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The incidence of esophageal adenocarcinoma (EA) and its precursor condition, Barrett's esophagus, has risen rapidly in the United States for reasons that are not fully understood. Therefore, we evaluated the association between use of supplemental vitamins and minerals and risk of neoplastic progression of Barrett's esophagus and EA. The Seattle Barrett's Esophagus Program is a prospective study based on 339 men and women with histologically confirmed Barrett's esophagus. Participants underwent baseline and periodic follow-up exams, which included endoscopy and self-administered questionnaires on diet, supplement use, and lifestyle characteristics. Use of multivitamins and 4 individual supplements was calculated using time-weighted averages of reported use over the observational period. Cox proportional-hazards models were used to calculate hazard ratios (HR) for each endpoint: EA, tetraploidy, and aneuploidy. During a mean follow-up of 5 yr, there were 37 cases of EA, 42 cases of tetraploidy, and 34 cases of aneuploidy. After controlling for multiple covariates including diet, nonsteroidal anti-inflammatory drug use, obesity, and smoking, participants who took 1 or more multivitamin pills/day had a significantly decreased risk of tetraploidy [HR = 0.19; 95% confidence interval (CI) = 0.08-0.47) and EA (HR = 0.38; 95% CI = 0.15-0.99] compared to those not taking multivitamins. Significant inverse associations were also observed between risk of EA and supplemental vitamin C (> or = 250 mg vs. none: HR = 0.25; 95% CI = 0.11-0.58) and vitamin E (> or = 180 mg vs. none: HR = 0.25; 95% CI = 0.10-0.60). In this cohort study, use of multivitamins and single antioxidant supplements was associated with a significantly reduced risk of EA and markers of neoplastic progression among individuals with Barrett's esophagus. [ABSTRACT FROM AUTHOR]

This cross-sectional study reports associations between anthropometric measures, serum antioxidant concentrations, and present diet with measures of elevated cell proliferation in 51 patients with Barrett's esophagus. Cell proliferation was assessed as fractions of cells in the S and G2 phases, measured in biopsies of Barrett's tissue and analyzed by DNA content flow cytometry. Elevated proportions in the S and G2 phases predict progression to adenocarcinoma. The percentage of cells in the S phase was positively associated with waist-to-hip ratio (r = 0.33, p < 0.05) and negatively associated with serum and dietary selenium (r = -0.34 and -0.32, respectively, p < 0.05). The percentage of cells in the G2 phase was positively associated with weight change from age 25 (r = 0.39, p < 0.01) and negatively associated with dietary selenium (r = -0.31, p < 0.05). Selenium from breads and grains was negatively associated with the percentage of cells in the S phase (r = -0.41, p < 0.01) and the percentage of cells in the G2 phase (r = -0.41, p < 0.01). These results suggest that increasing weight gain in adulthood, increasing waist-to-hip ratio, and decreasing dietary selenium intake and serum levels increase the risk of progression of Barrett's esophagus to adenocarcinoma. [ABSTRACT FROM AUTHOR]

Abstract Chest compression-only (CC-only) is now incorporated in the Norwegian protocol for dispatch guided CPR (cardiopulmonary resuscitation) in cardiac arrest of presumed cardiac aetiology. We present a case that is unique and instructive as well as unusual. It reminds us of the challenges that face bystanders, dispatch centres and ambulance services when faced with possible cardiac arrest. This case report describes a 50 year old man in a rural community. He had suffered a heart attack 8 months previously, and was found unconscious with respiratory arrest in his garden one morning. Due to the proximity to the ambulance station, the paramedics were on the scene within three minutes. A chain-saw was lying beside him, but no external injuries were seen. The patient had no radial pulse, central cyanosis and respiratory gasps approximately every 30 seconds. Ventilation with bag and mask was given, and soon a femoral pulse could be palpated. Blood sugar was elevated and ECG (electrocardiogram) was normal. GCS (Glasgow Coma Scale) was 3. Upon arrival of the physician staffed air ambulance, further examination revealed bilateral miosis of the pupils and continuing bradypnoea. Naloxone was given with an immediate effect and the patient woke up. The patient denied intake of narcotics, but additional information from the dispatch centre revealed that he was hepatitis C positive. After a few hours, the patient admitted to have obtained a fentanyl transdermal patch from an acquaintance, having chewed it before falling unconscious. This case report shows the importance as well as the challenges of identifying a non-cardiac cause of possible cardiac arrest, and the value of providing causal therapy.

BACKGROUND: Aspirin and other non-steroidal anti-inflammatory drugs (NSAID) probably decrease the risk of colorectal neoplasia; however their effect on development of oesophageal adenocarcinoma is less clear. We aimed to assess the role of NSAID in the development of oesophageal adenocarcinoma and precursor lesions in people with Barrett's oesophagus--a metaplastic disorder that confers a high risk of oesophageal adenocarcinoma. METHODS: We did a prospective study of the relation between duration, frequency, and recency of NSAID use and the risk of oesophageal adenocarcinoma, aneuploidy, and tetraploidy in a cohort of 350 people with Barrett's oesophagus followed for 20,770 person-months. We used proportional-hazards regression to calculate hazard ratios (HR) adjusted for age, sex, cigarette use, and anthropometric measurements. FINDINGS: Median follow-up was 65.5 months (range 3.1-106.9). Compared with never users, HR for oesophageal adenocarcinoma (n=37 cases) in current NSAID users was 0.32 (95% CI 0.14-0.76), and in former users was 0.70 (0.31-1.58). 5-year cumulative incidence of oesophageal adenocarcinoma was 14.3% (95% CI 9.3-21.6) for never users, 9.7% (4.5-20.5) for former users, and 6.6% (3.1-13.6) for current NSAID users. When changes in NSAID use during follow up were taken into account, the associations were strengthened: HR for oesophageal adenocarcinoma for current users at baseline or afterwards was 0.20 (95% CI 0.10-0.41) compared with never users. Compared with never users, current NSAID users (at baseline and follow-up) had less aneuploidy (n=35 cases; 0.25 [0.12-0.54]) and tetraploidy (n=45 cases; 0.44 [0.22-0.87]). INTERPRETATION: NSAID use might be an effective chemopreventive strategy, reducing the risk of neoplastic progression in Barrett's oesophagus. [ABSTRACT FROM AUTHOR]

Background: Dormant coronary collaterals are highly prevalent and clinically beneficial in cases of coronary occlusion. However, the magnitude of myocardial perfusion provided by immediate coronary collateral recruitment during acute occlusion is unknown. We aimed to quantify collateral myocardial perfusion during balloon occlusion in patients with coronary artery disease (CAD)., Methods: Patients without angiographically visible collaterals undergoing elective percutaneous transluminal coronary angioplasty (PTCA) to a single epicardial vessel underwent two scans with 99mTc-sestamibi myocardial perfusion single-photon emission computed tomography (SPECT). All subjects underwent at least three minutes of angiographically verified complete balloon occlusion, at which time an intravenous injection of the radiotracer was administered, followed by SPECT imaging. A second radiotracer injection followed by SPECT imaging was performed 24 h after PTCA., Results: The study included 22 patients (median [interquartile range] age 68 [54-72] years. The perfusion defect extent was 19 [11-38] % of the LV, and the collateral perfusion at rest was 64 [58-67]% of normal., Conclusion: This is the first study to describe the magnitude of short-term changes in coronary microvascular collateral perfusion in patients with CAD. On average, despite coronary occlusion and an absence of angiographically visible collateral vessels, collaterals provided more than half of the normal perfusion., (© 2023. The Author(s).)

Oncogene amplification on extrachromosomal DNA (ecDNA) drives the evolution of tumours and their resistance to treatment, and is associated with poor outcomes for patients with cancer 1-6 . At present, it is unclear whether ecDNA is a later manifestation of genomic instability, or whether it can be an early event in the transition from dysplasia to cancer. Here, to better understand the development of ecDNA, we analysed whole-genome sequencing (WGS) data from patients with oesophageal adenocarcinoma (EAC) or Barrett's oesophagus. These data included 206 biopsies in Barrett's oesophagus surveillance and EAC cohorts from Cambridge University. We also analysed WGS and histology data from biopsies that were collected across multiple regions at 2 time points from 80 patients in a case-control study at the Fred Hutchinson Cancer Center. In the Cambridge cohorts, the frequency of ecDNA increased between Barrett's-oesophagus-associated early-stage (24%) and late-stage (43%) EAC, suggesting that ecDNA is formed during cancer progression. In the cohort from the Fred Hutchinson Cancer Center, 33% of patients who developed EAC had at least one oesophageal biopsy with ecDNA before or at the diagnosis of EAC. In biopsies that were collected before cancer diagnosis, higher levels of ecDNA were present in samples from patients who later developed EAC than in samples from those who did not. We found that ecDNAs contained diverse collections of oncogenes and immunomodulatory genes. Furthermore, ecDNAs showed increases in copy number and structural complexity at more advanced stages of disease. Our findings show that ecDNA can develop early in the transition from high-grade dysplasia to cancer, and that ecDNAs progressively form and evolve under positive selection., (© 2023. The Author(s).)

Soil organic carbon can be increased through sympathetic land management and/or directly by incorporating carbon rich amendments. Herein, a field experiment amended paper crumble (PC) to soil at a normal deployment rate of 50 t ha -1 , and at higher rates up to 200 t ha -1 . The nominal 50 t ha -1 PC amendment resulted a mean increase in soil carbon of 12.5 g kg -1 . Using a modified Roth-C carbon fate model, the long-term (50 years) carbon storage potential of a 50 t ha -1 PC amendment was determined to be 0.36 t O C ha -1 . Modelling a rotational (4 yearly) 50 t ha -1 PC amendment indicated 6.65 t O C ha -1 uplift would accrue after 50 years. Contextualised for the average farm in the East of England (~120 ha, with 79 % as arable), PC derived increases in SOC would be equivalent to 2310 t CO 2 e. These results support the use of PC to deliver significant levels of soil recarbonisation. Beyond carbon, PC was observed to influence other soil properties. Benefits observed included, decreased bulk density, increased water holding capacity, and increased cation exchange capacity. While PC amendment did not significantly increase wheat (Triticum aestivum) crop yield, manifold benefits in terms of increased SOC, long-term carbon storage potential, and improved soil quality sustain PC as a beneficial soil conditioner., Competing Interests: Declaration of competing interest Brian Reid reports financial support was provided by Research England., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

While the genomes of normal tissues undergo dynamic changes over time, little is understood about the temporal-spatial dynamics of genomes in premalignant tissues that progress to cancer compared to those that remain cancer-free. Here we use whole genome sequencing to contrast genomic alterations in 427 longitudinal samples from 40 patients with stable Barrett's esophagus compared to 40 Barrett's patients who progressed to esophageal adenocarcinoma (ESAD). We show the same somatic mutational processes are active in Barrett's tissue regardless of outcome, with high levels of mutation, ESAD gene and focal chromosomal alterations, and similar mutational signatures. The critical distinction between stable Barrett's versus those who progress to cancer is acquisition and expansion of TP53-/- cell populations having complex structural variants and high-level amplifications, which are detectable up to six years prior to a cancer diagnosis. These findings reveal the timing of common somatic genome dynamics in stable Barrett's esophagus and define key genomic features specific to progression to esophageal adenocarcinoma, both of which are critical for cancer prevention and early detection strategies., (© 2022. The Author(s).)

Arsenic (As) pollution remains a major threat to the quality of global soils and drinking water. The health effects of As pollution are often severe and have been largely reported across Asia and South America. This study investigated the possibility of using unmodified biochar derived from rice husk (RB) and aspen wood (WB) at 400 °C and 700 °C to enhance the precipitation of calcium/arsenic compounds for the removal of As(III) from solution. The approach was based on utilizing calcium to precipitate arsenic in solution and adding unmodified biochar to enhance the process. Using this approach, As(III) concentration in aqueous solution decreased by 58.1% when biochar was added, compared to 25.4% in the absence of biochar. Varying the pH from acidic to alkaline enabled an investigation into the pH dependent dynamics of the approach. Results indicated that significant precipitation was only possible at near neutral pH (i.e. pH = 6.5) where calcium arsenites (i.e. Ca(AsO 2 ) 2 , and CaAsO 2 OH•½H 2 O) and arsenates (i.e. Ca 5 (AsO 4 ) 3 OH) were precipitated and deposited as aggregates in the pores of biochars. Arsenite was only slightly precipitated under acidic conditions (pH = 4.5) while no arsenite was precipitated under alkaline conditions (pH = 9.5). Arsenite desorption from wood biochar was lowest at pH 6.5 indicating that wood biochar was able to retain a large quantity of the precipitates formed at pH 6.5 compared to pH 4.5 and pH 9.5. Given that the removal of As(III) from solution is often challenging and that biochar modification invites additional cost, the study demonstrated that low cost unmodified biochar can be effective in enhancing the removal of As(III) from the environment through Ca-As precipitation., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Metaldehyde, a widely used molluscicide, is one of the most commonly detected pesticides in aquatic environments in the UK. In this study, metaldehyde concentrations and fluxes in stream water over a ten-year period (2008-2018) are reported for the River Colne catchment (Essex, southeast England), and the influence of hydrological conditions and application regimes are assessed. In general, peaks in metaldehyde concentration in river water occasionally exceeded 0.25 μg L -1 , and concentrations did not typically exceed the European Union Drinking Water Directive (EU DWD) regulatory limit of 0.1 μg L -1 . Metaldehyde concentration peaks displayed a seasonal pattern. Metaldehyde concentrations during periods when the molluscicide was not applied to agricultural land (January, July) and during the spring-summer application period (February to June) were generally low (0.01-0.03 μg L -1 ). Peaks in metaldehyde concentration mainly occurred during the autumn-winter application season (August to December), and were typically associated with high intensity hydrological regimes (daily rainfall ≥10 mm; stream flow up to 18 m 3 s -1 ). Where metaldehyde concentrations exceeded the EU DWD regulatory limit, this was short-lived. The annual flux at the top of the Colne catchment (0.2-0.6 kg a -1 ) tended to be lower than in the middle of the catchment (0.3-1.4 kg a -1 ), with maximum flux values observed at the bottom of the catchment (0.5-25.8 kg a -1 ). Metaldehyde losses from point of application to surface water varied between 0.01 and 0.25%, with a maximum of 1.18% (2012). Annual flux was primarily controlled by the annual precipitation and stream flow (R 2 = 0.9) rather than annual metaldehyde use (kg active applied). Precipitation explained 37% and 81% of variability in metaldehyde concentration and flux, respectively. Annual ranges in metaldehyde concentration were greater in the years 2012 and 2014 with an overall reduction in the range of metaldehyde concentrations evident over the period 2015-2018. It is the expectation that metaldehyde concentrations in stream water will continue to decrease following the withdrawal of metaldehyde for outdoor use in the UK from March 2022., Competing Interests: Declaration of competing interest The authors whose names are listed immediately below certify that they have NO affiliations with or involvement in any organization or entity with any financial interest (such as honoraria; educational grants; participation in speakers' bureaus; membership, employment, consultancies, stock ownership, or other equity interest; and expert testimony or patent-licensing arrangements), or non-financial interest (such as personal or professional relationships, affiliations, knowledge or beliefs) in the subject matter or materials discussed in this manuscript., (Crown Copyright © 2021. Published by Elsevier B.V. All rights reserved.)

Current carbon pricing and trading mechanisms, despite their efficacy in reducing GHG emissions from industry, will not be sufficient to achieve Net Zero targets. Current mechanisms that redress emissions are largely economic disincentives , in effect financial penalties for emitters. In order to attain Net Zero futures, financial incentives for activities that sequester carbon from the atmosphere are needed. Herein, we present the environmental and economic co-benefits of soil re-carbonization and justify support for soil carbon remuneration. With increasing momentum to develop green economies, and projected increases in carbon price, growth in the global carbon market is inevitable. The establishment of a soil-based carbon economy, within this emerging financial space, has the potential to deliver a paradigm shift that will accelerate climate change mitigation, and concurrently realize net gains for soil health and the delivery of soil ecosystem services. Pivotal to the emergence of a global soil carbon economy will be a consensus on certification instruments used for long-term soil carbon storage, and the development of robust institutional agreements and processes to facilitate soil carbon trading., (© 2021 The Authors.)

Soil ecosystem service (SES) approaches evidence the importance of soil for human well-being, contribute to improving dialogue between science and decision-making and encourage the translation of scientific results into public policies. Herein, through systematic review, we assess the state of the art of SES approaches in tropical regions. Through this review, 41 publications were identified; while most of these studies considered SES, a lack of a consistent framework to define SES was apparent. Most studies measured soil natural capital and processes, while only three studies undertook monetary valuation. Although the number of publications increased (from 1 to 41), between 2001 and 2019, the total number of publications for tropical regions is still small. Countries with the largest number of publications were Brazil ( n = 8), Colombia ( n = 6) and Mexico ( n = 4). This observation emphasizes an important knowledge gap pertaining to SES approaches and their link to tropical regions. With global momentum behind SES approaches, there is an opportunity to integrate SES approaches into policy and practice in tropical regions. The use of SES evaluation tools in tropical regions could transform how land use decisions are informed, mitigating soil degradation and protecting the ecosystems that soil underpins., (© 2021 The Authors.)

Background & Aims: Esophageal adenocarcinoma (EA) and its premalignant lesion, Barrett's esophagus (BE), are characterized by a strong and yet unexplained male predominance (with a male-to-female ratio in EA incidence of up to 6:1). Genome-wide association studies (GWAS) have identified more than 20 susceptibility loci for these conditions. However, potential sex differences in genetic associations with BE/EA remain largely unexplored., Methods: Given strong genetic overlap, BE and EA cases were combined into a single case group for analysis. These were compared with population-based controls. We performed sex-specific GWAS of BE/EA in 3 separate studies and then used fixed-effects meta-analysis to provide summary estimates for >9 million variants for male and female individuals. A series of downstream analyses were conducted separately in male and female individuals to identify genes associated with BE/EA and the genetic correlations between BE/EA and other traits., Results: We included 6758 male BE/EA cases, 7489 male controls, 1670 female BE/EA cases, and 6174 female controls. After Bonferroni correction, our meta-analysis of sex-specific GWAS identified 1 variant at chromosome 6q11.1 (rs112894788, KHDRBS2-MTRNR2L9, P BONF  = .039) that was statistically significantly associated with BE/EA risk in male individuals only, and 1 variant at chromosome 8p23.1 (rs13259457, PRSS55-RP1L1, P BONF  = 0.057) associated, at borderline significance, with BE/EA risk in female individuals only. We also observed strong genetic correlations of BE/EA with gastroesophageal reflux disease in male individuals and obesity in female individuals., Conclusions: The identified novel sex-specific variants associated with BE/EA could improve the understanding of the genetic architecture of the disease and the reasons for the male predominance., (Copyright © 2020 AGA Institute. All rights reserved.)

Background & Aims: Esophageal adenocarcinoma (EAC) occurs most frequently in men. We performed a Mendelian randomization analysis to investigate whether genetic factors that regulate levels of sex hormones are associated with risk of EAC or Barrett's esophagus (BE)., Methods: We conducted a Mendelian randomization analysis using data from patients with EAC (n = 2488) or BE (n = 3247) and control participants (n = 2127), included in international consortia of genome-wide association studies in Australia, Europe, and North America. Genetic risk scores or single-nucleotide variants were used as instrumental variables for 9 specific sex hormones. Logistic regression provided odds ratios (ORs) with 95% CIs., Results: Higher genetically predicted levels of follicle-stimulating hormones were associated with increased risks of EAC and/or BE in men (OR, 1.14 per allele increase; 95% CI, 1.01-1.27) and in women (OR, 1.28; 95% CI, 1.03-1.59). Higher predicted levels of luteinizing hormone were associated with a decreased risk of EAC in men (OR, 0.92 per SD increase; 95% CI, 0.87-0.99) and in women (OR, 0.93; 95% CI, 0.79-1.09), and decreased risks of BE (OR, 0.88; 95% CI, 0.77-0.99) and EAC and/or BE (OR, 0.89; 95% CI, 0.79-1.00) in women. We found no clear associations for other hormones studied, including sex hormone-binding globulin, dehydroepiandrosterone sulfate, testosterone, dihydrotestosterone, estradiol, progesterone, or free androgen index., Conclusions: In a Mendelian randomization analysis of data from patients with EAC or BE, we found an association between genetically predicted levels of follicle-stimulating and luteinizing hormones and risk of BE and EAC., (Copyright © 2020 AGA Institute. Published by Elsevier Inc. All rights reserved.)

Cancer genomes often harbor hundreds of somatic DNA rearrangement junctions, many of which cannot be easily classified into simple (e.g., deletion) or complex (e.g., chromothripsis) structural variant classes. Applying a novel genome graph computational paradigm to analyze the topology of junction copy number (JCN) across 2,778 tumor whole-genome sequences, we uncovered three novel complex rearrangement phenomena: pyrgo, rigma, and tyfonas. Pyrgo are "towers" of low-JCN duplications associated with early-replicating regions, superenhancers, and breast or ovarian cancers. Rigma comprise "chasms" of low-JCN deletions enriched in late-replicating fragile sites and gastrointestinal carcinomas. Tyfonas are "typhoons" of high-JCN junctions and fold-back inversions associated with expressed protein-coding fusions, breakend hypermutation, and acral, but not cutaneous, melanomas. Clustering of tumors according to genome graph-derived features identified subgroups associated with DNA repair defects and poor prognosis., Competing Interests: Declaration of Interests J.S.R.-F. reports receiving personal/consultancy fees from VolitionRx, Paige.AI, Goldman Sachs, REPARE Therapeutics, GRAIL, Ventana Medical Systems, Roche, Genentech, and InviCRO outside of the scope of the submitted work., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Barrett's Esophagus is a neoplastic condition which progresses to esophageal adenocarcinoma in 5% of cases. Key events affecting the outcome likely occur before diagnosis of Barrett's and cannot be directly observed; we use phylogenetic analysis to infer such past events. We performed whole-genome sequencing on 4-6 samples from 40 cancer outcome and 40 noncancer outcome patients with Barrett's Esophagus, and inferred within-patient phylogenies of deconvoluted clonal lineages. Spatially proximate lineages clustered in the phylogenies, but temporally proximate ones did not. Lineages with inferred loss-of-function mutations in both copies of TP53 and CDKN2A showed enhanced spatial spread, whereas lineages with loss-of-function mutations in other frequently mutated loci did not. We propose a two-phase model with expansions of TP53 and CKDN2A mutant lineages during initial growth of the segment, followed by relative stasis. Subsequent to initial expansion, mutations in these loci as well as ARID1A and SMARCA4 may show a local selective advantage but do not expand far: The spatial structure of the Barrett's segment remains stable during surveillance even in patients who go on to cancer. We conclude that the cancer/noncancer outcome is strongly affected by early steps in formation of the Barrett's segment., Competing Interests: None declared., (© 2020 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Thiol-modified rice straw biochar (RS) was prepared by an esterification reaction with β-mercaptoethanol and used for the remediation of Cd and Pb polluted soils. Modified biochar was characterized through elemental analysis, BET analysis, FE-SEM, FT-IR and XPS. These analytical results revealed that thiol groups were successfully grafted onto the surface of the biochar and were involved in metal ion complexation. Batch sorption experiments indicated that Cd 2+ and Pb 2+ sorption onto RS described well by a pseudo second order kinetic model and a Langmuir isotherm. The maximum adsorption capacities for Cd 2+ and Pb 2+ , in the single-metal systems, were 45.1 and 61.4 mg g -1 , respectively. In the binary-metal systems, RS selectively adsorbed Cd 2+ over Pb 2+ . Cd 2+ and Pb 2+ were removed mainly through surface complexation. In the soil incubation experiments (28 days), RS reduced the available Cd by 34.8-39.2 %; while, RS reduced the available Pb by 8.6 %-11.1 %. This research demonstrates RS as a potentially effective amendment for the remediation of heavy metal polluted soils., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Metaldehyde is a molluscicide used to control slugs and snails. Despite its extensive use, very little is known about the capacity of soil microbial communities to degrade this chemical. This research provides a synopsis of the latent capacity of soil microbial communities, present in agricultural (n=14), allotment (n=4) and garden (n=10) soils, to degrade metaldehyde. Extents of 14 C-metaldehyde mineralisation across all soils ranged from 17.7 to 60.0%. Pre-exposure (in situ, in the field) to metaldehyde was not observed to consistently increase extents of metaldehyde mineralisation. Where soils were augmented, (ex situ, in the laboratory) with metaldehyde (28 mg kg -1 ), the mineralisation capacity was increased in some, but not all, soils (uplift ranged from +0.10 to +16.9%). Results indicated that catabolic competence to degrade metaldehyde was evident in both surface (16.7-52.8%) and in sub-surface (30.0-66.4%) soil horizons. Collectively, the results suggest that catabolic competence to degrade metaldehyde was ubiquitous across a diverse range of soil environments; that varied in texture (from sand to silty clay loam), pH (6.15-8.20) and soil organic matter (SOM) content (1.2%-52.1%). Lighter texture soils, in general, were observed to have higher capacity to mineralise metaldehyde. Weak correlations between catabolic competence and soil pH and soil organic matter content were observed; it was noted that above a SOM threshold of 12% metaldehyde mineralisation was always >34%. It was concluded that the common occurrence of metaldehyde in EU waters is unlikely the consequence of low potential for this chemical to be degraded in soil. It is more likely that application regimes (quantities/timings) and meteorological drivers facilitate the transport of metaldehyde from point of application into water resources., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Background & Aims: Epidemiology studies of circulating concentrations of 25 hydroxy vitamin D (25(OH)D) and risk of esophageal adenocarcinoma (EAC) have produced conflicting results. We conducted a Mendelian randomization study to determine the associations between circulating concentrations of 25(OH)D and risks of EAC and its precursor, Barrett's esophagus (BE)., Methods: We conducted a Mendelian randomization study using a 2-sample (summary data) approach. Six single-nucleotide polymorphisms (SNPs; rs3755967, rs10741657, rs12785878, rs10745742, rs8018720, and rs17216707) associated with circulating concentrations of 25(OH)D were used as instrumental variables. We collected data from 6167 patients with BE, 4112 patients with EAC, and 17,159 individuals without BE or EAC (controls) participating in the Barrett's and Esophageal Adenocarcinoma Consortium, as well as studies from Bonn, Germany, and Cambridge and Oxford, United Kingdom. Analyses were performed separately for BE and EAC., Results: Overall, we found no evidence for an association between genetically estimated 25(OH)D concentration and risk of BE or EAC. The odds ratio per 20 nmol/L increase in genetically estimated 25(OH)D concentration for BE risk estimated by combining the individual SNP association using inverse variance weighting was 1.21 (95% CI, 0.77-1.92; P = .41). The odds ratio for EAC risk, estimated by combining the individual SNP association using inverse variance weighting, was 0.68 (95% CI, 0.39-1.19; P = .18)., Conclusions: In a Mendelian randomization study, we found that low genetically estimated 25(OH)D concentrations were not associated with risk of BE or EAC., (Copyright © 2019 AGA Institute. Published by Elsevier Inc. All rights reserved.)

It was highlighted that in the original article [1] the Availability of data and materials section was incorrect.

The "4 per mil" initiative recognizes the pivotal role of soil in carbon resequestration. The need for evidence to substantiate the influence of agricultural practices on chemical nature of soil carbon and microbial biodiversity has become a priority. However, owing to the molecular complexity of soil dissolved organic matter (DOM), specific linkages to microbial biodiversity have eluded researchers. Here, we characterized the chemodiversity of soil DOM, assessed the variation of soil bacterial community composition (BCC), and identified specific linkages between DOM traits and BCC. Sustained organic carbon amendment significantly ( P < 0.05) increased total organic matter reservoirs, resulted in higher chemodiversity of DOM and emergence of recalcitrant moieties (H/C < 1.5). In the meantime, sustained organic carbon amendment shaped the BCC to a more eutrophic state while long-term chemical fertilization directed the BCC toward an oligotrophic state. Meanwhile, higher connectivity and complexity were observed in organic carbon amendment by DOM-BCC network analysis, indicating that soil microbes tended to have more interaction with DOM molecules after organic matter inputs. These results highlight the potential for organic carbon amendments to not only build soil carbon stocks and increase their resilience but also mediate the functional state of soil bacterial communities.

Background & Aims: We developed comprehensive models to determine risk of Barrett's esophagus (BE) or esophageal adenocarcinoma (EAC) based on genetic and non-genetic factors., Methods: We used pooled data from 3288 patients with BE, 2511 patients with EAC, and 2177 individuals without either (controls) from participants in the international Barrett's and EAC consortium as well as the United Kingdom's BE gene study and stomach and esophageal cancer study. We collected data on 23 genetic variants associated with risk for BE or EAC, and constructed a polygenic risk score (PRS) for cases and controls by summing the risk allele counts for the variants weighted by their natural log-transformed effect estimates (odds ratios) extracted from genome-wide association studies. We also collected data on demographic and lifestyle factors (age, sex, smoking, body mass index, use of nonsteroidal anti-inflammatory drugs) and symptoms of gastroesophageal reflux disease (GERD). Risk models with various combinations of non-genetic factors and the PRS were compared for their accuracy in identifying patients with BE or EAC using the area under the receiver operating characteristic curve (AUC) analysis., Results: Individuals in the highest quartile of risk, based on genetic factors (PRS), had a 2-fold higher risk of BE (odds ratio, 2.22; 95% confidence interval, 1.89-2.60) or EAC (odds ratio, 2.46; 95% confidence interval, 2.07-2.92) than individual in the lowest quartile of risk based on PRS. Risk models developed based on only demographic or lifestyle factors or GERD symptoms identified patients with BE or EAC with AUC values ranging from 0.637 to 0.667. Combining data on demographic or lifestyle factors with data on GERD symptoms identified patients with BE with an AUC of 0.793 and patients with EAC with an AUC of 0.745. Including PRSs with these data only minimally increased the AUC values for BE (to 0.799) and EAC (to 0.754). Including the PRSs in the model developed based on non-genetic factors resulted in a net reclassification improvement for BE of 3.0% and for EAC of 5.6%., Conclusions: We used data from 3 large databases of patients from studies of BE or EAC to develop a risk prediction model based on genetic, clinical, and demographic/lifestyle factors. We identified a PRS that increases discrimination and net reclassification of individuals with vs without BE and EAC. However, the absolute magnitude of improvement is not sufficient to justify its clinical use., (Copyright © 2018 AGA Institute. Published by Elsevier Inc. All rights reserved.)

Background: Use of aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs) has been shown to protect against tetraploidy, aneuploidy, and chromosomal alterations in the metaplastic condition Barrett's esophagus (BE) and to lower the incidence and mortality of esophageal adenocarcinoma (EA). The esophagus is exposed to both intrinsic and extrinsic mutagens resulting from gastric reflux, chronic inflammation, and exposure to environmental carcinogens such as those found in cigarettes. Here we test the hypothesis that NSAID use inhibits accumulation of point mutations/indels during somatic genomic evolution in BE., Methods: Whole exome sequences were generated from 82 purified epithelial biopsies and paired blood samples from a cross-sectional study of 41 NSAID users and 41 non-users matched by sex, age, smoking, and continuous time using or not using NSAIDs., Results: NSAID use reduced overall frequency of point mutations across the spectrum of mutation types, lowered the frequency of mutations even when adjusted for both TP53 mutation and smoking status, and decreased the prevalence of clones with high variant allele frequency. Never smokers who consistently used NSAIDs had fewer point mutations in signature 17, which is commonly found in EA. NSAID users had, on average, a 50% reduction in functional gene mutations in nine cancer-associated pathways and also had less diversity in pathway mutational burden compared to non-users., Conclusions: These results indicate NSAID use functions to limit overall mutations on which selection can act and supports a model in which specific mutant cell populations survive or expand better in the absence of NSAIDs.

The low risk of progression of Barrett's esophagus (BE) to esophageal adenocarcinoma can lead to over-diagnosis and over-treatment of BE patients. This may be addressed through a better understanding of the dynamics surrounding BE malignant progression. Although genetic diversity has been characterized as a marker of malignant development, it is still unclear how BE arises and develops. Here we uncover the evolutionary dynamics of BE at crypt and biopsy levels in eight individuals, including four patients that experienced malignant progression. We assay eight individual crypts and the remaining epithelium by SNP array for each of 6-11 biopsies over 2 time points per patient (358 samples in total). Our results indicate that most Barrett's segments are clonal, with similar number and inferred rates of alterations observed for crypts and biopsies. Divergence correlates with geographical location, being higher near the gastro-esophageal junction. Relaxed clock analyses show that genomic instability precedes and is enhanced by genome doubling. These results shed light on the clinically relevant evolutionary dynamics of BE.

Excessive transport of fine sediment, and its associated pollutants, can cause detrimental impacts in aquatic environments. It is therefore important to perform accurate sediment source apportionment to identify hot spots of soil erosion. Various tracers have been adopted, often in combination, to identify sediment source type and its spatial origin; these include fallout radionuclides, geochemical tracers, mineral magnetic properties and bulk and compound-specific stable isotopes. In this review, the applicability of these techniques to particular settings and their advantages and limitations are reviewed. By synthesizing existing approaches, that make use of multiple tracers in combination with measured changes of channel geomorphological attributes, an integrated analysis of tracer profiles in deposited sediments in lakes and reservoirs can be made. Through a multi-scale approach for fine sediment tracking, temporal changes in soil erosion and sediment load can be reconstructed and the consequences of changing catchment practices evaluated. We recommend that long-term, as well as short-term, monitoring of riverine fine sediment and corresponding surface and subsurface sources at nested sites within a catchment are essential. Such monitoring will inform the development and validation of models for predicting dynamics of fine sediment transport as a function of hydro-climatic and geomorphological controls. We highlight that the need for monitoring is particularly important for hilly catchments with complex and changing land use. We recommend that research should be prioritized for sloping farmland-dominated catchments.

Understanding antibiotic biodegradation is important to the appreciation of their fate and removal from the environment. In this research an Isotope Ratio Mass Spectrometry (IRMS) method was developed to evaluate the extent of biodegradation of the antibiotic, sulphanilamide, in contaminated groundwater. Results indicted an enrichment in δ 13 C of 8.44‰ from -26.56 (at the contaminant source) to -18.12‰ (300m downfield of the source). These results confirm reductions in sulphanilamide concentrations (from 650 to 10mg/L) across the contaminant plume to be attributable to biodegradation (56%) vs. other natural attenuation processes, such as dilution or dispersion (42%). To understand the controls on sulphanilamide degradation ex-situ microcosms assessed the influence of sulphanilamide concentration, redox conditions and an alternative carbon source. Results indicated, high levels of anaerobic capacity (~50% mineralisation) to degrade sulphanilamide under high (263mg/L), moderate (10mg/L) and low (0.02mg/L) substrate concentrations. The addition of electron acceptors; nitrate and sulphate, did not significantly enhance the capacity of the groundwater to anaerobically biodegrade sulphanilamide. Interestingly, where alternative carbon sources were present, the addition of nitrate and sulphate inhibited sulphanilamide biodegradation. These results suggest, under in-situ conditions, when a preferential carbon source was available for biodegradation, sulphanilamide could be acting as a nitrogen and/or sulphur source. These findings are important as they highlight sulphanilamide being used as a carbon and a putative nitrogen and sulphur source, under prevailing iron reducing conditions., (Copyright © 2017. Published by Elsevier B.V.)

The inoculation of rice straw biochar with PAH-degrading Mycobacterium gilvum (1.27 × 10 11  ± 1.24 × 10 10  cell g -1 ), and the subsequent amendment of this composite material to PAHs contaminated (677 mg kg -1 ) coke plant soil, was conducted in order to investigate if would enhance PAHs biodegradation in soils. The microbe-biochar composite showed superior degradation capacity for phenanthrene, fluoranthene and pyrene. Phenanthrene loss in the microbe-biochar composite, free cell alone and biochar alone treatments was, respectively, 62.6 ± 3.2%, 47.3 ± 4.1% and non-significant (P > 0.05); whereas for fluoranthene loss it was 52.1 ± 2.3%; non-significant (P > 0.05) and non-significant (P > 0.05); and for pyrene loss it was 62.1 ± 0.9%; 19.7 ± 6.5% and 13.5 ± 2.8%. It was hypothesized that the improved remediation was underpinned by i) biochar enhanced mass transfer of PAHs from the soil to the carbonaceous biochar "sink", and ii) the subsequent degradation of the PAHs by the immobilized M. gilvum. To test this mechanism, a surfactant (Brij 30; 20 mg g -1 soil), was added to impede PAHs mass transfer to biochar and sorption. The surfactant increased solution phase PAH concentrations and significantly (P < 0.05) reduced PAH degradation in the biochar immobilized M. gilvum treatments; indicating the enhanced degradation occurred between the immobilized M. gilvum and biochar sorbed PAHs., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Cancer development is driven by genomic alterations, including copy number aberrations. The detection of copy number aberrations in tumor cells is often complicated by possible contamination of normal stromal cells in tumor samples and intratumor heterogeneity, namely the presence of multiple clones of tumor cells. In order to correctly quantify copy number aberrations, it is critical to successfully de-convolute the complex structure of the genetic information from tumor samples. In this article, we propose a general Bayesian method for estimating copy number aberrations when there are normal cells and potentially more than one tumor clones. Our method provides posterior probabilities for the proportions of tumor clones and normal cells. We incorporate prior information on the distribution of the copy numbers to prioritize biologically more plausible solutions and alleviate possible identifiability issues that have been observed by many researchers. Our model is flexible and can work for both SNP array and next-generation sequencing data. We compare our method to existing ones and illustrate the advantage of our approach in multiple datasets.

Globally, rapid urbanization, along with economic development, is dramatically changing the balance of biogeochemical cycles, impacting upon ecosystem services and impinging on United Nation global sustainability goals (inter alia: sustainable cities and communities; responsible consumption and production; good health and well-being; clean water and sanitation, and; to protect and conserve life on land and below water). A key feature of the urban ecosystems is that nutrient stocks, carbon (C), nitrogen (N) and phosphorus (P), are being enriched. Furthermore, urban ecosystems are highly engineered, biogeochemical cycling of nutrients within urban ecosystems is spatially segregated, and nutrients exported (e.g. in food) from rural/peri-urban areas are not being returned to support primary production in these environments. To redress these imbalances we propose the concept of the Peri-URban Ecosystem (PURE). Through the merging of conceptual approaches that relate to Critical Zone science and the dynamics of successional climax PURE serves at the symbiotic interface between rural/natural and urban ecosystems and allow re-coupling of resource flows. PURE provides a framework for tackling the most pressing of societal challenges and supporting global sustainability goals., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Introduction/objectives: Incidence of esophageal adenocarcinoma (EA), an often fatal cancer, has increased sharply over recent decades. Several important risk factors (reflux, obesity, smoking) have been identified for EA and its precursor, Barrett's esophagus (BE), but a key challenge remains identifying individuals at highest risk, since most with reflux do not develop BE, and most with BE do not progress to cancer. Metabolomics represents an emerging approach for identifying novel biomarkers associated with cancer development., Methods: We used targeted liquid chromatography-mass spectrometry (LC-MS) to profile 57 metabolites in 322 serum specimens derived from individuals with gastroesophageal reflux disease (GERD), BE, high-grade dysplasia (HGD), or EA, drawn from two well-annotated epidemiologic parent studies., Results: Multiple metabolites differed significantly (P<0.05) between BE versus GERD (n=9), and between HGD/EA versus BE (n=4). Several top candidates (FDR q≤0.15), including urate, homocysteine, and 3-nitrotyrosine, are linked to inflammatory processes, which may contribute to BE/EA pathogenesis. Multivariate modeling achieved moderate discrimination between HGD/EA and BE (AUC=0.75), with less pronounced separation for BE versus GERD (AUC=0.64)., Conclusion: Serum metabolite differences can be detected between individuals with GERD versus BE, and between those with BE versus HGD/EA, and may help differentiate patients at different stages of progression to EA., Competing Interests: Statement : D.R. holds equity and an executive role in Matrix-Bio, Inc. (IN, USA). The authors have no other potential conflicts of interest to disclose.

Greenhouse experiments were conducted to investigate the influence of rice straw biochar (RSB) on soil cadmium (Cd) availability and accumulation in lettuce. The RSB was applied either in bands or broadcast in the test site of four greenhouses with soil Cd concentrations ranging from 1.70-3.14 μg g -1 . Biochar doses applied in bands were half of those broadcast. The Cd levels in the shoots of lettuce were observed to be reduced by up to 57% with increasing RSB application rate (0, 6, 12, 18 t ha -1 ). Following RSB application, shoot Cd concentrations of lettuce were reduced to below the Chinese threshold value set for food, and hazard quotients for Cd associated with vegetable consumption were reduced from 0.70-1.11 to 0.42-0.65. A decrease in soil bulk density (11%) and increases in water holding capacity (16%), available phosphorus (30%), available potassium (197%), and lettuce yield (15%) were observed after RSB application. Multiple linear regression analysis suggested that the soil extractable Cd level (but not biomass dilution) and soil bulk density, as influenced by RSB addition, were the dominant contributors to the shoot Cd levels in lettuce and lettuce yield, respectively. These results highlight the potential for RSB to mitigate the phytoaccumulation of Cd and thereby to reduce human exposure from vegetable consumption. Application of biochar in band, rather than broadcasting over the entire area, represents an opportunity to halve the biochar cost while retaining a good remediation effect.

In The Cancer Genome Atlas the goals were to define how to treat advanced cancers with targeted therapy. However, the challenges facing cancer interception for early detection and prevention include length bias in which current screening and surveillance approaches frequently miss rapidly progressing cancers that then present at advanced stages in the clinic with symptoms (underdiagnosis). In contrast, many early detection strategies detect benign conditions that may never progress to cancer during a lifetime, and the patient dies of unrelated causes (overdiagnosis). This challenge to cancer interception is believed to be due to the speed at which the neoplasm evolves, called length bias sampling ; rapidly progressing cancers are missed by current early detection strategies. In contrast, slowly or non-progressing cancers or their precursors are selectively detected. This has led to the concept of cancer interception, which can be defined as active interception of a biological process that drives cancer development before the patient presents in the clinic with an advanced, symptomatic cancer. The solutions needed to advance strategies for cancer interception require assessing the rate at which the cancer evolves over time and space. This is an essential challenge that needs to be addressed by robust study designs including normal and non-progressing controls when known to be appropriate.

Understanding of the adsorption behavior of organic pollutants on carbon nanotubes (CNTs) and its governing factors are crucial for the assessment of transport and fate of organic pollutants. This study explored adsorption characteristics of linear alkylbenzene sulfonates (LAS) on carboxyl modified multi-walled carbon nanotubes (CMMWCNTs) and the effect of solution chemistry and temperature on LAS sorption. Results indicted LAS adsorption isotherms to display five distinct regions of sorption at 25°C and 60°C. Regardless of temperature, the adsorption isotherm of LAS on the CMMWCNTs was well described using the Freundlich equation. This result indicated heterogeneous distribution of adsorption sites on the CMMWCNT surface. At low initial LAS concentrations, below the critical micelle concentration, (2, 10 and 50mgL -1 ) LAS adsorption on the CMMWCNTs followed pseudo second-order kinetics. The highest LAS adsorption was observed at ionic strengths of 1.0molL -1 for NaCl; and 0.2molL -1 for both CaCl 2 and MgCl 2 . However, LAS sorption was greatest in the presence of sodium-divalent anion salts and at higher temperatures. These findings are of relevance to the fate and environmental risk of LAS in the presence of CMMWCNTs in high salinity wastewaters or effluents and brackish receiving surface water bodies (e.g., at estuaries)., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Many cancers offer an extended window of opportunity for early detection and therapeutic intervention that could lead to a reduction in cause-specific mortality. The pursuit of early detection in screening settings has resulted in decreased incidence and mortality for some cancers (e.g., colon and cervical cancers), and increased incidence with only modest or no effect on cause-specific mortality in others (e.g., breast and prostate). Whereas highly sensitive screening technologies are better at detecting a number of suspected "cancers" that are indolent and likely to remain clinically unimportant in the lifetime of a patient, defined as overdiagnosis, they often miss cancers that are aggressive and tend to present clinically between screenings, known as interval cancers. Unrecognized overdiagnosis leads to overtreatment with its attendant (often long-lasting) side effects, anxiety, and substantial financial harm. Existing methods often cannot differentiate indolent lesions from aggressive ones or understand the dynamics of neoplastic progression. To correctly identify the population that would benefit the most from screening and identify the lesions that would benefit most from treatment, the evolving genomic and molecular profiles of individual cancers during the clinical course of progression or indolence must be investigated, while taking into account an individual's genetic susceptibility, clinical and environmental risk factors, and the tumor microenvironment. Practical challenges lie not only in the lack of access to tissue specimens that are appropriate for the study of natural history, but also in the absence of targeted research strategies. This commentary summarizes the recommendations from a diverse group of scientists with expertise in basic biology, translational research, clinical research, statistics, and epidemiology and public health professionals convened to discuss research directions. J. Cell. Physiol. 231: 1870-1875, 2016. © 2015 Wiley Periodicals, Inc., (© 2015 Wiley Periodicals, Inc.)

Much research has considered the influence of biochars on the availability and phytoaccumulation of potentially toxic elements (PTEs) from soil. However, the vast majority of these studies use, what are arguably, unrealistic and unpractical amounts of biochar (10, 50 and even up to 100 t/ha). To offer a more realistic insight into the influence of biochar on PTE partitioning and phytoaccumulation, a field study, using modest rates of biochar application (1.5, 3.0 t/ha), was undertaken. Specifically, the research investigated the influence of sewage sludge biochar (SSBC) on the accumulation of Cd into rice (Oryza sativa L.) grown in Cd contaminated (0.82 ± 0.07 mg/kg) paddy soil. Results indicated, Cd concentrations in rice grains to significantly (p < 0.05) decrease from 1.35 ± 0.09 mg/kg in the control to 0.82 ± 0.07 mg/kg and 0.80 ± 0.21 mg/kg in the 1.5 t/ha and 3.0 t/ha treatments, respectively. Accordingly, the hazardous quotient (HQ) indices for Cd, associated with rice grain consumption, were also reduced by ∼40%. SSBC amendment significantly (p < 0.05) increased grain yields from 1.90 ± 0.08 g/plant in the control to 2.17 ± 0.30 g/plant and 3.40 ± 0.27 g/plant in the 1.5 t/ha and 3.0 t/ha treatments, respectively. Thus, the amendment of SSBC to contaminated paddy soils, even at low application rates, could be an effective approach to mitigate Cd accumulation into rice plants, to improve rice grain yields, and to thereby improve food security and protect public health., (Copyright © 2016 Elsevier Ltd. All rights reserved.)