Identification and validation of an immunotherapeutic signature for colon cancer based on the regulatory patterns of ferroptosis and their association with the tumor microenvironment.

The integrated landscape of ferroptosis regulatory patterns and their association with colon microenvironment have been demonstrated in recent studies. However, the ferroptosis-related immunotherapeutic signature for colon cancer (CC) remains unclear. We comprehensively evaluated 1623 CC samples, identified patterns of ferroptosis modification based on ferroptosis-associated genes, and systematically correlated these patterns with tumor microenvironment (TME) cell infiltration characteristics. In addition, the ferroptosis-regulated gene score (FRG-score) was constructed to quantify the pattern of ferroptosis alterations in individual tumors. Three distinct patterns of ferroptosis modification were identified, including antioxidant defense, iron toxicity, and lipid peroxidation. The characteristics of TME cell infiltration under these three patterns were highly consistent with the three immune phenotypes of tumors, including immune-inflamed, immune-excluded and immune-desert phenotypes. We also demonstrated that evaluation of ferroptosis regulatory patterns within individual tumors can predict tumor inflammatory status, tumor subtype, TME stromal activity, genetic variation, and clinical outcome. Immunotherapy cohorts confirmed that patients with low FRG-scores showed remarkable therapeutic and clinical benefits. Furthermore, the hub gene apolipoprotein L6 (APOL6), a drug-sensitive target associated with cancer cell ferroptosis, was identified through our proposed novel key gene screening process and validated in CC cell lines and scRNA-seq.

Staging liver fibrosis: comparison of radiomics model and fusion model based on multiparametric MRI in patients with chronic liver disease.

OBJECTIVES: To develop and compare radiomics model and fusion model based on multiple MR parameters for staging liver fibrosis in patients with chronic liver disease. MATERIALS AND METHODS: Patients with chronic liver disease who underwent multiparametric abdominal MRI were included in this retrospective study. Multiparametric MR images were imported into 3D-Slicer software for drawing bounding boxes on MR images. By using a 3D-Slicer extension of SlicerRadiomics, radiomics features were extracted from these MR images. The z-score normalization method was used for post-processing radiomics features. The least absolute shrinkage and selection operator method (LASSO) was performed for selecting significant radiomics features. The logistic regression analysis was used for building the radiomics model. A fusion model was built by integrating serum fibrosis biomarkers of aspartate transaminase-to-platelet ratio index (APRI) and the fibrosis-4 index (FIB-4) with radiomics signatures. RESULTS: In the training cohort, AUCs of radiomics and fusion model were 0.707-0.842 and 0.718-0.854 for differentiating different groups. In the testing cohort, AUCs were 0.514-0.724 and 0.609-0.728. For the training cohort, there was no significant difference of AUCs between radiomics and fusion model (p > 0.05). For the testing cohort, AUCs of fusion model were higher than those of radiomics model in differentiating F1-3 vs. F4 and F1-2 vs. F4 (p = 0.011 & 0.042). CONCLUSIONS: Radiomics model and fusion model based on multiparametric MRI exhibited the feasibility for staging liver fibrosis in patients with CLD, and APRI and FIB-4 could improve the diagnostic performance of radiomics model in differentiating F1-3 vs. F4 and F1-2 vs. F4.

Automatic liver segmentation and assessment of liver fibrosis using deep learning with MR T1-weighted images in rats.

OBJECTIVES: To validate the performance of nnU-Net in segmentation and CNN in classification for liver fibrosis using T1-weighted images. MATERIALS AND METHODS: In this prospective study, animal models of liver fibrosis were induced by injecting subcutaneously a mixture of Carbon tetrachloride and olive oil. A total of 99 male Wistar rats were successfully induced and underwent MR scanning with no contrast agent to get T1-weighted images. The regions of interest (ROIs) of the whole liver were delineated layer by layer along the liver edge by 3D Slicer. For segmentation task, all T1-weighted images were randomly divided into training and test cohorts in a ratio of 7:3. For classification, images containing the hepatic maximum diameter of every rat were selected and 80% images of no liver fibrosis (NLF), early liver fibrosis (ELF) and progressive liver fibrosis (PLF) stages were randomly selected for training, while the rest were used for testing. Liver segmentation was performed by the nnU-Net model. The convolutional neural network (CNN) was used for classification task of liver fibrosis stages. The Dice similarity coefficient was used to evaluate the segmentation performance of nnU-Net. Confusion matrix, ROC curve and accuracy were used to show the classification performance of CNN. RESULTS: A total of 2628 images were obtained from 99 Wistar rats by MR scanning. For liver segmentation by nnU-Net, the Dice similarity coefficient in the test set was 0.8477. The accuracies of CNN in staging NLF, ELF and PLF were 0.73, 0.89 and 0.84, respectively. The AUCs were 0.76, 0.88 and 0.79, respectively. CONCLUSION: The nnU-Net architecture is of high accuracy for liver segmentation and CNN for assessment of liver fibrosis with T1-weighted images.

Single-cell dissection, hdWGCNA and deep learning reveal the role of oxidatively stressed plasma cells in ulcerative colitis.

Ulcerative colitis (UC) develops as a result of complex interactions between various cell types in the mucosal microenvironment. In this study, we aim to elucidate the pathogenesis of ulcerative colitis at the single-cell level and unveil its clinical significance. Using single-cell RNA sequencing and high-dimensional weighted gene co-expression network analysis, we identify a subpopulation of plasma cells (PCs) with significantly increased infiltration in UC colonic mucosa, characterized by pronounced oxidative stress. Combining 10 machine learning approaches, we find that the PC oxidative stress genes accurately distinguish diseased mucosa from normal mucosa (independent external testing AUC=0.991, sensitivity=0.986, specificity=0.909). Using MCPcounter and non-negative matrix factorization, we identify the association between PC oxidative stress genes and immune cell infiltration as well as patient heterogeneity. Spatial transcriptome data is used to verify the infiltration of oxidatively stressed PCs in colitis. Finally, we develop a gene-immune convolutional neural network deep learning model to diagnose UC mucosa in different cohorts (independent external testing AUC=0.984, sensitivity=95.9%, specificity=100%). Our work sheds light on the key pathogenic cell subpopulations in UC and is essential for the development of future clinical disease diagnostic tools.

Instant deep sea debris detection for maneuverable underwater machines to build sustainable ocean using deep neural network.

Deep sea debris is any persistent man-made material that ends up in the deep sea. The scale and rapidly increasing amount of sea debris are endangering the health of the ocean. So, many marine communities are struggling for the objective of a clean, healthy, resilient, safe, and sustainably harvested ocean. That includes deep sea debris removal with maneuverable underwater machines. Previous studies have demonstrated that deep learning methods can successfully extract features from seabed images or videos, and are capable of identifying and detecting debris to facilitate debris collection. In this paper, the lightweight neural network (termed DSDebrisNet), which can leverage the detection speed and identification performance to achieve instant detection with high accuracy, is proposed to implement compound-scaled deep sea debris detection. In DSDebrisNet, a hybrid loss function considering the illumination and detection problem was also introduced to improve performance. In addition, the DSDebris dataset is constructed by extracting images and video frames from the JAMSTEC dataset and labeled using a graphical image annotation tool. The experiments are implemented on the deep sea debris dataset, and the results indicate that the proposed methodology can achieve promising detection accuracy in real-time. The in-depth study also provides significant evidence for the successful extension branch of artificial intelligence to the deep sea research domain.

A no-Reference Stereoscopic Image Quality Assessment Network Based on Binocular Interaction and Fusion Mechanisms.

In contemporary society full of stereoscopic images, how to assess visual quality of 3D images has attracted an increasing attention in field of Stereoscopic Image Quality Assessment (SIQA). Compared with 2D-IQA, SIQA is more challenging because some complicated features of Human Visual System (HVS), such as binocular interaction and binocular fusion, must be considered. In this paper, considering both binocular interaction and fusion mechanisms of the HVS, a hierarchical no-reference stereoscopic image quality assessment network (StereoIF-Net) is proposed to simulate the whole quality perception of 3D visual signals in human cortex, including two key modules: BIM and BFM. In particular, Binocular Interaction Modules (BIMs) are constructed to simulate binocular interaction in V2-V5 visual cortex regions, in which a novel cross convolution is designed to explore the interaction details in each region. In the BIMs, different output channel numbers are designed to imitate various receptive fields in V2-V5. Furthermore, a Binocular Fusion Module (BFM) with automatic learned weights is proposed to model binocular fusion of the HVS in higher cortex layers. The verification experiments are conducted on the LIVE 3D, IVC and Waterloo-IVC SIQA databases and three indices including PLCC, SROCC and RMSE are employed to evaluate the assessment consistency between StereoIF-Net and the HVS. The proposed StereoIF-Net achieves almost the best results compared with advanced SIQA methods. Specifically, the metric values on LIVE 3D, IVC and WIVC-I are the best, and are the second-best on the WIVC-II.