CT-based radiogenomic analysis dissects intratumor heterogeneity and predicts prognosis of colorectal cancer: a multi-institutional retrospective study.

BACKGROUND: This study aimed to develop a radiogenomic prognostic prediction model for colorectal cancer (CRC) by investigating the biological and clinical relevance of intratumoural heterogeneity. METHODS: This retrospective multi-cohort study was conducted in three steps. First, we identified genomic subclones using unsupervised deconvolution analysis. Second, we established radiogenomic signatures to link radiomic features with prognostic subclone compositions in an independent radiogenomic dataset containing matched imaging and gene expression data. Finally, the prognostic value of the identified radiogenomic signatures was validated using two testing datasets containing imaging and survival information collected from separate medical centres. RESULTS: This multi-institutional retrospective study included 1601 patients (714 females and 887 males; mean age, 65 years ± 14 [standard deviation]) with CRC from 5 datasets. Molecular heterogeneity was identified using unsupervised deconvolution analysis of gene expression data. The relative prevalence of the two subclones associated with cell cycle and extracellular matrix pathways identified patients with significantly different survival outcomes. A radiogenomic signature-based predictive model significantly stratified patients into high- and low-risk groups with disparate disease-free survival (HR = 1.74, P = 0.003). Radiogenomic signatures were revealed as an independent predictive factor for CRC by multivariable analysis (HR = 1.59, 95% CI:1.03-2.45, P = 0.034). Functional analysis demonstrated that the 11 radiogenomic signatures were predominantly associated with extracellular matrix and immune-related pathways. CONCLUSIONS: The identified radiogenomic signatures might be a surrogate for genomic signatures and could complement the current prognostic strategies.

Intervention Effect of Taurine on LPS-Induced Intestinal Mechanical Barrier Injury in Piglets.

Taurine has the advantages of being safe, highly efficient, chemically stabile, and biologically active, together with having versatile functions. Presently, it is employed as a veterinary feed additive in animal research. The tight junctions that constitute the intestinal epithelial cells are the most critical structures for ensuring regular and uninterrupted digestion and absorption of food by the intestinal mucosa, while at the same time resisting invasions by toxins. The purpose of this study was to investigate the protective effect and mechanism of taurine action on intestinal mechanical barrier function of piglets that were infected with LPS. The results showed that 0.3% taurine inhibits LPS-driven increase in intestinal permeability and intestinal mucosal injury, the rise in the ratio of villus length to crypt depth within the duodenum, jejunum, and ileum, and the significant enhancement in the expression of tight junction protein-related genes. In summary, dietary taurine significantly reduces intestinal mucosal structural damage and intestinal mucosal permeability while increasing gene expression of tight junction proteins of the intestinal mucosa of piglets induced by LPS, thereby enhancing the effect of intestinal mucosal mechanical barriers.

Taurine Prevents LPS-Induced Liver Injury in Weaned Piglets.

This study employed taurine as a feed additive to explore the prophylactic effect of taurine on LPS-induced hepatic injury in piglets. The pathological shifts within hepatic tissue were observed by HE staining. Serum levels of ALT and AST together with SOD, CAT, GSH-PX activity, and MDA serum and liver levels were detected. TUNEL was used to detect apoptosis, while qPCR was employed to detect HO-1, Nrf-2, Bcl2, BAX, Caspase-3, and NF- κB p65 transcriptomic expression levels. TRL4, Caspase-3, Nrf-2, and NF- κB p-p65/NF- κB p65 were detected by Western blot. The results revealed that taurine reduces LPS-induced pathological damage of hepatic tissue and reduces the levels of ALT and AST in pig serum. The transcriptomic expression levels of HO-1 and Nrf-2 were upregulated, and proteomic expression of Nrf-2 was increased. SOD, CAT, and GSH-PX activity was elevated, while MDA content was reduced in serum and liver. The levels of mRNA of BAX and Caspase-3 were downregulated, but mRNA content of Bcl2 was increased, and the protein levels of TRL4, NF-κB p-p65/NF-κB p65, and Caspase-3 were diminished. Overall, the degree of hepatocyte apoptosis was also significantly reduced. In conclusion, taurine reduces LPS-induced injury of piglet liver, while reducing hepatocyte apoptotic levels. These data provide a scientific basis for the selection of animal feed additives and lay a foundation for the healthy and sustainable development of the porcine industry.

Segmentation only uses sparse annotations: Unified weakly and semi-supervised learning in medical images.

Since segmentation labeling is usually time-consuming and annotating medical images requires professional expertise, it is laborious to obtain a large-scale, high-quality annotated segmentation dataset. We propose a novel weakly- and semi-supervised framework named SOUSA (Segmentation Only Uses Sparse Annotations), aiming at learning from a small set of sparse annotated data and a large amount of unlabeled data. The proposed framework contains a teacher model and a student model. The student model is weakly supervised by scribbles and a Geodesic distance map derived from scribbles. Meanwhile, a large amount of unlabeled data with various perturbations are fed to student and teacher models. The consistency of their output predictions is imposed by Mean Square Error (MSE) loss and a carefully designed Multi-angle Projection Reconstruction (MPR) loss. Extensive experiments are conducted to demonstrate the robustness and generalization ability of our proposed method. Results show that our method outperforms weakly- and semi-supervised state-of-the-art methods on multiple datasets. Furthermore, our method achieves a competitive performance with some fully supervised methods with dense annotation when the size of the dataset is limited.

CT-based radiomics for predicting the rapid progression of coronavirus disease 2019 (COVID-19) pneumonia lesions.

OBJECTIVES: To develop and validate a radiomic model to predict the rapid progression (defined as volume growth of pneumonia lesions > 50% within seven days) in patients with coronavirus disease 2019 (COVID-19). METHODS: Patients with laboratory-confirmed COVID-19 who underwent longitudinal chest CT between January 01 and February 18, 2020 were included. A total of 1316 radiomic features were extracted from the lung parenchyma window for each CT. The least absolute shrinkage and selection operator (LASSO), Relief, Las Vegas Wrapper (LVW), L1-norm-Support Vector Machine (L1-norm-SVM), and recursive feature elimination (RFE) were applied to select the features that associated with rapid progression. Four machine learning classifiers were used for modeling, including Support Vector Machine (SVM), Random Forest (RF), Logistic Regression (LR), and Decision Tree (DT). Accordingly, 20 radiomic models were developed on the basis of 296 CT scans and validated in 74 CT scans. Model performance was determined by the receiver operating characteristic curve. RESULTS: A total of 107 patients (median age, 49.0 years, interquartile range, 35-54) were evaluated. The patients underwent a total of 370 chest CT scans with a median interval of 4 days (interquartile range, 3-5 days). The combination methods of L1-norm SVM and SVM with 17 radiomic features yielded the highest performance in predicting the likelihood of rapid progression of pneumonia lesions on next CT scan, with an AUC of 0.857 (95% CI: 0.766-0.947), sensitivity of 87.5%, and specificity of 70.7%. CONCLUSIONS: Our radiomic model based on longitudinal chest CT data could predict the rapid progression of pneumonia lesions, which may facilitate the CT follow-up intervals and reduce the radiation. ADVANCES IN KNOWLEDGE: Radiomic features extracted from the current chest CT have potential in predicting the likelihood of rapid progression of pneumonia lesions on the next chest CT, which would improve clinical decision-making regarding timely treatment.

Development of a risk-stratification scoring system for predicting lymphovascular invasion in breast cancer.

BACKGROUND: Lymphovascular invasion (LVI) is a vital risk factor for prognosis across cancers. We aimed to develop a scoring system for stratifying LVI risk in patients with breast cancer. METHODS: A total of 301 consecutive patients (mean age, 49.8 ± 11.0 years; range, 29-86 years) with breast cancer confirmed by pathological reports were retrospectively evaluated at the authors' institution between June 2015 and October 2018. All patients underwent contrast-enhanced Magnetic Resonance Imaging (MRI) examinations before surgery. MRI findings and histopathologic characteristics of tumors were collected for analysis. Breast LVI was confirmed by postoperative pathology. We used a stepwise logistic regression to select variables and two cut-points were determined to create a three-tier risk-stratification scoring system. The patients were classified as having low, moderate and high probability of LVI. The area under the receiver operating characteristic curve (AUC) was used to evaluate the discrimination ability of the scoring system. RESULTS: Tumor margins, lobulation sign, diffusion-weighted imaging appearance, MRI-reported axillary lymph node metastasis, time to signal intensity curve pattern, and HER-2 were selected as predictors for LVI in the point-based scoring system. Patients were considered at low risk if the score was < 3.5, moderate risk if the score was 3.5 to 6.0, and high risk if the score was ≥6.0. LVI risk was segmented from 0 to 100.0% and was positively associated with an increase in risk scores. The AUC of the scoring system was 0.824 (95% confidence interval [CI]: 0.776--0.872). CONCLUSION: This study shows that a simple and reliable score-based risk-stratification system can be practically used in stratifying the risk of LVI in breast cancer.

Low humic acids promote in vitro lily bulblet enlargement by enhancing roots growth and carbohydrate metabolism.

Bulblet development is a problem in global lily bulb production and carbohydrate metabolism is a crucial factor. Micropropagation acts as an efficient substitute for faster propagation and can provide a controllable condition to explore bulb growth. The present study was conducted to investigate the effects of humic acid (HA) on bulblet swelling and the carbohydrate metabolic pathway in Lilium Oriental Hybrids 'Sorbonne' under in vitro conditions. HA greatly promoted bulblet growth at 0.2, 2.0, and 20.0 mg/L, and pronounced increases in bulblet sucrose, total soluble sugar, and starch content were observed for higher HA concentrations (≥2.0 mg/L) within 45 d after transplanting (DAT). The activities of three major starch synthetic enzymes (including adenosine 5'-diphosphate glucose pyrophosphorylase, granule-bound starch synthase, and soluble starch synthase) were enhanced dramatically after HA application especially low concentration HA (LHA), indicating a quick response of starch metabolism. However, higher doses of HA also caused excessive aboveground biomass accumulation and inhibited root growth. Accordingly, an earlier carbon starvation emerged by observing evident starch degradation. Relative bulblet weight gradually decreased with increased HA doses and thereby broke the balance between the source and sink. A low HA concentration at 0.2 mg/L performed best in both root and bulblet growth. The number of roots and root length peaked at 14.5 and 5.75 cm, respectively. The fresh bulblet weight and diameter reached 468 mg (2.9 times that under the control treatment) and 11.68 mm, respectively. Further, sucrose/starch utilization and conversion were accelerated and carbon famine was delayed as a result with an average relative bulblet weight of 80.09%. To our knowledge, this is the first HA application and mechanism research into starch metabolism in both in vitro and in vivo condition in bulbous crops.