140 results on '"Yafei, Qi"'
Search Results
2. LGAD: Local and Global Attention Distillation for Efficient Semantic Segmentation.
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Chen Wang, Yafei Qi, Qi Li 0025, and Huawen Liu
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- 2024
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3. PRRD: Pixel-Region Relation Distillation For Efficient Semantic Segmentation.
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Chen Wang, Jiang Zhong, Qizhu Dai, Yafei Qi, Rongzhen Li, Qin Lei, Bin Fang, and Xue Li 0001
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- 2023
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4. PointViG: A Lightweight GNN-based Model for Efficient Point Cloud Analysis.
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Qiang Zheng, Yafei Qi, Chen Wang, Chao Zhang, and Jian Sun
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- 2024
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5. MTED: multiple teachers ensemble distillation for compact semantic segmentation.
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Chen Wang, Jiang Zhong, Qizhu Dai, Qien Yu, Yafei Qi, Bin Fang, and Xue Li 0001
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- 2023
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6. Channel Correlation Distillation for Compact Semantic Segmentation.
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Chen Wang, Jiang Zhong, Qizhu Dai, Yafei Qi, Qien Yu, Fengyuan Shi 0003, Rongzhen Li, Xue Li 0001, and Bin Fang
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- 2023
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7. Medical hyperspectral image classification based weakly supervised single-image global learning network.
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Chenglong Zhang, Lichao Mou, Shihao Shan, Hao Zhang 0113, Yafei Qi, Dexin Yu, Xiao Xiang Zhu 0001, Nianzheng Sun, Xiangrong Zheng, and Xiaopeng Ma
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- 2024
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8. Using amide proton transfer-weighted MRI to non-invasively differentiate mismatch repair deficient and proficient tumors in endometrioid endometrial adenocarcinoma
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Yuan Li, Xinyu Liu, Xiaoqi Wang, Chengyu Lin, Yafei Qi, Bo Chen, Hailong Zhou, Qiaoling Wu, Jing Ren, Jia Zhao, Junjun Yang, Yang Xiang, Yonglan He, Zhengyu Jin, and Huadan Xue
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Amide proton transfer-weighted ,Magnetic resonance imaging ,Endometrioid endometrial adenocarcinoma ,Mismatch repair deficient ,Medical physics. Medical radiology. Nuclear medicine ,R895-920 - Abstract
Abstract Objectives To investigate the utility of three-dimensional (3D) amide proton transfer-weighted (APTw) imaging to differentiate mismatch repair deficient (dMMR) and mismatch repair proficient (pMMR) tumors in endometrioid endometrial adenocarcinoma (EEA). Methods Forty-nine patients with EEA underwent T1-weighted imaging, T2-weighted imaging, 3D APTw imaging, and diffusion-weighted imaging at 3 T MRI. Image quality and measurement confidence of APTw images were evaluated on a 5-point Likert scale. APTw and apparent diffusion coefficient (ADC) values were calculated and compared between the dMMR and pMMR groups and among the three EEA histologic grades based on the Federation of Gynecology and Obstetrics (FIGO) grading system criteria. Student’s t-test, analysis of variance with Scheffe post hoc test, and receiver operating characteristic analysis were performed. Statistical significance was set at p
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- 2021
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9. Prior knowledge-based precise diagnosis of blend sign from head computed tomography
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Chen Wang, Jiefu Yu, Jiang Zhong, Shuai Han, Yafei Qi, Bin Fang, and Xue Li
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blend sign ,intracranial hemorrhage ,hemorrhage expansion ,prior knowledge ,self-knowledge distillation ,convolutional neural network ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
IntroductionAutomated diagnosis of intracranial hemorrhage on head computed tomography (CT) plays a decisive role in clinical management. This paper presents a prior knowledge-based precise diagnosis of blend sign network from head CT scans.MethodWe employ the object detection task as an auxiliary task in addition to the classification task, which could incorporate the hemorrhage location as prior knowledge into the detection framework. The auxiliary task could help the model pay more attention to the regions with hemorrhage, which is beneficial for distinguishing the blend sign. Furthermore, we propose a self-knowledge distillation strategy to deal with inaccuracy annotations.ResultsIn the experiment, we retrospectively collected 1749 anonymous non-contrast head CT scans from the First Affiliated Hospital of China Medical University. The dataset contains three categories: no intracranial hemorrhage (non-ICH), normal intracranial hemorrhage (normal ICH), and blend sign. The experimental results demonstrate that our method performs better than other methods.DiscussionOur method has the potential to assist less-experienced head CT interpreters, reduce radiologists' workload, and improve efficiency in natural clinical settings.
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- 2023
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10. The effect of oral bacterial lysates on the respiratory microbiome in patients with chronic obstructive pulmonary disease exacerbations – A pilot study
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Yafei Qi, Zhou Zhu, Xiaomin Liu, Junhao Yang, Weimin Zhang, Jinlun Huang, Hong Li, Weijie Guan, Zhang Wang, and Yinhuan Li
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COPD ,Bacterial lysate ,Respiratory microbiome ,16S rRna ,Diseases of the digestive system. Gastroenterology ,RC799-869 ,Microbiology ,QR1-502 - Abstract
Background: Increasing evidence suggests that the airway microbiome plays an important role in chronic obstructive pulmonary disease (COPD). While oral bacterial lysates were found to reduce the number of acute exacerbations of COPD (AECOPD), little is known regarding the effects of bacterial lysates on COPD airway microbiome. Methods: Sixteen patients with AECOPD were enrolled in this pilot, prospective study from November 2020 to June 2021. Patients were randomly divided into two groups to receive conventional treatment (n = 8) or conventional treatment combined with bacterial lysates (n = 8), respectively. Sputum samples were collected upon hospital admission and at discharge. Patients were followed-up over 6 months after discharge. Results: The α-diversity was not significantly different pre- and post-treatment between the two treatment groups. There was a significantly greater weighted UniFrac distance between the paired pre- and post-treatment samples for patients receiving bacterial lysates compared to those receiving conventional treatment (P = 0.021). Among all taxa, a significantly decrease of Pseudomonadaceae was observed for patients receiving bacterial lysates group, while this trend was non-significant for the conventional treatment group. The frequency of acute exacerbations during the 6-month follow-up period was significantly lower for patients receiving bacterial lysates compared to those receiving conventional treatment (P = 0.042). Conclusions: Bacterial lysates resulted in greater alteration of the airway microbiota compared to conventional treatment. Pseudomonadaceae was significantly decreased in sputum samples of patients receiving bacterial lysate, which may be a microbiome-related mechanism by which bacterial lysates reduce COPD exacerbations.
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- 2022
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11. The value of CT radiomic in differentiating mycoplasma pneumoniae pneumonia from streptococcus pneumoniae pneumonia with similar consolidation in children under 5 years
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Dongdong Wang, Jianshe Zhao, Ran Zhang, Qinghu Yan, Lu Zhou, Xiaoyu Han, Yafei Qi, and Dexin Yu
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pneumonia ,mycoplasma pneumoniae pneumonia ,streptococcus pneumoniae pneumonia ,nomogram ,CT radiomics ,Pediatrics ,RJ1-570 - Abstract
ObjectiveTo investigate the value of CT radiomics in the differentiation of mycoplasma pneumoniae pneumonia (MPP) from streptococcus pneumoniae pneumonia (SPP) with similar CT manifestations in children under 5 years.MethodsA total of 102 children with MPP (n = 52) or SPP (n = 50) with similar consolidation and surrounding halo on CT images in Qilu Hospital and Qilu Children’s Hospital between January 2017 and March 2022 were enrolled in the retrospective study. Radiomic features of the both lesions on plain CT images were extracted including the consolidation part of the pneumonia or both consolidation and surrounding halo area which were respectively delineated at region of interest (ROI) areas on the maximum axial image. The training cohort (n = 71) and the validation cohort (n = 31) were established by stratified random sampling at a ratio of 7:3. By means of variance threshold, the effective radiomics features, SelectKBest and least absolute shrinkage and selection operator (LASSO) regression method were employed for feature selection and combined to calculate the radiomics score (Rad-score). Six classifiers, including k-nearest neighbor (KNN), support vector machine (SVM), extreme gradient boosting (XGBoost), random forest (RF), logistic regression (LR), and decision tree (DT) were used to construct the models based on radiomic features. The diagnostic performance of these models and the radiomic nomogram was estimated and compared using the area under the receiver operating characteristic (ROC) curve (AUC), and the decision curve analysis (DCA) was used to evaluate which model achieved the most net benefit.ResultsRF outperformed other classifiers and was selected as the backbone in the classifier with the consolidation + the surrounding halo was taken as ROI to differentiate MPP from SPP in validation cohort. The AUC value of MPP in validation cohort was 0.822, the sensitivity and specificity were 0.81 and 0.81, respectively.ConclusionThe RF model has the best classification efficiency in the identification of MPP from SPP in children, and the ROI with both consolidation and surrounding halo is most suitable for the delineation.
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- 2022
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12. Grain yield and food security evaluation in the yellow river basin under climate change and water resources constraints
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Chen Niu, Yafei Qi, Aijun Guo, and Jianxia Chang
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climate change ,water resources constraint ,grain yield (GY) ,food security ,yellow river basin ,Environmental technology. Sanitary engineering ,TD1-1066 - Abstract
With climate change, the amount of global water resources is decreasing and crop growth patterns are changing. Global food security will face severe challenges in future. Hence, it is of great significance to study the change in grain production under climate change and the water resources constraint to ensure national and regional food security. In this study, a complex system coupled with the hydrological model, crop model, and optimal regulation model of water resources has been constructed to explore the changes in future grain yield in the Yellow River Basin (YRB) under climate change and the water resources constraint, and further evaluate the future food security of the basin. The models show good adaptability. The results show that the precipitation and temperature in the YRB will be higher than the historical level and show an upward trend in future. On the contrary, runoff and irrigation water demand in the basin are lower than historical levels. Although the grain yield would decrease in future, the food security of YRB would be well-guaranteed. However, the level of food security in different provinces would be quite different. And some provinces will face serious food security problems without grain trade. This study will help relevant institutions in the YRB to deal with possible food security problems in future, and can also provide a reference for other countries and institutions in the world.
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- 2022
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13. Multi-view knowledge distillation for efficient semantic segmentation.
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Chen Wang, Jiang Zhong, Qizhu Dai, Yafei Qi, Fengyuan Shi 0003, Bin Fang, and Xue Li 0001
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- 2023
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14. Use of magnetic resonance elastography to gauge meningioma intratumoral consistency and histotype
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Yu Shi, Yunlong Huo, Chen Pan, Yafei Qi, Ziying Yin, Richard L. Ehman, Zhenyu Li, Xiaoli Yin, Bai Du, Ziyang Qi, and Yang Hong
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Meningiomas ,Magnetic resonance imaging ,Elastography ,Mechanical properties ,Stiffness ,Computer applications to medicine. Medical informatics ,R858-859.7 ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Objective: To determine whether tumor shear stiffness, as measured by magnetic resonance elastography, corresponds with intratumoral consistency and histotype. Materials and methods: A total of 88 patients with 89 meningiomas (grade 1, 74 typical [13 fibroblastic, 61 non-fibroblastic]; grade 2, 12 atypical; grade 3, 3 anaplastic) were prospectively studied, each undergoing preoperative MRE in conjunction with T1-, T2- and diffusion-weighted imaging. Contrast-enhanced T1-weighted sequences were also obtained. Tumor consistency was evaluated as heterogeneous or homogenous, and graded on a 5-point scale intraoperatively. MRE-determined shear stiffness was associated with tumor consistency by surgeon’s evaluation and whole-slide histologic analyses. Results: Mean tumor stiffness overall was 3.81+/-1.74 kPa (range, 1.57–12.60 kPa), correlating well with intraoperative scoring (r = 0.748; p = 0.001). MRE performed well as a gauge of tumor consistency (AUC = 0.879, 95 % CI: 0.792–0.938) and heterogeneity (AUC = 0.773, 95 % CI: 0.618–0.813), significantly surpassing conventional MR techniques (DeLong test, all p 0.05). Small (
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- 2022
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15. Human spatial navigation: benchmark behavioral findings
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Weimin Mou and Yafei Qi
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- 2024
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16. Computed tomography-adjusted fistula risk score for predicting clinically relevant postoperative pancreatic fistula after pancreatoduodenectomy: Training and external validation of model upgrade
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Yu Shi, Feng Gao, Yafei Qi, Hong Lu, Fulu Ai, Yang Hou, Chang Liu, Youli Xu, Xianyi Zhang, and Xiaoli Cai
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Postoperative pancreatic fistula ,Pancreaticoduodenectomy ,Computed tomography ,Risk prediction ,Medicine ,Medicine (General) ,R5-920 - Abstract
Background: To develop a modified Fistula Risk Score (FRS) for predicting clinically relevant postoperative pancreatic fistula (CR-POPF) after pancreatoduodenectomy (PD) based on both FRS and contrast-enhanced computed tomography (CE-CT). Methods: In this multicenter retrospective analysis, we focused on 990 consecutive patients with pancreatoduodenectomy performed at four institutions between 2009 and 2019. The enhanced CT-FRS model initially targeted 26 pre- and intraoperative factors, including CT descriptors, FRS elements and clinical factors, using LASSO-penalized multivariable logistic regression for predicting CR-POPF events in discovery (n = 718) and externally validated (n = 272) datasets. Probabilities generated were further correlated with histologic features of pancreatic stumps in 356 patients. C-indices were analyzed to compare the predictive potential between the original FRS and the CT-FRS. Findings: CR-POPF developed in 112 (15.6%) and 36 (13.2%) patients in discovery and validation datasets, respectively. The final CT-FRS construct, incorporating remnant pancreatic volume (RPV), stump area, fat and atrophy scores by CT, and main pancreatic duct size, offered significantly greater overall predictability than the original FRS in discovery (C-index: 0.825 vs 0.794; p = 0.04) and validation (0.807 vs 0.741; p = 0.05) cohorts. Importantly, it outperformed the FRS in patients at moderate risk levels (FRS: 3–6), showing remarkably improved C-indices (discovery: 0.729 vs 0.626 [p
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- 2020
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17. Sources of systematic errors in human path integration
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Yafei Qi and Weimin Mou
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Behavioral Neuroscience ,Arts and Humanities (miscellaneous) ,Experimental and Cognitive Psychology - Abstract
Triangle completion is a task widely used to study human path integration, an important navigation method relying on idiothetic cues. Systematic biases (compression patterns in the inbound responses) have been well documented in human triangle completion. However, the sources of systematic biases remain controversial. We used cross-validation modeling to compare three plausible theoretical models that assume that systematic errors occur in the encoding outbound path solely (encoding-error model), executing the inbound responses solely (execution-error model), and both (bicomponent model), respectively. The data for cross-validation modeling are from a previous study (Qi et al., 2021), in which participants learned three objects' locations (one at the path origin, that is, home) very well before walking each outbound path and then pointed to the objects' original locations after walking the outbound path. The modeling algorithm used one inbound response (i.e., response to the home) or multiple inbound responses (i.e., responses to two nonhome locations and the home) for each outbound path. The algorithm of using multiple inbound responses demonstrated that the bicomponent model outperformed the other models in accounting for the systematic errors. This finding suggests that both encoding the outbound path and executing the inbound responses contribute to the systematic biases in human path integration. In addition, the results showed that the algorithm using only the home response could not distinguish among these 3 models, suggesting that the typical triangle-completion task with only the home response for each outbound path cannot determine the sources of the systematic biases. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
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- 2023
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18. Optimisation and performance test of fibre-based large-area surface contamination monitor
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Jie Hou, Yafei Qi, Haiyan Luan, Lihua Ren, Yantao Qu, Wei Wang, Ying Wang, Xia Li, Zhiping Luo, and Jizeng Ma
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Physics ,QC1-999 - Abstract
A portable large-area radiological contamination surface monitor of advanced design is now under research and development. This monitor, whose detection area is 1200 cm2, is mainly applied for hot-spot searching for nuclear emergency response or facility decommissioning. It consists of a thin plastic scintillation tile and wavelength-shifting fibres coupled to a photomultiplier tube. To improve the detector performance, it is necessary to calculate the collection efficiency of optical photons from the scintillator. The optical photon transportation processes in the plastic scintillator and wavelength-shifting fibres are simulated using the Monte Carlo code Geant4. For further optimisation, experiments with different fibre arrangements are conducted to verify uniformity. In conclusion, an arrangement of ten neighbouring wavelength-shifting fibres, with alternating fibres connected on opposite sides of a organic support for the plastic scintillator presents a better performance for detection. Keywords: GEANT4, Monte Carlo, Surface contamination monitor, Wavelength shifting fibre, Plastic scintillation
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- 2019
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19. Chloroplast Translation Elongation Factor EF-Tu/SVR11 Is Involved in var2-Mediated Leaf Variegation and Leaf Development in Arabidopsis
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Siyu Liu, Lu Zheng, Jia Jia, Jia Guo, Mengdi Zheng, Jun Zhao, Jingxia Shao, Xiayan Liu, Lijun An, Fei Yu, and Yafei Qi
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EF-Tu ,chloroplast development ,leaf variegation ,retrograde signal ,VAR2 ,Plant culture ,SB1-1110 - Abstract
Chloroplasts are semiautonomous organelles, retaining their own genomes and gene expression apparatuses but controlled by nucleus genome encoded protein factors during evolution. To analyze the genetic regulatory network of FtsH-mediated chloroplast development in Arabidopsis, a set of suppressor mutants of yellow variegated (var2) have been identified. In this research, we reported the identification of another new var2 suppressor locus, SUPPRESSOR OF VARIEGATION11 (SVR11), which encodes a putative chloroplast-localized prokaryotic type translation elongation factor EF-Tu. SVR11 is likely essential to chloroplast development and plant survival. GUS activity reveals that SVR11 is abundant in the juvenile leaf tissue, lateral roots, and root tips. Interestingly, we found that SVR11 and SVR9 together regulate leaf development, including leaf margin development and cotyledon venation patterns. These findings reinforce the notion that chloroplast translation state triggers retrograde signals regulate not only chloroplast development but also leaf development.
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- 2019
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20. Synergistic ferroptosis-gemcitabine chemotherapy of the gemcitabine loaded carbonaceous nanozymes to enhance the treatment and magnetic resonance imaging monitoring of pancreatic cancer
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Gaorui Zhang, Nianlu Li, Yafei Qi, Quanqin Zhao, Jinhua Zhan, and Dexin Yu
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Glutathione Peroxidase ,Biomedical Engineering ,Antineoplastic Agents ,General Medicine ,Adenocarcinoma ,Deoxycytidine ,Magnetic Resonance Imaging ,Gemcitabine ,Biochemistry ,Pancreatic Neoplasms ,Biomaterials ,Cell Line, Tumor ,Ferroptosis ,Humans ,Reactive Oxygen Species ,Molecular Biology ,Peroxidase ,Biotechnology - Abstract
Pancreatic adenocarcinoma (PDAC) is one of the deadliest cancers, and it is resistant to most conventional antineoplastic therapies. To address this challenge, gemcitabine (Gem)-loaded carbonaceous nanoparticles (MFC-Gem) as nanozymes and a theranostic platform were fabricated and used for MR-guided ferroptosis-chemo synergetic therapy of PDAC. As a biocompatible carrier, MFC-Gem nanoparticles are regarded as peroxidase-like and glutathione peroxidase-like nanozymes that promote ferroptosis therapy by effectively generating ROS and consuming GSH. Meanwhile, the combination of MnFe
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- 2022
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21. Statistically Optimal Cue Integration During Human Spatial Navigation
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Phillip M. Newman, Yafei Qi, Weimin Mou, and Timothy P. McNamara
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Arts and Humanities (miscellaneous) ,Developmental and Educational Psychology ,Experimental and Cognitive Psychology - Published
- 2023
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22. Chloroplast SRP54 and FtsH protease coordinate thylakoid membrane-associated proteostasis in Arabidopsis
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Yang Lei, Bilang Li, Xiaomin Wang, Junyou Wei, Peiyi Wang, Jun Zhao, Fei Yu, and Yafei Qi
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Physiology ,Genetics ,Plant Science - Abstract
Thylakoid membrane protein quality control (PQC), which requires the coordination of membrane protein translocation and degradation of unassembled proteins, determines chloroplast development during de-etiolation. Despite numerous efforts, the regulation of this process in land plants is largely unknown. Here, we report the isolation and characterization of pale green Arabidopsis4 (pga4) mutants in Arabidopsis (Arabidopsis thaliana) with defects in chloroplast development during de-etiolation. Map-based cloning and complementation assays confirmed that PGA4 encodes the chloroplast Signal Recognition Particle 54 kDa (cpSRP54) protein. A heterogeneous Light-Harvesting Chlorophyll a/b Binding-Green Fluorescent Protein (LhcB2-GFP) fusion protein was generated as an indicative reporter for cpSRP54-mediated thylakoid translocation. LhcB2-GFP was dysfunctional and degraded to a short-form dLhcB2-GFP during de-etiolation through an N-terminal degradation initiated on thylakoid membranes. Further biochemical and genetic evidence demonstrated that the degradation of LhcB2-GFP to dLhcB2-GFP was disrupted in pga4 and yellow variegated2 (var2) mutants caused by mutations in the Filamentous Temperature-Sensitive H2 (VAR2/AtFtsH2) subunit of thylakoid FtsH. The yeast two-hybrid assay showed that the N-terminus of LhcB2-GFP interacts with the protease domain of VAR2/AtFtsH2. Moreover, the over-accumulated LhcB2-GFP in pga4 and var2 formed protein aggregates, which were insoluble in mild nonionic detergents. Genetically, cpSRP54 is a suppressor locus for the leaf variegation phenotype of var2. Together, these results demonstrate the coordination of cpSRP54 and thylakoid FtsH in maintaining thylakoid membrane PQC during the assembly of photosynthetic complexes and provide a trackable substrate and product for monitoring cpSRP54-dependent protein translocation and FtsH-dependent protein degradation.
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- 2023
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23. A New Allele of the SPIKE1 Locus Reveals Distinct Regulation of Trichome and Pavement Cell Development and Plant Growth
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Shuang Liang, Xuying Yang, Meng Deng, Jun Zhao, Jingxia Shao, Yafei Qi, Xiayan Liu, Fei Yu, and Lijun An
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branching ,cell morphogenesis ,cytoskeleton ,nucleus positioning ,SPIKE1 ,trichome ,Plant culture ,SB1-1110 - Abstract
The single-celled trichomes of Arabidopsis thaliana have long served as an elegant model for elucidating the mechanisms of cell differentiation and morphogenesis due to their unique growth patterns. To identify new components in the genetic network that governs trichome development, we carried out exhaustive screens for additional Arabidopsis mutants with altered trichome morphology. Here, we report one mutant, aberrantly branched trichome1-1 (abt1-1), with a reduced trichome branching phenotype. After positional cloning, a point mutation in the SPIKE1 (SPK1) gene was identified in abt1-1. Further genetic complementation experiments confirmed that abt1-1 is a new allele of SPK1, so abt1-1 was renamed as spk1-7 according to the literatures. spk1-7 and two other spk1 mutant alleles, covering a spectrum of phenotypic severity, highlighted the distinct responses of developmental programs to different SPK1 mutations. Although null spk1 mutants are lethal and show defects in plant stature, trichome and epidermal pavement cell development, only trichome branching is affected in spk1-7. Surprisingly, we found that SPK1 is involved in the positioning of nuclei in the trichome cells. Lastly, through double mutant analysis, we found the coordinated regulation of trichome branching between SPK1 and two other trichome branching regulators, ANGUSTIFOLIA (AN) and ZWICHEL (ZWI). SPK1 might serve for the precise positioning of trichome nuclei, while AN and ZWI contribute to the formation of branch points through governing the cMTs dynamics. In summary, this study presented a fully viable new mutant allele of SPK1 and shed new light on the regulation of trichome branching and other developmental processes by SPK1.
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- 2019
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24. Back Cover: PD‐L1 Aptamer‐Functionalized Metal–Organic Framework Nanoparticles for Robust Photo‐Immunotherapy against Cancer with Enhanced Safety (Angew. Chem. Int. Ed. 5/2023)
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Jingfang Zhang, Wenzhe Li, Yafei Qi, Guorong Wang, Lele Li, Zhengyu Jin, Jie Tian, and Yang Du
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General Chemistry ,Catalysis - Published
- 2023
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25. Rücktitelbild: PD‐L1 Aptamer‐Functionalized Metal–Organic Framework Nanoparticles for Robust Photo‐Immunotherapy against Cancer with Enhanced Safety (Angew. Chem. 5/2023)
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Jingfang Zhang, Wenzhe Li, Yafei Qi, Guorong Wang, Lele Li, Zhengyu Jin, Jie Tian, and Yang Du
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General Medicine - Published
- 2023
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26. Distinct Molecular Features In Early-Onset Lung Adenocarcinoma
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Ye Tian, Rui Ma, Shumin Wang, Teng Fei, Chuanjiang Zhou, Weibing Wu, Bo Yang, Hua Xin, Hongyan Wang, Pengfei Li, Ranhua Li, Changhong Liu, Chengyang Song, Jizhe Tong, Lei Zhang, Di Zhou, Xitong Zhao, Zhuo Wu, Yao Lu, Qian Yu, Yafei Qi, Rui Wang, and Xueying Yang
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- 2023
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27. Radiomics analysis potentially reduces over-diagnosis of prostate cancer with PSA levels of 4-10 ng/ml based on DWI data.
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Shuaitong Zhang, Yafei Qi, Jingwei Wei, Jianxing Niu, Dongsheng Gu, Yuqi Han, Xiaohan Hao, Yali Zang, and Jie Tian 0001
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- 2019
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28. Tumoral Morphologic Features From Cervical Biopsies That Are Predictive of a Negligible Risk for Nodal Metastasis and Tumor Recurrence in Usual-type Cervical Adenocarcinomas
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Aijun Liu, Li-Li Liu, Jayanthi S. Lea, Yan Wang, Steven Holloway, Jun Wang, Oluwole Fadare, M.R. Quddus, Ming Li, Feng Zhou, Ruby Chang, Xiujie Sheng, Yun Wang, Natalie Banet, Huiting Zhu, Xiaofei Zhang, Beihua Kong, Yue Wang, J. Li, Ruijiao Zhao, Wanrun Lin, Rongzhen Luo, Rui Bi, Yan-Lin Wen, Qingping Jiang, Jihong Liu, Hao Chen, Glorimar Rivera, Wentao Yang, Yiying Wang, Xianghong Yang, Wenxin Zheng, Li Li, C.J. Sung, Yafei Qi, and Jing Yu
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medicine.medical_specialty ,Lymphovascular invasion ,Biopsy ,Uterine Cervical Neoplasms ,Adenocarcinoma ,Gastroenterology ,Pathology and Forensic Medicine ,Stromal Invasion ,Internal medicine ,Eosinophilic ,medicine ,Humans ,Stage (cooking) ,Papillomaviridae ,medicine.diagnostic_test ,business.industry ,Carcinoma ,Odds ratio ,Confidence interval ,Cohort ,Female ,Surgery ,Neoplasm Recurrence, Local ,Anatomy ,business - Abstract
The metastatic or recurrent potential of localized human papillomavirus-associated endocervical adenocarcinoma (HPVA EAC) is difficult to predict, especially based upon biopsy alone. Recent analyses of small cohorts indicate that high tumor nuclear grade (TNG) and the presence of necrotic tumor debris (NTD) from HPVA EACs in cervical biopsy specimens are highly predictive of nodal metastasis (NM). In the present study, we aimed to investigate how reliably tumoral morphologic features from cervical biopsy specimens predict NM or tumor recurrence (TR) and patient outcomes in a large cohort of endocervical adenocarcinoma patients. A cohort comprised of 397 patients with HPVA EAC treated at 18 institutions was identified, and cervical biopsies were paired with their associated complete tumor resections for a total of 794 specimens. A variety of tumoral histologic features were examined for each paired specimen, including TNG (assessed on a 3-tiered scale of increasing abnormalities-TNG1, TNG2, TNG3) and NTD (defined by the presence of necrotic and apoptotic tumor cells within tumor glandular lumens admixed with granular and eosinophilic amorphous material and inflammatory cells), which were correlated with outcomes. The distribution of TNG in biopsies was as follows: 86 (21.7%) TNG1, 223 (56.2%) TNG2, and 88 (22.2%) TNG3. NTD was identified in 176 (44%) of the biopsy specimens. The sensitivity, specificity, positive predictive value, and negative predictive value of a TNG1 assignment in the biopsy being predictive of the same assignment in the full resection were 0.82 (95% confidence interval [CI]: 0.7-0.9), 0.895 (0.86-0.93), 0.593 (0.48-0.696), and 0.96 (0.94-0.98), respectively. Respective values for an NTD-negative status were 0.89 (95% CI: 0.83-0.92), 0.715 (0.64-0.77), 0.72 (0.65-0.77), and 0.89 (0.83-0.93), respectively. Compared with the other cases in each category, both TNG1 and an NTD-negative status were each significantly associated with lower rates of NM (odds ratio for TNG1=0.245, 95% CI: 0.070-0.857, P=0.0277; for NTD=0.199, 95% CI: 0.094-0.421, P
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- 2021
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29. Three-dimensional MR Elastography Depicts Liver Inflammation, Fibrosis, and Portal Hypertension in Chronic Hepatitis B or C
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Yu Shi, Ruoyun Ji, Yang Hong, Xianyi Zhang, Bing Ma, Gongyu Lan, Yafei Qi, Yu-Jia Ma, and Qijun Wu
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Adult ,Liver Cirrhosis ,Male ,medicine.medical_specialty ,Portal venous pressure ,Gastroenterology ,Hepatitis B, Chronic ,Imaging, Three-Dimensional ,Fibrosis ,Interquartile range ,Internal medicine ,Hypertension, Portal ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Prospective Studies ,Stage (cooking) ,Inflammation ,medicine.diagnostic_test ,Receiver operating characteristic ,business.industry ,Hepatitis C, Chronic ,Middle Aged ,medicine.disease ,Cross-Sectional Studies ,Liver ,Liver biopsy ,Elasticity Imaging Techniques ,Portal hypertension ,Female ,Elastography ,business - Abstract
Background The value of measuring mechanical properties to categorize various pathophysiologic states of the liver is as yet undetermined in chronic hepatitis B (CHB) or C (CHC). Purpose To evaluate multiparametric three-dimensional (3D) MR elastography as a means of detecting early necroinflammation, distinguishing necroinflammation from fibrosis, and gauging the severity of portal hypertension (PH) in CHB or CHC. Materials and Methods From January 2015 to September 2019, participants with CHB or CHC were prospectively enrolled from a single institution and were divided into two groups: those with liver biopsy and no evidence of PH (group 1) and those with PH and a hepatic venous pressure gradient (HVPG) measurement (group 2). For group 3, healthy volunteers were separately recruited from a nearby community. Multiple viscoelastic parameters (shear stiffness [SS], storage modulus, loss modulus, and damping ratio [DR]) were determined at 3D MR elastography at 60 Hz, and multivariable logistic or linear regression analysis was used to assess associations of mechanical parameters with histologic scores and HVPG. Results A total of 155 participants (median age, 41 years [interquartile range, 32-48 years]; 85 women) were in group 1 (training set: n = 78, validation set: n = 77), 85 participants (median age, 57 years [interquartile range, 43-61 years]; 51 women) in group 2, and 60 healthy volunteers (median age, 49 years [interquartile range, 27-64 years]; 38 men) in group 3. The liver DR was higher in participants with necroinflammation (DR, 0.13 ± 0.03) versus those without (at liver fibrosis stage F0) (DR, 0.10 ± 0.02; P < .001). Liver DR and SS together performed well in the diagnosis of necroinflammation (area under the receiver operating characteristic curve [AUC], 0.88 [95% CI: 0.79, 0.96]) and the scoring of moderate to severe activity (AUC, 0.88 [95% CI: 0.81, 0.95]) in the validation data set. Liver DR (regression coefficient [β] = -30.3 [95% CI: -58.0, -2.5]; P = .03) and splenic SS (β = 2.3 [95% CI: 1.7, 2.9]; P < .001) were independently associated with HVPG. Conclusion Three-dimensional MR elastography may detect early necroinflammation, distinguish necroinflammation from liver fibrosis, and correlate with hepatic venous pressure gradient in chronic hepatitis B and C. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Reeder in this issue.
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- 2021
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30. Hepatic perivascular epithelioid cell tumor: Five case reports and literature review
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Zhen Liu, Yafei Qi, Chuanzhuo Wang, Xiaobo Zhang, and Baosheng Wang
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hepatectomy ,Human Melanoma Black-45 ,liver ,perivascular epithelioid cell tumor ,Surgery ,RD1-811 - Abstract
Perivascular epithelioid cell tumor (PEComa) is a rare tumor. Here, we present data regarding clinical presentations, diagnoses, management, and prognosis of five cases of hepatic PEComa between January 2002 and December 2008. Ultrasonography showed hyperechoic masses in all patients. Precontrast computed tomography (CT) showed that all lesions scanned were heterogeneous in density and were heterogeneously enhanced in arterial phase images. In two cases, magnetic resonance imaging showed hypointensity on T1-weighted images and hyperintensity on T2-weighted images. In enhanced scanning, lesions showed asymmetrical enhancement during arterial phase imaging. All tumors were composed of varying proportions of smooth muscle, adipose tissue, and thick-walled blood vessels, and showed positive immunohistochemical staining for Human Melanoma Black-45. All patients underwent hepatectomy, and there was no evidence of recurrence or metastasis during the follow-up period.
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- 2015
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31. Mutations in the Arabidopsis AtMRS2-11/AtMGT10/VAR5 Gene Cause Leaf Reticulation
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Shuang Liang, Yafei Qi, Jun Zhao, Yuanfeng Li, Rui Wang, Jingxia Shao, Xiayan Liu, Lijun An, and Fei Yu
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AtMRS2-11/AtMGT10/VAR5 ,chloroplast development ,leaf variegation ,Mg2+ transporters ,chloroplast envelope ,Plant culture ,SB1-1110 - Abstract
In higher plants, the development of functional chloroplasts is essential for photosynthesis and many other physiological processes. With a long-term goal of elucidating the genetic regulation of chloroplast development, we identified two allelic leaf variegation mutants, variegated5-1 (var5-1) and var5-2. Both mutants showed a distinct leaf reticulation phenotype of yellow paraveinal regions and green interveinal regions, and the leaf reticulation phenotype correlated with photosynthetic defects. Through the identification of mutation sites in the two mutant alleles and the molecular complementation, we confirmed that VAR5 encodes a CorA family of Mg2+ transporters also known as AtMRS2-11/AtMGT10. Using protoplast transient expression and biochemical fractionation assays, we demonstrated that AtMRS2-11/AtMGT10/VAR5 likely localizes to the chloroplast envelope. Moreover, we established that AtMRS2-11/AtMGT10/VAR5 forms large molecular weight complexes in the chloroplast and the sizes of these complexes clearly exceed those of their bacterial counterparts, suggesting the compositions of CorA Mg2+ transporter complex is different between the chloroplast and bacteria. Our findings indicate that AtMRS2-11/AtMGT10/VAR5 plays an important role in the tissue specific regulation of chloroplast development.
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- 2017
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32. PD-L1 Aptamer-Functionalized Metal-Organic Framework Nanoparticles for Robust Photo-Immunotherapy against Cancer with Enhanced Safety
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Jingfang Zhang, Wenzhe Li, Yafei Qi, Guorong Wang, Lele Li, Zhengyu Jin, Jie Tian, and Yang Du
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General Chemistry ,General Medicine ,Catalysis - Abstract
Immune checkpoint blockade has become a paradigm-shifting treatment modality to combat cancer, while conventional administration of immune checkpoint inhibitors, such as anti-PD-L1 antibody (α-PD-L1), often shows unsatisfactory immune responses and lead to severe immune-related adverse effects (irAEs). Herein, we develop a PD-L1 aptamer-based spherical nucleic acids (SNAs), which consists of oxaliplatin (OXA) encapsulated in a metal-organic framework nanoparticle core and a dense shell of aptPD-L1 (denoted as M@O-A). Upon light irradiation, this nanosystem enables concurrent photodynamic therapy (PDT), chemotherapy, and enhanced immunotherapy in one shot to inhibit both primary colorectal tumors and untreated distant tumors in mice. Notably, M@O-A shows scarcely any systemic immunotoxicity in a clinical irAEs-mimic transgenic mouse model. Collectively, this study presents a novel strategy for priming robust photo-immunotherapy against cancer with enhanced safety.
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- 2022
33. Endometrial T2 values and thickness measured during the spontaneous menstrual cycle: potential imaging biomarker related to female physiological hormones
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Liangkun Ma, Jing Lei, Ling Yuan, Haibo Zhang, Ning Ding, Yafei Qi, Xue Huadan, Jia Xu, Yonglan He, and Zhengyu Jin
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medicine.medical_specialty ,business.industry ,media_common.quotation_subject ,Luteal phase ,Endometrium ,Basal (phylogenetics) ,Follicle-stimulating hormone ,medicine.anatomical_structure ,Endocrinology ,Internal medicine ,Follicular phase ,medicine ,Radiology, Nuclear Medicine and imaging ,Luteinizing hormone ,business ,Menstrual cycle ,media_common ,Hormone - Abstract
The endometrium undergoes morphological and functional changes during menstrual cycles, regulated by female hormones. MRI T2 weighted imaging (T2WI) plays an essential role in endometrial disease evaluation. This study aims to define the cyclic course of endometrial T2 values and thickness and explore their relationship with basal female sex hormones. We prospectively recruited 38 healthy volunteers (20–30 years:22; 30–40 years:16), 3.0 T MR were performed during the menstrual phase (MP), follicular phase (FP), peri-ovulation phase (OP), and luteal phase (LP). Basal serum oestradiol (E), progesterone (P), luteinizing hormone (LH) and follicle stimulating hormone (FSH) hormone was tested. Endometrium thicknesses, T2 values were obtained in each phase. Pearson correlation test, Fisher's least significant difference (LSD) test, the analysis of variance (ANOVA) test, and the paired sample t test were applied. The endometrium thickness was significantly thinner in the younger age group (p
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- 2021
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34. Deep Learning for Fully Automated Prediction of Overall Survival in Patients Undergoing Resection for Pancreatic Cancer
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Jiawen Yao, Kai Cao, Yang Hou, Jian Zhou, Yingda Xia, Isabella Nogues, Qike Song, Hui Jiang, Xianghua Ye, Jianping Lu, Gang Jin, Hong Lu, Chuanmiao Xie, Rong Zhang, Jing Xiao, Zaiyi Liu, Feng Gao, Yafei Qi, Xuezhou Li, Yang Zheng, Le Lu, Yu Shi, and Ling Zhang
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Surgery - Abstract
To develop an imaging-derived biomarker for prediction of overall survival (OS) of pancreatic cancer by analyzing preoperative multiphase contrast-enhanced computed topography (CECT) using deep learning.Exploiting prognostic biomarkers for guiding neoadjuvant and adjuvant treatment decisions may potentially improve outcomes in patients with resectable pancreatic cancer.This multicenter, retrospective study included 1516 patients with resected pancreatic ductal adenocarcinoma (PDAC) from 3 centers located in China. The discovery cohort (n=763), which included preoperative multiphase CECT scans and OS data from 2 centers, was used to construct a fully automated imaging-derived prognostic biomarker-DeepCT-PDAC-by training scalable deep segmentation and prognostic models (via self-learning) to comprehensively model the tumor-anatomy spatial relations and their appearance dynamics in multiphase CECT for OS prediction. The marker was independently tested using internal (n=574) and external validation cohorts (n=179, 3 centers) to evaluate its performance, robustness, and clinical usefulness.Preoperatively, DeepCT-PDAC was the strongest predictor of OS in both internal and external validation cohorts [hazard ratio (HR) for high versus low risk 2.03, 95% confidence interval (CI): 1.50-2.75; HR: 2.47, CI: 1.35-4.53] in a multivariable analysis. Postoperatively, DeepCT-PDAC remained significant in both cohorts (HR: 2.49, CI: 1.89-3.28; HR: 2.15, CI: 1.14-4.05) after adjustment for potential confounders. For margin-negative patients, adjuvant chemoradiotherapy was associated with improved OS in the subgroup with DeepCT-PDAC low risk (HR: 0.35, CI: 0.19-0.64), but did not affect OS in the subgroup with high risk.Deep learning-based CT imaging-derived biomarker enabled the objective and unbiased OS prediction for patients with resectable PDAC. This marker is applicable across hospitals, imaging protocols, and treatments, and has the potential to tailor neoadjuvant and adjuvant treatments at the individual level.
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- 2022
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35. Chloroplast SRP54 and FtsH protease coordinate thylakoid membrane-associated proteostasis in Arabidopsis.
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(雷洋), Yang Lei, (李碧浪), Bilang Li, (王晓敏), Xiaomin Wang, (卫俊佑), Junyou Wei, (王佩仪), Peiyi Wang, (赵军), Jun Zhao, (郁飞), Fei Yu, and (齐亚飞), Yafei Qi
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- 2023
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36. A Hepatocellular Carcinoma Targeting Nanostrategy with Hypoxia-Ameliorating and Photothermal Abilities that, Combined with Immunotherapy, Inhibits Metastasis and Recurrence
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Xiaolong Liang, Yafei Qi, Jie Tian, Peifeng Wang, Yang Du, Chihua Fang, Yueyang Hu, Tianjun Zhou, and Yu-Shen Jin
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Sorafenib ,Biodistribution ,Carcinoma, Hepatocellular ,medicine.medical_treatment ,General Physics and Astronomy ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Metastasis ,Cell Line, Tumor ,medicine ,Humans ,Tissue Distribution ,General Materials Science ,Hypoxia ,Tumor hypoxia ,business.industry ,Liver Neoplasms ,General Engineering ,Abscopal effect ,Immunotherapy ,Phototherapy ,Photothermal therapy ,021001 nanoscience & nanotechnology ,medicine.disease ,0104 chemical sciences ,Cancer research ,Nanoparticles ,Immunogenic cell death ,0210 nano-technology ,business ,medicine.drug - Abstract
Hepatocellular carcinoma (HCC) is a common and highly malignant tumor that is prone to recurrence and metastasis and has no effective treatment. Unsurprisingly, its prognosis is quite poor; early detection methods and effective low-toxicity treatments are urgently needed. To achieve these goals, we designed a multifunctional, U.S. Food and Drug Administration-approved Prussian blue (PB) nanoparticle (NP) with a porous metal organic frame loaded with sorafenib (SF), conjugated with HCC-specific targeting peptide SP94 and the near-infrared dye cyanine (Cy)5.5. These NPs are amenable to multimodal imaging for dynamic monitoring of their biodistribution and tumor-targeting effects. The SP94-PB-SF-Cy5.5 NPs achieved targeted delivery and controlled SF release and exhibited good photothermal effects. In this strategy, photothermal therapy and SF treatment complement each other, reducing the side effects of SF and achieving a therapeutic effect without local tumor recurrence. In addition, the catalase-like ability of the NPs alleviates tumor hypoxia, and their photothermal effects induce immunogenic cell death, leading to the release of tumor-associated antigens. These effects combine to trigger an antitumor immune response; the NPs also displayed promising inhibitory effects on tumor metastasis and recurrence and produced an abscopal effect and long-term immunological memory when combined with antiprogrammed death-ligand 1 (PD-L1) immunotherapy. These safe, multifunctional NPs represent a valuable treatment option for HCC. In addition, this next-generation treatment model may provide some ideas for the management of HCC and other cancers.
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- 2020
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37. Morphological description of uterine scar 1 year after cesarean section by 3D-SPACE 3.0T MR
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Ning Ding, Yafei Qi, Yonglan He, Liangkun Ma, Huadan Xue, and Zhengyu Jin
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History ,Polymers and Plastics ,3d space ,Section (typography) ,Anatomy ,General Environmental Science - Abstract
Poster: "ECR 2017 / C-2942 / Morphological description of uterine scar one year after cesarean section by T2 3D SPACE 3.0T MR" by: "N. Ding, Y. Qi, Y. He, H. D. Xue, Z. Jin; Beijing/CN"
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- 2020
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38. Pancreatic adenocarcinoma: quantitative CT features are correlated with fibrous stromal fraction and help predict outcome after resection
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Xiaoli Cai, Yu Shi, Ruoyun Ji, Yafei Qi, Youli Xu, Xianyi Zhang, Gongyu Lan, Chang Liu, and Feng Gao
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Male ,medicine.medical_specialty ,Stromal cell ,medicine.medical_treatment ,Contrast Media ,Kaplan-Meier Estimate ,Disease-Free Survival ,030218 nuclear medicine & medical imaging ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Pancreas ,Aged ,Proportional Hazards Models ,Retrospective Studies ,Neuroradiology ,business.industry ,Retrospective cohort study ,Histology ,General Medicine ,Middle Aged ,Prognosis ,medicine.disease ,Pancreatic Neoplasms ,Survival Rate ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Pancreatectomy ,Cohort ,Adenocarcinoma ,Female ,Radiology ,Neoplasm Grading ,Tomography, X-Ray Computed ,business ,Carcinoma, Pancreatic Ductal - Abstract
To identify quantitative imaging features of contrast-enhanced computed tomography (CE-CT) that may be prognostically favorable after resection of smaller (≤ 30 mm) pancreatic ductal adenocarcinomas (PDACs) located at head. This retrospective study included two independent cohorts (discovery cohort, n = 212; test cohort, n = 100) of patients who underwent resection of head PDACs ≤ 30 mm and preoperative CE-CT. We examined tumor and surrounding parenchymal attenuation differences (deltas), and tumor attenuation changes across phases (ratios). Semantic features of PDACs were evaluated by two radiologists. Clinicopathologic and imaging features for predicting disease-free survival (DFS) and overall survival (OS) were analyzed via multivariate Lasso-penalized Cox proportional-hazards models. Survival rates were derived by Kaplan-Meier method. Imaging features achieved C-indices of 0.766 (discovery cohort) and 0.739 (test cohort) for DFS, and 0.790 (discovery cohort) and 0.772 (test cohort) for OS estimates through incorporation of clinicopathologic features. The most decisive imaging feature was delta 3, denoting attenuation differences between tumor and surrounding pancreas at pancreatic phase (DFS: HR = 2.122; OS: HR = 2.375; both p
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- 2020
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39. Radiomics Based on MRI as a Biomarker to Guide Therapy by Predicting Upgrading of Prostate Cancer From Biopsy to Radical Prostatectomy
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Hao Sun, Jingwei Wei, Yu Xiao, Dongsheng Gu, Zhengyu Jin, Jing Lei, Feng Feng, Wei-Gang Yan, Yafei Qi, Jie Tian, Gumuyang Zhang, Huadan Xue, and Yuqi Han
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Male ,medicine.medical_specialty ,Biopsy ,medicine.medical_treatment ,Population ,Logistic regression ,030218 nuclear medicine & medical imaging ,03 medical and health sciences ,Prostate cancer ,0302 clinical medicine ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Stage (cooking) ,education ,Multiparametric Magnetic Resonance Imaging ,Retrospective Studies ,Prostatectomy ,education.field_of_study ,Receiver operating characteristic ,business.industry ,Prostatic Neoplasms ,Nomogram ,medicine.disease ,Magnetic Resonance Imaging ,Radiology ,business ,Biomarkers - Abstract
Background Biopsy Gleason score (GS) is crucial for prostate cancer (PCa) treatment decision-making. Upgrading in GS from biopsy to radical prostatectomy (RP) puts a proportion of patients at risk of undertreatment. Purpose To develop and validate a radiomics model based on multiparametric magnetic resonance imaging (mp-MRI) to predict PCa upgrading. Study type Retrospective, radiomics. Population A total of 166 RP-confirmed PCa patients (training cohort, n = 116; validation cohort, n = 50) were included. Field strength/sequence 3.0T/T2 -weighted (T2 W), apparent diffusion coefficient (ADC), and dynamic contrast enhancement (DCE) sequences. Assessment PI-RADSv2 score for each tumor was recorded. Radiomic features were extracted from T2 W, ADC, and DCE sequences and Mutual Information Maximization criterion was used to identify the optimal features on each sequence. Multivariate logistic regression analysis was used to develop predictive models and a radiomics nomogram and their performance was evaluated. Statistical tests Student's t or chi-square were used to assess the differences in clinicopathologic data between the training and validation cohorts. Receiver operating characteristic (ROC) curve analysis was performed and the area under the curve (AUC) was calculated. Results In PI-RADSv2 assessment, 67 lesions scored 5, 70 lesions scored 4, and 29 lesions scored 3. For each sequence, 4404 features were extracted and the top 20 best features were selected. The radiomics model incorporating signatures from the three sequences achieved better performance than any single sequence (AUC: radiomics model 0.868, T2 W 0.700, ADC 0.759, DCE 0.726). The combined mode incorporating radiomics signature, clinical stage, and time from biopsy to RP outperformed the clinical model and radiomics model (AUC: combined model 0.910, clinical model 0.646, radiomics model 0.868). The nomogram showed good performance (AUC 0.910) and calibration (P-values: training cohort 0.624, validation cohort 0.294). Data conclusion Radiomics based on mp-MRI has potential to predict upgrading of PCa from biopsy to RP. Level of evidence 3 TECHNICAL EFFICACY: Stage 5 J. Magn. Reson. Imaging 2020;52:1239-1248.
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- 2020
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40. Chloroplast envelope ATPase PGA1/AtFtsH12 is required for chloroplast protein accumulation and cytosol-chloroplast protein homeostasis in Arabidopsis
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Qinglong Li, Xiaomin Wang, Yang Lei, Yanling Wang, Bilang Li, Xiayan Liu, Lijun An, Fei Yu, and Yafei Qi
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Adenosine Triphosphatases ,Chloroplast Proteins ,Chloroplasts ,Cytosol ,Arabidopsis Proteins ,Gene Expression Regulation, Plant ,Mutation ,Arabidopsis ,Proteostasis ,Cell Biology ,Molecular Biology ,Biochemistry - Abstract
The establishment of photosynthetic protein complexes during chloroplast development requires the influx of a large number of chloroplast proteins that are encoded by the nuclear genome, which is critical for cytosol and chloroplast protein homeostasis and chloroplast development. However, the mechanisms regulating this process are still not well understood in higher plants. Here, we report the isolation and characterization of the pale green Arabidopsis pga1-1 mutant, which is defective in chloroplast development and chloroplast protein accumulation. Using genetic and biochemical evidence, we reveal that PGA1 encodes AtFtsH12, a chloroplast envelope-localized protein of the FtsH family proteins. We determined a G703R mutation in the GAD motif of the conserved ATPase domain renders the pga1-1 a viable hypomorphic allele of the essential gene AtFtsH12. In de-etiolation assays, we showed that the accumulation of photosynthetic proteins and the expression of photosynthetic genes were impaired in pga1-1. Using the FNR
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- 2022
41. VAR2/AtFtsH2 and EVR2/BCM1/CBD1 synergistically regulate the accumulation of PSII reaction centre D1 protein during de-etiolation in Arabidopsis
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Xiaomin Wang, Qinglong Li, Yalin Zhang, Mi Pan, Ruijuan Wang, Yifan Sun, Lijun An, Xiayan Liu, Fei Yu, and Yafei Qi
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Chlorophyll ,Chloroplasts ,ATP-Dependent Proteases ,Physiology ,Arabidopsis Proteins ,Etiolation ,Mutation ,Arabidopsis ,Membrane Proteins ,Photosystem II Protein Complex ,Plant Science - Abstract
Thylakoid FtsH complex participates in PSII repair cycle during high light-induced photoinhibition. The Arabidopsis yellow variegated2 (var2) mutants are defective in the VAR2/AtFtsH2 subunit of thylakoid FtsH complex. Taking advantage of the var2 leaf variegation phenotype, dissections of genetic enhancer loci have yielded novel paradigms in understanding functions of thylakoid FtsH complex. Here, we report the isolation of a new var2 enhancer, enhancer of variegation2-1 (evr2-1). We confirmed that EVR2 encodes a chloroplast protein that was known as BALANCE OF CHLOROPHYLL METABOLISM 1 (BCM1), or CHLOROPHYLL BIOSYNTHETIC DEFECT 1 (CBD1). We showed that EVR2/BCM1/CBD1 was involved in the oligomerization of photosystem I complexes. Genetic assays indicated that general defects in chlorophyll biosynthesis and the accumulation of photosynthetic complexes do not necessarily enhance var2 leaf variegation. In addition, we found that VAR2/AtFtsH2 is required for the accumulation of photosynthetic proteins during de-etiolation. Moreover, we identified PSII core proteins D1 and PsbC as potential EVR2-associated proteins using Co-IP/MS. Furthermore, the accumulation of D1 protein was greatly compromised in the var2-5 evr2-1 double mutant during de-etiolation. Together, our findings reveal a functional link between VAR2/AtFtsH2 and EVR2/BCM1/CBD1 in regulating chloroplast development and the accumulation of PSII reaction centre D1 protein during de-etiolation.
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- 2022
42. The value of CT radiomics in differentiating mycoplasma pneumoniae pneumonia from streptococcus pneumoniae pneumonia with similar consolidation in children
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Dongdong Wang, Jianshe Zhao, Ran Zhang, Qinghu Yan, Lu Zhou, Xiaoyu Han, Yafei Qi, and Dexin YU
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Objective To investigate the value of CT radiomics in the differentiation of mycoplasma pneumoniae pneumonia (MPP) from streptococcus pneumoniae pneumonia (SPP) with similar CT manifestations in children. Methods 63 children with MPP (n=30) or SPP (n=33) with similar consolidation and surrounding halo on CT images in Qilu Hospital and Qilu Children's Hospital between January 2017 and July 2019 were enrolled in the retrospective study. Radiomic features of the both lesions on plain CT images were extracted including the consolidation part of the pneumonia or both consolidation and surrounding halo area which were respectively delineated at region of interest (ROI) areas on the maximum axial image. The training set (n=43) and the validation set (n=20) were established by stratified random sampling at a ratio of 7:3. By means of variance threshold, the effective radiomics features, Select Best and least absolute shrinkage and selection operator (LASSO) regression method were employed for feature selection. Six classifiers, including k-nearest neighbor(KNN), support vector machine (SVM),extreme gradient boosting(XGBoost), random forest(RF), logistic regression(LR), and decision tree(DT) were used to construct the models based on radiomic features. The diagnostic performance of these models was estimated and compared using the area under the receiver operating characteristic (ROC) curve (AUC), and the accuracy (score) matrix was established to compare and evaluate the results of different radiomics models. Results XGBoost outperformed other classifiers and was selected as the backbone in the classifier with the consolidation + the surrounding halo was taken as ROI to differentiate MPP from SPP in validation set. The AUC value of MPP in validation set was 0.889, the sensitivity and specificity were 0.89 and 0.82, respectively; and the AUC value of SPP validation set was 0.889, the sensitivity and specificity were 0.82 and 0.89, respectively. Conclusion The XGBoost model has the best classification efficiency in the identification of MPP from SPP in children, and the ROI with both consolidation and surrounding halo is most suitable for the delineation.
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- 2022
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43. Sources of systematic errors in human path integration
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Yafei Qi, Weimin Mou
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- 2022
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44. Three-Dimensional Visualization and Imaging of the Entry Tear and Intimal Flap of Aortic Dissection Using CT Virtual Intravascular Endoscopy.
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Yafei Qi, Xiaoyuan Ma, Gang Li, Xiangxing Ma, Qing Wang, and Dexin Yu
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Medicine ,Science - Abstract
Conventional computed tomography (CT) approaches provides limited visualization of the entire endoluminal changes of aortic dissection (AD), which is essential for its treatment. As an important supplement, three-dimensional CT virtual intravascular endoscopy (VIE) can show relevant details. This study aims to determine the value of VIE in displaying the entry tear and intimal flap of AD.Among 127 consecutive symptomatic patients with suspected AD who underwent CT angiography (CTA), 84 subjects were confirmed to have AD and were included in the study. Conventional CT and VIE images were observed and evaluated. From the 92 entry tears revealed via conventional CT, 88 (95.7%) tears appeared on VIE with round (n = 26), slit-shaped (n = 9), or irregular (n = 53) shapes, whereas the intimal flaps were sheetlike (n = 34), tubular (n = 34), wavelike (n = 13), or irregular (n = 7) in shape. The VIE also showed the spatial relationship between the torn flap and adjacent structures. Among 58 entry tears with multiple-line type flap shown on conventional CT, 41 (70.7%) appeared with an irregular shape on VIE, whereas among 30 tears with single-line type flap, 17 (56.7%) appeared as round or slit-shaped on VIE. These results demonstrated a significant difference (P < 0.05). The poor display of tears on VIE was related to the low CT attenuation values in lumen or in neighboring artifacts (P < 0.01).CT VIE presents the complete configurations and details of the intimal tears and flaps of AD better than conventional CT approaches. Accordingly, it should be recommended as a necessary assessment tool for endovascular therapy and as part of strategy planning in pre-surgical patients.
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- 2016
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45. The Cloning and Functional Characterization of Peach CONSTANS and FLOWERING LOCUS T Homologous Genes PpCO and PpFT.
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Xiang Zhang, Lijun An, Thi Hung Nguyen, Huike Liang, Rui Wang, Xiayan Liu, Tianhong Li, Yafei Qi, and Fei Yu
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Medicine ,Science - Abstract
Flowering is an essential stage of plant growth and development. The successful transition to flowering not only ensures the completion of plant life cycles, it also serves as the basis for the production of economically important seeds and fruits. CONSTANS (CO) and FLOWERING LOCUS T (FT) are two genes playing critical roles in flowering time control in Arabidopsis. Through homology-based cloning and rapid-amplifications of cDNA ends (RACE), we obtained full-lengths cDNA sequences of Prunus persica CO (PpCO) and Prunus persica FT (PpFT) from peach (Prunus persica (L.) Batsch) and investigated their functions in flowering time regulation. PpCO and PpFT showed high homologies to Arabidopsis CO and FT at DNA, mRNA and protein levels. We showed that PpCO and PpFT were nucleus-localized and both showed transcriptional activation activities in yeast cells, consistent with their potential roles as transcription activators. Moreover, we established that the over-expression of PpCO could restore the late flowering phenotype of the Arabidopsis co-2 mutant, and the late flowering defect of the Arabidopsis ft-1 mutant can be rescued by the over-expression of PpFT, suggesting functional conservations of CO and FT genes in peach and Arabidopsis. Our results suggest that PpCO and PpFT are homologous genes of CO and FT in peach and they may function in regulating plant flowering time.
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- 2015
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46. The chloroplast metalloproteases VAR2 and EGY1 act synergistically to regulate chloroplast development in Arabidopsis
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Jingxia Shao, Yafei Qi, Pei Lei, Liru Yan, Xiayan Liu, Xiaomin Wang, Jingjing Meng, Lijun An, Jun Zhao, Huimin Li, and Fei Yu
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0106 biological sciences ,0301 basic medicine ,Chloroplasts ,Mutant ,Arabidopsis ,Plant Biology ,Photosystem I ,01 natural sciences ,Biochemistry ,03 medical and health sciences ,ATP-Dependent Proteases ,Etiolation ,Arabidopsis thaliana ,Amino Acid Sequence ,Photosynthesis ,Molecular Biology ,Variegation ,Base Sequence ,Photosystem I Protein Complex ,biology ,Arabidopsis Proteins ,Protein Stability ,food and beverages ,Membrane Proteins ,Photosystem II Protein Complex ,Cell Biology ,biology.organism_classification ,Cell biology ,Chloroplast ,030104 developmental biology ,Proteostasis ,Genetic Loci ,Thylakoid ,Mutation ,Metalloproteases ,Protein Multimerization ,010606 plant biology & botany - Abstract
Chloroplast development and photosynthesis require the proper assembly and turnover of photosynthetic protein complexes. Chloroplasts harbor a repertoire of proteases to facilitate proteostasis and development. We have previously used an Arabidopsis leaf variegation mutant, yellow variegated2 (var2), defective in thylakoid FtsH protease complexes, as a tool to dissect the genetic regulation of chloroplast development. Here, we report a new genetic enhancer mutant of var2, enhancer of variegation3–1 (evr3–1). We confirm that EVR3 encodes a chloroplast metalloprotease, reported previously as ethylene-dependent gravitropism-deficient and yellow-green1 (EGY1)/ammonium overly sensitive1 (AMOS1). We observed that mutations in EVR3/EGY1/AMOS1 cause more severe leaf variegation in var2–5 and synthetic lethality in var2–4. Using a modified blue-native PAGE system, we reveal abnormal accumulations of photosystem I, photosystem II, and light-harvesting antenna complexes in EVR3/EGY1/AMOS1 mutants. Moreover, we discover distinct roles of VAR2 and EVR3/EGY1/AMOS1 in the turnover of photosystem II reaction center under high light stress. In summary, our findings indicate that two chloroplast metalloproteases, VAR2/AtFtsH2 and EVR3/EGY1/AMOS1, function coordinately to regulate chloroplast development and reveal new roles of EVR3/EGY1/AMOS1 in regulating chloroplast proteostasis in Arabidopsis.
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- 2019
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47. Noninvasive imaging in cancer immunotherapy: The way to precision medicine
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Yang Du, Zhengyu Jin, Jie Tian, and Yafei Qi
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0301 basic medicine ,Oncology ,Cancer Research ,medicine.medical_specialty ,medicine.medical_treatment ,Cancer Vaccines ,Immunotherapy, Adoptive ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,Cancer immunotherapy ,Neoplasms ,Internal medicine ,medicine ,Animals ,Humans ,Immunologic Factors ,Molecular Targeted Therapy ,Precision Medicine ,business.industry ,Cancer ,Immunotherapy ,Precision medicine ,medicine.disease ,Molecular medicine ,Chimeric antigen receptor ,Molecular Imaging ,030104 developmental biology ,030220 oncology & carcinogenesis ,Molecular imaging ,business - Abstract
Molecular medicine requires a more precise treatment directed at molecular aberrations detected in tumors on an individual patient level. Immunotherapies empower the body's own immune system to confront tumor cells; however, their efficacy is often affected by tumor heterogeneity. Numerous noninvasive imaging techniques are available to monitor changes in tumor function reflecting therapeutic response, including immunotherapy, and to realize personalized response evaluation. For immunotherapy, strategies for using noninvasive imaging as a prognostic biomarker to identify patients who could benefit from targeted immunotherapy and predict early responders/nonresponders may ultimately lead to improved clinical management, individualized therapy regimens, and better prediction of patient outcomes. Herein, we summarize the recent progress in noninvasive imaging of immunotherapeutic targets such as immune cells, immune checkpoint inhibitors, immune vaccines, and T-cell therapy with chimeric antigen receptor, and review the clinical application of noninvasive imaging in immunotherapy. Finally, we describe the application of multimodal/multispectral imaging and radiomics, which may offer future direction for precision imaging in immunotherapy. With further progress of noninvasive imaging, guiding cancer immunotherapy into the era of precision medicine would be a promising option.
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- 2019
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48. CT radiomics nomogram for the preoperative prediction of lymph node metastasis in gastric cancer
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Huadan Xue, Zhengyu Jin, Jian-Chun Yu, Yafei Qi, Wei Liu, Yue Wang, Jing-Juan Liu, Yang Yu, and Jing Lei
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Adult ,Male ,medicine.medical_specialty ,030218 nuclear medicine & medical imaging ,Metastasis ,Cohort Studies ,03 medical and health sciences ,0302 clinical medicine ,Predictive Value of Tests ,Stomach Neoplasms ,Preoperative Care ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Lymph node ,Aged ,Neoplasm Staging ,Retrospective Studies ,Receiver operating characteristic ,business.industry ,Area under the curve ,Cancer ,Retrospective cohort study ,General Medicine ,Middle Aged ,Nomogram ,medicine.disease ,Nomograms ,medicine.anatomical_structure ,ROC Curve ,Lymphatic Metastasis ,030220 oncology & carcinogenesis ,Cohort ,Female ,Radiology ,Tomography, X-Ray Computed ,business ,Algorithms - Abstract
To investigate the role of computed tomography (CT) radiomics for the preoperative prediction of lymph node (LN) metastasis in gastric cancer. This retrospective study included 247 consecutive patients (training cohort, 197 patients; test cohort, 50 patients) with surgically proven gastric cancer. Dedicated radiomics prototype software was used to segment lesions on preoperative arterial phase (AP) CT images and extract features. A radiomics model was constructed to predict the LN metastasis by using a random forest (RF) algorithm. Finally, a nomogram was built incorporating the radiomics scores and selected clinical predictors. Receiver operating characteristic (ROC) curves were used to validate the capability of the radiomics model and nomogram on both the training and test cohorts. The radiomics model showed a favorable discriminatory ability in the training cohort with an area under the curve (AUC) of 0.844 (95% CI, 0.759 to 0.909), which was confirmed in the test cohort with an AUC of 0.837 (95% CI, 0.705 to 0.926). The nomogram consisted of radiomics scores and the CT-reported LN status showed excellent discrimination in the training and test cohorts with AUCs of 0.886 (95% CI, 0.808 to 0.941) and 0.881 (95% CI, 0.759 to 0.956), respectively. The CT-based radiomics nomogram holds promise for use as a noninvasive tool in the individual prediction of LN metastasis in gastric cancer. • CT radiomics showed a favorable performance for the prediction of LN metastasis in gastric cancer. • Radiomics model outperformed the routine CT in predicting LN metastasis in gastric cancer. • The radiomics nomogram holds potential in the individualized prediction of LN metastasis in gastric cancer.
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- 2019
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49. DNMT3a promotes proliferation by activating the STAT3 signaling pathway and depressing apoptosis in pancreatic cancer
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Xianghong Yang, Kezuo Hou, Yafei Qi, Xiaofang Che, Yunpeng Liu, Na Song, Ce Li, Xiujuan Qu, and Wei Jing
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0301 basic medicine ,Gene knockdown ,Cell cycle checkpoint ,endocrine system diseases ,Cell growth ,Cell ,Cell cycle ,Biology ,medicine.disease_cause ,Stat3 Signaling Pathway ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,Oncology ,Apoptosis ,030220 oncology & carcinogenesis ,embryonic structures ,medicine ,Cancer research ,Carcinogenesis - Abstract
Background Although aberrant DNA methyltransferase 3a (DNMT3a) expression is important to the tumorigenesis of pancreatic ductal adenocarcinoma (PDAC), the role of DNMT3a in PDAC prognosis is not clarified yet due to the limited studies and lacking of underlying molecular mechanism. Methods The expression of DNMT3a was examined by immunohistochemistry in PDAC tissues. Gene expression profiles assays were conducted to explore the impact of DNMT3a on biological processes and signal pathways. Cell cycle and apoptosis were measured by flow cytometry. Western blotting and real-time qPCR assays were used to explore the impact of DNMT3a on expression of protein and mRNA related to cell cycle, STAT3 signaling pathway and apoptosis. Results DNMT3a was overexpressed and closely associated with poor outcomes of PDAC. DNMT3a knockdown restrained PDAC cell proliferation, induced cell cycle arrest and promoted apoptosis in vitro. Affymetrix GeneChip Human Transcriptome Array identified that the cell cycle-related process was most significantly associated with DNMT3a. DNMT3a knockdown induced G1-S phase transition arrest by decreasing the expression of cyclin D1, which was mediated by the reduction of IL8 and the subsequent inactivation of STAT3 signaling pathway. Furthermore, exogenous apoptosis was also promoted after DNMT3a knockdown, probably via up-regulation of DNA transcription and expression in CASP8. Conclusion These findings indicate that DNMT3a plays an important role in PDAC progression. DNMT3a may serve as a prognostic biomarker and a therapeutic strategy candidate in PDAC.
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- 2019
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50. Three‐dimensional turbo‐spin‐echo amide proton transfer‐weighted mri for cervical cancer: A preliminary study
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Xiaoqi Wang, Zhengyu Jin, Yafei Qi, Yang Xiang, Hai‐Long Zhou, Huadan Xue, Yuan Li, Yong-lan He, Cheng-Yu Lin, and Junjun Yang
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Adult ,Interclass correlation ,Population ,Uterine Cervical Neoplasms ,Cervix Uteri ,Sensitivity and Specificity ,030218 nuclear medicine & medical imaging ,Young Adult ,03 medical and health sciences ,Imaging, Three-Dimensional ,0302 clinical medicine ,Region of interest ,Image Interpretation, Computer-Assisted ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Prospective Studies ,Stage (cooking) ,education ,Aged ,Cervical cancer ,education.field_of_study ,medicine.diagnostic_test ,business.industry ,Area under the curve ,Reproducibility of Results ,Cancer ,Magnetic resonance imaging ,Middle Aged ,medicine.disease ,Amides ,Magnetic Resonance Imaging ,Female ,Protons ,Nuclear medicine ,business - Abstract
BACKGROUND Amide proton transfer-weighted (APTw) imaging has shown great potential in the diagnosis of cancer, but has yet not been well studied in cervical cancer. PURPOSE To evaluate the image quality and clinical feasibility of APTw MRI for cervical cancer. STUDY TYPE Prospective. POPULATION In all, 75 patients with cervical lesions and 49 healthy volunteers. FIELD STRENGTH/SEQUENCE 3.0 T, 3D turbo spin echo (TSE) APTw sequence. ASSESSMENT Three radiologists, blinded to the clinical data, independently evaluated APTw image quality with a 5-point Likert scale on 64 patients with pathologically confirmed cervical cancer. APT values, calculated based on asymmetry of acquired Z-spectrum with respect to water frequency, using 3D turbo spin echo volume acquisition with B0 correction, were independently measured by two radiologists, twice for each observer, on 52 cervical cancer lesions and 49 normal cervical stroma with a mean region of interest area of 638.6 mm2 and 557.5 mm2 , respectively. STATISTICAL TESTS Interobserver agreement was evaluated by Kendall's W test. Intra- and interobserver interclass correlation coefficients (ICC) were computed. Student's t-test was used to compare the differences of APT values between cervical cancer and normal cervix; receiver operating characteristic analysis was performed. RESULTS Most cases revealed good APTw image quality with excellent agreement (Kendall's W = 0.850, P
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- 2019
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