Automating Data Analysis for Two-Dimensional Gas Chromatography/Time-of-Flight Mass Spectrometry Non-Targeted Analysis of Comparative Samples

Non-targeted analysis of environmental samples, using comprehensive two‐dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC/ToF-MS), poses significant data analysis challenges due to the large number of possible analytes. Non-targeted data analysis of complex mixtures is prone to human bias and is laborious, particularly for comparative environmental samples such as contaminated soil pre- and post-bioremediation. To address this research bottleneck, we developed OCTpy, a Python™ script that acts as a data reduction filter to automate GC × GC/ToF-MS data analysis from LECO® ChromaTOF® software and facilitates selection of analytes of interest based on peak area comparison between comparative samples. We used data from polycyclic aromatic hydrocarbon (PAH) contaminated soil, pre- and post‐bioremediation, to assess the effectiveness of OCTpy in facilitating the selection of analytes that have formed or degraded following treatment. Using datasets from the soil extracts pre- and post‐bioremediation, OCTpy selected, on average, 18% of the initial suggested analytes generated by the LECO® ChromaTOF® software Statistical Compare feature. Based on this list, 63–100% of the candidate analytes identified by a highly trained individual were also selected by OCTpy. This process was accomplished in several minutes per sample, whereas manual data analysis took several hours per sample. OCTpy automates the analysis of complex mixtures of comparative samples, reduces the potential for human error during heavy data handling and decreases data analysis time by at least tenfold

Aerobic Bioremediation of PAH Contaminated Soil Results in Increased Genotoxicity and Developmental Toxicity

This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society and can be found at: https://doi.org/10.1021/acs.est.5b00499The formation of more polar and toxic polycyclic aromatic hydrocarbon (PAH) transformation products is one of the concerns associated with the bioremediation of PAH-contaminated soils. Soil contaminated with coal tar (pre-bioremediation) from a former manufactured gas plant (MGP) site was treated in a laboratory scale bioreactor (post-bioremediation) and extracted using pressurized liquid extraction. The soil extracts were fractionated, based on polarity, and analyzed for 88 PAHs (unsubstituted, oxygenated, nitrated, and heterocyclic PAHs). The PAH concentrations in the soil tested, post-bioremediation, were lower than their regulatory maximum allowable concentrations (MACs), with the exception of the higher molecular weight PAHs (BaA, BkF, BbF, BaP, and IcdP), most of which did not undergo significant biodegradation. The soil extract fractions were tested for genotoxicity using the DT40 chicken lymphocyte bioassay and developmental toxicity using the embryonic zebrafish (Danio rerio) bioassay. A statistically significant increase in genotoxicity was measured in the unfractionated soil extract, as well as in four polar soil extract fractions, post-bioremediation (p < 0.05). In addition, a statistically significant increase in developmental toxicity was measured in one polar soil extract fraction, post-bioremediation (p < 0.05). A series of morphological abnormalities, including peculiar caudal fin malformations and hyperpigmentation in the tail, were measured in several soil extract fractions in embryonic zebrafish, both pre- and post-bioremediation. The increased toxicity measured post-bioremediation is not likely due to the 88 PAHs measured in this study (including quinones), because most were not present in the toxic polar fractions and/or because their concentrations did not increase post-bioremediation. However, the increased toxicity measured post-bioremediation is likely due to hydroxylated and carboxylated transformation products of the 3- and 4-ring PAHs (PHE, 1MPHE, 2MPHE, PRY, BaA, and FLA) that were most degraded

Immobilization, Trapping, and Anion Exchange of Perrhenate Ion Using Copper-Based Tripodal Complexes

We describe a multidentate tripodal ligand in which three pendant arms carrying di(2-picolyl)amine units are linked to the ortho positions of a tris(o-xylyl) scaffold, providing N(CH[subscript 2]-o-C[subscript 6]H[subscript 4]CH[subscript 2]N(CH2py)[subscript 2])[subscript 3] (L). Reaction of L with CuCl[subscript 2] in the presence of hexafluorophosphate anion afforded blue cubes of [(CuCl)[subscript 3]L](PF[subscript 6])[subscript 3]·5H[subscript 2]O (1). Crystallographic studies of 1 revealed that the three symmetry-related arms each coordinate a {Cu[superscript II]Cl} unit, and two molecules of 1 are connected to one another through a Cu(μ-Cl)[subscript 2]Cu bridge, extending the molecular structure to form a two-dimensional (2-D) layer. These 2-D layers pack in an ABCABC... fashion with PF[subscript 6]– anions located in between. Reaction of 1 with a stoichiometric amount of perrhenate ion afforded blue plates of [(CuCl)[subscript 3]L](PF[subscript 6])(ReO[subscript 4])[subscript 2]·3H[subscript 2]O (2). Compound 2 has the same lattice structure as 1, but the tricopper unit backbone now traps one ReO[subscript 4]– anion through Coulombic interactions. In addition, three molecules of 2 are bridged by a perrhenate ion, forming a Cu[subscript 3](μ[superscript 3]-ReO[subscript 4]) cluster, to give a different 2-D structure displaying a rare tridentate bridging ReO[subscript 4]– mode. Thus, in addition to classic perrhenate trapping through weak Coulombic interactions, 2 represents an exceptional example in which the ReO[subscript 4]– anion is immobilized in an extended framework through tight covalent interactions. The interlamellar PF[subscript 6]– anions in 1 can be exchanged with other anions including perrhenate, perchlorate, or periodate. The structural similarity between perrhenate and pertechnetate makes these materials of potential interest for pertechnetate trapping

Omicron B.1.1.529 variant infections associated with severe disease are uncommon in a COVID-19 under-vaccinated, high SARS-CoV-2 seroprevalence population in Malawi.

BACKGROUND: The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the fourth COVID-19 pandemic wave across the southern African region, including Malawi. The seroprevalence of SARS-CoV-2 antibodies and their association with epidemiological trends of hospitalisations and deaths are needed to aid locally relevant public health policy decisions. METHODS: We conducted a population-based serosurvey from December 27, 2021 to January 17, 2022, in 7 districts across Malawi to determine the seroprevalence of SARS-CoV-2 antibodies. Serum samples were tested for antibodies against SARS-CoV-2 receptor binding domain using WANTAI SARS-CoV-2 Receptor Binding Domain total antibody commercial enzyme-linked immunosorbent assay (ELISA). We also evaluated COVID-19 epidemiologic trends in Malawi, including cases, hospitalisations and deaths from April 1, 2021 through April 30, 2022, collected using the routine national COVID-19 reporting system. A multivariable logistic regression model was developed to investigate the factors associated with SARS-CoV-2 seropositivity. FINDINGS: Serum samples were analysed from 4619 participants (57% female; 60% aged 18-50 years), of whom 878/3794 (23%) of vaccine eligible adults had received a single dose of any COVID-19 vaccine. The overall assay-adjusted seroprevalence was 83.7% (95% confidence interval (CI), 79.3%-93.4%). Seroprevalence was lowest among children <13 years of age (66%) and highest among adults 18-50 years of age (82%). Seroprevalence was higher among vaccinated compared to unvaccinated participants (1 dose, 94% vs. 77%, adjusted odds ratio 4.89 [95% CI, 3.43-7.22]; 2 doses, 97% vs. 77%, aOR 6.62 [95% CI, 4.14-11.3]). Urban residents were more likely to be seropositive than those from rural settings (91% vs. 78%, aOR 2.76 [95% CI, 2.16-3.55]). There was at least a two-fold reduction in the proportion of hospitalisations and deaths among the reported cases in the fourth wave compared to the third wave (hospitalisations, 10.7% (95% CI, 10.2-11.3) vs. 4.86% (95% CI, 4.52-5.23), p < 0.0001; deaths, 3.48% (95% CI, 3.18-3.81) vs. 1.15% (95% CI, 1.00-1.34), p < 0.0001). INTERPRETATION: We report reduction in proportion of hospitalisations and deaths from SARS-CoV-2 infections during the Omicron variant dominated wave in Malawi, in the context of high SARS-CoV-2 seroprevalence and low COVID-19 vaccination coverage. These findings suggest that COVID-19 vaccination policy in high seroprevalence settings may need to be amended from mass campaigns to targeted vaccination of reported at-risk populations. FUNDING: Supported by the Bill and Melinda Gates Foundation (INV-039481)

Organic contaminants in western pond turtles in remote habitat in California

Remote aquatic ecosystems are exposed to an assortment of semivolatile organic compounds (SOCs) originating from current and historic uses, of local and global origin. Here, a representative suite of 57 current- and historic-use pesticides, polychlorinated biphenyls, and polycyclic aromatic hydrocarbons were surveyed in the plasma of the western pond turtle (Emys marmorata) and their potential prey items and habitat. California study sites included Sequoia National Park, Whiskeytown National Recreation Area, and Six Rivers National Forest. Each was downstream of undeveloped watersheds and varied in distance from agricultural and urban pollution sources. SOCs were detected frequently in all sites with more found in turtle plasma and aquatic macroinvertebrates in the two sites closest to agricultural and urban sources. Summed PCBs were highest in Whiskeytown National Recreation Area turtle plasma (mean; 1.56&nbsp;ng/g ww) compared to plasma from Sequoia National Park (0.16&nbsp;ng/g&nbsp;ww; p&nbsp;=&nbsp;0.002) and Six Rivers National Forest (0.07&nbsp;ng/g ww; p&nbsp;=&nbsp;0.001). While no current-use pesticides were detected in turtle plasma at any site, both current- and historic-use pesticides were found prominently in sediment and macroinvertebrates at the Sequoia National Park site, which is immediately downwind of Central Valley agriculture. SOC classes associated with urban and industrial pollution were found more often and at higher concentrations at Whiskeytown National Recreation Area. These findings demonstrate a range of SOC exposure in a turtle species with current and proposed conservation status and shed additional light on the fate of environmental contaminants in remote watersheds

CFD Modeling of Multiphase Flow in an SKS Furnace: The Effect of Tuyere Arrangements

Funding Information: Open access funding provided by Aalto University. This work was supported by the China Scholarship Council, and School of Chemical engineering, Aalto university. Publisher Copyright: © 2021, The Author(s). Copyright: Copyright 2021 Elsevier B.V., All rights reserved.The emerging bottom blown copper smelting (SKS) technology has attracted growing interest since it came into production. To further reveal the agitation behavior inside the bath and optimize the variable parameters, CFD simulation was conducted on a scaled down SKS furnace model with different tuyere arrangements. The Multi-Fluid VOF model was used for the first time in SKS furnace simulation and the simulated results show good agreement with an experimental water model reported in the literature, in terms of plume shape and surface wave. It was found that a low velocity region would appear on the opposite side of the bubble plume and persisted for a long time. To enhance the agitation in the low velocity region and reduce the dead zone area, an arrangement with tuyeres installed at each side of the furnace was recommended. Results suggested that a smaller tuyere angle difference would help to strengthen the agitation in the system. However, further investigation indicated that the difference in tuyere angle between two rows of tuyeres should be limited within a certain range to balance the requirements of higher agitation efficiency and longer lining refractory lifespan.Peer reviewe

SimonichStaciEnvironmentalMolecularToxicologyAerobicBioremediationPAH.pdf

This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society and can be found at: https://doi.org/10.1021/acs.est.5b00499The formation of more polar and toxic polycyclic aromatic hydrocarbon (PAH) transformation products is one of the concerns associated with the bioremediation of PAH-contaminated soils. Soil contaminated with coal tar (pre-bioremediation) from a former manufactured gas plant (MGP) site was treated in a laboratory scale bioreactor (post-bioremediation) and extracted using pressurized liquid extraction. The soil extracts were fractionated, based on polarity, and analyzed for 88 PAHs (unsubstituted, oxygenated, nitrated, and heterocyclic PAHs). The PAH concentrations in the soil tested, post-bioremediation, were lower than their regulatory maximum allowable concentrations (MACs), with the exception of the higher molecular weight PAHs (BaA, BkF, BbF, BaP, and IcdP), most of which did not undergo significant biodegradation. The soil extract fractions were tested for genotoxicity using the DT40 chicken lymphocyte bioassay and developmental toxicity using the embryonic zebrafish (Danio rerio) bioassay. A statistically significant increase in genotoxicity was measured in the unfractionated soil extract, as well as in four polar soil extract fractions, post-bioremediation (p < 0.05). In addition, a statistically significant increase in developmental toxicity was measured in one polar soil extract fraction, post-bioremediation (p < 0.05). A series of morphological abnormalities, including peculiar caudal fin malformations and hyperpigmentation in the tail, were measured in several soil extract fractions in embryonic zebrafish, both pre- and post-bioremediation. The increased toxicity measured post-bioremediation is not likely due to the 88 PAHs measured in this study (including quinones), because most were not present in the toxic polar fractions and/or because their concentrations did not increase post-bioremediation. However, the increased toxicity measured post-bioremediation is likely due to hydroxylated and carboxylated transformation products of the 3- and 4-ring PAHs (PHE, 1MPHE, 2MPHE, PRY, BaA, and FLA) that were most degraded

Organic contaminants in western pond turtles in remote habitat in California.

Remote aquatic ecosystems are exposed to an assortment of semivolatile organic compounds (SOCs) originating from current and historic uses, of local and global origin. Here, a representative suite of 57 current- and historic-use pesticides, polychlorinated biphenyls, and polycyclic aromatic hydrocarbons were surveyed in the plasma of the western pond turtle (Emys marmorata) and their potential prey items and habitat. California study sites included Sequoia National Park, Whiskeytown National Recreation Area, and Six Rivers National Forest. Each was downstream of undeveloped watersheds and varied in distance from agricultural and urban pollution sources. SOCs were detected frequently in all sites with more found in turtle plasma and aquatic macroinvertebrates in the two sites closest to agricultural and urban sources. Summed PCBs were highest in Whiskeytown National Recreation Area turtle plasma (mean; 1.56&nbsp;ng/g ww) compared to plasma from Sequoia National Park (0.16&nbsp;ng/g&nbsp;ww; p&nbsp;=&nbsp;0.002) and Six Rivers National Forest (0.07&nbsp;ng/g ww; p&nbsp;=&nbsp;0.001). While no current-use pesticides were detected in turtle plasma at any site, both current- and historic-use pesticides were found prominently in sediment and macroinvertebrates at the Sequoia National Park site, which is immediately downwind of Central Valley agriculture. SOC classes associated with urban and industrial pollution were found more often and at higher concentrations at Whiskeytown National Recreation Area. These findings demonstrate a range of SOC exposure in a turtle species with current and proposed conservation status and shed additional light on the fate of environmental contaminants in remote watersheds