•A nationwide survey of animal manure-based composts was carried out in China.•As was present mainly as AsⅤ, with DMA and MMA as the minor species in composts.•Zn, Cu, As, Cd and Hg were the most ...cautionary elements with composts application.
A nationwide survey of animal manure-based composts was carried out in China. Two hundred and twelve samples were collected and analyzed for the concentrations of 9 heavy metals or metalloids and arsenic (As) speciation. The concentrations of heavy metals vary widely (Zn 11.8–3692, Cu 3.6–916, Cr 0.7–6603, Ni 0.7–73, Pb 0.05–189, As 0.4–72, Co 0.1–94, Cd 0.01–8.7 and Hg 0.01–1.9mgkg−1 dry weight). Compared with the maximum permissible values of the Chinese standard for organic fertilizers, 13.7% and 2.4% of the composts exceeded the limits for As (15mgkg−1) and Cd (3mgkg−1), respectively. Some samples contained very high concentrations of Zn and Cu, although no limits have been set for these two metals in China. Further analysis showed that As was present mainly as arsenate (AsⅤ), with dimethylarsenate (DMA) and monomethylarsenate (MMA) as the minor species in composts. There were significant correlations between the concentrations of Zn, Cu and As, suggesting co-contamination of these elements in some composts. Monte Carlo simulations based on the distributions of metal concentrations and application rate showed that repeated applications of compost likely increase the concentrations of Zn, Cu, Cd and Hg in soil significantly compared with the soil background levels. This study highlights a need to minimize the concentrations of Zn, Cu, Cd, Hg and As in animal manures to ensure their safe recycling to agricultural soils.
Considerable proportions of rice grains produced in some areas in southern China contain high concentrations of cadmium (Cd), leading to unsafe levels of dietary Cd intake. Cultivars of Indica rice, ...widely grown in southern China, are particularly prone to high Cd accumulation in the grain. Effective methods are needed to decrease Cd accumulation in Indica rice.
OsHMA3, encoding a tonoplast Cd transporter, was overexpressed in an elite Indica rice cultivar (Zhongjiazao 17) driven by CaMV 35S promoter. The effects on Cd translocation, accumulation and tolerance, as well as on the agronomic traits and micronutrient concentrations were evaluated.
OsHMA3 overexpression markedly decreased Cd translocation from roots to shoots and increased Cd tolerance. OsHMA3 overexpression decreased Cd concentrations in brown rice by 94–98%, to levels just above the detection limit, when rice plants were grown in two Cd-contaminated paddy soils. OsHMA3 overexpression generally had no significant effect on grain yield and the concentrations of the essential micronutrients including zinc, iron, copper and manganese in field trials.
Overexpression of OsHMA3 is a highly effective method to reduce Cd accumulation in Indica rice, producing rice grains that were almost Cd free with little effect on grain yield or essential micronutrient concentrations.
•High Cd concentrations of Cd are found in some rice produced in southern China.•Transgenic rice overexpressing OsHMA3 gene was developed in an elite Indica cultivar.•Overexpressing OsHMA3 decreased grain Cd concentration by 94–98%.•Overexpressing OsHMA3 had little effect on grain yield and essential micronutrients.
Background
Computed tomography (CT) is essential for pulmonary nodule detection in diagnosing lung cancer. As deep learning algorithms have recently been regarded as a promising technique in medical ...fields, we attempt to integrate a well‐trained deep learning algorithm to detect and classify pulmonary nodules derived from clinical CT images.
Materials and Methods
Open‐source data sets and multicenter data sets have been used in this study. A three‐dimensional convolutional neural network (CNN) was designed to detect pulmonary nodules and classify them into malignant or benign diseases based on pathologically and laboratory proven results.
Results
The sensitivity and specificity of this well‐trained model were found to be 84.4% (95% confidence interval CI, 80.5%–88.3%) and 83.0% (95% CI, 79.5%–86.5%), respectively. Subgroup analysis of smaller nodules (<10 mm) have demonstrated remarkable sensitivity and specificity, similar to that of larger nodules (10–30 mm). Additional model validation was implemented by comparing manual assessments done by different ranks of doctors with those performed by three‐dimensional CNN. The results show that the performance of the CNN model was superior to manual assessment.
Conclusion
Under the companion diagnostics, the three‐dimensional CNN with a deep learning algorithm may assist radiologists in the future by providing accurate and timely information for diagnosing pulmonary nodules in regular clinical practices.
Implications for Practice
The three‐dimensional convolutional neural network described in this article demonstrated both high sensitivity and high specificity in classifying pulmonary nodules regardless of diameters as well as superiority compared with manual assessment. Although it still warrants further improvement and validation in larger screening cohorts, its clinical application could definitely facilitate and assist doctors in clinical practice.
摘要
背景。在肺癌的诊断中，计算机断层扫描 (CT) 对于肺结节的检测必不可少。近几年，随着医学领域逐渐认识到深度学习算法这种技术的价值，本研究试图集成一种训练有素的深度学习算法，对临床 CT 图像中的肺结节进行检测和分类。
材料和方法。本研究使用了开源数据集和多中心数据集。本文设计了一种三维卷积神经网络 (CNN) 来检测肺结节，然后根据病理和实验室证实的结果，判断为恶性或良性结节。
结果。这种训练有素的模型敏感性和特异性分别为 84.4% 95% 可信区间 (CI)， 80.5%‐88.3%和83.0%(95% CI，79.5%‐86.5%)。小结节 (< 10mm) 亚组分析显示的敏感性和特异性显著，与大结节 (10‐30mm) 相似。对比不同级别医生的人工评估结果与三维 CNN 的评估结果，进行了额外的模型验证。结果表明，CNN 模型的表现优于人工评估。
结论。通过伴随诊断可知，加入深度学习算法的三维 CNN 能够提供准确、及时的信息，有助于放射科医生在常规临床实践中的肺结节诊断工作。
实践意义:在对各种直径的肺结节分类中，本文所述的三维卷积神经网络具有较高的敏感性和特异性，与人工评估结果相比具有优越性。虽然仍需在更大的筛选队列中进行进一步改进和验证，但可以肯定的是，临床应用三维卷积神经网络可以促进和协助医生的临床实践工作。
Interest in deep convolutional neural networks (CNN) is growing because of demonstrated accuracy with less manual intervention in computer vision tasks. This article describes efforts to use a pre‐trained CNN model integrating with multi‐centers datasets for detection and classification of pulmonary nodules.
The cellular and subcellular distributions of trace elements can provide important clues to understanding how the elements are transported and stored in plant cells, but mapping their distributions ...is a challenging task.
The distributions of arsenic, iron, zinc, manganese and copper, as well as physiologically related macro-elements, were mapped in the node, internode and leaf sheath of rice (Oryza sativa) using synchrotron X-ray fluorescence (S-XRF) and high-resolution secondary ion mass spectrometry (NanoSIMS).
Although copper and silicon generally showed cell wall localization, arsenic, iron and zinc were strongly localized in the vacuoles of specific cell types. Arsenic was highly localized in the companion cell vacuoles of the phloem in all vascular bundles, showing a strong co-localization with sulfur, consistent with As(III)–thiol complexation. Within the node, zinc was localized in the vacuoles of the parenchyma cell bridge bordering the enlarged and diffuse vascular bundles, whereas iron and manganese were localized in the fundamental parenchyma cells, with iron being strongly co-localized with phosphorus in the vacuoles.
The highly heterogeneous and contrasting distribution patterns of these elements imply different transport activities and/or storage capacities among different cell types. Sequestration of arsenic in companion cell vacuoles may explain the limited phloem mobility of arsenite.
Improvement in managing HPV‐positive women is urgently needed. Based on a population‐based study which included 2112 women aged 49 to 69 from Shanxi, China, we aimed to evaluate the clinical ...performance of multiple triage strategies based on liquid‐based cytology (LBC), p16INK4a, viral load and partial genotyping, as a single or combined strategy for detecting cervical intraepithelial neoplasia grade 2/3 or higher (CIN2+/CIN3+) in women who tested positive by Hybrid Capture 2 (HC2). Among 452 HC2‐positive women, the test positivity of LBC (ASC‐US+), p16INK4a, HPV16/18 and HPV16/18/31/33/45 were 39.6%, 38.5%, 18.0% and 40.0%, respectively. Compared to LBC (ASC‐US+) triage, a single triage strategies using p16INK4a or extended genotyping (SureX HPV16/18/31/33/45) achieved comparable sensitivity (relative sensitivity: 1.08, 95% confidence interval CI: 0.93‐1.26 and 0.96, 95% CI: 0.76‐1.22) and specificity (relative specificity: 1.05, 95% CI: 0.96‐1.14 and 1.02, 95% CI: 0.92‐1.14) for CIN3+. Viral load triage using a ≥50 RLU/CO cut‐point also yielded similar results with LBC (ASC‐US+). Among combined triage strategies, HPV16/18 genotyping with reflex p16INK4a showed higher sensitivity and slightly lower specificity than LBC (ASC‐US+) for CIN3+ detection, however, the differences were not statistically significant. Of note, after a negative result by p16INK4a or LBC among HPV16/18 negative women, the posttest probability of CIN3+ was lower than 1%. Our study suggested that p16INK4a, extended genotyping and increased viral load cut‐point could be promising alternatives to cytology triage. Combined triage algorithms of HPV16/18 with reflex p16INK4a or cytology, if negative, are associated with the substantial low posttest risk sufficient to release women to next screening round.
What's new?
Cytology triage is widely used to manage the care of women with positive human papillomavirus (HPV) results following HPV‐based screening. Challenges with cytology in low‐resource settings, however, has fueled the development of other triage strategies. Whether these strategies are superior to cytology remains unclear. In this population‐based evaluation, promising alternatives to cytology triage were identified, including p16INK4a biomarker testing, extended genotyping, and viral load with increased cut‐point. These methods were especially suitable for settings that lack trained cytologists. Combined HPV16/18 with reflex p16INK4a or cytology provided optimal risk stratification, enabling double‐negative cases to be released to routine screening.
Selenite can be a dominant form of selenium (Se) in aerobic soils; however, unlike selenate, the mechanism of selenite uptake by plants remains unclear. Uptake, translocation and Se speciation in ...wheat (Triticum aestivum) supplied with selenate or selenite, or both, were investigated in hydroponic experiments. The kinetics of selenite influx was determined in short-term (30 min) experiments. Selenium speciation in the water-extractable fraction of roots and shoots was determined by HPLC-ICPMS. Plants absorbed similar amounts of Se within 1 d when supplied with selenite or selenate. Selenate and selenite uptake were enhanced in sulphur-starved and phosphorus-starved plants, respectively. Phosphate markedly increased Km of the selenite influx. Selenate and selenite uptake were both metabolically dependent. Selenite was rapidly converted to organic forms in roots, with limited translocation to shoots. Selenomethionine, selenomethionine Se-oxide, Se-methyl-selenocysteine and several other unidentified Se species were detected in the root extracts and xylem sap from selenite-treated plants. Selenate was highly mobile in xylem transport, but little was assimilated to organic forms in 1 d. The presence of selenite decreased selenate uptake and xylem transport. Selenite uptake is an active process likely mediated, at least partly, by phosphate transporters. Selenite and selenate differ greatly in the ease of assimilation and xylem transport.
Summary
Arsenic (As) biomethylation is an important component of the As biogeochemical cycle that can influence As toxicity and mobility in the environment. Biomethylation of As is catalyzed by the ...enzyme arsenite (AsIII) S‐adenosylmethionine methyltransferase (ArsM). To date, all identified ArsM orthologs with As(III) methylation activities have four conserved cysteine residues, which are thought to be essential for As(III) methylation. Here, we isolated an As(III)‐methylating bacterium, Bacillus sp. CX‐1, and identified a gene encoding a S‐adenosylmethionine methyltranserase termed BlArsM with low sequence similarities (≤ 39%) to other ArsMs. BlArsM has six cysteine residues (Cys10, Cys11, Cys145, Cys193, Cys195 and Cys268), three of which (Cys10, Cys145 and Cys195) align with conserved cysteine residues found in most ArsMs. BlarsM is constitutively expressed in Bacillus sp. CX‐1. Heterologous expression of BlarsM conferred As(III) resistance. Purified BlArsM methylated both As(III) and methylarsenite (MAsIII), with a final product of dimethylarsenate (DMAsV). When all six cysteines were individually altered to serine residues, only C145S and C195S derivatives lost the ability to methylate As(III) and MAs(III). The derivative C10S/C11S/C193S/C268S was still active. These results suggest that BlArsM is a novel As(III) S‐adenosylmethionine methyltransferase requiring only two conserved cysteine residues. A model of As(III) methylation by BlArsM is proposed.
Arsenic biomethylation is an important component of the arsenic biogeochemical cycle. We isolated an arsenite‐methylating bacterium, Bacillus sp. CX‐1, and identified a novel arsenite S‐adenosylmethionine methyltransferase (BlArsM) that can catalyze arsenic biomethylation. Different from ArsMs reported previously, BlArsM requires only two conserved cysteine residues for its catalytic activity.
Microbe-mediated arsenic (As) redox reactions play an important role in the biogeochemical cycling of As. Reduction of arsenate As(V) generally leads to As mobilization in paddy soils and increased ...As availability to rice plants, whereas oxidation of arsenite As(III) results in As immobilization. A novel chemoautotrophic As(III)-oxidizing bacterium, designated strain SY, was isolated from an As-contaminated paddy soil. The isolate was able to derive energy from the oxidation of As(III) to As(V) under both aerobic and anaerobic conditions using O2 or NO3(-) as the respective electron acceptor. Inoculation of the washed SY cells into a flooded soil greatly enhanced As(III) oxidation to As(V) both in the solution and adsorbed phases of the soil. Strain SY is phylogenetically closely related to Paracoccus niistensis with a 16S rRNA gene similarity of 96.79%. The isolate contains both the denitrification and ribulose 1,5-bisphosphate carboxylase/oxygenase gene clusters, underscoring its ability to denitrify and to fix CO2 while coupled to As(III) oxidation. Deletion of the aioA gene encoding the As(III) oxidase subunit A abolished the As(III) oxidation ability of strain SY and led to increased sensitivity to As(III), suggesting that As(III) oxidation is a detoxification mechanism in this bacterium under aerobic and heterotrophic growth conditions. Analysis of the aioA gene clone library revealed that the majority of the As(III)-oxidizing bacteria in the soil were closely related to the genera Paracoccus of α-Proteobacteria. Our results provide direct evidence for As(III) oxidation by Paracoccus species and suggest that these species may play an important role in As(III) oxidation in paddy soils under both aerobic and denitrifying conditions.
In order to give full play to the role of regional logistics in the regional economic development of the metropolitan area, a kind of hub-and-spoke regional logistics network based on hub-and-spoke ...model was established, which has the characteristics of hub-and-spoke network scale economy, scope economy, density economy and structure economy. Seventeen technical and economic indicators are sorted out from regional economy, industrial and commercial development, transportation infrastructure development and logistics industry development, and 35 counties and districts in the Capital metropolitan area are used as the research objects in 2020. The model is used to determine the network layout among node cities and to optimize the logistics network in the Capital metropolitan area.
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