: 9223532 PMCID: PMC191898 DOI: 10.1128/jvi.71.8.6271-6275.1997] [Citation(s) in RCA: 176] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Seminal viral load is likely to be directly related to the sexual transmissibility of human immunodeficiency virus type 1 (HIV-1). However, it is not clear whether the level of HIV-1 in semen varies with the stage of infection and whether antiretroviral therapy reduces seminal viral load. A nucleic acid sequence-based amplification (NASBA) technique was used to quantify HIV-1 RNA as an indicator of infectious viral load in semen and blood plasma of homosexual men with different stages and durations of HIV-1 infection. The median viral load in a cross section of 34 men was 11,000 HIV-1 RNA copies/ml (range, <400 to 1.3 x 10(7) copies/ml) in whole semen and 5,238 HIV-1 RNA copies/ml (range, <400 to 2.8 x 10(5) copies/ml) in seminal plasma, which is 10- to 1,000-fold higher than previous estimates. Viral loads in whole semen and seminal plasma were strongly correlated with blood plasma viral load (P < 0.001) but not with blood CD4+ T-cell count (P = 0.420). Longitudinal analysis of eight subjects who progressed to AIDS showed that seminal viral load increased in most cases, with viral load consistently higher in blood plasma than in semen. Viral loads in semen and blood plasma decreased markedly in six other patients following initiation of potent combination therapy with a protease inhibitor (indinavir) and a nonnucleoside reverse transcriptase inhibitor (DMP-266). These findings have important implications for the biology of sexual transmission of HIV-1 and its potential reduction by antiretroviral therapy.
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research-article |
28 |
176 |
9
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Clark R, Olson K, Fuh G, Marian M, Mortensen D, Teshima G, Chang S, Chu H, Mukku V, Canova-Davis E, Somers T, Cronin M, Winkler M, Wells JA. Long-acting growth hormones produced by conjugation with polyethylene glycol. J Biol Chem 1996; 271:21969-77. [PMID: 8703002 DOI: 10.1074/jbc.271.36.21969] [Citation(s) in RCA: 173] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Derivatives of human growth hormone (hGH) of increasing size were produced by reaction with the N-hydroxysuccinimide ester of polyethylene glycol-5000 (PEG5000), a 5-kDa reagent that selectively conjugates to primary amines. By adjusting the reaction conditions and purification procedure, it was possible to isolate hGH derivatives containing up to seven PEG moieties that altered the Stokes radius and thereby the effective molecular masses of the unmodified hormone from 22 to 300 kDa. Fortunately, the most reactive amines were ones that did not lie in either of the two sites important for receptor binding. Nonetheless, increasing the level of PEG modification linearly reduced the affinity of hGH for its receptor and increased the EC50 in a cell-based assay up to 1500-fold. Most of the reduction in affinity was the result of slowing the association rate for the receptor. The clearance rate of hGH in rats was inversely proportional to effective molecular weight and closely fit a filtration model. We have tested the potency of these analogs by injecting them daily or every 6 days into hypophysectomized rats and determining the effects on body and organ growth. The efficacy of these analogs was optimal for hGH conjugated with 5 eq of PEG5000, and the potency was increased by about 10-fold compared with unmodified hGH. Such PEG-hGH derivatives show promise as long-acting alternatives to daily injections of hGH. More generally these studies show that improving hormone clearance properties, even at the expense of reducing receptor binding affinity, can lead to dramatic increases in hormone efficacy.
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Comparative Study |
29 |
173 |
10
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Moss GP, Dearden JC, Patel H, Cronin MTD. Quantitative structure-permeability relationships (QSPRs) for percutaneous absorption. Toxicol In Vitro 2002; 16:299-317. [PMID: 12020604 DOI: 10.1016/s0887-2333(02)00003-6] [Citation(s) in RCA: 167] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Quantitative structure-permeability relationships (QSPRs) have been derived by many researchers to model the passive, diffusion-controlled, percutaneous penetration of exogenous chemicals. Most of these relationships are based on experimental data from the published literature. They indicate that molecular size (as molecular weight) and hydrophobicity (as the logarithm of the octanol-water partition coefficient; log k(ow)) are the main determinants of transdermal penetration. This article reviews the current state of the art in QSPRs for absorption of chemicals through the skin, and where this technology can be exploited in future research. The main shortfalls in QSPR models result from inconsistency and error of the experimental values used to derive them. This is probably caused by the manner in which they employ data from a variety of sources and, in some cases, slightly different experimental protocols. Further, most current models are based on data generated from either aqueous or ethanolic solution, where each penetrant is present at its saturated solubility or a fraction of its saturated solubility. No models currently account for the influences of formulation upon percutaneous penetration. Current QSPR models provide a significant tool for assessing the percutaneous penetration of chemicals. They may be important in determining the bioavailability of a range of topically applied exogenous chemicals, and in issues of dermal toxicology and risk assessment. However, their current use may be limited by their lack of applicability across different formulation types. As a consequence, their true value may be to make predictions within specific formulation types, as opposed to a general model based on a range of formulation types. In addition, the endpoint of models may be inappropriate for specific applications other than the systemic delivery of topically applied chemicals.
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Review |
23 |
167 |
11
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Chou WH, Yan FX, de Leon J, Barnhill J, Rogers T, Cronin M, Pho M, Xiao V, Ryder TB, Liu WW, Teiling C, Wedlund PJ. Extension of a pilot study: impact from the cytochrome P450 2D6 polymorphism on outcome and costs associated with severe mental illness. J Clin Psychopharmacol 2000; 20:246-51. [PMID: 10770465 DOI: 10.1097/00004714-200004000-00019] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The influence of cytochrome P450 2D6 (CYP2D6) genetic variability was examined in psychiatric inpatients by evaluating adverse drug events (ADEs), hospital stays, and total costs over a 1-year period in an extension of a previously published brief report. One hundred consecutive psychiatric patients from Eastern State Hospital in Lexington, Kentucky, were genotyped for CYP2D6 expression. ADEs were evaluated by a neurologic rating scale, modified Udvalg for Kliniske Undersogelser Side Effect Rating Scale, or chart review. Information on total hospitalization days and total costs were gathered for a 1-year period. Forty-five percent of the patients received medications that were primarily dependent on the CYP2D6 enzyme for their elimination. When the analysis was restricted to just those patients in each group receiving medication heavily dependent on the CYP2D6 enzyme, the following were observed: (1) a trend toward greater numbers of ADEs from medications as one moved from the group with ultrarapid CYP2D6 activity (UM) to the group with absent CYP2D6 activity (PM); (2) the cost of treating patients with extremes in CYP2D6 activity (UM and PM) was on average $4,000 to $6,000 per year greater than the cost of treating patients in the efficient metabolizer (EM) and intermediate metabolizer (IM) groups; and (3) total duration of hospital stay was more pronounced for those in CYP2D6 PM group. Variance of hospital stays and costs calculated from these preliminary data suggests that 1,500 to 2,000 patients must be evaluated over at least a 1-year period to determine whether the CYP2D6 genetic variation significantly alters the duration of hospital stay and costs.
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25 |
164 |
12
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Patel H, ten Berge W, Cronin MTD. Quantitative structure-activity relationships (QSARs) for the prediction of skin permeation of exogenous chemicals. CHEMOSPHERE 2002; 48:603-613. [PMID: 12143935 DOI: 10.1016/s0045-6535(02)00114-5] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Quantitative structure-activity relationships (QSARs) for the skin permeability coefficients of 158 compounds through excised human skin in vitro have been developed. A number of compounds, including hydrocortisone derivatives, were removed from the dataset as reported permeability data for these compounds was considered to be in error. QSARs developed for the dataset with the outliers removed included terms for hydrophobicity, molecular size, and hydrogen bonding. These descriptors provided an excellent fit to the data (r2 = 0.90), are easily calculated from molecular structure, and are mechanistically interpretable. Further analyses of the dataset indicated that good QSARs could be developed utilising hydrophobicity and molecular size alone, with molecular volume and molecular weight providing good quantification of molecular size.
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23 |
159 |
13
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Cronin MTD, Jaworska JS, Walker JD, Comber MHI, Watts CD, Worth AP. Use of QSARs in international decision-making frameworks to predict health effects of chemical substances. ENVIRONMENTAL HEALTH PERSPECTIVES 2003; 111:1391-401. [PMID: 12896862 PMCID: PMC1241622 DOI: 10.1289/ehp.5760] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
This article is a review of the use of quantitative (and qualitative) structure-activity relationships (QSARs and SARs) by regulatory agencies and authorities to predict acute toxicity, mutagenicity, carcinogenicity, and other health effects. A number of SAR and QSAR applications, by regulatory agencies and authorities, are reviewed. These include the use of simple QSAR analyses, as well as the use of multivariate QSARs, and a number of different expert system approaches.
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Review |
22 |
159 |
14
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Drakvik E, Altenburger R, Aoki Y, Backhaus T, Bahadori T, Barouki R, Brack W, Cronin MTD, Demeneix B, Hougaard Bennekou S, van Klaveren J, Kneuer C, Kolossa-Gehring M, Lebret E, Posthuma L, Reiber L, Rider C, Rüegg J, Testa G, van der Burg B, van der Voet H, Warhurst AM, van de Water B, Yamazaki K, Öberg M, Bergman Å. Statement on advancing the assessment of chemical mixtures and their risks for human health and the environment. ENVIRONMENT INTERNATIONAL 2020; 134:105267. [PMID: 31704565 PMCID: PMC6979318 DOI: 10.1016/j.envint.2019.105267] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/01/2019] [Accepted: 10/13/2019] [Indexed: 05/20/2023]
Abstract
The number of anthropogenic chemicals, manufactured, by-products, metabolites and abiotically formed transformation products, counts to hundreds of thousands, at present. Thus, humans and wildlife are exposed to complex mixtures, never one chemical at a time and rarely with only one dominating effect. Hence there is an urgent need to develop strategies on how exposure to multiple hazardous chemicals and the combination of their effects can be assessed. A workshop, "Advancing the Assessment of Chemical Mixtures and their Risks for Human Health and the Environment" was organized in May 2018 together with Joint Research Center in Ispra, EU-funded research projects and Commission Services and relevant EU agencies. This forum for researchers and policy-makers was created to discuss and identify gaps in risk assessment and governance of chemical mixtures as well as to discuss state of the art science and future research needs. Based on the presentations and discussions at this workshop we want to bring forward the following Key Messages.
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Letter |
5 |
155 |
15
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Schwöbel JAH, Koleva YK, Enoch SJ, Bajot F, Hewitt M, Madden JC, Roberts DW, Schultz TW, Cronin MTD. Measurement and Estimation of Electrophilic Reactivity for Predictive Toxicology. Chem Rev 2011; 111:2562-96. [DOI: 10.1021/cr100098n] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14 |
150 |
16
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Brockmeier EK, Hodges G, Hutchinson TH, Butler E, Hecker M, Tollefsen KE, Garcia-Reyero N, Kille P, Becker D, Chipman K, Colbourne J, Collette TW, Cossins A, Cronin M, Graystock P, Gutsell S, Knapen D, Katsiadaki I, Lange A, Marshall S, Owen SF, Perkins EJ, Plaistow S, Schroeder A, Taylor D, Viant M, Ankley G, Falciani F. The Role of Omics in the Application of Adverse Outcome Pathways for Chemical Risk Assessment. Toxicol Sci 2017; 158:252-262. [PMID: 28525648 PMCID: PMC5837273 DOI: 10.1093/toxsci/kfx097] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In conjunction with the second International Environmental Omics Symposium (iEOS) conference, held at the University of Liverpool (United Kingdom) in September 2014, a workshop was held to bring together experts in toxicology and regulatory science from academia, government and industry. The purpose of the workshop was to review the specific roles that high-content omics datasets (eg, transcriptomics, metabolomics, lipidomics, and proteomics) can hold within the adverse outcome pathway (AOP) framework for supporting ecological and human health risk assessments. In light of the growing number of examples of the application of omics data in the context of ecological risk assessment, we considered how omics datasets might continue to support the AOP framework. In particular, the role of omics in identifying potential AOP molecular initiating events and providing supportive evidence of key events at different levels of biological organization and across taxonomic groups was discussed. Areas with potential for short and medium-term breakthroughs were also discussed, such as providing mechanistic evidence to support chemical read-across, providing weight of evidence information for mode of action assignment, understanding biological networks, and developing robust extrapolations of species-sensitivity. Key challenges that need to be addressed were considered, including the need for a cohesive approach towards experimental design, the lack of a mutually agreed framework to quantitatively link genes and pathways to key events, and the need for better interpretation of chemically induced changes at the molecular level. This article was developed to provide an overview of ecological risk assessment process and a perspective on how high content molecular-level datasets can support the future of assessment procedures through the AOP framework.
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Review |
8 |
144 |
17
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Kekow J, Wachsman W, McCutchan JA, Cronin M, Carson DA, Lotz M. Transforming growth factor beta and noncytopathic mechanisms of immunodeficiency in human immunodeficiency virus infection. Proc Natl Acad Sci U S A 1990; 87:8321-5. [PMID: 1700428 PMCID: PMC54947 DOI: 10.1073/pnas.87.21.8321] [Citation(s) in RCA: 136] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
This study examines the contribution of transforming growth factor beta (TGF beta), one of the most potent endogenous immunosuppressive factors, to the development of immunodeficiency in human immunodeficiency virus (HIV) infection. Increased titers of TGF beta were found in supernatants of peripheral blood mononuclear cells (PBMCs) from HIV-infected donors as compared to uninfected controls (P less than 0.001). This correlated closely with defective responses of CD4+ lymphocytes to the recall antigens tuberculin purified protein derivative or tetanus toxoid. The addition of TGF beta-neutralizing antibody to PBMCs partially restored these defective T-cell responses. Furthermore, purified TGF beta or HIV+ PBMC culture supernatants preferentially inhibited proliferation of CD4+ lymphocytes as compared to CD8+ cells. The increased expression of the TGF beta protein was associated with increased TGF beta mRNA as determined by a polymerase chain reaction assay. This increase in TGF beta protein and mRNA was due to a selective upregulation of the TGF beta 1 isoform. These results indicate that overexpression of TGF beta 1 occurs in HIV-infected individuals and that this cytokine can contribute to impaired immune functions and to depletion of CD4+ T lymphocytes.
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research-article |
35 |
136 |
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Myatt GJ, Ahlberg E, Akahori Y, Allen D, Amberg A, Anger LT, Aptula A, Auerbach S, Beilke L, Bellion P, Benigni R, Bercu J, Booth ED, Bower D, Brigo A, Burden N, Cammerer Z, Cronin MTD, Cross KP, Custer L, Dettwiler M, Dobo K, Ford KA, Fortin MC, Gad-McDonald SE, Gellatly N, Gervais V, Glover KP, Glowienke S, Van Gompel J, Gutsell S, Hardy B, Harvey JS, Hillegass J, Honma M, Hsieh JH, Hsu CW, Hughes K, Johnson C, Jolly R, Jones D, Kemper R, Kenyon MO, Kim MT, Kruhlak NL, Kulkarni SA, Kümmerer K, Leavitt P, Majer B, Masten S, Miller S, Moser J, Mumtaz M, Muster W, Neilson L, Oprea TI, Patlewicz G, Paulino A, Lo Piparo E, Powley M, Quigley DP, Reddy MV, Richarz AN, Ruiz P, Schilter B, Serafimova R, Simpson W, Stavitskaya L, Stidl R, Suarez-Rodriguez D, Szabo DT, Teasdale A, Trejo-Martin A, Valentin JP, Vuorinen A, Wall BA, Watts P, White AT, Wichard J, Witt KL, Woolley A, Woolley D, Zwickl C, Hasselgren C. In silico toxicology protocols. Regul Toxicol Pharmacol 2018; 96:1-17. [PMID: 29678766 DOI: 10.1016/j.yrtph.2018.04.014] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 03/16/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022]
Abstract
The present publication surveys several applications of in silico (i.e., computational) toxicology approaches across different industries and institutions. It highlights the need to develop standardized protocols when conducting toxicity-related predictions. This contribution articulates the information needed for protocols to support in silico predictions for major toxicological endpoints of concern (e.g., genetic toxicity, carcinogenicity, acute toxicity, reproductive toxicity, developmental toxicity) across several industries and regulatory bodies. Such novel in silico toxicology (IST) protocols, when fully developed and implemented, will ensure in silico toxicological assessments are performed and evaluated in a consistent, reproducible, and well-documented manner across industries and regulatory bodies to support wider uptake and acceptance of the approaches. The development of IST protocols is an initiative developed through a collaboration among an international consortium to reflect the state-of-the-art in in silico toxicology for hazard identification and characterization. A general outline for describing the development of such protocols is included and it is based on in silico predictions and/or available experimental data for a defined series of relevant toxicological effects or mechanisms. The publication presents a novel approach for determining the reliability of in silico predictions alongside experimental data. In addition, we discuss how to determine the level of confidence in the assessment based on the relevance and reliability of the information.
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Journal Article |
7 |
135 |
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Cronin MTD, Walker JD, Jaworska JS, Comber MHI, Watts CD, Worth AP. Use of QSARs in international decision-making frameworks to predict ecologic effects and environmental fate of chemical substances. ENVIRONMENTAL HEALTH PERSPECTIVES 2003; 111:1376-90. [PMID: 12896861 PMCID: PMC1241621 DOI: 10.1289/ehp.5759] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
This article is a review of the use, by regulatory agencies and authorities, of quantitative structure-activity relationships (QSARs) to predict ecologic effects and environmental fate of chemicals. For many years, the U.S. Environmental Protection Agency has been the most prominent regulatory agency using QSARs to predict the ecologic effects and environmental fate of chemicals. However, as increasing numbers of standard QSAR methods are developed and validated to predict ecologic effects and environmental fate of chemicals, it is anticipated that more regulatory agencies and authorities will find them to be acceptable alternatives to chemical testing.
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Review |
22 |
128 |
20
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Ball N, Cronin MTD, Shen J, Blackburn K, Booth ED, Bouhifd M, Donley E, Egnash L, Hastings C, Juberg DR, Kleensang A, Kleinstreuer N, Kroese ED, Lee AC, Luechtefeld T, Maertens A, Marty S, Naciff JM, Palmer J, Pamies D, Penman M, Richarz AN, Russo DP, Stuard SB, Patlewicz G, van Ravenzwaay B, Wu S, Zhu H, Hartung T. Toward Good Read-Across Practice (GRAP) guidance. ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION 2016; 33:149-66. [PMID: 26863606 PMCID: PMC5581000 DOI: 10.14573/altex.1601251] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/11/2016] [Indexed: 12/04/2022]
Abstract
Grouping of substances and utilizing read-across of data within those groups represents an important data gap filling technique for chemical safety assessments. Categories/analogue groups are typically developed based on structural similarity and, increasingly often, also on mechanistic (biological) similarity. While read-across can play a key role in complying with legislation such as the European REACH regulation, the lack of consensus regarding the extent and type of evidence necessary to support it often hampers its successful application and acceptance by regulatory authorities. Despite a potentially broad user community, expertise is still concentrated across a handful of organizations and individuals. In order to facilitate the effective use of read-across, this document presents the state of the art, summarizes insights learned from reviewing ECHA published decisions regarding the relative successes/pitfalls surrounding read-across under REACH, and compiles the relevant activities and guidance documents. Special emphasis is given to the available existing tools and approaches, an analysis of ECHA's published final decisions associated with all levels of compliance checks and testing proposals, the consideration and expression of uncertainty, the use of biological support data, and the impact of the ECHA Read-Across Assessment Framework (RAAF) published in 2015.
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Research Support, Non-U.S. Gov't |
9 |
125 |
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Walsh FS, Cronin M, Koblar S, Doherty P, Winer J, Leon A, Hughes RA. Association between glycoconjugate antibodies and Campylobacter infection in patients with Guillain-Barré syndrome. J Neuroimmunol 1991; 34:43-51. [PMID: 1894733 DOI: 10.1016/0165-5728(91)90097-q] [Citation(s) in RCA: 125] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In a retrospective study, we have analysed sera from a well-characterised Guillain-Barré syndrome (GBS) patient group for antibodies that react with gangliosides. Of 95 GBS patients and 85 control patients analysed, we found that 14 (15%) of GBS patients but only one control patient had antibodies that react with the gangliosides GM1 and/or GD1b but not GM2, GD1a and GT1b using a sensitive enzyme-linked immunosorbent assay (ELISA). This pattern of reactivity suggests binding to the carbohydrate structure Gal(beta 1-3)GalNAc which is shared between some glycolipids and glycoproteins. Similar antibodies have been found previously in a subpopulation of patients with lower motor neuron disease. In the present study, the predominant immunoglobulin class of these anti-glycoconjugate antibodies was IgG rather than IgM. A correlation was found between the presence of these antibodies and prognosis in terms of disability at 3 and 12 months after presentation. Patients with anti-glycoconjugate antibodies also had a higher incidence of previous Campylobacter infections than the rest of the patient group, although the significance of this remains to be determined.
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34 |
125 |
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Golbamaki N, Rasulev B, Cassano A, Marchese Robinson RL, Benfenati E, Leszczynski J, Cronin MTD. Genotoxicity of metal oxide nanomaterials: review of recent data and discussion of possible mechanisms. NANOSCALE 2015; 7:2154-98. [PMID: 25580680 DOI: 10.1039/c4nr06670g] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nanotechnology has rapidly entered into human society, revolutionized many areas, including technology, medicine and cosmetics. This progress is due to the many valuable and unique properties that nanomaterials possess. In turn, these properties might become an issue of concern when considering potentially uncontrolled release to the environment. The rapid development of new nanomaterials thus raises questions about their impact on the environment and human health. This review focuses on the potential of nanomaterials to cause genotoxicity and summarizes recent genotoxicity studies on metal oxide/silica nanomaterials. Though the number of genotoxicity studies on metal oxide/silica nanomaterials is still limited, this endpoint has recently received more attention for nanomaterials, and the number of related publications has increased. An analysis of these peer reviewed publications over nearly two decades shows that the test most employed to evaluate the genotoxicity of these nanomaterials is the comet assay, followed by micronucleus, Ames and chromosome aberration tests. Based on the data studied, we concluded that in the majority of the publications analysed in this review, the metal oxide (or silica) nanoparticles of the same core chemical composition did not show different genotoxicity study calls (i.e. positive or negative) in the same test, although some results are inconsistent and need to be confirmed by additional experiments. Where the results are conflicting, it may be due to the following reasons: (1) variation in size of the nanoparticles; (2) variations in size distribution; (3) various purities of nanomaterials; (4) variation in surface areas for nanomaterials with the same average size; (5) differences in coatings; (6) differences in crystal structures of the same types of nanomaterials; (7) differences in size of aggregates in solution/media; (8) differences in assays; (9) different concentrations of nanomaterials in assay tests. Indeed, due to the observed inconsistencies in the recent literature and the lack of adherence to appropriate, standardized test methods, reliable genotoxicity assessment of nanomaterials is still challenging.
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Review |
10 |
123 |
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Yen-Lieberman B, Brambilla D, Jackson B, Bremer J, Coombs R, Cronin M, Herman S, Katzenstein D, Leung S, Lin HJ, Palumbo P, Rasheed S, Todd J, Vahey M, Reichelderfer P. Evaluation of a quality assurance program for quantitation of human immunodeficiency virus type 1 RNA in plasma by the AIDS Clinical Trials Group virology laboratories. J Clin Microbiol 1996; 34:2695-701. [PMID: 8897167 PMCID: PMC229388 DOI: 10.1128/jcm.34.11.2695-2701.1996] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A number of quantitative assays have been developed by using amplification techniques to measure human immunodeficiency virus type 1 RNA in the plasma of infected individuals. The Virology Committee of the AIDS Clinical Trials Group in the Division of AIDS, National Institute of Allergy and Infectious Diseases, has established a quality assurance program (QAP) for quantitative assays of HIV-1 RNA levels in plasma. The primary objective of the QAP was to ascertain that a laboratory could maintain the precision required to have a 90% power to detect a fivefold difference in RNA copy number between two samples in the same batch. To achieve this goal, the QAP required an intra-assay standard deviation of no greater than 0.15 log10 RNA copies per ml. Panels for proficiency testing consisted of coded replicate samples and a common set of standards. To date, 41 laboratories have participated in the program and have used both commercial and in-house assays. We demonstrated that 65% of the laboratories were capable of attaining the necessary level of intra-assay precision. The fitted regressions indicated that the differences among laboratories that used the same kit were generally greater than the differences among population-average regressions for the kits themselves. The use of an external QAP and a common set of standards reduced differences both among laboratories that used the same kit and among laboratories that used different kits. Thus, use of a common set of standards across clinical trial protocols would allow for cross-protocol comparisons.
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research-article |
29 |
121 |
24
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30 |
115 |
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Brozek JL, Canelo-Aybar C, Akl EA, Bowen JM, Bucher J, Chiu WA, Cronin M, Djulbegovic B, Falavigna M, Guyatt GH, Gordon AA, Hilton Boon M, Hutubessy RCW, Joore MA, Katikireddi V, LaKind J, Langendam M, Manja V, Magnuson K, Mathioudakis AG, Meerpohl J, Mertz D, Mezencev R, Morgan R, Morgano GP, Mustafa R, O'Flaherty M, Patlewicz G, Riva JJ, Posso M, Rooney A, Schlosser PM, Schwartz L, Shemilt I, Tarride JE, Thayer KA, Tsaioun K, Vale L, Wambaugh J, Wignall J, Williams A, Xie F, Zhang Y, Schünemann HJ. GRADE Guidelines 30: the GRADE approach to assessing the certainty of modeled evidence-An overview in the context of health decision-making. J Clin Epidemiol 2020; 129:138-150. [PMID: 32980429 DOI: 10.1016/j.jclinepi.2020.09.018] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 09/08/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The objective of the study is to present the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) conceptual approach to the assessment of certainty of evidence from modeling studies (i.e., certainty associated with model outputs). STUDY DESIGN AND SETTING Expert consultations and an international multidisciplinary workshop informed development of a conceptual approach to assessing the certainty of evidence from models within the context of systematic reviews, health technology assessments, and health care decisions. The discussions also clarified selected concepts and terminology used in the GRADE approach and by the modeling community. Feedback from experts in a broad range of modeling and health care disciplines addressed the content validity of the approach. RESULTS Workshop participants agreed that the domains determining the certainty of evidence previously identified in the GRADE approach (risk of bias, indirectness, inconsistency, imprecision, reporting bias, magnitude of an effect, dose-response relation, and the direction of residual confounding) also apply when assessing the certainty of evidence from models. The assessment depends on the nature of model inputs and the model itself and on whether one is evaluating evidence from a single model or multiple models. We propose a framework for selecting the best available evidence from models: 1) developing de novo, a model specific to the situation of interest, 2) identifying an existing model, the outputs of which provide the highest certainty evidence for the situation of interest, either "off-the-shelf" or after adaptation, and 3) using outputs from multiple models. We also present a summary of preferred terminology to facilitate communication among modeling and health care disciplines. CONCLUSION This conceptual GRADE approach provides a framework for using evidence from models in health decision-making and the assessment of certainty of evidence from a model or models. The GRADE Working Group and the modeling community are currently developing the detailed methods and related guidance for assessing specific domains determining the certainty of evidence from models across health care-related disciplines (e.g., therapeutic decision-making, toxicology, environmental health, and health economics).
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Research Support, N.I.H., Extramural |
5 |
111 |