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1.
J Cheminform ; 16(1): 19, 2024 Feb 20.
Article in English | MEDLINE | ID: mdl-38378618

ABSTRACT

The rapid increase of publicly available chemical structures and associated experimental data presents a valuable opportunity to build robust QSAR models for applications in different fields. However, the common concern is the quality of both the chemical structure information and associated experimental data. This is especially true when those data are collected from multiple sources as chemical substance mappings can contain many duplicate structures and molecular inconsistencies. Such issues can impact the resulting molecular descriptors and their mappings to experimental data and, subsequently, the quality of the derived models in terms of accuracy, repeatability, and reliability. Herein we describe the development of an automated workflow to standardize chemical structures according to a set of standard rules and generate two and/or three-dimensional "QSAR-ready" forms prior to the calculation of molecular descriptors. The workflow was designed in the KNIME workflow environment and consists of three high-level steps. First, a structure encoding is read, and then the resulting in-memory representation is cross-referenced with any existing identifiers for consistency. Finally, the structure is standardized using a series of operations including desalting, stripping of stereochemistry (for two-dimensional structures), standardization of tautomers and nitro groups, valence correction, neutralization when possible, and then removal of duplicates. This workflow was initially developed to support collaborative modeling QSAR projects to ensure consistency of the results from the different participants. It was then updated and generalized for other modeling applications. This included modification of the "QSAR-ready" workflow to generate "MS-ready structures" to support the generation of substance mappings and searches for software applications related to non-targeted analysis mass spectrometry. Both QSAR and MS-ready workflows are freely available in KNIME, via standalone versions on GitHub, and as docker container resources for the scientific community. Scientific contribution: This work pioneers an automated workflow in KNIME, systematically standardizing chemical structures to ensure their readiness for QSAR modeling and broader scientific applications. By addressing data quality concerns through desalting, stereochemistry stripping, and normalization, it optimizes molecular descriptors' accuracy and reliability. The freely available resources in KNIME, GitHub, and docker containers democratize access, benefiting collaborative research and advancing diverse modeling endeavors in chemistry and mass spectrometry.

2.
ACS Sustain Chem Eng ; 11: 7986-7996, 2023 May 15.
Article in English | MEDLINE | ID: mdl-37476647

ABSTRACT

One type of firefighting foam, referred to as aqueous filmforming foams (AFFF), is known to contain per- and polyfluoroalkyl substances (PFAS). The concerns raised with PFAS, and their potential environmental and health impacts, have led to a surge in research on fluorine-free alternatives both in the United States and globally. Particularly, in January 2023, a new military specification (MIL-PRF-32725) for fluorine-free foam was released in accordance with Congressional requirements for the U.S. Department of Defense. This paper provides a critical analysis of the present state of the various fluorine-free options that have been developed to date. A nuanced perspective of the challenges and opportunities of more sustainable replacements is explored by examining the performance, cost, and regulatory considerations associated with these fluorine-free alternatives. Ultimately, this evaluation shows that the transition to fluorine-free replacements is likely to be complex and multifaceted, requiring careful consideration of the trade-offs involved. Yet, the ongoing work will provide valuable insights for future research on alternatives to AFFF and enhancing the safety and sustainability of fire suppression systems.

3.
Chem Res Toxicol ; 36(3): 465-478, 2023 03 20.
Article in English | MEDLINE | ID: mdl-36877669

ABSTRACT

The need for careful assembly, training, and validation of quantitative structure-activity/property models (QSAR/QSPR) is more significant than ever as data sets become larger and sophisticated machine learning tools become increasingly ubiquitous and accessible to the scientific community. Regulatory agencies such as the United States Environmental Protection Agency must carefully scrutinize each aspect of a resulting QSAR/QSPR model to determine its potential use in environmental exposure and hazard assessment. Herein, we revisit the goals of the Organisation for Economic Cooperation and Development (OECD) in our application and discuss the validation principles for structure-activity models. We apply these principles to a model for predicting water solubility of organic compounds derived using random forest regression, a common machine learning approach in the QSA/PR literature. Using public sources, we carefully assembled and curated a data set consisting of 10,200 unique chemical structures with associated water solubility measurements. This data set was then used as a focal narrative to methodically consider the OECD's QSA/PR principles and how they can be applied to random forests. Despite some expert, mechanistically informed supervision of descriptor selection to enhance model interpretability, we achieved a model of water solubility with comparable performance to previously published models (5-fold cross validated performance 0.81 R2 and 0.98 RMSE). We hope this work will catalyze a necessary conversation around the importance of cautiously modernizing and explicitly leveraging OECD principles while pursuing state-of-the-art machine learning approaches to derive QSA/PR models suitable for regulatory consideration.


Subject(s)
Organisation for Economic Co-Operation and Development , Quantitative Structure-Activity Relationship , Solubility , Algorithms , Water/chemistry
4.
J Solution Chem ; 51: 838-849, 2022 Jul 01.
Article in English | MEDLINE | ID: mdl-35967985

ABSTRACT

A solvent has many different types of impact on the environment. This article describes a method that combines several different types of impacts together into one environmental index so that similar solvents may be compared by their cumulative impact to the environment. The software tool PARIS III (Program for Assisting the Replacement of Industrial Solvents III) initially finds thousands of solvents mixtures with behaviors as close as possible to those of the original solvent entered. The overall environmental impacts of these solvent mixtures are estimated and assigned to environmental indexes. Users of the software tool can then choose replacements for the original solvent with similar activities but with significantly smaller environmental indexes. These solvent mixtures may act as practical substitutes for the industrial solvents but substantially reduce the overall environmental impact of the original harmful solvents. Potential replacements like this are found for three of the U.S. Environmental Protection Agency's Toxic Release Inventory solvents, carbon tetrachloride, toluene, and N-methylpyrrolidone.

5.
Chemosphere ; 287(Pt 1): 131845, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34523441

ABSTRACT

"Green" pyrotechnics seek to remove known environmental pollutants and health hazards from their formulations. This chemical engineering approach often focuses on maintaining performance effects upon replacement of objectionable ingredients, yet neglects the chemical products formed by the exothermic reaction. In this work, milligram quantities of a lab-scale pyrotechnic red smoke composition were functioned within a thermal probe for product identification by pyrolysis-gas chromatography-mass spectrometry. Thermally decomposed ingredients and new side product derivatives were identified at lower relative abundances to the intact organic dye (as the engineered sublimation product). Side products included chlorination of the organic dye donated by the chlorate oxidizer. Machine learning quantitative structure-activity relationship models computed impacts to health and environmental hazards. High to very high toxicities were predicted for inhalation, mutagenicity, developmental, and endocrine disruption for common military pyrotechnic dyes and their analogous chlorinated side products. These results underscore the need to revise objectives of "green" pyrotechnic engineering.


Subject(s)
Coloring Agents , Smoke , Anthraquinones/toxicity , Coloring Agents/toxicity , Mutagens , Nicotiana
6.
J Air Waste Manag Assoc ; 72(6): 540-555, 2022 06.
Article in English | MEDLINE | ID: mdl-34905459

ABSTRACT

The release of persistent per- and polyfluoroalkyl substances (PFAS) into the environment is a major concern for the United States Environmental Protection Agency (U.S. EPA). To complement its ongoing research efforts addressing PFAS contamination, the U.S. EPA's Office of Research and Development (ORD) commissioned the PFAS Innovative Treatment Team (PITT) to provide new perspectives on treatment and disposal of high priority PFAS-containing wastes. During its six-month tenure, the team was charged with identifying and developing promising solutions to destroy PFAS. The PITT examined emerging technologies for PFAS waste treatment and selected four technologies for further investigation. These technologies included mechanochemical treatment, electrochemical oxidation, gasification and pyrolysis, and supercritical water oxidation. This paper highlights these four technologies and discusses their prospects and the development needed before potentially becoming available solutions to address PFAS-contaminated waste.Implications: This paper examines four novel, non-combustion technologies or applications for the treatment of persistent per- and polyfluoroalkyl substances (PFAS) wastes. These technologies are introduced to the reader along with their current state of development and areas for further development. This information will be useful for developers, policy makers, and facility managers that are facing increasing issues with disposal of PFAS wastes.


Subject(s)
Fluorocarbons , Water Pollutants, Chemical , Fluorocarbons/analysis , United States , United States Environmental Protection Agency , Water Pollutants, Chemical/analysis
8.
Comput Toxicol ; 182021 May 01.
Article in English | MEDLINE | ID: mdl-34504984

ABSTRACT

Regulatory agencies world-wide face the challenge of performing risk-based prioritization of thousands of substances in commerce. In this study, a major effort was undertaken to compile a large genotoxicity dataset (54,805 records for 9299 substances) from several public sources (e.g., TOXNET, COSMOS, eChemPortal). The names and outcomes of the different assays were harmonized, and assays were annotated by type: gene mutation in Salmonella bacteria (Ames assay) and chromosome mutation (clastogenicity) in vitro or in vivo (chromosome aberration, micronucleus, and mouse lymphoma Tk +/- assays). This dataset was then evaluated to assess genotoxic potential using a categorization scheme, whereby a substance was considered genotoxic if it was positive in at least one Ames or clastogen study. The categorization dataset comprised 8442 chemicals, of which 2728 chemicals were genotoxic, 5585 were not and 129 were inconclusive. QSAR models (TEST and VEGA) and the OECD Toolbox structural alerts/profilers (e.g., OASIS DNA alerts for Ames and chromosomal aberrations) were used to make in silico predictions of genotoxicity potential. The performance of the individual QSAR tools and structural alerts resulted in balanced accuracies of 57-73%. A Naïve Bayes consensus model was developed using combinations of QSAR models and structural alert predictions. The 'best' consensus model selected had a balanced accuracy of 81.2%, a sensitivity of 87.24% and a specificity of 75.20%. This in silico scheme offers promise as a first step in ranking thousands of substances as part of a prioritization approach for genotoxicity.

10.
Environ Health Perspect ; 129(4): 47013, 2021 04.
Article in English | MEDLINE | ID: mdl-33929906

ABSTRACT

BACKGROUND: Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silico models built using existing data facilitate rapid acute toxicity predictions without using animals. OBJECTIVES: The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organized an international collaboration to develop in silico models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50≤50mg/kg)], and nontoxic chemicals (LD50>2,000mg/kg). METHODS: An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. RESULTS: The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in vivo results. DISCUSSION: CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemicals have been made available via the National Toxicology Program's Integrated Chemical Environment tools and data sets (ice.ntp.niehs.nih.gov). The models are also implemented in a free, standalone, open-source tool, OPERA, which allows predictions of new and untested chemicals to be made. https://doi.org/10.1289/EHP8495.


Subject(s)
Government Agencies , Animals , Computer Simulation , Rats , Toxicity Tests, Acute , United States , United States Environmental Protection Agency
11.
Comput Toxicol ; 20: 1-100185, 2021 Nov 01.
Article in English | MEDLINE | ID: mdl-35128218

ABSTRACT

The Toxic Substances Control Act (TSCA) became law in the U.S. in 1976 and was amended in 2016. The amended law requires the U.S. EPA to perform risk-based evaluations of existing chemicals. Here, we developed a tiered approach to screen potential candidates based on their genotoxicity and carcinogenicity information to inform the selection of candidate chemicals for prioritization under TSCA. The approach was underpinned by a large database of carcinogenicity and genotoxicity information that had been compiled from various public sources. Carcinogenicity data included weight-of-evidence human carcinogenicity evaluations and animal cancer data. Genotoxicity data included bacterial gene mutation data from the Salmonella (Ames) and Escherichia coli WP2 assays and chromosomal mutation (clastogenicity) data. Additionally, Ames and clastogenicity outcomes were predicted using the alert schemes within the OECD QSAR Toolbox and the Toxicity Estimation Software Tool (TEST). The evaluation workflows for carcinogenicity and genotoxicity were developed along with associated scoring schemes to make an overall outcome determination. For this case study, two sets of chemicals, the TSCA Active Inventory non-confidential portion list available on the EPA CompTox Chemicals Dashboard (33,364 chemicals, 'TSCA Active List') and a representative proof-of-concept (POC) set of 238 chemicals were profiled through the two workflows to make determinations of carcinogenicity and genotoxicity potential. Of the 33,364 substances on the 'TSCA Active List', overall calls could be made for 20,371 substances. Here 46.67%% (9507) of substances were non-genotoxic, 0.5% (103) were scored as inconclusive, 43.93% (8949) were predicted genotoxic and 8.9% (1812) were genotoxic. Overall calls for genotoxicity could be made for 225 of the 238 POC chemicals. Of these, 40.44% (91) were non-genotoxic, 2.67% (6) were inconclusive, 6.22% (14) were predicted genotoxic, and 50.67% (114) genotoxic. The approach shows promise as a means to identify potential candidates for prioritization from a genotoxicity and carcinogenicity perspective.

12.
Environ Prog Sustain Energy ; 39(1): 1-13331, 2020 Jan 01.
Article in English | MEDLINE | ID: mdl-32832013

ABSTRACT

PARIS III (Program for Assisting the Replacement of Industrial Solvents III, Version 1.4.0) is a pollution prevention solvent substitution software tool used to find mixtures of solvents that are less harmful to the environment than the industrial solvents to be replaced. By searching extensively though hundreds of millions of possible solvent combinations, mixtures that perform the same as the original solvents may be found. Greener solvent substitutes may then be chosen from those mixtures that behave similarly but have less environmental impact. These extensive searches may be enhanced by fine-tuning impact weighting factors to better reflect regional environmental concerns; and by adjusting how close the properties of the replacement must be to those of the original solvent. Optimal replacements can then be compared again and selected for better performance, but less environmental impact. This method can be a very effective way of finding greener replacements for harmful solvents used by industry.

13.
Environ Health Perspect ; 128(2): 27002, 2020 02.
Article in English | MEDLINE | ID: mdl-32074470

ABSTRACT

BACKGROUND: Endocrine disrupting chemicals (EDCs) are xenobiotics that mimic the interaction of natural hormones and alter synthesis, transport, or metabolic pathways. The prospect of EDCs causing adverse health effects in humans and wildlife has led to the development of scientific and regulatory approaches for evaluating bioactivity. This need is being addressed using high-throughput screening (HTS) in vitro approaches and computational modeling. OBJECTIVES: In support of the Endocrine Disruptor Screening Program, the U.S. Environmental Protection Agency (EPA) led two worldwide consortiums to virtually screen chemicals for their potential estrogenic and androgenic activities. Here, we describe the Collaborative Modeling Project for Androgen Receptor Activity (CoMPARA) efforts, which follows the steps of the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP). METHODS: The CoMPARA list of screened chemicals built on CERAPP's list of 32,464 chemicals to include additional chemicals of interest, as well as simulated ToxCast™ metabolites, totaling 55,450 chemical structures. Computational toxicology scientists from 25 international groups contributed 91 predictive models for binding, agonist, and antagonist activity predictions. Models were underpinned by a common training set of 1,746 chemicals compiled from a combined data set of 11 ToxCast™/Tox21 HTS in vitro assays. RESULTS: The resulting models were evaluated using curated literature data extracted from different sources. To overcome the limitations of single-model approaches, CoMPARA predictions were combined into consensus models that provided averaged predictive accuracy of approximately 80% for the evaluation set. DISCUSSION: The strengths and limitations of the consensus predictions were discussed with example chemicals; then, the models were implemented into the free and open-source OPERA application to enable screening of new chemicals with a defined applicability domain and accuracy assessment. This implementation was used to screen the entire EPA DSSTox database of ∼875,000 chemicals, and their predicted AR activities have been made available on the EPA CompTox Chemicals dashboard and National Toxicology Program's Integrated Chemical Environment. https://doi.org/10.1289/EHP5580.


Subject(s)
Computer Simulation , Endocrine Disruptors , Androgens , Databases, Factual , High-Throughput Screening Assays , Humans , Receptors, Androgen , United States , United States Environmental Protection Agency
14.
Clean Technol Environ Policy ; 22(2): 441-458, 2020 Mar 01.
Article in English | MEDLINE | ID: mdl-33867908

ABSTRACT

Comparative chemical hazard assessment, which compares hazards for several endpoints across several chemicals, can be used for a variety of purposes including alternatives assessment and the prioritization of chemicals for further assessment. A new framework was developed to compile and integrate chemical hazard data for several human health and ecotoxicity endpoints from public online sources including hazardous chemical lists, Globally Harmonized System hazard codes (H-codes) or hazard categories from government health agencies, experimental quantitative toxicity values, and predicted values using Quantitative Structure-Activity Relationship (QSAR) models. QSAR model predictions were obtained using EPA's Toxicity Estimation Software Tool. Java programming was used to download hazard data, convert data from each source into a consistent score record format, and store the data in a database. Scoring criteria based on the EPA's Design for the Environment Program Alternatives Assessment Criteria for Hazard Evaluation were used to determine ordinal hazard scores (i.e., low, medium, high, or very high) for each score record. Different methodologies were assessed for integrating data from multiple sources into one score for each hazard endpoint for each chemical. The chemical hazard assessment (CHA) Database developed in this study currently contains more than 990,000 score records for more than 85,000 chemicals. The CHA Database and the methods used in its development may contribute to several cheminformatics, public health, and environmental activities.

15.
Environ Toxicol Chem ; 38(10): 2294-2304, 2019 10.
Article in English | MEDLINE | ID: mdl-31269286

ABSTRACT

Multiple mode of action (MOA) frameworks have been developed in aquatic ecotoxicology, mainly based on fish toxicity. These frameworks provide information on a key determinant of chemical toxicity, but the MOA categories and level of specificity remain unique to each of the classification schemes. The present study aimed to develop a consensus MOA assignment within EnviroTox, a curated in vivo aquatic toxicity database, based on the following MOA classification schemes: Verhaar (modified) framework, Assessment Tool for Evaluating Risk, Toxicity Estimation Software Tool, and OASIS. The MOA classifications from each scheme were first collapsed into one of 3 categories: non-specifically acting (i.e., narcosis), specifically acting, or nonclassifiable. Consensus rules were developed based on the degree of concordance among the 4 individual MOA classifications to attribute a consensus MOA to each chemical. A confidence rank was also assigned to the consensus MOA classification based on the degree of consensus. Overall, 40% of the chemicals were classified as narcotics, 17% as specifically acting, and 43% as unclassified. Sixty percent of chemicals had a medium to high consensus MOA assignment. When compared to empirical acute toxicity data, the general trend of specifically acting chemicals being more toxic is clearly observed for both fish and invertebrates but not for algae. EnviroTox is the first approach to establishing a high-level consensus across 4 computationally and structurally distinct MOA classification schemes. This consensus MOA classification provides both a transparent understanding of the variation between MOA classification schemes and an added certainty of the MOA assignment. In terms of regulatory relevance, a reliable understanding of MOA can provide information that can be useful for the prioritization (ranking) and risk assessment of chemicals. Environ Toxicol Chem 2019;38:2294-2304. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.


Subject(s)
Consensus , Ecotoxicology , Animals , Databases, Factual , Fishes/physiology , Invertebrates/physiology , Risk Assessment , Toxicity Tests, Acute
16.
Toxicol Sci ; 169(2): 317-332, 2019 06 01.
Article in English | MEDLINE | ID: mdl-30835285

ABSTRACT

The U.S. Environmental Protection Agency (EPA) is faced with the challenge of efficiently and credibly evaluating chemical safety often with limited or no available toxicity data. The expanding number of chemicals found in commerce and the environment, coupled with time and resource requirements for traditional toxicity testing and exposure characterization, continue to underscore the need for new approaches. In 2005, EPA charted a new course to address this challenge by embracing computational toxicology (CompTox) and investing in the technologies and capabilities to push the field forward. The return on this investment has been demonstrated through results and applications across a range of human and environmental health problems, as well as initial application to regulatory decision-making within programs such as the EPA's Endocrine Disruptor Screening Program. The CompTox initiative at EPA is more than a decade old. This manuscript presents a blueprint to guide the strategic and operational direction over the next 5 years. The primary goal is to obtain broader acceptance of the CompTox approaches for application to higher tier regulatory decisions, such as chemical assessments. To achieve this goal, the blueprint expands and refines the use of high-throughput and computational modeling approaches to transform the components in chemical risk assessment, while systematically addressing key challenges that have hindered progress. In addition, the blueprint outlines additional investments in cross-cutting efforts to characterize uncertainty and variability, develop software and information technology tools, provide outreach and training, and establish scientific confidence for application to different public health and environmental regulatory decisions.


Subject(s)
Computational Biology/methods , High-Throughput Screening Assays/methods , Toxicology/methods , Decision Making , Humans , Information Technology , Risk Assessment , Toxicokinetics , United States , United States Environmental Protection Agency
17.
ACS Sustain Chem Eng ; 7(8): 7630-7641, 2019 Apr 15.
Article in English | MEDLINE | ID: mdl-33123418

ABSTRACT

The evaluation of potential alternatives for chemicals of concern (CoC) requires an understanding of their potential human health and environmental impacts during the manufacture, use, recycle and disposal life stages. During the manufacturing phase, the processes used to produce a desired chemical are defined based on the sequence of chemical reactions and unit operations required to produce the molecule and separate it from other materials used or produced during its manufacture. This paper introduces and demonstrates a tool that links a chemical's structure to information about its synthesis route and the manufacturing process for that chemical. The structure of the chemical is entered using either a SMILES string or the molecule MOL file, and the molecule is searched to identify functional groups present. Based on those functional groups present, the respective named reactions that can be used in its synthesis routes are identified. This information can be used to identify input and output materials for each named reaction, along with reaction conditions, solvents, and catalysts that participate in the reaction. Additionally, the reaction database contains links to internet references and appropriate reaction-specific keywords, further increasing its comprehensiveness. The tool is designed to facilitate the cataloging and use of the chemical literature in a way that allows user to identify and evaluate information about the reactions, such as alternative solvents, catalysts, reaction conditions and other reaction products which enable the comparison of various reaction pathways for the manufacture of the subject chemical. The chemical manufacturing processing steps can be linked to a chemical process ontology to estimate releases and exposures occurring during the manufacturing phase of a chemical.

18.
Clean Technol Environ Policy ; 19(4): 1067-1086, 2017 May 01.
Article in English | MEDLINE | ID: mdl-29333139

ABSTRACT

The goal of alternatives assessment (AA) is to facilitate a comparison of alternatives to a chemical of concern, resulting in the identification of safer alternatives. A two stage methodology for comparing chemical alternatives was developed. In the first stage, alternatives are compared using a variety of human health effects, ecotoxicity, and physicochemical properties. Hazard profiles are completed using a variety of online sources and quantitative structure activity relationship models. In the second stage, alternatives are evaluated utilizing an exposure/risk assessment over the entire life cycle. Exposure values are calculated using screening-level near-field and far-field exposure models. The second stage allows one to more accurately compare potential exposure to each alternative and consider additional factors that may not be obvious from separate binned persistence, bioaccumulation, and toxicity scores. The methodology was utilized to compare phosphate-based alternatives for decabromodiphenyl ether (decaBDE) in electronics applications.

19.
Aquat Toxicol ; 180: 11-24, 2016 Nov.
Article in English | MEDLINE | ID: mdl-27640153

ABSTRACT

The mode of toxic action (MoA) has been recognized as a key determinant of chemical toxicity, but development of predictive MoA classification models in aquatic toxicology has been limited. We developed a Bayesian network model to classify aquatic toxicity MoA using a recently published dataset containing over one thousand chemicals with MoA assignments for aquatic animal toxicity. Two dimensional theoretical chemical descriptors were generated for each chemical using the Toxicity Estimation Software Tool. The model was developed through augmented Markov blanket discovery from the dataset of 1098 chemicals with the MoA broad classifications as a target node. From cross validation, the overall precision for the model was 80.2%. The best precision was for the AChEI MoA (93.5%) where 257 chemicals out of 275 were correctly classified. Model precision was poorest for the reactivity MoA (48.5%) where 48 out of 99 reactive chemicals were correctly classified. Narcosis represented the largest class within the MoA dataset and had a precision and reliability of 80.0%, reflecting the global precision across all of the MoAs. False negatives for narcosis most often fell into electron transport inhibition, neurotoxicity or reactivity MoAs. False negatives for all other MoAs were most often narcosis. A probabilistic sensitivity analysis was undertaken for each MoA to examine the sensitivity to individual and multiple descriptor findings. The results show that the Markov blanket of a structurally complex dataset can simplify analysis and interpretation by identifying a subset of the key chemical descriptors associated with broad aquatic toxicity MoAs, and by providing a computational chemistry-based network classification model with reasonable prediction accuracy.


Subject(s)
Ecotoxicology/methods , Models, Biological , Models, Chemical , Water Pollutants, Chemical/toxicity , Animals , Bayes Theorem , Computational Biology , Databases, Factual , Markov Chains , Reproducibility of Results
20.
Kidney Blood Press Res ; 41(3): 278-87, 2016.
Article in English | MEDLINE | ID: mdl-27160585

ABSTRACT

BACKGROUND/AIMS: Clinical benefits of percutaneous treatment of renal artery stenosis (RAS) remain controversial. The aim of this study was to evaluate the effects of renal artery stenting on kidney function and blood pressure (BP) control in the log-term follow-up. Additionally angiographic follow up was performed in selected subgroup of patients. METHODS: The study was designed as international registry of 265 consecutive patients with RAS treated with renal artery stenting. The primary end-point of the study was the change in renal function and blood pressure at long-term follow-up as compared with baseline values. Evaluation of the renal function was based on estimated glomerular filtration rate (eGFR) with the use of the modification of diet in renal disease (MDRD) formula. RESULTS: All patients had clinical follow-up at the median time of 23.8 (interquartile range: 3-90) months during ambulatory visits. At follow-up eGFR improved in 53,9% of patients. These patients had lower pre-procedural systolic BP, more severe lesion type at baseline and lower diameter stenosis in control angiography. At follow up visits, SBP improvement was observed in 77,4% of patients. The average number of anti-hypertensive medications before the procedure and at follow up did not change significantly (2,70±1,0 vs 2,49±0,9, p=0,1). Restenosis rate based on control angiography performed at median time of 15 months was 12%. CONCLUSION: The results of the study suggest that interventional treatment of RAS may preserve renal function and improve blood pressure control at long-term follow-up.


Subject(s)
Blood Pressure , Kidney/physiology , Renal Artery Obstruction/therapy , Stents , Follow-Up Studies , Humans , Renal Artery/surgery
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