Deep unfolding as iterative regularization for imaging inverse problems

Recently, deep unfolding methods that guide the design of deep neural networks (DNNs) through iterative algorithms have received increasing attention in the field of inverse problems. Unlike general end-to-end DNNs, unfolding methods have better interpretability and performance. However, to our knowledge, their accuracy and stability in solving inverse problems cannot be fully guaranteed. To bridge this gap, we modified the training procedure and proved that the unfolding method is an iterative regularization method. More precisely, we jointly learn a convex penalty function adversarially by an input-convex neural network (ICNN) to characterize the distance to a real data manifold and train a DNN unfolded from the proximal gradient descent algorithm with this learned penalty. Suppose the real data manifold intersects the inverse problem solutions with only the unique real solution. We prove that the unfolded DNN will converge to it stably. Furthermore, we demonstrate with an example of MRI reconstruction that the proposed method outperforms conventional unfolding methods and traditional regularization methods in terms of reconstruction quality, stability and convergence speed

SPIRiT-Diffusion: Self-Consistency Driven Diffusion Model for Accelerated MRI

Diffusion models are a leading method for image generation and have been successfully applied in magnetic resonance imaging (MRI) reconstruction. Current diffusion-based reconstruction methods rely on coil sensitivity maps (CSM) to reconstruct multi-coil data. However, it is difficult to accurately estimate CSMs in practice use, resulting in degradation of the reconstruction quality. To address this issue, we propose a self-consistency-driven diffusion model inspired by the iterative self-consistent parallel imaging (SPIRiT), namely SPIRiT-Diffusion. Specifically, the iterative solver of the self-consistent term in SPIRiT is utilized to design a novel stochastic differential equation (SDE) for diffusion process. Then $\textit{k}$-space data can be interpolated directly during the reverse diffusion process, instead of using CSM to separate and combine individual coil images. This method indicates that the optimization model can be used to design SDE in diffusion models, driving the diffusion process strongly conforming with the physics involved in the optimization model, dubbed model-driven diffusion. The proposed SPIRiT-Diffusion method was evaluated on a 3D joint Intracranial and Carotid Vessel Wall imaging dataset. The results demonstrate that it outperforms the CSM-based reconstruction methods, and achieves high reconstruction quality at a high acceleration rate of 10

Convex Latent-Optimized Adversarial Regularizers for Imaging Inverse Problems

Recently, data-driven techniques have demonstrated remarkable effectiveness in addressing challenges related to MR imaging inverse problems. However, these methods still exhibit certain limitations in terms of interpretability and robustness. In response, we introduce Convex Latent-Optimized Adversarial Regularizers (CLEAR), a novel and interpretable data-driven paradigm. CLEAR represents a fusion of deep learning (DL) and variational regularization. Specifically, we employ a latent optimization technique to adversarially train an input convex neural network, and its set of minima can fully represent the real data manifold. We utilize it as a convex regularizer to formulate a CLEAR-informed variational regularization model that guides the solution of the imaging inverse problem on the real data manifold. Leveraging its inherent convexity, we have established the convergence of the projected subgradient descent algorithm for the CLEAR-informed regularization model. This convergence guarantees the attainment of a unique solution to the imaging inverse problem, subject to certain assumptions. Furthermore, we have demonstrated the robustness of our CLEAR-informed model, explicitly showcasing its capacity to achieve stable reconstruction even in the presence of measurement interference. Finally, we illustrate the superiority of our approach using MRI reconstruction as an example. Our method consistently outperforms conventional data-driven techniques and traditional regularization approaches, excelling in both reconstruction quality and robustness

Matrix Completion-Informed Deep Unfolded Equilibrium Models for Self-Supervised k-Space Interpolation in MRI

Recently, regularization model-driven deep learning (DL) has gained significant attention due to its ability to leverage the potent representational capabilities of DL while retaining the theoretical guarantees of regularization models. However, most of these methods are tailored for supervised learning scenarios that necessitate fully sampled labels, which can pose challenges in practical MRI applications. To tackle this challenge, we propose a self-supervised DL approach for accelerated MRI that is theoretically guaranteed and does not rely on fully sampled labels. Specifically, we achieve neural network structure regularization by exploiting the inherent structural low-rankness of the $k$-space data. Simultaneously, we constrain the network structure to resemble a nonexpansive mapping, ensuring the network's convergence to a fixed point. Thanks to this well-defined network structure, this fixed point can completely reconstruct the missing $k$-space data based on matrix completion theory, even in situations where full-sampled labels are unavailable. Experiments validate the effectiveness of our proposed method and demonstrate its superiority over existing self-supervised approaches and traditional regularization methods, achieving performance comparable to that of supervised learning methods in certain scenarios

Stem cell factor SALL4, a potential prognostic marker for myelodysplastic syndromes

Background: Myelodysplastic syndromes (MDS) are a group of heterogeneous diseases with variable clinical course. Predicting disease progression is difficult due to lack of specific molecular marker(s). SALL4 plays important roles in normal hematopoiesis and leukemogenesis. SALL4 transgenic mice develop MDS prior to acute myeloid leukemia (AML) transformation. However, the role of SALL4 in human MDS has not been extensively investigated. In this study, we evaluate the diagnostic/prognostic value of SALL4 in MDS by examining its expression levels in a cohort of MDS patients. Methods: Fifty-five newly diagnosed MDS, twenty MDS-AML, and sixteen post-treatment MDS patients were selected for our study along with ten healthy donors. Results: We demonstrated that SALL4 was over-expressed in MDS patients and proportionally increased in MDS patients with high grade/IPSS scores. This expression pattern was similar to that of Bmi-1, an important marker in predicting MDS/AML progression. In addition, the level of SALL4 was positively correlated with increased blast counts, high-risk keryotypes and increased significantly in MDS-AML transformation. Furthermore, higher level of SALL4 expression was associated with worse survival rates and SALL4 level decreased following effective therapy. Conclusions: To the best of our knowledge, this is the largest series and the first to report the expression pattern of SALL4 in detail in various subtypes of MDS in comparison to that of Bmi-1. We conclude that SALL4 is a potential molecular marker in predicting the prognosis of MDS

Macrophages Phenotype Regulated by IL-6 Are Associated with the Prognosis of Platinum-Resistant Serous Ovarian Cancer: Integrated Analysis of Clinical Trial and Omics

Background. The treatment of platinum-resistant recurrent ovarian cancer (PROC) is a clinical challenge and a hot topic. Tumor microenvironment (TME) as a key factor promoting ovarian cancer progression. Macrophage is a component of TME, and it has been reported that macrophage phenotype is related to the development of PROC. However, the mechanism underlying macrophage polarization and whether macrophage phenotype can be used as a prognostic indicator of PROC remains unclear. Methods. We used ESTIMATE to calculate the number of immune and stromal components in high-grade serous ovarian cancer (HGSOC) cases from The Cancer Genome Atlas database. The differential expression genes (DEGs) were analyzed via protein–protein interaction network, Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) analysis to reveal major pathways of DEGs. CD80 was selected for survival analysis. IL-6 was selected for gene set enrichment analysis (GSEA). A subsequent cohort study was performed to confirm the correlation of IL-6 expression with macrophage phenotype in peripheral blood and to explore the clinical utility of macrophage phenotype for the prognosis of PROC patients. Results. A total of 993 intersecting genes were identified as candidates for further survival analysis. Further analysis revealed that CD80 expression was positively correlated with the survival of HGSOC patients. The results of GO and KEGG analysis suggested that macrophage polarization could be regulated via chemokine pathway and cytokine–cytokine receptor interaction. GSEA showed that the genes were mainly enriched in IL-6-STAT-3. Correlation analysis for the proportion of tumor infiltration macrophages revealed that M2 was correlated with IL-6. The results of a cohort study demonstrated that the regulation of macrophage phenotype by IL-6 is bidirectional. The high M1% was a protective factor for progression-free survival. Conclusion. Thus, the macrophage phenotype is a prognostic indicator in PROC patients, possibly via a hyperactive IL-6-related pathway, providing an additional clue for the therapeutic intervention of PROC

Accelerating Magnetic Resonance Parametric Mapping Using Simultaneously Spatial Patch-based and Parametric Group-based Low-rank Tensors (SMART)

Quantitative magnetic resonance (MR) parametric mapping is a promising approach for characterizing intrinsic tissue-dependent information. However, long scan time significantly hinders its widespread applications. Recently, low-rank tensor has been employed and demonstrated good performance in accelerating MR parametricmapping. In this study, we propose a novel method that uses spatial patch-based and parametric group-based low rank tensors simultaneously (SMART) to reconstruct images from highly undersampled k-space data. The spatial patch-based low-rank tensor exploits the high local and nonlocal redundancies and similarities between the contrast images in parametric mapping. The parametric group based low-rank tensor, which integrates similar exponential behavior of the image signals, is jointly used to enforce the multidimensional low-rankness in the reconstruction process. In vivo brain datasets were used to demonstrate the validity of the proposed method. Experimental results have demonstrated that the proposed method achieves 11.7-fold and 13.21-fold accelerations in two-dimensional and three-dimensional acquisitions, respectively, with more accurate reconstructed images and maps than several state-of-the-art methods. Prospective reconstruction results further demonstrate the capability of the SMART method in accelerating MR quantitative imaging.Comment: 15 pages, 12 figure

Exploring the safety, effectiveness, and cost-effectiveness of a Chinese patent medicine (Fufang E’jiao syrup) for alleviating cancer-related fatigue : a protocol for a randomized, double-blinded, placebo-controlled, multicenter trial

Objective: To provide higher level evidence on the benefits of a Chinese patent medicine (CPM) (Fufang E’jiao Syrup, FFEJS) for alleviating cancer-related fatigue (CRF), this article describes a protocol for a randomized controlled trial. Methods/design: We designed a double-blind, placebo-controlled stratified permuted block randomization clinical trial on CRF among 3 types of cancer in China. Participants will be equally allocated to FFEJS group or placebo group according to the randomization sequence and the hospitals they were enrolled at. Each patient will receive 20 ml of either the study formula FFEJS or a placebo formula, 3 times a day for 6 weeks. The follow-up period will be another 4 weeks for safety evaluation. The primary outcome is the difference in improvement of fatigue as measured with the Revised Piper Fatigue Scale-Chinese Version (RPFS-CV). Secondary outcomes include change in fatigue (measured by routine blood panel and hormones in peripheral blood) and QoL (measured by Edmonton symptom assessment scale and Functional Assessment of Cancer Therapy). Patient safety will be measured by liver, renal or cardiac damage, and the risk of FFEJS having a tumor promotion and progression effect will be monitored throughout this study. Cost-effectiveness will also be evaluated mainly by incremental cost per each quality-adjusted life year gained. Discussion: This article describes the study design of a CPM for CRF in patients with advanced cancer through exploring the effectiveness, safety, and cost-effectiveness of FFEJS. Trial registration: ClinicalTrials.gov, NCT04147312. Registered on 1 Sep 2019

Label-free quantitative proteomic analysis of molting-related proteins of Trichinella spiralis intestinal infective larvae

International audienceAbstractMolting is a key step for body-size expansion and environmental adaptation of parasitic nematodes, and it is extremely important for Trichinella spiralis growth and development, but the molting mechanism is not fully understood. In this work, label-free LC–MS/MS was used to determine the proteome differences between T. spiralis muscle larvae (ML) at the encapsulated stage and intestinal infective larvae (IIL) at the molting stage. The results showed that a total of 2885 T. spiralis proteins were identified, 323 of which were differentially expressed. These proteins were involved in cuticle structural elements, regulation of cuticle synthesis, remodeling and degradation, and hormonal regulation of molting. These differential proteins were also involved in diverse intracellular pathways, such as fatty acid biosynthesis, arachidonic acid metabolism, and mucin type O-glycan biosynthesis. qPCR results showed that five T. spiralis genes (cuticle collagen 14, putative DOMON domain-containing protein, glutamine synthetase, cathepsin F and NADP-dependent isocitrate dehydrogenase) had significantly higher transcriptional levels in 10 h IIL than ML (P < 0.05), which were similar to their protein expression levels, suggesting that they might be T. spiralis molting-related genes. Identification and characterization of T. spiralis molting-related proteins will be helpful for developing vaccines and new drugs against the early enteral stage of T. spiralis