Thomas Miller

Dr. Thomas Miller

College of Health, Medicine and Life Sciences, King's College London, London, UK

Research Focus & Metrics

Academic Career Length

14Years (2013-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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1 August 2018 in Environmental Pollution
Verified
Journal Article
Open access
Thomas MillerThomas Miller
Thomas Miller
NBNicolas R. Bury
Nicolas R. Bury
SOStewart F. Owen
Stewart F. Owen
JMJames I. MacRae
James I. MacRae
LBLeon P. Barron
Leon P. Barron
Pharmaceuticals have been considered 'contaminants of emerging concern' for more than 20 years. In that time, many laboratory studies have sought to identify hazard and assess risk in the aquatic environment, whilst field studies have searched for targeted candidates and occurrence trends using advanced analytical techniques. However, a lack of a systematic approach to the detection and quantification of pharmaceuticals has provided a fragmented literature of serendipitous approaches. Evaluation of the extent of the risk for the plethora of human and veterinary pharmaceuticals available requires the reliable measurement of trace levels of contaminants across different environmental compartments (water, sediment, biota - of which biota has been largely neglected). The focus on pharmaceutical concentrations in surface waters and other exposure media have therefore limited both the characterisation of the exposome in aquatic wildlife and the understanding of cause and effect relationships. Here, we compile the current analytical approaches and available occurrence and accumulation data in biota to review the current state of research in the field. Our analysis provides evidence in support of the 'Matthew Effect' and raises critical questions about the use of targeted analyte lists for biomonitoring. We provide six recommendations to stimulate and improve future research avenues.

1 May 2017 in Forensic Science International: Genetics
Verified
Journal Article
Open access
AVAthina Vidaki
Athina Vidaki
DBDavid Ballard
David Ballard
AAAnastasia Aliferi
Anastasia Aliferi
Thomas MillerThomas Miller
Thomas Miller
LBLeon P. Barron
Leon P. Barron
DCDenise Syndercombe Court
Denise Syndercombe Court
The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging can be complex and is associated with various molecular modifications in cells that accumulate over a person's lifetime including epigenetic patterns. The aim of this study was to use age-specific DNA methylation patterns to generate an accurate model for the prediction of chronological age using data from whole blood. In total, 45 age-associated CpG sites were selected based on their reported age coefficients in a previous extensive study and investigated using publicly available methylation data obtained from 1156 whole blood samples (aged 2-90 years) analysed with Illumina's genome-wide methylation platforms (27K/450K). Applying stepwise regression for variable selection, 23 of these CpG sites were identified that could significantly contribute to age prediction modelling and multiple regression analysis carried out with these markers provided an accurate prediction of age (R2=0.92, mean absolute error (MAE)=4.6 years). However, applying machine learning, and more specifically a generalised regression neural network model, the age prediction significantly improved (R2=0.96) with a MAE=3.3 years for the training set and 4.4 years for a blind test set of 231 cases. The machine learning approach used 16 CpG sites, located in 16 different genomic regions, with the top 3 predictors of age belonged to the genes NHLRC1, SCGN and CSNK1D. The proposed model was further tested using independent cohorts of 53 monozygotic twins (MAE=7.1 years) and a cohort of 1011 disease state individuals (MAE=7.2 years). Furthermore, we highlighted the age markers' potential applicability in samples other than blood by predicting age with similar accuracy in 265 saliva samples (R2=0.96) with a MAE=3.2 years (training set) and 4.0 years (blind test). In an attempt to create a sensitive and accurate age prediction test, a next generation sequencing (NGS)-based method able to quantify the methylation status of the selected 16 CpG sites was developed using the Illumina MiSeq® platform. The method was validated using DNA standards of known methylation levels and the age prediction accuracy has been initially assessed in a set of 46 whole blood samples. Although the resulted prediction accuracy using the NGS data was lower compared to the original model (MAE=7.5years), it is expected that future optimization of our strategy to account for technical variation as well as increasing the sample size will improve both the prediction accuracy and reproducibility.

1 August 2019 in Environment International
Verified
Journal Article
Open access
Thomas MillerThomas Miller
Thomas Miller
KNKeng Tiong Ng
Keng Tiong Ng
SBSamuel T. Bury
Samuel T. Bury
SBSophie E. Bury
Sophie E. Bury
NBNicolas R. Bury
Nicolas R. Bury
LBLeon P. Barron
Leon P. Barron
Multiple classes of environmental contaminants have been found in aquatic environments, globally. Understanding internalised concentrations in the organism could further improve the risk assessment process. The present study is concerned with the determination of several contaminant classes (107 compounds) in Gammarus pulex collected from 15 sites covering 5 river catchments across Suffolk, UK. Quantitative method performance was acceptable for 67 compounds including pharmaceuticals, pesticides, illicit drugs and drugs of abuse. A total of 56 compounds were detectable and ranged from

1 December 2015 in Science of The Total Environment
Verified
Journal Article
Open access
RBRichard Bade
Richard Bade
LBLubertus Bijlsma
Lubertus Bijlsma
Thomas MillerThomas Miller
Thomas Miller
LBLeon P. Barron
Leon P. Barron
JSJuan Vicente Sancho
Juan Vicente Sancho
FHfelix hernandez hernandez
felix hernandez hernandez
The recent development of broad-scope high resolution mass spectrometry (HRMS) screening methods has resulted in a much improved capability for new compound identification in environmental samples. However, positive identifications at the ng/L concentration level rely on analytical reference standards for chromatographic retention time (tR) and mass spectral comparisons. Chromatographic tR prediction can play a role in increasing confidence in suspect screening efforts for new compounds in the environment, especially when standards are not available, but reliable methods are lacking. The current work focuses on the development of artificial neural networks (ANNs) for tR prediction in gradient reversed-phase liquid chromatography and applied along with HRMS data to suspect screening of wastewater and environmental surface water samples. Based on a compound tR dataset of >500 compounds, an optimized 4-layer back-propagation multi-layer perceptron model enabled predictions for 85% of all compounds to within 2min of their measured tR for training (n=344) and verification (n=100) datasets. To evaluate the ANN ability for generalization to new data, the model was further tested using 100 randomly selected compounds and revealed 95% prediction accuracy within the 2-minute elution interval. Given the increasing concern on the presence of drug metabolites and other transformation products (TPs) in the aquatic environment, the model was applied along with HRMS data for preliminary identification of pharmaceutically-related compounds in real samples. Examples of compounds where reference standards were subsequently acquired and later confirmed are also presented. To our knowledge, this work presents for the first time, the successful application of an accurate retention time predictor and HRMS data-mining using the largest number of compounds to preliminarily identify new or emerging contaminants in wastewater and surface waters.

1 January 2019 in Science of The Total Environment
Verified
Journal Article
Open access
Thomas MillerThomas Miller
Thomas Miller
Matteo Davide GallidabinoMatteo Davide Gallidabino
Matteo Davide Gallidabino
JMJames I. MacRae
James I. MacRae
SOStewart F. Owen
Stewart F. Owen
NBNicolas R. Bury
Nicolas R. Bury
LBLeon Barron
Leon Barron
The application of machine learning has recently gained interest from ecotoxicological fields for its ability to model and predict chemical and/or biological processes, such as the prediction of bioconcentration. However, comparison of different models and the prediction of bioconcentration in invertebrates has not been previously evaluated. A comparison of 24 linear and machine learning models is presented herein for the prediction of bioconcentration in fish and important factors that influenced accumulation identified. R2 and root mean square error (RMSE) for the test data (n = 110 cases) ranged from 0.23-0.73 and 0.34-1.20, respectively. Model performance was critically assessed with neural networks and tree-based learners showing the best performance. An optimised 4-layer multi-layer perceptron (14 descriptors) was selected for further testing. The model was applied for cross-species prediction of bioconcentration in a freshwater invertebrate, Gammarus pulex. The model for G. pulex showed good performance with R2 of 0.99 and 0.93 for the verification and test data, respectively. Important molecular descriptors determined to influence bioconcentration were molecular mass (MW), octanol-water distribution coefficient (logD), topological polar surface area (TPSA) and number of nitrogen atoms (nN) among others. Modelling of hazard criteria such as PBT, showed potential to replace the need for animal testing. However, the use of machine learning models in the regulatory context has been minimal to date and is critically discussed herein. The movement away from experimental estimations of accumulation to in silico modelling would enable rapid prioritisation of contaminants that may pose a risk to environmental health and the food chain.

1 April 2015 in Science of The Total Environment
Verified
Journal Article
Open access
Thomas MillerThomas Miller
Thomas Miller
GMGillian L. McEneff
Gillian L. McEneff
RBRebecca J. Brown
Rebecca J. Brown
SOStewart F. Owen
Stewart F. Owen
NBNicolas R. Bury
Nicolas R. Bury
LBLeon Barron
Leon Barron
The development, characterisation and application of a new analytical method for multi-residue PPCP determination in the freshwater amphipod, Gammarus pulex are presented. Analysis was performed using pulverised liquid extraction (PuLE), solid phase extraction (SPE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Qualitative method performance offered excellent limits of detection at <20 ng g(-1) for 18 out of 29 compounds. For quantitative application, linearity and precision were considered acceptable for 10 compounds across the ng-μg g(-1) range (R2≥0.99; ≤20% relative standard deviation respectively). The method was applied to the analysis of G. pulex and river water sourced from six tributaries of the River Thames. Carbamazepine, diazepam, nimesulide, trimethoprim and warfarin were determined in G. pulex samples at low ng g(-1) (dry weight) concentrations across these sites. Temazepam and diclofenac were also detected, but were not quantifiable. Six pharmaceuticals were quantified in surface waters across the eight sites at concentrations ranging from 3 to 344 ng L(-1). The possibility for confirmatory detection and subsequent quantification of pharmaceutical residues in benthic organisms such as G. pulex will enable further understanding on the susceptibility and ecological effects of PPCPs in the aquatic environment.