A Two-Stream Mutual Attention Network for Semi-supervised Biomedical Segmentation with Noisy Labels

\begin{abstract} Learning-based methods suffer from a deficiency of clean annotations, especially in biomedical segmentation. Although many semi-supervised methods have been proposed to provide extra training data, automatically generated labels are usually too noisy to retrain models effectively. In this paper, we propose a Two-Stream Mutual Attention Network (TSMAN) that weakens the influence of back-propagated gradients caused by incorrect labels, thereby rendering the network robust to unclean data. The proposed TSMAN consists of two sub-networks that are connected by three types of attention models in different layers. The target of each attention model is to indicate potentially incorrect gradients in a certain layer for both sub-networks by analyzing their inferred features using the same input. In order to achieve this purpose, the attention models are designed based on the propagation analysis of noisy gradients at different layers. This allows the attention models to effectively discover incorrect labels and weaken their influence during the parameter updating process. By exchanging multi-level features within the two-stream architecture, the effects of noisy labels in each sub-network are reduced by decreasing the updating gradients. Furthermore, a hierarchical distillation is developed to provide more reliable pseudo labels for unlabelded data, which further boosts the performance of our retrained TSMAN. The experiments using both the HVSMR 2016 and BRATS 2015 benchmarks demonstrate that our semi-supervised learning framework surpasses the state-of-the-art fully-supervised results

Distinguishing Lymphomatous and Cancerous Lymph Nodes in 18F-Fluorodeoxyglucose Positron Emission Tomography/Computed Tomography by Radiomics Analysis

Background. The National Comprehensive Cancer Network guidelines recommend excisional biopsies for the diagnosis of lymphomas. However, resection biopsies in all patients who are suspected of having malignant lymph nodes may cause unnecessary injury and increase medical costs. We investigated the usefulness of 18F-fluorodeoxyglucose positron emission/computed tomography- (18F-FDG-PET/CT-) based radiomics analysis for differentiating between lymphomatous lymph nodes (LLNs) and cancerous lymph nodes (CLNs). Methods. Using texture analysis, radiomic parameters from the 18F-FDG-PET/CT images of 492 lymph nodes (373 lymphomatous lymph nodes and 119 cancerous lymph nodes) were extracted with the LIFEx package. Predictive models were generated from the six parameters with the largest area under the receiver operating characteristics curve (AUC) in PET or CT images in the training set (70% of the data), using binary logistic regression. These models were applied to the test set to calculate predictive variables, including the combination of PET and CT predictive variables (PREcombination). The AUC, sensitivity, specificity, and accuracy were used to compare the differentiating ability of the predictive variables. Results. Compared with the pathological diagnosis of the patient’s primary tumor, the AUC, sensitivity, specificity, and accuracy of PREcombination in differentiating between LLNs and CLNs were 0.95, 91.67%, 94.29%, and 92.96%, respectively. Moreover, PREcombination could effectively distinguish LLNs caused by various lymphoma subtypes (Hodgkin’s lymphoma and non-Hodgkin’s lymphoma) from CLNs, with the AUC, sensitivity, specificity, and accuracy being 0.85 and 0.90, 77.78% and 77.14%, 97.22% and 88.89%, and 90.74% and 83.10%, respectively. Conclusions. Radiomics analysis of 18F-FDG-PET/CT images may provide a noninvasive, effective method to distinguish LLN and CLN and inform the choice between fine-needle aspiration and excision biopsy for sampling suspected lymphomatous lymph nodes

Identification of PAL genes related to anthocyanin synthesis in tea plants and its correlation with anthocyanin content

The phenylalanine ammonia-lyase (PAL) gene family in tea plants (Camellia sinensis L.) encodes the enzyme that catalyzes the first reaction of the phenylpropane metabolic pathway. The present study aimed to characterize the PAL genes in tea plants, and get better insights on the CsPALs in anthocyanins accumulation. Seven CsPAL genes were identified and characterized in tea plants by bioinformatics analysis. Systematic analysis of CsPALs was conducted for its phylogenetic relationship, gene structure, chromosomal location, and protein conserved motifs based on tea plant genome. The cis-elements of CsPALs were responsive to light, abiotic stress, hormone, and MYB-binding site. Furthermore, tissue-specific expression analysis showed that CsPAL4 was expressed preferentially in young leaves and buds. Correlation analysis was performed in purple-leaf tea with anthocyanin components, and it was suggested that CsPAL4 was closely related with different anthocyanin accumulated, especially with cyanidin 3-O-galactoside, cyanidin 3-O-glucoside, and delphinidin 3-O-glucoside. Additionally, the putative upstream regulation factors CsMYBs (CsMYB59, CsARR1, CsSRM1, CsMYB101, and CsMYB52) and CsbHLHs (CsbHLH104, CsbHLH3, CsbIM1, CsTCP14, and CsPIF4) could bind to the promoter of CsPALs, thereby activating its transcription. This study provides a theoretical basis for further research to elucidate the functions of the CsPAL genes

GLP-2 Prevents Intestinal Mucosal Atrophy and Improves Tissue Antioxidant Capacity in a Mouse Model of Total Parenteral Nutrition

We investigated the effects of exogenous glucagon-like peptide-2 (GLP-2) on mucosal atrophy and intestinal antioxidant capacity in a mouse model of total parenteral nutrition (TPN). Male mice (6–8 weeks old) were divided into three groups (n = 8 for each group): a control group fed a standard laboratory chow diet, and experimental TPN (received standard TPN solution) and TPN + GLP-2 groups (received TPN supplemented with 60 µg/day of GLP-2 for 5 days). Mice in the TPN group had lower body weight and reduced intestinal length, villus height, and crypt depth compared to the control group (all p < 0.05). GLP-2 supplementation increased all parameters compared to TPN only (all p < 0.05). Intestinal total superoxide dismutase activity and reduced-glutathione level in the TPN + GLP-2 group were also higher relative to the TPN group (all p < 0.05). GLP-2 administration significantly upregulated proliferating cell nuclear antigen expression and increased glucose-regulated protein (GRP78) abundance. Compared with the control and TPN + GLP-2 groups, intestinal cleaved caspase-3 was increased in the TPN group (all p < 0.05). This study shows GLP-2 reduces TPN-associated intestinal atrophy and improves tissue antioxidant capacity. This effect may be dependent on enhanced epithelial cell proliferation, reduced apoptosis, and upregulated GRP78 expression