Swin transformer for fast MRI

Magnetic resonance imaging (MRI) is an important non-invasive clinical tool that can produce high-resolution and reproducible images. However, a long scanning time is required for high-quality MR images, which leads to exhaustion and discomfort of patients, inducing more artefacts due to voluntary movements of the patients and involuntary physiological movements. To accelerate the scanning process, methods by k-space undersampling and deep learning based reconstruction have been popularised. This work introduced SwinMR, a novel Swin transformer based method for fast MRI reconstruction. The whole network consisted of an input module (IM), a feature extraction module (FEM) and an output module (OM). The IM and OM were 2D convolutional layers and the FEM was composed of a cascaded of residual Swin transformer blocks (RSTBs) and 2D convolutional layers. The RSTB consisted of a series of Swin transformer layers (STLs). The shifted windows multi-head self-attention (W-MSA/SW-MSA) of STL was performed in shifted windows rather than the multi-head self-attention (MSA) of the original transformer in the whole image space. A novel multi-channel loss was proposed by using the sensitivity maps, which was proved to reserve more textures and details. We performed a series of comparative studies and ablation studies in the Calgary-Campinas public brain MR dataset and conducted a downstream segmentation experiment in the Multi-modal Brain Tumour Segmentation Challenge 2017 dataset. The results demonstrate our SwinMR achieved high-quality reconstruction compared with other benchmark methods, and it shows great robustness with different undersampling masks, under noise interruption and on different datasets. The code is publicly available at https://github.com/ayanglab/SwinMR.This work was supported in part by the UK Research and Inno- vation Future Leaders Fellowship [MR/V023799/1], in part by the Medical Research Council [MC/PC/21013], in part by the European Research Council Innovative Medicines Initiative [DRAGON, H2020-JTI-IMI2 101005122], in part by the AI for Health Imaging Award [CHAIMELEON, H2020-SC1-FA-DTS-2019-1 952172], in part by the British Heart Foundation [Project Number: TG/18/5/34111, PG/16/78/32402], in part by the NVIDIA Academic Hardware Grant Program, in part by the Project of Shenzhen International Cooper- ation Foundation [GJHZ20180926165402083], in part by the Bas- que Government through the ELKARTEK funding program [KK- 2020/00049], and in part by the consolidated research group MATHMODE [IT1294-19

Clinical factors of post-chemoradiotherapy as valuable indicators for pathological complete response in locally advanced rectal cancer

OBJECTIVES: Pathological complete response has shown a better prognosis for patients with locally advanced rectal cancer after preoperative chemoradiotherapy. However, correlations between post-chemoradiotherapy clinical factors and pathologic complete response are not well confirmed. The aim of the current study was to identify post-chemoradiotherapy clinical factors that could serve as indicators of pathologic complete response in locally advanced rectal cancer. METHODS: This study retrospectively analyzed 544 consecutive patients with locally advanced rectal cancer treated at Sun Yat-sen University Cancer Center from December 2003 to June 2014. All patients received preoperative chemoradiotherapy followed by surgery. Univariate and multivariate regression analyses were performed to identify post-chemoradiotherapy clinical factors that are significant indicators of pathologic complete response. RESULTS: In this study, 126 of 544 patients (23.2%) achieved pathological complete response. In multivariate analyses, increased pathological complete response rate was significantly associated with the following factors: post-chemoradiotherapy clinical T stage 0-2 (odds ratio=2.098, 95% confidence interval=1.023-4.304, p=0.043), post-chemoradiotherapy clinical N stage 0 (odds ratio=2.011, 95% confidence interval=1.264-3.201, p=0.003), interval from completion of preoperative chemoradiotherapy to surgery of >;7 weeks (odds ratio=1.795, 95% confidence interval=1.151-2.801, p=0.010) and post-chemoradiotherapy carcinoembryonic antigen ≤2 ng/ml (odds ratio=1.579, 95% confidence interval=1.026-2.432, p=0.038). CONCLUSIONS: Post-chemoradiotherapy clinical T stage 0-2, post-chemoradiotherapy clinical N stage 0, interval from completion of chemoradiotherapy to surgery of >;7 weeks and post-chemoradiotherapy carcinoembryonic antigen ≤2 ng/ml were independent clinical indicators for pathological complete response. These findings demonstrate that post-chemoradiotherapy clinical factors could be valuable for post-operative assessment of pathological complete response

Experimental research on the effect caused by effective stress change in injection production capacity of carbonate reservoir

The effective stress of the reservoir rock in the underground gas storage (UGS) changes with the multi cycle injection and production, which changes the physical characteristics of the reservoir and affects the injection production capacity of the UGS. Taking carbonate fracture-pore type gas storage as the research object, combined with the actual production of UGS, establish a set of experimental evaluation methods based on production characteristics; Core damage evaluator, overburden pressure porosimeter and scanning electron microscope are used to carry out experimental research on the impact of effective stress change on injection production capacity, quantitative analysis of reservoir internal characteristics, multi cycle injection and production and effect of effective stress action time on injection-production capacity. The results show, the experimental method established based on the actual production characteristics of the UGS, simulation of multi cycle injection and production by forward and reverse displacement, simulation of effective stress change under constant confining pressure and variable internal pressure, the experimental evaluation of the injection production capacity of the simulation multi cycle injection and production of the UGS is realized; The change of effective stress makes the reservoir seepage characteristics worse and the reservoir space smaller, injection-production coefficient (Szc) is positively correlated with the internal characteristic value of the reservoir, the larger the internal characteristic value of the reservoir, the higher Szc, and the better the injection production capacity; The injection production capacity of the UGS reservoir deteriorates with the increase of the injection production cycle, in the 4th injection production cycle, the injection production capacity of the UGS changes from moderately strong to moderately weak; The damage of effective stress to the injection production capacity of UGS mainly occurs in the initial stage of injection production, and the damage tends to be stable with the progress of injection production. The conclusion is that the change of effective stress in carbonate fracture-pore type gas storage makes the injection-production capacity of the reservoir worse, it is proposed to carry out reservoir reconstruction before the UGS is put into operation, and expand the capacity of the gas storage after the completion of the 3rd injection and production cycle, which can effectively offset the impact of the decline of injection production capacity of the UGS and play the role of reservoir protection, it provides a constructive idea for improving the operation efficiency of the UGS

Shared data of "Automated Detection Framework of the Calcified Plaque with Acoustic Shadowing in IVUS Images" in PLOS One

<p>The file includes the shared data of the PLOS One paper "Automated Detection Framework of the Calcified Plaque with Acoustic Shadowing in IVUS Images"</p