Publications by authors named "Bill Lee"

3 Publications

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Alignment free sequence comparison methods and reservoir host prediction.

Bioinformatics 2021 May 8. Epub 2021 May 8.

State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Rd., Pok Fu Lam, Hong Kong.

Motivation: The emergence and subsequent pandemic of the SARS-CoV-2 virus raised urgent questions about its origin and, particularly, its reservoir host. These types of questions are long-standing problems in the management of emerging infectious diseases and are linked to virus discovery programs and the prediction of viruses that are likely to become zoonotic. Conventional means to identify reservoir hosts have relied on surveillance, experimental studies and phylogenetics. More recently, machine learning approaches have been applied to generate tools to swiftly predict reservoir hosts from sequence data.

Results: Here, we extend a recent work that combined sequence alignment and a mixture of alignment-free approaches using a gradient boosting machines (GBMs) machine learning model, which integrates genomic traits (GT) and phylogenetic neighbourhood (PN) signatures to predict reservoir hosts. We add a more uniform approach by applying Machine Learning with Digital Signal Processing (MLDSP)-based structural patterns (M-SP). The extended model was applied to an existing virus/reservoir host dataset and to the SARS-CoV-2 and related viruses and generated an improvement in prediction accuracy.

Availability And Implementation: The source code used in this work is freely available at

Supplementary Information: Supplementary data are available at Bioinformatics online.
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May 2021

Macro practice--cornerstone of our profession!

Bill Lee

Soc Work 2014 Oct;59(4):376

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October 2014

Occurrence and reductions of pharmaceuticals and personal care products and estrogens by municipal wastewater treatment plants in Ontario, Canada.

Sci Total Environ 2006 Aug 12;367(2-3):544-58. Epub 2006 May 12.

Environment Canada, National Water Research Institute, 867 Lakeshore Road, P. O. Box 5050, Burlington, Ontario, Canada L7R 4A6.

Over the last ten years there have been reports of pharmaceuticals and personal care product (PPCP) residuals in municipal wastewater treatment plant (WWTP) effluents. The principle goal of this study was specifically to expand and in some cases establish a Canadian database for the presence of selected acidic drugs, triclosan, polycyclic musks, and selected estrogens in MWWTP influent and effluent. The impact of treatment configuration (e.g. lagoons, conventional activated sludge (CAS), and CAS followed by media filtration (CAS+filtration)) was also examined. For CAS systems, the most prevalent treatment type, the effect of operating temperature and SRT was evaluated. Selected PPCPs included ten acidic pharmaceuticals (i.e. a group of pharmaceuticals that are extractable at a pH of 2 or less), triclosan, five polycyclic musks and two estrogens. The pharmaceuticals and musks were selected on the basis of levels of use in Canada; reported aquatic toxicity effects; and the ability to analyze for the compounds at low levels. Twelve MWWTPs discharging into the Thames River, the second largest river in southwestern Ontario, were surveyed. The only common characteristic of acidic drugs is their extraction pH as they differ in their intended biological function and chemical structure. Many organics degraded by WWTP processes benefit from warm temperatures and long SRTs so the impact of these variables warranted additional attention. Influent concentrations and reductions for acidic drugs reported by this study were compared to other Canadian studies, when available, and European investigations. The data of this study seems consistent with other reports. Ten acidic drugs were considered by this study. Three were consistently present at non-quantifiable levels (e.g. CLF, FNP and FNF). Additionally, one analyte, SYL, presented results that were so inconsistent that the values were not analysed. The remaining six acidic pharmaceuticals were placed into three categories. IBU and NPX members of the first category had consistently high reductions. At the level of reduction achieved (i.e. median reduction of greater than 93%) and any effect of treatment type or operating characteristics would be subtle and non-discernable given the analytical noise. In the second group are KTP and IND, and definitive comments are difficult to make on the impact of treatment type and operational considerations due to a sparse data set (i.e. many influent values were at non-quantifiable concentrations). Median reductions were in the 23% to 44% range. In the last category are GMF and DCF which have median reductions of 66% and -34%, respectively. Several negative reduction values in the data set (i.e. twelve of twenty six sampling events) suggest that DCF may be deconjugated under certain conditions. This warrants further evaluation when analytical methods for measuring human metabolites of DCF are available. For both GMF and DCF, reduction does not appear to be strongly influenced by SRTs up to 15 days, while SRTs over 30 days were associated with more frequent non-quantifiable effluent levels of DCF. This would suggest that better treatment would be provided by lagoons and CAS systems with extended aeration. Preliminary data suggests that temperature does not play a strong role in the reduction of these compounds. Triclosan (TCL) was detected at concentrations of 0.01-4.01 microg/L in influent samples and 0.01-0.324 microg/L in effluent samples. Reduction of TCL ranged from 74% to 98%. Lagoon treatment seems to be the best TCL reduction as it was present in the influent and effluent at quantifiable and non-quantifiable concentrations, respectively, on nine of nine sampling occasions. Influent and reduction values of five polycyclic musks (e.g. ADBI, AHMI, ATII, HHCB, and AHTN) were examined over the course of this study. AHMI was predominantly present at non-quantifiable concentrations. HHCB and AHTN were present at the highest concentrations. A comparison between Canadian values and those of European studies indicate that in general polycyclic musk concentrations in Canadian MWWTP effluents are 5-10 times lower. More extensive European and Canadian databases would be useful in confirming this initial observation. Median reductions for the five remaining musks range between 37% and 65% in CAS systems. CAS+filtration systems would be expected to have higher reductions if musks were bound to the effluent solids. This trend is not apparent but this may be due to the small size of the data set. In lagoon systems, musk reduction for HHCB and AHTN are approximately 98-99%. For ADBI and ATII musk, there are no numerical reduction values as most often the effluent concentration was non-quantifiable. In some instances, both the influent and effluent concentrations were non-quantifiable. The hormones 17-beta-estradiol (E2) and estrone (E1) were detected at concentrations of 0.006 to 0.014 and 0.016 to 0.049 microg/L, respectively. E2 was not detected in any effluent samples (<0.005 microg/L) whereas E1 was detected in effluent samples from CAS treatment plants (median of 0.008 microg/L), and in one sample from lagoons. These data demonstrate that there are detectable levels of PPCPs entering Canadian waterways at trace levels, and that only some of these compounds are being reduced in a significant proportion by municipal wastewater treatment processes.
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August 2006