MRI-based Quantification of Intratumoral Heterogeneity for Predicting Treatment Response to Neoadjuvant Chemotherapy in Breast Cancer.

Background Breast cancer is highly heterogeneous, resulting in different treatment responses to neoadjuvant chemotherapy (NAC) among patients. A noninvasive quantitative measure of intratumoral heterogeneity (ITH) may be valuable for predicting treatment response. Purpose To develop a quantitative measure of ITH on pretreatment MRI scans and test its performance for predicting pathologic complete response (pCR) after NAC in patients with breast cancer. Materials and Methods Pretreatment MRI scans were retrospectively acquired in patients with breast cancer who received NAC followed by surgery at multiple centers from January 2000 to September 2020. Conventional radiomics (hereafter, C-radiomics) and intratumoral ecological diversity features were extracted from the MRI scans, and output probabilities of imaging-based decision tree models were used to generate a C-radiomics score and ITH index. Multivariable logistic regression analysis was used to identify variables associated with pCR, and significant variables, including clinicopathologic variables, C-radiomics score, and ITH index, were combined into a predictive model for which performance was assessed using the area under the receiver operating characteristic curve (AUC). Results The training data set was comprised of 335 patients (median age, 48 years [IQR, 42-54 years]) from centers A and B, and 590, 280, and 384 patients (median age, 48 years [IQR, 41-55 years]) were included in the three external test data sets. Molecular subtype (odds ratio [OR] range, 4.76-8.39 [95% CI: 1.79, 24.21]; all P < .01), ITH index (OR, 30.05 [95% CI: 8.43, 122.64]; P < .001), and C-radiomics score (OR, 29.90 [95% CI: 12.04, 81.70]; P < .001) were independently associated with the odds of achieving pCR. The combined model showed good performance for predicting pCR to NAC in the training data set (AUC, 0.90) and external test data sets (AUC range, 0.83-0.87). Conclusion A model that combined an index created from pretreatment MRI-based imaging features quantitating ITH, C-radiomics score, and clinicopathologic variables showed good performance for predicting pCR to NAC in patients with breast cancer. © RSNA, 2023 Supplemental material is available for this article. See also the editorial by Rauch in this issue.

Using Machine Learning Methods to Assess Lymphovascular Invasion and Survival in Breast Cancer: Performance of Combining Preoperative Clinical and MRI Characteristics.

BACKGROUND: Preoperative assessment of lymphovascular invasion (LVI) in invasive breast cancer (IBC) is of high clinical relevance for treatment decision-making and prognosis. PURPOSE: To investigate the associations of preoperative clinical and magnetic resonance imaging (MRI) characteristics with LVI and disease-free survival (DFS) by using machine learning methods in patients with IBC. STUDY TYPE: Retrospective. POPULATION: Five hundred and seventy-five women (range: 24-79 years) with IBC who underwent preoperative MRI examinations at two hospitals, divided into the training (N = 386) and validation datasets (N = 189). FIELD STRENGTH/SEQUENCE: Axial fat-suppressed T2-weighted turbo spin-echo sequence and dynamic contrast-enhanced with fat-suppressed T1-weighted three-dimensional gradient echo imaging. ASSESSMENT: MRI characteristics (clinical T stage, breast edema score, MRI axillary lymph node status, multicentricity or multifocality, enhancement pattern, adjacent vessel sign, and increased ipsilateral vascularity) were reviewed independently by three radiologists. Logistic regression (LR), eXtreme Gradient Boosting (XGBoost), k-Nearest Neighbor (KNN), and Support Vector Machine (SVM) algorithms were used to establish the models by combing preoperative clinical and MRI characteristics for assessing LVI status in the training dataset, and the methods were further applied in the validation dataset. The LVI score was calculated using the best-performing of the four models to analyze the association with DFS. STATISTICAL TESTS: Chi-squared tests, variance inflation factors, receiver operating characteristics (ROC), Kaplan-Meier curve, log-rank, Cox regression, and intraclass correlation coefficient were performed. The area under the ROC curve (AUC) and hazard ratios (HR) were calculated. A P-value <0.05 was considered statistically significant. RESULTS: The model established by the XGBoost algorithm had better performance than LR, SVM, and KNN models, achieving an AUC of 0.832 (95% confidence interval [CI]: 0.789, 0.876) in the training dataset and 0.838 (95% CI: 0.775, 0.901) in the validation dataset. The LVI score established by the XGBoost model was an independent indicator of DFS (adjusted HR: 2.66, 95% CI: 1.22-5.80). DATA CONCLUSION: The XGBoost model based on preoperative clinical and MRI characteristics may help to investigate the LVI status and survival in patients with IBC. LEVEL OF EVIDENCE: 3 TECHNICAL EFFICACY: Stage 2.

Automated whole-slide images assessment of immune infiltration in resected non-small-cell lung cancer: towards better risk-stratification.

BACKGROUND: High immune infiltration is associated with favourable prognosis in patients with non-small-cell lung cancer (NSCLC), but an automated workflow for characterizing immune infiltration, with high validity and reliability, remains to be developed. METHODS: We performed a multicentre retrospective study of patients with completely resected NSCLC. We developed an image analysis workflow for automatically evaluating the density of CD3+ and CD8+ T-cells in the tumour regions on immunohistochemistry (IHC)-stained whole-slide images (WSIs), and proposed an immune scoring system "I-score" based on the automated assessed cell density. RESULTS: A discovery cohort (n = 145) and a validation cohort (n = 180) were used to assess the prognostic value of the I-score for disease-free survival (DFS). The I-score (two-category) was an independent prognostic factor after adjusting for other clinicopathologic factors. Compared with a low I-score (two-category), a high I-score was associated with significantly superior DFS in the discovery cohort (adjusted hazard ratio [HR], 0.54; 95% confidence interval [CI] 0.33-0.86; P = 0.010) and validation cohort (adjusted HR, 0.57; 95% CI 0.36-0.92; P = 0.022). The I-score improved the prognostic stratification when integrating it into the Cox proportional hazard regression models with other risk factors (discovery cohort, C-index 0.742 vs. 0.728; validation cohort, C-index 0.695 vs. 0.685). CONCLUSION: This automated workflow and immune scoring system would advance the clinical application of immune microenvironment evaluation and support the clinical decision making for patients with resected NSCLC.

Multi-scale pathology image texture signature is a prognostic factor for resectable lung adenocarcinoma: a multi-center, retrospective study.

BACKGROUND: Tumor histomorphology analysis plays a crucial role in predicting the prognosis of resectable lung adenocarcinoma (LUAD). Computer-extracted image texture features have been previously shown to be correlated with outcome. However, a comprehensive, quantitative, and interpretable predictor remains to be developed. METHODS: In this multi-center study, we included patients with resectable LUAD from four independent cohorts. An automated pipeline was designed for extracting texture features from the tumor region in hematoxylin and eosin (H&E)-stained whole slide images (WSIs) at multiple magnifications. A multi-scale pathology image texture signature (MPIS) was constructed with the discriminative texture features in terms of overall survival (OS) selected by the LASSO method. The prognostic value of MPIS for OS was evaluated through univariable and multivariable analysis in the discovery set (n = 111) and the three external validation sets (V1, n = 115; V2, n = 116; and V3, n = 246). We constructed a Cox proportional hazards model incorporating clinicopathological variables and MPIS to assess whether MPIS could improve prognostic stratification. We also performed histo-genomics analysis to explore the associations between texture features and biological pathways. RESULTS: A set of eight texture features was selected to construct MPIS. In multivariable analysis, a higher MPIS was associated with significantly worse OS in the discovery set (HR 5.32, 95%CI 1.72-16.44; P = 0.0037) and the three external validation sets (V1: HR 2.63, 95%CI 1.10-6.29, P = 0.0292; V2: HR 2.99, 95%CI 1.34-6.66, P = 0.0075; V3: HR 1.93, 95%CI 1.15-3.23, P = 0.0125). The model that integrated clinicopathological variables and MPIS had better discrimination for OS compared to the clinicopathological variables-based model in the discovery set (C-index, 0.837 vs. 0.798) and the three external validation sets (V1: 0.704 vs. 0.679; V2: 0.728 vs. 0.666; V3: 0.696 vs. 0.669). Furthermore, the identified texture features were associated with biological pathways, such as cytokine activity, structural constituent of cytoskeleton, and extracellular matrix structural constituent. CONCLUSIONS: MPIS was an independent prognostic biomarker that was robust and interpretable. Integration of MPIS with clinicopathological variables improved prognostic stratification in resectable LUAD and might help enhance the quality of individualized postoperative care.

Methodological quality of machine learning-based quantitative imaging analysis studies in esophageal cancer: a systematic review of clinical outcome prediction after concurrent chemoradiotherapy.

PURPOSE: Studies based on machine learning-based quantitative imaging techniques have gained much interest in cancer research. The aim of this review is to critically appraise the existing machine learning-based quantitative imaging analysis studies predicting outcomes of esophageal cancer after concurrent chemoradiotherapy in accordance with PRISMA guidelines. METHODS: A systematic review was conducted in accordance with PRISMA guidelines. The citation search was performed via PubMed and Embase Ovid databases for literature published before April 2021. From each full-text article, study characteristics and model information were summarized. We proposed an appraisal matrix with 13 items to assess the methodological quality of each study based on recommended best-practices pertaining to quality. RESULTS: Out of 244 identified records, 37 studies met the inclusion criteria. Study endpoints included prognosis, treatment response, and toxicity after concurrent chemoradiotherapy with reported discrimination metrics in validation datasets between 0.6 and 0.9, with wide variation in quality. A total of 30 studies published within the last 5 years were evaluated for methodological quality and we found 11 studies with at least 6 "good" item ratings. CONCLUSION: A substantial number of studies lacked prospective registration, external validation, model calibration, and support for use in clinic. To further improve the predictive power of machine learning-based models and translate into real clinical applications in cancer research, appropriate methodologies, prospective registration, and multi-institution validation are recommended.

MRI characteristics of breast edema for assessing axillary lymph node burden in early-stage breast cancer: a retrospective bicentric study.

OBJECTIVES: To investigate whether breast edema characteristics at preoperative T2-weighted imaging (T2WI) could help evaluate axillary lymph node (ALN) burden in patients with early-stage breast cancer. METHODS: This retrospective study included women with clinical T1 and T2 stage breast cancer and preoperative MRI examination in two independent cohorts from May 2014 to December 2020. Low (< 3 LNs+) and high (≥ 3 LNs+) pathological ALN (pALN) burden were recorded as endpoint. Breast edema score (BES) was evaluated at T2WI. Univariable and multivariable analyses were performed by the logistic regression model. The added predictive value of BES was examined utilizing the area under the curve (AUC), net reclassification improvement (NRI), and integrated discrimination improvement (IDI). RESULTS: A total of 1092 patients were included in this study. BES was identified as the independent predictor of pALN burden in primary (n = 677) and validation (n = 415) cohorts. The analysis using MRI-ALN status showed that BES significantly improved the predictive performance of pALN burden (AUC: 0.65 vs 0.71, p < 0.001; IDI = 0.045, p < 0.001; continuous NRI = 0.159, p = 0.050). These results were confirmed in the validation cohort (AUC: 0.64 vs 0.69, p = 0.009; IDI = 0.050, p < 0.001; continuous NRI = 0.213, p = 0.047). Furthermore, BES was positively correlated with biologically invasive clinicopathological factors (p < 0.05). CONCLUSIONS: In individuals with early-stage breast cancer, preoperative MRI characteristics of breast edema could be a promising predictor for pALN burden, which may aid in treatment planning. KEY POINTS: • In this retrospective study of 1092 patients with early-stage breast cancer from two cohorts, the MRI characteristic of breast edema has independent and additive predictive value for assessing axillary lymph node burden. • Breast edema characteristics at T2WI positively correlated with biologically invasive clinicopathological factors, which may be useful for preoperative diagnosis and treatment planning for individual patients with breast cancer.

Systematic review of radiomic biomarkers for predicting immune checkpoint inhibitor treatment outcomes.

BACKGROUND: Systemic therapy agents targeting immune checkpoint inhibitors have been approved for use since 2011. This type of therapy aims to trigger a patient's immune response to attack tumor cells, rather than acting against the tumor directly. Radiomics is an automated method of medical image analysis that is now being actively investigated for predictive markers of treatment response in immunotherapy. OBJECTIVE: To conduct an early systematic review determining the current status of radiomic features as potential predictive markers of immunotherapy response. Provide a detailed critical appraisal of methodological quality of models, as this informs the degree of confidence about current reports of model performance. In addition, to offer some recommendations for future studies that could establish robust evidence for radiomic features as immunotherapy response markers. METHOD: A PubMed citation search was conducted for publications up to and including April 2020, followed by full-text screening. A total of seven articles meeting the eligibility criteria were examined in detail for study characteristics, model information and methodological quality. The review was conducted in the Cochrane style but has not been prospectively registered. Results are reported following Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA) guidelines. RESULTS: A total of seven studies were examined in detail, comprising non-small cell lung cancer, metastatic melanoma and a diverse assortment of solid tumors. Methodological robustness of reviewed studies varied greatly. Principal shortcomings were lack of prospective registration, and deficiencies in feature selection and dimensionality reduction, model calibration, clinical utility and external validation. A few studies with overall moderate to good methodological quality were identified. These results suggest that current state-of-the-art performance of radiomics in regards to discrimination (area under the curve or concordance index) is in the vicinity of 0.7, but the very small number of studies to date prevents any conclusive remarks to be made. We recommended future improvements in regards to prospective study registration, clinical utility, methodological procedure and data sharing. CONCLUSIONS: Radiomics has a potentially significant role for predicting immunotherapy response. Additional multi-institutional studies with robust methodological underpinning and repeated external validations are required to establish the (added) value of radiomics within the pantheon of clinical tools for decision-making in immunotherapy.

A deep learning quantified stroma-immune score to predict survival of patients with stage II-III colorectal cancer.

BACKGROUND: Profound heterogeneity in prognosis has been observed in colorectal cancer (CRC) patients with intermediate levels of disease (stage II-III), advocating the identification of valuable biomarkers that could improve the prognostic stratification. This study aims to develop a deep learning-based pipeline for fully automatic quantification of immune infiltration within the stroma region on immunohistochemical (IHC) whole-slide images (WSIs) and further analyze its prognostic value in CRC. METHODS: Patients from two independent cohorts were divided into three groups: the development group (N = 200), the internal (N = 134), and the external validation group (N = 90). We trained a convolutional neural network for tissue classification of CD3 and CD8 stained WSIs. A scoring system, named stroma-immune score, was established by quantifying the density of CD3+ and CD8+ T-cells infiltration in the stroma region. RESULTS: Patients with higher stroma-immune scores had much longer survival. In the development group, 5-year survival rates of the low and high scores were 55.7% and 80.8% (hazard ratio [HR] for high vs. low 0.39, 95% confidence interval [CI] 0.24-0.63, P < 0.001). These results were confirmed in the internal and external validation groups with 5-year survival rates of low and high scores were 57.1% and 78.8%, 63.9% and 88.9%, respectively (internal: HR for high vs. low 0.49, 95% CI 0.28-0.88, P = 0.017; external: HR for high vs. low 0.35, 95% CI 0.15-0.83, P = 0.018). The combination of stroma-immune score and tumor-node-metastasis (TNM) stage showed better discrimination ability for survival prediction than using the TNM stage alone. CONCLUSIONS: We proposed a stroma-immune score via a deep learning-based pipeline to quantify CD3+ and CD8+ T-cells densities within the stroma region on WSIs of CRC and further predict survival.

High Mobility Group Protein 1 Reverses Immune System Paralysis in Late-Phase Sepsis.

High mobility group protein 1 (HMGB1) is considered to be the primary inflammatory factor triggering immune paralysis in late-phase sepsis. In this study, however, we wanted to explore the possibility of using HMGB1 to boost local differentiation of bone marrow cells (BMCs) into regulatory dendritic cells (DCs) in vivo, thereby inducing immune reversal in late-phase sepsis and improving the prognosis. For this purpose, sepsis was induced by cecal ligation and puncture (CLP). Mice were injected intraperitoneally with HMGB1 (10, 50, or 250 µg/kg of body weight) 7 days before CLP. BMCs and liver immune cells were isolated at 0, 3, 5, and 7 days post-CLP. Mice were intranasally infected with Pseudomonas aeruginosa 3 days post-CLP as a secondary pneumonia infection model. BMCs and liver cells isolated from septic mice pretreated with HMGB1 were adoptively transferred into CLP mice. GFP+-C57BL/6 and C3H/HeN-C3H/HeJ parabiosis models were established. We found that HMGB1 pretreatment improved the survival of sepsis and increased the numbers of BMCs and liver immune cells in CLP mice. Furthermore, HMGB1 stimulation improved survival in the secondary pneumonia infection model. HMGB1 increased the number as well as the percentage of CD11c- CD45RBhigh DCs in septic BM and liver. Adoptive transfer of septic cells pretreated with HMGB1 into CLP mice attenuated sepsis. HMGB1 enhanced the redistribution of CD11c- CD45RBhigh DCs through TLR4 signaling in parabiosis models. We conclude that HMGB1 triggers immune reversal through the mobilization, redistribution, and local immune differentiation of BMCs, thereby compensating for impaired immunity and leading to sufficient bacterial eradication.

Vasonatrin peptide attenuates myocardial ischemia-reperfusion injury in diabetic rats and underlying mechanisms.

Diabetes mellitus increases morbidity/mortality of ischemic heart disease. Although atrial natriuretic peptide and C-type natriuretic peptide reduce the myocardial ischemia-reperfusion damage in nondiabetic rats, whether vasonatrin peptide (VNP), the artificial synthetic chimera of atrial natriuretic peptide and C-type natriuretic peptide, confers cardioprotective effects against ischemia-reperfusion injury, especially in diabetic patients, is still unclear. This study was designed to investigate the effects of VNP on ischemia-reperfusion injury in diabetic rats and to further elucidate its mechanisms. The high-fat diet-fed streptozotocin-induced diabetic Sprague-Dawley rats were subjected to ischemia-reperfusion operation. VNP treatment (100 µg/kg iv, 10 min before reperfusion) significantly improved the instantaneous first derivation of left ventricle pressure (±LV dP/dtmax) and LV systolic pressure and reduced LV end-diastolic pressure, apoptosis index, caspase-3 activity, plasma creatine kinase (CK), and lactate dehydrogenase (LDH) activities. Moreover, VNP inhibited endoplasmic reticulum (ER) stress by suppressing glucose-regulated protein 78 (GRP78) and C/EBP homologous protein (CHOP). These effects were mimicked by 8-bromine-cyclic guanosinemonophosphate (8-Br-cGMP), a cGMP analog, whereas they were inhibited by KT-5823, the selective inhibitor of PKG. In addition, pretreatment with tauroursodeoxycholic acid (TUDCA), a specific inhibitor of ER stress, could not further promote the VNP's cardioprotective effect in diabetic rats. In vitro H9c2 cardiomyocytes were subjected to hypoxia/reoxygenation and incubated with or without VNP (10(-8) mol/l). Gene knockdown of PKG1α with siRNA blunted VNP inhibition of ER stress and apoptosis, while overexpression of PKG1α resulted in significant decreased ER stress and apoptosis. VNP protects the diabetic heart against ischemia-reperfusion injury by inhibiting ER stress via the cGMP-PKG signaling pathway. These results suggest that VNP may have potential therapeutic value for the diabetic patients with ischemic heart disease.

Tremella Polysaccharides attenuated sepsis through inhibiting abnormal CD4⁺CD25(high) regulatory T cells in mice.

Tremella Polysaccharides (TPS) have been reported to play an important role in regulating immune responses. Tregs are widely identified as the critical reason for immune dysfunction during sepsis. However, whether TPS could influence the immunomodulatory activities of Tregs in post-burn sepsis mice remains unclear. In this experiment, we researched the effects of TPS on peripheral blood Tregs in sepsis mouse induced by burn plus Pseudomonas aeruginosa infection. Results showed that TPS reversed the influences of Tregs on CD4⁺T cells proliferation and polarization and declined the level of IL-10 in burn plus P. aeruginosa infection mice. In addition, TPS notably reduced the mortality of post-burn sepsis mice. Therefore, TPS could inhibit the abnormal activities of CD4⁺CD25(high) Tregs in burn with P. aeruginosa infection mice, at least in part via inhibiting IL-10 secretion, and trigger a shift of Th2 to Th1 with activation of CD4⁺T cells in burn with P. aeruginosa infection mice.

Learning At a Glance: Towards Interpretable Data-Limited Continual Semantic Segmentation Via Semantic-Invariance Modelling.

Continual semantic segmentation (CSS) based on incremental learning (IL) is a great endeavour in developing human- like segmentation models. However, current CSS approaches encounter challenges in the trade-off between preserving old knowledge and learning new ones, where they still need large-scale annotated data for incremental training and lack interpretability. In this paper, we present Learning at a Glance (LAG), an efficient, robust, human- like and interpretable approach for CSS. Specifically, LAG is a simple and model-agnostic architecture, yet it achieves competitive CSS efficiency with limited incremental data. Inspired by human- like recognition patterns, we propose a semantic-invariance modelling approach via semantic features decoupling that simultaneously reconciles solid knowledge inheritance and new-term learning. Concretely, the proposed decoupling manner includes two ways, i.e., channel- wise decoupling and spatial-level neuron-relevant semantic consistency. Our approach preserves semantic-invariant knowledge as solid prototypes to alleviate catastrophic forgetting, while also constraining sample-specific contents through an asymmetric contrastive learning method to enhance model robustness during IL steps. Experimental results in multiple datasets validate the effectiveness of the proposed method. Furthermore, we introduce a novel CSS protocol that better reflects realistic data-limited CSS settings, and LAG achieves superior performance under multiple data-limited conditions.

Traffic safety comprehensive evaluation of urban tunnel visual guiding system based on extension matter-element model: a case study in tunnel curves.

OBJECTIVE: The visual guiding system, as a tunnel traffic safety improvement method by using visual guiding facilities to actively guide driving safely, has been widely used in countries with many tunnels, in recent years. This paper aims to quantitatively study the comprehensive evaluation of traffic safety of the visual guiding system in tunnels, which has certain engineering application value and can provide support for the quantitative evaluation and optimal design of tunnel traffic safety. METHODS: Based on the analysis of the relevant factors of urban tunnel traffic safety, a multi-factor comprehensive evaluation system with 5 upper-level indicators and 12 basic-level indicators was proposed. Considering the independent and incompatible indicators, a comprehensive evaluation method of traffic safety of the visual guiding system in urban tunnels was constructed by using the extension matter-element model. Taking the scene of 4 types of tunnel curves, such as no facilities, horizontal stripe, chevron alignment sign, and LED arch, as examples, the comprehensive evaluation of various schemes were carried out by using simulation tests. RESULTS: The traffic safety comprehensive evaluation system of visual guiding system in urban tunnels can be analyzed from five aspects: perception reaction, guidance ability, driver factor, driving task, and facility appearance. The results demonstrated significant the comprehensive evaluation result of the target level of scene 1 was L4, scene 2 was L3, scene 3 was L2, and scene 4 was L1. That is, the final results of the comprehensive evaluation of the four scenes were poor, medium, good, and very good, respectively. CONCLUSIONS: In the scheme of visual guiding system for urban tunnel curves, the effectiveness of the three types of designs, from high to low, was the LED arch, chevron alignment sign, and horizontal stripe, and the safety of the scene without facilities was the lowest. Hence, setting the LED arch in the urban tunnel curve has a good effect in the aspects of guidance ability, sight distance, and sight zone, and is conducive to the driver's perception reaction and driving task.

PA-Net: A phase attention network fusing venous and arterial phase features of CT images for liver tumor segmentation.

BACKGROUND AND OBJECTIVE: Liver cancer seriously threatens human health. In clinical diagnosis, contrast-enhanced computed tomography (CECT) images provide important supplementary information for accurate liver tumor segmentation. However, most of the existing methods of liver tumor automatic segmentation focus only on single-phase image features. And the existing multi-modal methods have limited segmentation effect due to the redundancy of fusion features. In addition, the spatial misalignment of multi-phase images causes feature interference. METHODS: In this paper, we propose a phase attention network (PA-Net) to adequately aggregate multi-phase information of CT images and improve segmentation performance for liver tumors. Specifically, we design a PA module to generate attention weight maps voxel by voxel to efficiently fuse multi-phase CT images features to avoid feature redundancy. In order to solve the problem of feature interference in the multi-phase image segmentation task, we design a new learning strategy and prove its effectiveness experimentally. RESULTS: We conduct comparative experiments on the in-house clinical dataset and achieve the SOTA segmentation performance on multi-phase methods. In addition, our method has improved the mean dice score by 3.3% compared with the single-phase method based on nnUNet, and our learning strategy has improved the mean dice score by 1.51% compared with the ML strategy. CONCLUSION: The experimental results show that our method is superior to the existing multi-phase liver tumor segmentation method, and provides a scheme for dealing with missing modalities in multi-modal tasks. In addition, our proposed learning strategy makes more effective use of arterial phase image information and is proven to be the most effective in liver tumor segmentation tasks using thick-layer CT images. The source code is released on (https://github.com/Houjunfeng203934/PA-Net).

Exploring the S Protein of SARS-CoV-2 to Design a Novel Multi-Epitope Vaccine against COVID-19 Based on Immunoinformatics Approaches.

BACKGROUND: Developing a novel COVID-19 multi-epitope vaccine (CoVMEV) is essential to containing the SARS-CoV-2 pandemic. METHODS: The virus's immunodominant B and T cell epitopes from the S protein were found and joined to create the CoVMEV. Bioinformatics techniques were used to investigate the secondary and tertiary structures, as well as the physical and chemical properties of CoVMEV. RESULTS: CoVMEV exhibited high antigenicity and immunogenicity scores, together with good water solubility and stability. Toll-like receptor 2 (TLR2) and toll-like receptor4 (TLR4), which are critical in triggering immunological responses, were also strongly favoured by CoVMEV. Molecular dynamics simulation and immune stimulation studies revealed that CoVMEV effectively activated T and B lymphocytes, and increased the number of active CD8+ T cells than similar vaccines. CONCLUSION: CoVMEV holds promise as a potential vaccine candidate for COVID-19, given its robust immunogenicity, stability, antigenicity, and capacity to stimulate a strong immune response. This study presents a significant design concept for the development of peptidyl vaccines targeting SARS-CoV-2. Further investigation and clinical trials will be crucial in assessing the efficacy and safety of CoVMEV as a potential vaccine for COVID-19.

Protecting Prostate Cancer Classification From Rectal Artifacts via Targeted Adversarial Training.

Magnetic resonance imaging (MRI)-based deep neural networks (DNN) have been widely developed to perform prostate cancer (PCa) classification. However, in real-world clinical situations, prostate MRIs can be easily impacted by rectal artifacts, which have been found to lead to incorrect PCa classification. Existing DNN-based methods typically do not consider the interference of rectal artifacts on PCa classification, and do not design specific strategy to address this problem. In this study, we proposed a novel Targeted adversarial training with Proprietary Adversarial Samples (TPAS) strategy to defend the PCa classification model against the influence of rectal artifacts. Specifically, based on clinical prior knowledge, we generated proprietary adversarial samples with rectal artifact-pattern adversarial noise, which can severely mislead PCa classification models optimized by the ordinary training strategy. We then jointly exploited the generated proprietary adversarial samples and original samples to train the models. To demonstrate the effectiveness of our strategy, we conducted analytical experiments on multiple PCa classification models. Compared with ordinary training strategy, TPAS can effectively improve the single- and multi-parametric PCa classification at patient, slice and lesion level, and bring substantial gains to recent advanced models. In conclusion, TPAS strategy can be identified as a valuable way to mitigate the influence of rectal artifacts on deep learning models for PCa classification.

FedDBL: Communication and Data Efficient Federated Deep-Broad Learning for Histopathological Tissue Classification.

Histopathological tissue classification is a fundamental task in computational pathology. Deep learning (DL)-based models have achieved superior performance but centralized training suffers from the privacy leakage problem. Federated learning (FL) can safeguard privacy by keeping training samples locally, while existing FL-based frameworks require a large number of well-annotated training samples and numerous rounds of communication which hinder their viability in real-world clinical scenarios. In this article, we propose a lightweight and universal FL framework, named federated deep-broad learning (FedDBL), to achieve superior classification performance with limited training samples and only one-round communication. By simply integrating a pretrained DL feature extractor, a fast and lightweight broad learning inference system with a classical federated aggregation approach, FedDBL can dramatically reduce data dependency and improve communication efficiency. Five-fold cross-validation demonstrates that FedDBL greatly outperforms the competitors with only one-round communication and limited training samples, while it even achieves comparable performance with the ones under multiple-round communications. Furthermore, due to the lightweight design and one-round communication, FedDBL reduces the communication burden from 4.6 GB to only 138.4 KB per client using the ResNet-50 backbone at 50-round training. Extensive experiments also show the scalability of FedDBL on model generalization to the unseen dataset, various client numbers, model personalization and other image modalities. Since no data or deep model sharing across different clients, the privacy issue is well-solved and the model security is guaranteed with no model inversion attack risk. Code is available at https://github.com/tianpeng-deng/FedDBL.

A computed tomography-based multitask deep learning model for predicting tumour stroma ratio and treatment outcomes in patients with colorectal cancer: a multicentre cohort study.

BACKGROUND: Tumour-stroma interactions, as indicated by tumour-stroma ratio (TSR), offer valuable prognostic stratification information. Current histological assessment of TSR is limited by tissue accessibility and spatial heterogeneity. The authors aimed to develop a multitask deep learning (MDL) model to noninvasively predict TSR and prognosis in colorectal cancer (CRC). MATERIALS AND METHODS: In this retrospective study including 2268 patients with resected CRC recruited from four centres, the authors developed an MDL model using preoperative computed tomography (CT) images for the simultaneous prediction of TSR and overall survival. Patients in the training cohort ( n =956) and internal validation cohort (IVC, n =240) were randomly selected from centre I. Patients in the external validation cohort 1 (EVC1, n =509), EVC2 ( n =203), and EVC3 ( n =360) were recruited from other three centres. Model performance was evaluated with respect to discrimination and calibration. Furthermore, the authors evaluated whether the model could predict the benefit from adjuvant chemotherapy. RESULTS: The MDL model demonstrated strong TSR discrimination, yielding areas under the receiver operating curves (AUCs) of 0.855 (95% CI, 0.800-0.910), 0.838 (95% CI, 0.802-0.874), and 0.857 (95% CI, 0.804-0.909) in the three validation cohorts, respectively. The MDL model was also able to predict overall survival and disease-free survival across all cohorts. In multivariable Cox analysis, the MDL score (MDLS) remained an independent prognostic factor after adjusting for clinicopathological variables (all P <0.05). For stage II and stage III disease, patients with a high MDLS benefited from adjuvant chemotherapy [hazard ratio (HR) 0.391 (95% CI, 0.230-0.666), P =0.0003; HR=0.467 (95% CI, 0.331-0.659), P <0.0001, respectively], whereas those with a low MDLS did not. CONCLUSION: The multitask DL model based on preoperative CT images effectively predicted TSR status and survival in CRC patients, offering valuable guidance for personalized treatment. Prospective studies are needed to confirm its potential to select patients who might benefit from chemotherapy.