Modeling Organic Contaminant Transport through Reactive Media

We modeled the transport of 12 organic compounds through five different reactive media under diffusion and advection using deterministic and Monte Carlo methods to evaluate their effectiveness for sediment capping and/or liners. A broad range of media contaminant site scenarios are provided to aid in the selection of reactive media to address a broad range of organic sediment contaminants under diffusion or advection scenarios. Organic compounds evaluated include monoaromatics, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and alkanes covering a wide range of organic pollutants commonly found in contaminated sites. We investigated the performance of the reactive media granular activated carbon (GAC), organoclay (OC), shredded tires (ST), and apatite (AP) in comparison with the performance of conventional sand media. Based on the modeling results, a 2-cm GAC layer is predicted to be as effective to reduce organic contaminant transport as a 1- to 3-m-thick sand layer. Performances of GAC and OC were similar under both diffusion and advection due to their low observed diffusivity coefficients. As expected, low molecular weight compounds (e.g., monoaromatics and naphthalene) present a higher potential release risk. In contrast, pyrene, hexachlorobiphenyl, and tetradecane do not present toxicity concerns at the 95% confidence level after 100 years under diffusion and/or advection (except in AP/sand configurations). Lower acute toxicity contaminants such as benzene and dichlorobiphenyl are predicted to behave similarly for most media under advection, with partial breakthrough within 100 years. Performance uncertainty is substantially lower for organic contaminant transport simulations compared with those in a previous metal contaminant transport study. The relative GAC and OC effectiveness increases with increasing contaminant hydrophobicity. This behavior may be a key decision factor to select GAC and/or OC media at sites with highly hydrophobic and low toxicity/solubility ratio contaminants such as dichlorobiphenyls

Field Measurements and Modeling of Ebullition-Facilitated Flux of Heavy Metals and Polycyclic Aromatic Hydrocarbons from Sediments to the Water Column

Gas ebullition-facilitated transport of metals and polycyclic aromatic hydrocarbons (PAHs) from sediment was investigated in 14 urban waterway locations. Gas ebullition varied widely over four seasons (range 2–450 mmol m^–2 d^–1, mean 140 ± 90 mmol m^–2 d^–1) and was highly temperature dependent. Ebullition-facilitated metal fluxes were large: 50 ± 13 mg m^–2 d^–1 (Fe), 2.6 ± 0.71 mg m^–2 d^–1 (Zn), 1.5 ± 0.28 mg m^–2 d^–1 (Pb), and 0.19 ± 0.06 mg m^–2 d^–1 (Cr). Ebullition-facilitated PAH fluxes were also large: 0.61 ± 0.27 mg m^–2 d^–1 for anthracene, 0.65 ± 0.28 mg m^–2 d^–1 for benzo­[a]­pyrene, 0.72 ± 0.28 mg m^–2 d^–1 for chrysene, 3.51 ± 1.23 mg m^–2 d^–1 for fluoranthene, 0.23 ± 0.08 mg m^–2 d^–1 for naphthalene, 3.84 ± 1.47 mg m^–2 d^–1 for phenanthrene, and 2.46 ± 0.86 mg m^–2 d^–1 for pyrene. The magnitude of these fluxes indicates that gas ebullition is an important pathway for release of both PAHs and heavy metals from buried sediments. Multivariate regression analysis of the in situ gas ebullition flux and ebullition-facilitated contaminant flux suggests that metal transport likely is due to sediment particle resuspension, whereas PAH transport is due to both contaminant partitioning to gas bubbles and to sediment resuspension. These results indicate that assumptions regarding the natural recovery potential of ebullition-active sediments should be made with caution

DataSheet_1_Co-expression network analysis reveals PbTGA4 and PbAPRR2 as core transcription factors of drought response in an important timber species Phoebe bournei.xlsx

Phoebe bournei is one of the main afforestation tree species in subtropical regions of China and is famous for its timber. Its distribution and growth are significantly impaired by water conditions. Thus, it is essential to understand the mechanism of the stress response in P. bournei. Here, we analyzed the phenotypic changes and transcriptomic rearrangement in the leaves and roots of P. bournei seedlings grown for 0 h, 1 h, 24 h, and 72 h under simulated drought conditions (10% PEG 6000). The results showed that drought stress inhibited plant photosynthesis and increased oxidoreductase activity and abscisic acid (ABA) accumulation. Spatio-temporal transcriptomic analysis identified 2836 and 3704 differentially expressed genes (DEGs) in leaves and roots, respectively. The responsive genes in different organs presented various expression profiles at different times. Gene co-expression network analysis identified two core transcription factors, TGA4 and APRR2, from two modules that showed a strong positive correlation with ABA accumulation. Our study investigated the different responses of aboveground and belowground organs of P. bournei to drought stress and provides critical information for improving the drought resistance of this timber species.</p

Image_1_Co-expression network analysis reveals PbTGA4 and PbAPRR2 as core transcription factors of drought response in an important timber species Phoebe bournei.tif

Phoebe bournei is one of the main afforestation tree species in subtropical regions of China and is famous for its timber. Its distribution and growth are significantly impaired by water conditions. Thus, it is essential to understand the mechanism of the stress response in P. bournei. Here, we analyzed the phenotypic changes and transcriptomic rearrangement in the leaves and roots of P. bournei seedlings grown for 0 h, 1 h, 24 h, and 72 h under simulated drought conditions (10% PEG 6000). The results showed that drought stress inhibited plant photosynthesis and increased oxidoreductase activity and abscisic acid (ABA) accumulation. Spatio-temporal transcriptomic analysis identified 2836 and 3704 differentially expressed genes (DEGs) in leaves and roots, respectively. The responsive genes in different organs presented various expression profiles at different times. Gene co-expression network analysis identified two core transcription factors, TGA4 and APRR2, from two modules that showed a strong positive correlation with ABA accumulation. Our study investigated the different responses of aboveground and belowground organs of P. bournei to drought stress and provides critical information for improving the drought resistance of this timber species.</p

dynamics.mp4

This video illustrates the modulation of the depletion region induced by ultrafast photo-carrier dynamics

DataSheet_1_Single-cell mapping of N6-methyladenosine in esophageal squamous cell carcinoma and exploration of the risk model for immune infiltration.zip

BackgroundN6-methyladenosine (m6A) modification is the most common RNA modification, but its potential role in the development of esophageal cancer and its specific mechanisms still need to be further investigated.MethodsBulk RNA-seq of 174 patients with esophageal squamous carcinoma from the TCGA-ESCC cohort, GSE53625, and single-cell sequencing data from patients with esophageal squamous carcinoma from GSE188900 were included in this study. Single-cell analysis of scRNA-seq data from GSE188900 of 4 esophageal squamous carcinoma samples and calculation of PROGENy scores. Demonstrate the scoring of tumor-associated pathways for different cell populations. Cell Chat was calculated for cell populations. thereafter, m6A-related differential genes were sought and risk models were constructed to analyze the relevant biological functions and impact pathways of potential m6A genes and their impact on immune infiltration and tumor treatment sensitivity in ESCC was investigated.ResultsBy umap downscaling analysis, ESCC single-cell data were labelled into clusters of seven immune cell classes. Cellchat analysis showed that the network interactions of four signaling pathways, MIF, AFF, FN1 and CD99, all showed different cell type interactions. The prognostic risk model constructed by screening for m6A-related differential genes was of significant value in the prognostic stratification of ESCC patients and had a significant impact on immune infiltration and chemotherapy sensitivity in ESCC patients.ConclusionIn our study, we explored a blueprint for the distribution of single cells in ESCC based on m6A methylation and constructed a risk model for immune infiltration analysis and tumor efficacy stratification in ESCC on this basis. This may provide important potential guidance for revealing the role of m6A in immune escape and treatment resistance in esophageal cancer. </p

DataSheet_2_Single-cell mapping of N6-methyladenosine in esophageal squamous cell carcinoma and exploration of the risk model for immune infiltration.docx

BackgroundN6-methyladenosine (m6A) modification is the most common RNA modification, but its potential role in the development of esophageal cancer and its specific mechanisms still need to be further investigated.MethodsBulk RNA-seq of 174 patients with esophageal squamous carcinoma from the TCGA-ESCC cohort, GSE53625, and single-cell sequencing data from patients with esophageal squamous carcinoma from GSE188900 were included in this study. Single-cell analysis of scRNA-seq data from GSE188900 of 4 esophageal squamous carcinoma samples and calculation of PROGENy scores. Demonstrate the scoring of tumor-associated pathways for different cell populations. Cell Chat was calculated for cell populations. thereafter, m6A-related differential genes were sought and risk models were constructed to analyze the relevant biological functions and impact pathways of potential m6A genes and their impact on immune infiltration and tumor treatment sensitivity in ESCC was investigated.ResultsBy umap downscaling analysis, ESCC single-cell data were labelled into clusters of seven immune cell classes. Cellchat analysis showed that the network interactions of four signaling pathways, MIF, AFF, FN1 and CD99, all showed different cell type interactions. The prognostic risk model constructed by screening for m6A-related differential genes was of significant value in the prognostic stratification of ESCC patients and had a significant impact on immune infiltration and chemotherapy sensitivity in ESCC patients.ConclusionIn our study, we explored a blueprint for the distribution of single cells in ESCC based on m6A methylation and constructed a risk model for immune infiltration analysis and tumor efficacy stratification in ESCC on this basis. This may provide important potential guidance for revealing the role of m6A in immune escape and treatment resistance in esophageal cancer. </p

Table_1_Single-cell mapping of N6-methyladenosine in esophageal squamous cell carcinoma and exploration of the risk model for immune infiltration.xlsx

BackgroundN6-methyladenosine (m6A) modification is the most common RNA modification, but its potential role in the development of esophageal cancer and its specific mechanisms still need to be further investigated.MethodsBulk RNA-seq of 174 patients with esophageal squamous carcinoma from the TCGA-ESCC cohort, GSE53625, and single-cell sequencing data from patients with esophageal squamous carcinoma from GSE188900 were included in this study. Single-cell analysis of scRNA-seq data from GSE188900 of 4 esophageal squamous carcinoma samples and calculation of PROGENy scores. Demonstrate the scoring of tumor-associated pathways for different cell populations. Cell Chat was calculated for cell populations. thereafter, m6A-related differential genes were sought and risk models were constructed to analyze the relevant biological functions and impact pathways of potential m6A genes and their impact on immune infiltration and tumor treatment sensitivity in ESCC was investigated.ResultsBy umap downscaling analysis, ESCC single-cell data were labelled into clusters of seven immune cell classes. Cellchat analysis showed that the network interactions of four signaling pathways, MIF, AFF, FN1 and CD99, all showed different cell type interactions. The prognostic risk model constructed by screening for m6A-related differential genes was of significant value in the prognostic stratification of ESCC patients and had a significant impact on immune infiltration and chemotherapy sensitivity in ESCC patients.ConclusionIn our study, we explored a blueprint for the distribution of single cells in ESCC based on m6A methylation and constructed a risk model for immune infiltration analysis and tumor efficacy stratification in ESCC on this basis. This may provide important potential guidance for revealing the role of m6A in immune escape and treatment resistance in esophageal cancer. </p