HoVer-Trans: Anatomy-aware HoVer-Transformer for ROI-free Breast Cancer Diagnosis in Ultrasound Images

Ultrasonography is an important routine examination for breast cancer diagnosis, due to its non-invasive, radiation-free and low-cost properties. However, the diagnostic accuracy of breast cancer is still limited due to its inherent limitations. It would be a tremendous success if we can precisely diagnose breast cancer by breast ultrasound images (BUS). Many learning-based computer-aided diagnostic methods have been proposed to achieve breast cancer diagnosis/lesion classification. However, most of them require a pre-define ROI and then classify the lesion inside the ROI. Conventional classification backbones, such as VGG16 and ResNet50, can achieve promising classification results with no ROI requirement. But these models lack interpretability, thus restricting their use in clinical practice. In this study, we propose a novel ROI-free model for breast cancer diagnosis in ultrasound images with interpretable feature representations. We leverage the anatomical prior knowledge that malignant and benign tumors have different spatial relationships between different tissue layers, and propose a HoVer-Transformer to formulate this prior knowledge. The proposed HoVer-Trans block extracts the inter- and intra-layer spatial information horizontally and vertically. We conduct and release an open dataset GDPH&SYSUCC for breast cancer diagnosis in BUS. The proposed model is evaluated in three datasets by comparing with four CNN-based models and two vision transformer models via five-fold cross validation. It achieves state-of-the-art classification performance with the best model interpretability. In the meanwhile, our proposed model outperforms two senior sonographers on the breast cancer diagnosis when only one BUS image is given

Responses in the population growth and reproduction of freshwater rotifer

In China, although the production and use of organochlorine pesticides (OCPs) have been banned for decades, relatively high levels of OCP residues have still been found in some water bodies, and can result in adverse acute and chronic effects on zooplankton including rotifers, which have  caused public concern for many years. Responses in the population growth and reproduction of freshwater rotifer Brachionus calyciflorus to four OCPs including aldrin, dieldrin, β-hexachlorocyclohexane (β-HCH) and chlordecone were studied by 3-day population growth and 4-day resting eggs (RE) production tests. In comparison with control, aldrin at 10 μg.L−1, β-HCH at 1000 μg.L−1 and chlordecone at 0.05 μg.L−1 significantly increased the population growth rate (r); but aldrin at 100 μg.L−1, dieldrin at 0.001 and 0.1 μg.L−1, β-HCH at 0.1–100 μg.L−1 and chlordecone at 50 μg.L−1 markedly decreased it. Aldrin at concentrations higher than 1 μg.L−1, dieldrin at 0.01 and 1000 μg.L−1, β-HCH at concentrations 0.1 and higher than 1 μg.L−1, and chlordecone at concentrations 0.005 and higher than 0.5 μg.L−1 significantly decreased the ratio of ovigerous females to non-ovigerous females (OF/NOF), but the reverse was true for aldrin at 0.1 μg.L−1 and β-HCH at 0.001 μg.L−1. Dieldrin at 0.001, 0.01 and 1000 μg.L−1 significantly decreased the ratio of mictic females to amictic females (MF/AF), but β-HCH at 1 and 10 μg.L−1 highly significantly increased it. Dieldrin at 1000 μg.L−1 and β-HCH at concentrations higher than 10 μg.L−1 markedly decreased the fertilization rate (FR). Both aldrin and chlordecone have no significant effect on the MF/AF and FR of rotifers. Aldrin at concentrations higher than 1 μg.L−1, dieldrin at lower than 0.1 and higher than 10 μg.L−1, β-HCH at 1000 μg.L−1 and chlordecone at 0.005, 0.05 and 50.0 μg.L−1 significantly decreased the mictic rate (MR) of rotifers, but the reverse was true for β-HCH at 1 μg.L−1. Aldrin at 10 μg.L−1, dieldrin at 0.001, 0.1 and 1000 μg.L−1, β-HCH at concentrations higher than 1 μg.L−1 and chlordecone at concentrations higher than 0.005 μg.L−1 markedly decreased RE production of rotifers, but β-HCH at 0.01 μg.L−1 significantly increased it. A clear dose–response relationship existed between the RE and the concentration of dieldrin, β-HCH and chlordecone, and the OF/NOF and the aldrin concentration. The RE and OF/NOF in rotifer population might be suitable endpoints for monitoring the low concentration of three OCPs (dieldrin, β-HCH and chlordecone) and aldrin, respectively

Soil Microbial Properties and Plant Growth Responses to Carbon and Water Addition in a Temperate Steppe: The Importance of Nutrient Availability

Background: Global climatic change is generally expected to stimulate net primary production, and consequently increase soil carbon (C) input. The enhanced C input together with potentially increased precipitation may affect soil microbial processes and plant growth. Methodology/Principal Findings: To examine the effects of C and water additions on soil microbial properties and plant growth, we conducted an experiment lasting two years in a temperate steppe of northeastern China. We found that soil C and water additions significantly affected microbial properties and stimulated plant growth. Carbon addition significantly increased soil microbial biomass and activity but had a limited effect on microbial community structure. Water addition significantly increased soil microbial activity in the first year but the response to water decreased in the second year. The water-induced changes of microbial activity could be ascribed to decreased soil nitrogen (N) availability and to the shift in soil microbial community structure. However, no water effect on soil microbial activity was visible under C addition during the two years, likely because C addition alleviated nutrient limitation of soil microbes. In addition, C and water additions interacted to affect plant functional group composition. Water addition significantly increased the ratio of grass to forb biomass in C addition plots but showed only minor effects under ambient C levels. Our results suggest that soil microbial activity and plant growth are limited by nutrient (C and N) and water availability, and highlight the importance of nutrien

Root Exudates Mediate the Processes of Soil Organic Carbon Input and Efflux

Root exudates, as an important form of material input from plants to the soil, regulate the carbon input and efflux of plant rhizosphere soil and play an important role in maintaining the carbon and nutrient balance of the whole ecosystem. Root exudates are notoriously difficult to collect due to their underlying characteristics (e.g., low concentration and fast turnover rate) and the associated methodological challenges of accurately measuring root exudates in native soils. As a result, up until now, it has been difficult to accurately quantify the soil organic carbon input from root exudates to the soil in most studies. In recent years, the contribution and ecological effects of root exudates to soil organic carbon input and efflux have been paid more and more attention. However, the ecological mechanism of soil organic carbon input and efflux mediated by root exudates are rarely analyzed comprehensively. In this review, the main processes and influencing factors of soil organic carbon input and efflux mediated by root exudates are demonstrated. Soil minerals and soil microbes play key roles in the processes. The carbon allocation from plants to soil is influenced by the relationship between root exudates and root functional traits. Compared with the quantity of root exudates, the response of root exudate quality to environmental changes affects soil carbon function more. In the future, the contribution of root exudates in different plants to soil carbon turnover and their relationship with soil nutrient availability will be accurately quantified, which will be helpful to understand the mechanism of soil organic carbon sequestration

The total biomass phospholipid fatty acids (PLFAs), percentages of fungal and bacterial PLFAs to the total biomass PLFAs, and the ratio of fungal to bacterial PLFAs as influenced by carbon addition (+60%) and water addition (+30%) in temperate steppe of northeastern China.

<p>Values show the monthly means from June to September in the growing season. Vertical bars indicate standard errors of means (n = 6). Difference lowercase letters indicate statistically significant differences (<i>P</i><0.05). A = ambient condition (control), C = carbon addition, W = water addition, CW = combined carbon and water additions.</p

Figure 1

<p>Daily precipitation (bars) and daily mean air temperature (line) in 2010 and 2011 (A). Data are from the eddy tower adjacent (approximately 100 m) to the experimental site. Seasonal variations of soil temperature (B) and water content (C) at topsoil layer (0–10 cm) in response to carbon addition (+60%) and water addition (+30%) in the temperate steppe of northeastern China. Insets represent the two seasonal mean values of soil temperature (ST) and water content (SWC). Vertical bars indicate standard errors of means (n = 6). Difference lowercase letters indicate statistically significant differences (<i>P</i><0.05). A = ambient condition (control), C = carbon addition, W = water addition, CW = combined carbon and water additions.</p

Responses of aboveground biomass carbon (C) and nitrogen (N), root biomass C and N, peak aboveground biomass of grass and forb and the grass: forb ratio to carbon addition (+60%) and water addition (+30%) in 2010 and 2011 in temperate steppe of northeastern China.

<p>Vertical bars indicate standard errors of means (n = 6). Difference lowercase letters indicate statistically significant differences (<i>P</i><0.05). A = ambient condition (control), C = carbon addition, W = water addition, CW = combined carbon and water additions.</p

Results (<i>F</i>-values) of Four-way ANOVAs on the effects of carbon addition (C), water addition (W), sampling date (D), year (Y), and their interactions on soil temperature (ST), soil water content (SWC), microbial biomass C (MBC), microbial biomass N (MBN), microbial activity (SMA), metabolic quotient (<i>q</i>CO₂), soil inorganic N (IN), soil total PLFAs (TP), contribution of soil fungal PLFAs (F) and bacterial PLFAs (B), and the ratio of fungal to bacterial PLFAs (F: B).

*<p>, **, <i>and</i> ***<i>represent significant at P<0.05, 0.01, and 0.001, respectively.</i></p

Monitoring the major taste components during black tea fermentation using multielement fusion information in decision level

Hitherto, the intelligent detection of black tea fermentation quality is still a thought-provoking problem because of one-side sample information and poor model performance. This study proposed a novel method for the prediction of major chemical components including total catechins, soluble sugar and caffeine using hyperspectral imaging technology and electrical properties. The multielement fusion information were used to establish quantitative prediction models. The performance of model using multielement fusion information was better than that of model using single information. Subsequently, the stacking combination model using fusion data combined with feature selection algorithms for evaluating the fermentation quality of black tea. Our proposed strategy achieved better performance than classical linear and nonlinear algorithms, with the correlation coefficient of the prediction set (Rp) for total catechins, soluble sugar and caffeine being 0.9978, 0.9973 and 0.9560, respectively. The results demonstrated that our proposed strategy could effectively evaluate the fermentation quality of black tea

Significant enhancement of UV emission in ZnO nanorods subject to Ga+ ion beam irradiation

Applications of ZnO nanomaterials in optoelectronics are still limited due to their insufficient photoluminescence efficiency. In order to optimize the photoluminescence properties of ZnO nanorods, the UV emission of vertically aligned ZnO nanorods grown on a Si substrate, in correlation with Ga+ ion irradiation at different ion energies (0.5 keV–16 keV), was investigated in the present study. We found that the UV intensity increased rapidly with increasing Ga+ ion energy, up to its maximum around 2 keV, at which point the intensity was approximately 50 times higher than that produced by as-grown ZnO nanorods. The gentle bombardment of low-energy Ga+ ions removes defects from ZnO nanorod surfaces. The Ga+ ions, on the other hand, implant into the nanorods, resulting in compressive strain. It is believed that the perfect arrangement of the crystal lattice upon removal of surface defects and the introduction of compressive strain are two factors that contribute to the significant enhancement of UV light generation.MOE (Min. of Education, S’pore)Accepted versio