206 results on '"Yida, Zhang"'
Search Results
2. Exploring the brittle-to-ductile transition and microstructural responses of γ−TiAl alloy with a crystal plasticity model incorporating dislocation and twinning
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Hao Wu, Yida Zhang, Dong Lu, Xiufang Gong, Liming Lei, Hong Zhang, Yongjie Liu, and Qingyuan Wang
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γ−TiAl ,Crystal plasticity ,Brittle-to-ductile transition ,Dislocation ,Twinning ,Materials of engineering and construction. Mechanics of materials ,TA401-492 - Abstract
γ−TiAl alloy, with its high specific strength and creep resistance, is ideal for aerospace engines and gas turbines, but its brittleness poses significant manufacturing and processing challenges. To address these issues, this study employs a crystal plasticity finite element method incorporating dislocation and twinning to analyze the brittle-to-ductile transition behavior of γ−TiAl alloy at different temperatures. Additionally, the Bayesian optimization methods are employed to efficiently and accurately obtain parameters related to numerical calculations of crystal plasticity. The results indicate that at room temperature, the high activation resistance of the slip systems in the α2 phase leads to limited slip activity, resulting in poor plasticity. However, at 750 °C and 850 °C, the strength of the slip systems decreases significantly, allowing more α2 phase lamellae in the γ-TiAl alloy to undergo greater plastic deformation. This enhancement in the plastic deformation capacity of the α2phase lamellae reduce the overall deformation incompatibility in the TiAl alloy, thereby improving the overall ductile of the γ-TiAl alloy.
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- 2024
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3. Turning anecdotal irradiation-induced anticancer immune responses into reproducible in situ cancer vaccines via disulfiram/copper-mediated enhanced immunogenic cell death of breast cancer cells
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Wei Guo, Lin Jia, Ling Xie, Juliann G. Kiang, Yangyang Wang, Fengfei Sun, Zunwen Lin, Enwen Wang, Yida Zhang, Peigen Huang, Ting Sun, Xiao Zhang, Zhengying Bian, Tiejun Tang, Jingtian Guo, Soldano Ferrone, and Xinhui Wang
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Cytology ,QH573-671 - Abstract
Abstract Irradiation (IR) induces immunogenic cell death (ICD) in tumors, but it rarely leads to the abscopal effect (AE); even combining IR with immune checkpoint inhibitors has shown only anecdotal success in inducing AEs. In this study, we aimed to enhance the IR-induced immune response and generate reproducible AEs using the anti-alcoholism drug, disulfiram (DSF), complexed with copper (DSF/Cu) to induce tumor ICD. We measured ICD in vitro and in vivo. In mouse tumor models, DSF/Cu was injected intratumorally followed by localized tumor IR, creating an in situ cancer vaccine. We determined the anticancer response by primary tumor rejection and assessed systemic immune responses by tumor rechallenge and the occurrence of AEs relative to spontaneous lung metastasis. In addition, we analyzed immune cell subsets and quantified proinflammatory and immunosuppressive chemokines/cytokines in the tumor microenvironment (TME) and blood of the vaccinated mice. Immune cell depletion was investigated for its effects on the vaccine-induced anticancer response. The results showed that DSF/Cu and IR induced more potent ICD under hypoxia than normoxia in vitro. Low-dose intratumoral (i.t.) injection of DSF/Cu and IR(12Gy) demonstrated strong anti-primary and -rechallenged tumor effects and robust AEs in mouse models. These vaccinations also increased CD8+ and CD4+ cell numbers while decreasing Tregs and myeloid-derived suppressor cells in the 4T1 model, and increased CD8+, dendritic cells (DC), and decreased Treg cell numbers in the MCa-M3C model. Depleting both CD8+ and CD4+ cells abolished the vaccine’s anticancer response. Moreover, vaccinated tumor-bearing mice exhibited increased TNFα levels and reduced levels of immunosuppressive chemokines/cytokines. In conclusion, our novel approach generated an anticancer immune response that results in a lack of or low tumor incidence post-rechallenge and robust AEs, i.e., absence of or decreased spontaneous lung metastasis in tumor-bearing mice. This approach is readily translatable to clinical settings and may increase IR-induced AEs in cancer patients.
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- 2024
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4. Mapping human tissues with highly multiplexed RNA in situ hybridization
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Kian Kalhor, Chien-Ju Chen, Ho Suk Lee, Matthew Cai, Mahsa Nafisi, Richard Que, Carter R. Palmer, Yixu Yuan, Yida Zhang, Xuwen Li, Jinghui Song, Amanda Knoten, Blue B. Lake, Joseph P. Gaut, C. Dirk Keene, Ed Lein, Peter V. Kharchenko, Jerold Chun, Sanjay Jain, Jian-Bing Fan, and Kun Zhang
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Science - Abstract
Abstract In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ mapping techniques but their application to human tissues has been limited due to their large size, general lower tissue quality and high autofluorescence. Here we report DART-FISH, a padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections. We introduce an omni-cell type cytoplasmic stain that substantially improves the segmentation of cell bodies. Our enzyme-free isothermal decoding procedure allows us to image 121 genes in large sections from the human neocortex in 20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.
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- 2024
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5. Manipulating photogenerated electron flow in nickel single‐atom catalysts for photocatalytic CO2 reduction into tunable syngas
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Yida Zhang, Qingyu Wang, Lihui Wu, Haibin Pan, Chengyuan Liu, Yue Lin, Gongming Wang, and Xusheng Zheng
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carbon nitride ,CO2 photoreduction ,electron flow ,Ni single atoms ,syngas ,Production of electric energy or power. Powerplants. Central stations ,TK1001-1841 - Abstract
Abstract The key to designing photocatalysts is to orient the migration of photogenerated electrons to the target active sites rather than dissipate at inert sites. Herein, we demonstrate that the doping of phosphorus (P) significantly enriches photogenerated electrons at Ni active sites and enhances the performance for CO2 reduction into syngas. During photocatalytic CO2 reduction, Ni single‐atom‐anchored P‐modulated carbon nitride showed an impressive syngas yield rate of 85 μmol gcat−1 h−1 and continuously adjustable CO/H2 ratios ranging from 5:1 to 1:2, which exceeded those of most of the reported carbon nitride‐based single‐atom catalysts. Mechanistic studies reveal that P doping improves the conductivity of catalysts, which promotes photogenerated electron transfer to the Ni active sites rather than dissipate randomly at low‐activity nonmetallic sites, facilitating the CO2‐to‐syngas photoreduction process.
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- 2024
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6. Gene panel selection for targeted spatial transcriptomics
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Yida Zhang, Viktor Petukhov, Evan Biederstedt, Richard Que, Kun Zhang, and Peter V. Kharchenko
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Gene panel selection ,Targeted spatial transcriptomics ,Single-cell RNA sequencing ,Platform effect ,Cell type hierarchy ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types or processes being studied. A limitation of existing gene selection methods is their reliance on scRNA-seq data, ignoring platform effects between technologies. Here we describe gpsFISH, a computational method performing gene selection through optimizing detection of known cell types. By modeling and adjusting for platform effects, gpsFISH outperforms other methods. Furthermore, gpsFISH can incorporate cell type hierarchies and custom gene preferences to accommodate diverse design requirements.
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- 2024
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7. Single-cell analysis of immune and stroma cell remodeling in clear cell renal cell carcinoma primary tumors and bone metastatic lesions
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Shenglin Mei, Adele M. Alchahin, Ioanna Tsea, Youmna Kfoury, Taghreed Hirz, Nathan Elias Jeffries, Ting Zhao, Yanxin Xu, Hanyu Zhang, Hirak Sarkar, Shulin Wu, Alexander O. Subtelny, John Inge Johnsen, Yida Zhang, Keyan Salari, Chin-Lee Wu, Mark A. Randolph, David T. Scadden, Douglas M. Dahl, John Shin, Peter V. Kharchenko, Philip J. Saylor, David B. Sykes, and Ninib Baryawno
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Medicine ,Genetics ,QH426-470 - Abstract
Abstract Background Despite therapeutic advances, once a cancer has metastasized to the bone, it represents a highly morbid and lethal disease. One third of patients with advanced clear cell renal cell carcinoma (ccRCC) present with bone metastasis at the time of diagnosis. However, the bone metastatic niche in humans, including the immune and stromal microenvironments, has not been well-defined, hindering progress towards identification of therapeutic targets. Methods We collected fresh patient samples and performed single-cell transcriptomic profiling of solid metastatic tissue (Bone Met), liquid bone marrow at the vertebral level of spinal cord compression (Involved), and liquid bone marrow from a different vertebral body distant from the tumor site but within the surgical field (Distal), as well as bone marrow from patients undergoing hip replacement surgery (Benign). In addition, we incorporated single-cell data from primary ccRCC tumors (ccRCC Primary) for comparative analysis. Results The bone marrow of metastatic patients is immune-suppressive, featuring increased, exhausted CD8 + cytotoxic T cells, T regulatory cells, and tumor-associated macrophages (TAM) with distinct transcriptional states in metastatic lesions. Bone marrow stroma from tumor samples demonstrated a tumor-associated mesenchymal stromal cell population (TA-MSC) that appears to be supportive of epithelial-to mesenchymal transition (EMT), bone remodeling, and a cancer-associated fibroblast (CAFs) phenotype. This stromal subset is associated with poor progression-free and overall survival and also markedly upregulates bone remodeling through the dysregulation of RANK/RANKL/OPG signaling activity in bone cells, ultimately leading to bone resorption. Conclusions These results provide a comprehensive analysis of the bone marrow niche in the setting of human metastatic cancer and highlight potential therapeutic targets for both cell populations and communication channels.
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- 2024
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8. Impact of the Draft Plate on the Wall Erosion and Flow Field Stability of a Cyclone Separator
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Yida Zhang, Xiaodong Zhang, and Yanjiao Gao
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cyclone separator ,draft plate ,gas–solid phases ,computational fluid dynamics ,erosion ,Hydraulic engineering ,TC1-978 ,Water supply for domestic and industrial purposes ,TD201-500 - Abstract
Cyclone separators are commonly employed in the mining, metallurgy and chemical industries due to their simple structure, easy maintenance and high recovery efficiency. However, with the wide application of cyclone separators, many problems have become exposed in their practical operation, restricting their development. Among these, wall erosion is becoming a significant problem. In this study, to resolve the problem of severe erosion on the walls, the Eulerian–Lagrangian framework was employed to investigate a cyclone separator with a draft plate at the inlet and to evaluate the effect of a draft plate with angles of 0°, 45° and 90° on the degree of erosion and the stabilization of flow fields. Moreover, after verifying the reliability of the numerical model via data from experiments, the characteristics of gas–solid flow were analyzed and the effects of the new structure on the degree of wear were investigated. The results demonstrated that unfavorable phenomena such as secondary flow and wall erosion generated during the operation could be mitigated by the draft plate. When the plate angle was 90°, the wall erosion was the lightest and the range of influence of the secondary flow was the smallest. When the plate angle was 45°, the comprehensive performance was the best, and there was a better balance between the energy loss and the degree of wall erosion. Therefore, the presence of the draft plate has a significant impact on the interaction of gas–solid phases in a cyclone separator.
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- 2024
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9. Stressed target cancer cells drive nongenetic reprogramming of CAR T cells and solid tumor microenvironment
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Yufeng Wang, David L. Drum, Ruochuan Sun, Yida Zhang, Feng Chen, Fengfei Sun, Emre Dal, Ling Yu, Jingyu Jia, Shahrzad Arya, Lin Jia, Song Fan, Steven J. Isakoff, Allison M. Kehlmann, Gianpietro Dotti, Fubao Liu, Hui Zheng, Cristina R. Ferrone, Alphonse G. Taghian, Albert B. DeLeo, Marco Ventin, Giulia Cattaneo, Yongxiang Li, Youssef Jounaidi, Peigen Huang, Cristina Maccalli, Hanyu Zhang, Cheng Wang, Jibing Yang, Genevieve M. Boland, Ruslan I. Sadreyev, LaiPing Wong, Soldano Ferrone, and Xinhui Wang
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Science - Abstract
Abstract The poor efficacy of chimeric antigen receptor T-cell therapy (CAR T) for solid tumors is due to insufficient CAR T cell tumor infiltration, in vivo expansion, persistence, and effector function, as well as exhaustion, intrinsic target antigen heterogeneity or antigen loss of target cancer cells, and immunosuppressive tumor microenvironment (TME). Here we describe a broadly applicable nongenetic approach that simultaneously addresses the multiple challenges of CAR T as a therapy for solid tumors. The approach reprograms CAR T cells by exposing them to stressed target cancer cells which have been exposed to the cell stress inducer disulfiram (DSF) and copper (Cu)(DSF/Cu) plus ionizing irradiation (IR). The reprogrammed CAR T cells acquire early memory-like characteristics, potent cytotoxicity, enhanced in vivo expansion, persistence, and decreased exhaustion. Tumors stressed by DSF/Cu and IR also reprogram and reverse the immunosuppressive TME in humanized mice. The reprogrammed CAR T cells, derived from peripheral blood mononuclear cells of healthy donors or metastatic female breast cancer patients, induce robust, sustained memory and curative anti-solid tumor responses in multiple xenograft mouse models, establishing proof of concept for empowering CAR T by stressing tumor as a promising therapy for solid tumors.
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- 2023
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10. An Efficient Fault Tolerance Strategy for Multi-task MapReduce Models Using Coded Distributed Computing.
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Zaipeng Xie, Jianan Zhang, Yida Zhang, Chenghong Xu, Peng Chen, Zhihao Qu, and WenZhan Song 0001
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- 2023
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11. Germinated brown rice extract reduces brain lipid peroxidation and Aβ levels via regulations of BACE1, RAGE, IDE and LRP1 expressions in high fat/cholesterol diet-fed rats
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Azmi, Nur Hanisah, Ismail, Norsharina, Imam, Mustapha Umar, Ooi, Der Jiun, Yida, Zhang, Abdul Aziz, Ahmad Hazim, and Mohamad Rosdi, Mohamad Norisham
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- 2023
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12. Featherweight Soft Error Resilience for GPUs.
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Yida Zhang and Changhee Jung
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- 2022
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13. 食用植物油中黄曲霉毒素和赭曲霉毒素的 污染状况及特征分析Analysis of contamination status and characteristics of aflatoxin and ochratoxin in edible vegetable oils
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孙嘉笛,徐洪文,徐一达,张银志,孙秀兰 SUN Jiadi,XU Hongwen, XU Yida, ZHANG Yinzhi, SUN Xiulan
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食用植物油;黄曲霉毒素;赭曲霉毒素;混合污染 ,edible vegetable oil ,aflatoxin ,ochratoxin ,mixed pollution ,Oils, fats, and waxes ,TP670-699 - Abstract
针对市场在售的调和油、玉米油、大豆油、花生油和菜籽油等食用植物油,随机购买20种共290份食用植物油样品。采用液相色谱法测定AFB1、AFB2、AFG1、AFG2以及OTA、OTB真菌毒素的含量,对食用植物油中黄曲霉毒素和赭曲霉毒素的污染水平和分布特征进行分析。结果表明:20种290份食用植物油样品中,有16种共67份样品存在不同程度的真菌毒素污染,总污染率达到23.1%,不同种类食用植物油污染呈现“多种类、共分布”的特点,其中AFG1污染率(14.8%)最高,其次为OTA(13.4%)。绝大多数阳性样本受1~4种真菌毒素污染,仅有少数阳性样本受真菌毒素污染数量达到5种。总体上食用植物油样品受到多种真菌毒素的混合污染情况比较严重,应引起一定的重视。 A total of 290 samples from 20 kinds of edible vegetable oils such as blended oil, corn oil, soybean oil, peanut oil, and rapeseed oil on the market were randomly purchased. Then, the contents of AFB1, AFB2, AFG1, AFG2, OTA and OTB were accurately determined by HPLC to investigate the pollution levels and distribution characteristics of aflatoxins and ochratoxins in edible vegetable oils. The results showed that among the 20 kinds of 290 edible vegetable oil samples, 16 kinds of 67 samples suffered from different degrees of mycotoxin contamination, and the total pollution rate reached 23.1%. The pollution of different kinds of edible vegetable oils presented the characteristics of multi-species and co-distribution. AFG1 had the highest pollution rate (14.8%), followed by OTA (13.4%). Besides, the vast majority of positive samples were contaminated by 1-4 kinds of mycotoxins, only a few positive samples were contaminated with 5 kinds of mycotoxins. Overall, the problem that the edible vegetable oil samples are polluted by multiple mycotoxins is serious and should be paid attention to.
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- 2022
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14. Modified anterior approach preserving Retzius space versus standard anterior approach robot-assisted radical prostatectomy: A matched-pair analysis
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Hui Li, Chao Yang, Zhonghong Liao, Kaihong Wang, Yida Zhang, and Runfu Cao
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prostate cancer ,prostatectomy ,robotic-assisted surgery ,Retzius sparing ,modified anterior approach ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
ObjectiveTo compare our initial perioperative and postoperative outcomes of the modified anterior approach (MA) with Retzius space preservation robot-assisted radical prostatectomy (RARP) with the standard anterior approach (SA) RARP.Materials and methodsA retrospective analysis was performed on 116 patients with RARP completed by the same surgeon between September 2019 and March 2022. They were divided into SA-RARP group (77 cases) and MA-RARP group (39 cases). Propensity score matching was performed using eight preoperative variables, including age, BMI, preoperative PSA, biopsy Gleason score, prostate volume, D’Amico risk classification, SHIM, and clinical T stage. Functional outcome was assessed by urine pad count and SHIM after surgery, and oncological outcome was assessed by statistics of postoperative pathological findings as well as follow-up postoperative PSA. The median follow-up was 13 months and 17 months for MA-RARP and SA-RARP groups respectively.ResultsPropensity score matching was performed 1:1, and baseline data were comparable between the two groups after matching. Comparison of postoperative data: MA-RARP group had less mean EBL than SA-RARP group (200 vs 150 ml, p = 0.033). PSM did not differ between groups (p = 1). In terms of urinary control recovery, the MA-RARP group showed significant advantages in urinary control recovery at 24 h, 2 weeks, 1 month and 3 months after catheter removal, respectively (48.6% vs 5.7%, p < 0.001; 80% vs 22.9%, p < 0.001; 94.3% vs 51.4%, p < 0.001; 100% vs 74.3%, p = 0.002). This advantage gradually disappeared 6 months or more after surgery. The median time to recovery of sexual function was shorter in the MA-RARP group (165 vs 255 d, p = 0.001).ConclusionMA-RARP is safe and reliable, and can achieve better early urinary control function and sexual function recovery while achieving the primary tumor control goal.
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- 2023
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15. Targeting keystone species helps restore the dysbiosis of butyrate‐producing bacteria in nonalcoholic fatty liver disease
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Dingfeng Wu, Lei Liu, Na Jiao, Yida Zhang, Li Yang, Chuan Tian, Ping Lan, Lixin Zhu, Rohit Loomba, and Ruixin Zhu
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causal inference ,dynamic intervention simulation ,gut microbiota ,keystone species ,nonalcoholic fatty liver disease ,Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
Abstract The dysbiosis of the gut microbiome is one of the pathogenic factors of nonalcoholic fatty liver disease (NAFLD) and also affects the treatment and intervention of NAFLD. Among gut microbiomes, keystone species that regulate the integrity and stability of an ecological community have become the potential intervention targets for NAFLD. Here, we collected stool samples from 22 patients with nonalcoholic steatohepatitis (NASH), 25 obese patients, and 16 healthy individuals from New York for 16S rRNA gene sequencing. An algorithm was implemented to identify keystone species based on causal inference theories and dynamic intervention simulation. External validation was performed in an independent cohort from California. Eight keystone species in the gut of NAFLD, represented by Porphyromonas loveana, Alistipes indistinctus, and Dialister pneumosintes, were identified, which could efficiently restore the microbial composition of the NAFLD toward a normal gut microbiome with 92.3% recovery. These keystone species regulate intestinal amino acid metabolism and acid–base environment to promote the growth of the butyrate‐producing Lachnospiraceae and Ruminococcaceae species that are significantly reduced in NAFLD patients. Our findings demonstrate the importance of keystone species in restoring the microbial composition toward a normal gut microbiome, suggesting a novel potential microbial treatment for NAFLD.
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- 2022
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16. Construction and validation of a prognostic model for predicting overall survival of primary adrenal malignant tumor patients: A population-based study with 1,080 patients
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Wenhao Xie, Yida Zhang, and Runfu Cao
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adrenal malignant tumor ,SEER ,prognosis ,overall survival ,nomogram ,construct ,Surgery ,RD1-811 - Abstract
ObjectivePrimary adrenal malignant tumor is rare. The factors affecting the prognosis remain poorly defined. This study targeted to construct and corroborate a model for predicting the overall survival of adrenal malignant tumor patients.MethodsWe investigated the SEER database for patients with primary adrenal malignant tumor. 1,080 patients were divided into a construction cohort (n = 756) and a validation cohort (n = 324), randomly. The prognostic factors for overall survival were evaluated using univariate and multivariate Cox analyses. The nomogram was constructed and then validated with C-index, calibration curve, time-dependent ROC curve, and decision curve analysis in both cohorts. Then we divided the patients into 3 different risk groups according to the total points of the nomogram and analyzed their survival status by Kaplan-Meier curve with log-rank test.ResultsThe baseline characteristics of these two cohorts were not statistically different (P > 0.05). Using univariate and multivariate Cox analyses, 5 variables, including age, tumor size, histological type, tumor stage, and surgery of primary site, were distinguished as prognostic factors (P
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- 2022
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17. Microstructure-Based Multiscale Modeling of Deformation in MarBN Steel under Uniaxial Tension: Experiments and Finite Element Simulations
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Yida Zhang, Hong Zhang, Tongfei Zou, Meng Liu, Quanyi Wang, Yubing Pei, Yongjie Liu, and Qingyuan Wang
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MarBN steel ,uniaxial tension ,microstructure ,crystal plasticity ,finite element simulation ,Technology ,Electrical engineering. Electronics. Nuclear engineering ,TK1-9971 ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Microscopy ,QH201-278.5 ,Descriptive and experimental mechanics ,QC120-168.85 - Abstract
In the current work, a multiscale model was developed coupling a macro-model with the macromechanical physically based yield strength and a crystal plasticity model with micromechanical properties and realistic grain orientation based on the representative volume element. The simulation results show that the effect of microstructure on the macromechanical properties can be considered in the macro constitutive model due to a good consistency between experimental and computed results; whereas solid strengthening, grain boundaries, and dislocation density played a more crucial role than others. Besides coupling simulation and microstructure by EBSD, the microstructure evolution can be well explained by the micromechanical model. Strain is related to the grain orientation, leading to inhomogeneous deformation, forming the various Schmid factor and slip systems. A plastic strain occurs close to the grain boundaries and declines into the grain, resulting in higher kernel average misorientation (KAM) and geometry necessary dislocations (GNDs) in the grain boundaries. The higher the loading, the higher the local strain. Shear bands with around 45 degrees can be formed, resulting in crack initiation and tensile shear failure. This work has developed the guidance of structural integrity assessment and prediction of mechanical properties for the engineering material and components.
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- 2023
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18. Identification of microbial markers across populations in early detection of colorectal cancer
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Yuanqi Wu, Na Jiao, Ruixin Zhu, Yida Zhang, Dingfeng Wu, An-Jun Wang, Sa Fang, Liwen Tao, Yichen Li, Sijing Cheng, Xiaosheng He, Ping Lan, Chuan Tian, Ning-Ning Liu, and Lixin Zhu
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Science - Abstract
Abstract Associations between gut microbiota and colorectal cancer (CRC) have been widely investigated. However, the replicable markers for early-stage adenoma diagnosis across multiple populations remain elusive. Here, we perform an integrated analysis on 1056 public fecal samples, to identify adenoma-associated microbial markers for early detection of CRC. After adjusting for potential confounders, Random Forest classifiers are constructed with 11 markers to discriminate adenoma from control (area under the ROC curve (AUC) = 0.80), and 26 markers to discriminate adenoma from CRC (AUC = 0.89), respectively. Moreover, we validate the classifiers in two independent cohorts achieving AUCs of 0.78 and 0.84, respectively. Functional analysis reveals that the altered microbiome is characterized with increased ADP-l-glycero-beta-d-manno-heptose biosynthesis in adenoma and elevated menaquinone-10 biosynthesis in CRC. These findings are validated in a newly-collected cohort of 43 samples using quantitative real-time PCR. This work proves the validity of adenoma-specific markers across multi-populations, which would contribute to the early diagnosis and treatment of CRC.
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- 2021
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19. Short-range order in amorphous nickel oxide nanosheets enables selective and efficient electrochemical hydrogen peroxide production
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Ruilong Li, Shaokang Yang, Yida Zhang, Ge Yu, Chao Wang, Cai Chen, Geng Wu, Rongbo Sun, Guanzhong Wang, Xusheng Zheng, Wensheng Yan, Gongming Wang, Dewei Rao, and Xun Hong
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Physics ,QC1-999 - Abstract
Summary: Achieving high selectivity and activity with the oxygen reduction reaction (ORR) is significant for developing efficient energy conversion techniques and chemical production. Here, we report that selective ORRs can be achieved by tuning short-range order in amorphous and crystalline NiO nanosheets (a-NiO NSs and c-NiO NSs, respectively). X-ray absorption spectroscopy analysis reveals that the short-range order of a-NiO NSs and c-NiO NSs mainly adopt the NiO5 pyramidal and NiO6 octahedral structures, respectively. The a-NiO NSs for electrochemical H2O2 production in 0.1 M KOH exhibits both high selectivity over 90% and high activity (1 mA cm−2 at 0.66 V versus RHE), while c-NiO NSs tends to catalyze ORRs through 4-electron pathways to generate H2O. Theoretical calculations indicate that the changed short-range order of a-NiO NSs leads to alteration of Ni d-orbital states, which can regulate the adsorption orientation and strength of ∗OOH intermediates to achieve high selectivity and activity of 2-electron ORRs.
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- 2022
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20. Tmub1 Suppresses Hepatocellular Carcinoma by Promoting the Ubiquitination of ΔNp63 Isoforms
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Hangwei Fu, Yida Zhang, Junying Chen, Bo Zhou, Geng Chen, and Ping Chen
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transmembrane and ubiquitin-like domain containing 1 protein ,hepatocellular carcinoma ,tumor suppressor ,cell apoptosis ,tumor protein 63 ,post-translational modification ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Transmembrane and ubiquitin-like domain-containing 1 (Tmub1) inhibits hepatocyte proliferation during liver regeneration, but its role in hepatocellular carcinoma (HCC) has yet to be revealed. In this study, we show that the levels of Tmub1 were significantly lower in HCC tissues and cells than they were in adjacent tissues and normal hepatic cells, and the low levels of Tmub1 indicated a poor prognosis in HCC patients. Xenograft growth assay revealed that Tmub1 represses HCC growth in vivo. In addition, Tmub1 formed a protein complex with apoptosis-associated protein tumor protein 63 (p63), especially with the ΔN isoforms (ΔNp63α, β, and γ). Further loss- and gain-of-function analyses indicated that Tmub1 promotes apoptosis of Hep3B and MHCC-LM3 cells. Tmub1 decreased the protein expression of ΔNp63, and the pro-apoptotic effect of Tmub1 can be reversed by ΔNp63 isoforms (α, β, and γ). Additionally, we report that Tmub1 promotes the ubiquitination and degradation of ΔNp63 proteins. Finally, we confirmed in HCC tissues that Tmub1 is negatively correlated with ΔNp63 and positively correlated with the level of apoptosis. Taken together, Tmub1 suppresses HCC by enhancing the ubiquitination and degradation of ΔNp63 isoforms to induce HCC cell apoptosis. These findings provide a potential strategy for the management of HCC.
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- 2020
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21. Dual‐Metal Sites Boosting Polarization of Nitrogen Molecules for Efficient Nitrogen Photofixation
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Yida Zhang, Tingting Hou, Quan Xu, Qingyu Wang, Yu Bai, Shaokang Yang, Dewei Rao, Lihui Wu, Haibin Pan, Jiafu Chen, Gongming Wang, Junfa Zhu, Tao Yao, and Xusheng Zheng
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dual‐metal sites ,manganese ,nitrogen fixation ,polarization ,tungsten oxides ,Science - Abstract
Abstract Constructing nitrogen (N2) adsorption and activation sites on semiconductors is the key to achieving efficient N2 photofixation. Herein, Mn–W dual‐metal sites on WO3 are designed toward efficient N2 photoreduction via controlled Mn doping. Impressively, the optimal 2.3% Mn‐doped WO3 (Mn‐WO3) exhibits a remarkable ammonia (NH3) production rate of 425 µmol gcat.−1 h−1, representing the best catalytic performance among the ever‐reported tungsten oxide‐based photocatalysts for N2 fixation. Quasi in situ synchrotron radiation X‐ray spectroscopy directly identifies that the Mn–W dual‐metal sites can enhance the polarization of the adsorbed N2, which is beneficial to the N2 activation. Further theoretical calculations reveal that the increased polarization is originated from the electron back‐donation into the antibonding orbitals of the adsorbed N2, hence lowering the reaction energy barrier toward the N2 photofixation. The concept of dual sites construction for inert molecule activation offers a powerful platform toward rational design of highly efficient catalysts for nitrogen fixation and beyond.
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- 2021
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22. A Multi-Sensory Guidance System for the Visually Impaired Using YOLO and ORB-SLAM
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Zaipeng Xie, Zhaobin Li, Yida Zhang, Jianan Zhang, Fangming Liu, and Wei Chen
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multi-sensory guidance system ,visually impaired ,ORB-SLAM ,YOLO ,point map building ,indoor navigation ,Information technology ,T58.5-58.64 - Abstract
Guidance systems for visually impaired persons have become a popular topic in recent years. Existing guidance systems on the market typically utilize auxiliary tools and methods such as GPS, UWB, or a simple white cane that exploits the user’s single tactile or auditory sense. These guidance methodologies can be inadequate in a complex indoor environment. This paper proposes a multi-sensory guidance system for the visually impaired that can provide tactile and auditory advice using ORB-SLAM and YOLO techniques. Based on an RGB-D camera, the local obstacle avoidance system is realized at the tactile level through point cloud filtering that can inform the user via a vibrating motor. Our proposed method can generate a dense navigation map to implement global obstacle avoidance and path planning for the user through the coordinate transformation. Real-time target detection and a voice-prompt system based on YOLO are also incorporated at the auditory level. We implemented the proposed system as a smart cane. Experiments are performed using four different test scenarios. Experimental results demonstrate that the impediments in the walking path can be reliably located and classified in real-time. Our proposed system can function as a capable auxiliary to help visually impaired people navigate securely by integrating YOLO with ORB-SLAM.
- Published
- 2022
- Full Text
- View/download PDF
23. Evidence of a unique critical fabric surface for granular soils
- Author
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Yida Zhang and Yuxuan Wen
- Subjects
Surface (mathematics) ,Soil water ,Earth and Planetary Sciences (miscellaneous) ,Liquefaction ,Geotechnical engineering ,Geotechnical Engineering and Engineering Geology ,Anisotropy ,Geology - Abstract
The critical state of granular soils needs to make proper reference to the fabric that develops at critical state. This study substantialises the concept of critical fabric surface (CFS), which attracts the fabric state of granular soils upon continuous shearing. Numerical experiments using discrete-element method (DEM) modelling are conducted under drained and undrained conditions with varying Lode angles. Fabric tensors are defined based on the normals of all contacts and of the strong force contacts only. Both tensors have their spherical component preserved such that the information of coordination number can be carried. A separate series of low-confining-pressure undrained tests is conducted to probe the fabric states of soils in the post-liquefaction regime. Finally, a single CFS spanning across a wide range of coordination numbers is established based on the DEM results. The CFS concept provides an important reference state for soils sheared to large strains, complementary to the traditionally defined critical state. This provides a new perspective to interpret and model the mechanics of granular soils in both pre- and post-liquefied regimes. The evolution of fabric shows that the normalised strong-contact fabric evolves linearly with the stress ratio even for liquefied or anisotropically consolidated soils.
- Published
- 2023
24. Sp1 S-Sulfhydration Induced by Hydrogen Sulfide Inhibits Inflammation via HDAC6/MyD88/NF-κB Signaling Pathway in Adjuvant-Induced Arthritis
- Author
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Meng Li, Wei Hu, Ran Wang, Zhaoyi Li, Yue Yu, Yue Zhuo, Yida Zhang, Zhou Wang, Yuanye Qiu, Keyuan Chen, Qian Ding, Wei Qi, Menglin Zhu, and Yizhun Zhu
- Subjects
HDAC6 ,Sp1 ,H2S ,rheumatoid arthritis ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Histone deacetylase 6 (HDAC6) acts as a regulator of the nuclear factor kappa-B (NF-κB) signaling pathway by deacetylating the non-histone protein myeloid differentiation primary response 88 (MyD88) at lysine residues, which is an adapter protein for the Toll-like receptor (TLR) and interleukin (IL)-1β receptor. Over-activated immune responses, induced by infiltrated immune cells, excessively trigger the NF-κB signaling pathway in other effector cells and contribute to the development of rheumatoid arthritis (RA). It has also been reported that HDAC6 can promote the activation of the NF-κB signaling pathway. In the present study, we showed that HDAC6 protein level was increased in the synovium tissues of adjuvant-induced arthritis rats. In addition, hydrogen sulfide (H2S) donor S-propargyl-cysteine (SPRC) can inhibit HDAC6 expression and alleviate inflammatory response in vivo. In vitro study revealed that HDAC6 overexpression activated the NF-κB signaling pathway by deacetylating MyD88. Meanwhile, sodium hydrosulfide (NaHS) or HDAC6 inhibitor tubastatin A (tubA) suppressed the pro-inflammatory function of HDAC6. Furthermore, the reduced expression of HDAC6 appeared to result from transcriptional inhibition by S-sulfhydrating specificity protein 1 (Sp1), which is a transcription factor of HDAC6. Our results demonstrate that Sp1 can regulate HDAC6 expression, and S-sulfhydration of Sp1 by antioxidant molecular H2S ameliorates RA progression via the HDAC6/MyD88/NF-κB signaling pathway.
- Published
- 2022
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- View/download PDF
25. Constructing asymmetrical dual catalytic sites in manganese oxides enables fast and stable lithium–oxygen catalysis
- Author
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Bo Liu, Xinmiao Liu, Cong Wei, Ya Zhou, Zixuan Zhu, Xin Lei, Yanyan Fang, Yida Zhang, Jun Liu, Yitai Qian, and Gongming Wang
- Subjects
Renewable Energy, Sustainability and the Environment ,General Materials Science ,General Chemistry - Abstract
A general asymmetrical dual-site (Mn–Ru or Mn–Ir) construction strategy on manganese oxides is demonstrated to significantly improve the oxygen catalytic activity and cycling stability toward lithium–oxygen batteries.
- Published
- 2023
26. Research on High-frequency stock price prediction based on Chebyshev-Stacking and Weighted LSTM neural network [1]
- Author
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Yiwen Wang, Yida Zhang, and Zixuan Pan
- Abstract
To solve the problem of high-frequency stock price prediction, this paper proposed a prediction model based on Chebyshev-Stacking and a weighted LSTM neural network. The proposed method extracts the function characteristic information of the high-frequency stock price series through Chebyshev orthogonal polynomial basis expansion. Considering that the potential model structure between each component of the function feature vector and the residual sequence predicted by the LSTM neural network is unknown and there is a certain noise, this paper used the Stacking framework to enhance the data and weighed the bias and variance of the prediction model. In addition, since the number of predictor variable periods of the LSTM neural network is a hyperparameter, the model averaging method based on distance covariance is used for optimization. The results of actual data analysis show that the proposed method is significantly better than the original LSTM neural network in terms of mean square error, absolute error, and relative error. By selecting the different number of training sets, the robustness of the improved model is verified. Finally, the proposed method can also be used in practical applications such as daily average temperature prediction, missile trajectory prediction, and real-time monitoring of atmospheric environment quality.
- Published
- 2022
27. Characterization of covalent protein modification by triclosan in vivo and in vitro via three-dimensional liquid chromatography-mass spectrometry: New insight into its adverse effects
- Author
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Meixian Liu, Na Li, Yida Zhang, Zhiyuan Zheng, Yue Zhuo, Baoqing Sun, Li-Ping Bai, Mingming Zhang, Ming-Quan Guo, and Jian-Lin Wu
- Subjects
Environmental sciences ,GE1-350 - Abstract
Triclosan (TCS), an antimicrobial agent widely used in personal care products and ubiquitously exists in environment, has drawn increasing concern due to its potential to exert multiple adverse effects, ranging from endocrine disruption to carcinogenesis. However, the mechanism of these adverse effects is still not fully elucidated. More and more studies have shown that chemical reactive metabolites (RMs) covalently binding to proteins is a possible reason for these adverse effects, but there is still a lack of appropriate methods to predict or evaluate these adverse effects due to the extremely low abundance of the modified proteins in complex biological samples. In this study, we attempted to address this problem and investigate the possible mechanism of TCS adverse effects by a shotgun proteomics approach based on three-dimensional-liquid chromatography-mass spectrometry (3D-LC-MS). First, the in vitro incubation with model amino acids and protein in microsomes showed that TCS could react with cysteine residue of proteins through 3 types of RMs. Then, a 3D-LC-MS approach was developed to sensitively determine the low abundant modified proteins, which resulted in the identification of 45 TCS-modified proteins, including albumin, haptoglobin and NR1I2, in rats. STRING analysis indicated that these modified proteins mainly were involved in reproductive and development system, endocrine and immune system, and carcinogenesis, which were in accord with the main reported TCS-induced adverse effects and suggested that the covalent modification of TCS RMs for proteins might affect their activities and functions, thus inducing serious adverse effects. This study provided a new insight into the mechanism of TCS adverse effects and may serve as a valuable method to predict or evaluate adverse effects of ubiquitous chemicals. Keywords: Triclosan, Adverse effects, Reactive metabolites, Covalent protein modification, In vivo, Three-dimensional-liquid chromatography-mass spectrometry
- Published
- 2020
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28. Metal Coordination‐Mediated Functional Grading and Self‐Healing in Mussel Byssus Cuticle
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Quan Xu, Meng Xu, Chun‐Yu Lin, Qiang Zhao, Rui Zhang, Xiaoxiao Dong, Yida Zhang, Shouceng Tian, Yu Tian, and Zhenhai Xia
- Subjects
density functional theory ,iron complex ,mussels ,self‐healing ,tensile tests ,Science - Abstract
Abstract Metal‐containing polymer networks are ubiquitous in biological systems, and their unique structures enable a variety of fascinating biological behaviors. Cuticle of mussel byssal threads, containing Fe‐catecholate complexes, shows remarkably high hardness, high extensibility, and self‐healing capability. Understanding strengthening and self‐healing mechanisms is essential for elucidating animal behaviors and rationally designing mussel‐inspired materials. Here, direct evidence of Fe3+ and Fe2+ gradient distribution across the cuticle thickness is demonstrated, which shows more Fe2+ inside the inner cuticle, to support the hypothesis that the cuticle is a functionally graded material with high stiffness, extensibility, and self‐healing capacity. The mechanical tests of the mussel threads show that both strength and extensibility of the threads decrease with increasing oxygen contents, but this property degradation can be restored upon removing the oxygen. The first‐principles calculations explain the change in iron coordination, which plays a key role in strengthening, degradation, and self‐healing of the polymer networks. The oxygen absorbs on metal ions, weakening the iron‐catecholate bonds in the cuticle and collagen core, but this process can be reversed by sea water. These findings can have important implications in the design of next‐generation bioinspired robust, highly extensible materials, and catalysis.
- Published
- 2019
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29. Thymoquinone-rich fraction nanoemulsion (TQRFNE) decreases Aβ40 and Aβ42 levels by modulating APP processing, up-regulating IDE and LRP1, and down-regulating BACE1 and RAGE in response to high fat/cholesterol diet-induced rats
- Author
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Ismail, Norsharina, Ismail, Maznah, Azmi, Nur Hanisah, Bakar, Muhammad Firdaus Abu, Yida, Zhang, Abdullah, Maizaton Atmadini, and Basri, Hamidon
- Published
- 2017
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30. Development of a Novel Deep Learning-Based Prediction Model for the Prognosis of Operable Cervical Cancer
- Author
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Taotao Dong, Linlin Wang, Ruowen Li, Qingqing Liu, Yiyue Xu, Yuan Wei, Xinlin Jiao, Xiaofeng Li, Yida Zhang, Youzhong Zhang, Kun Song, Xingsheng Yang, and Baoxia Cui
- Subjects
Deep Learning ,Article Subject ,General Immunology and Microbiology ,Applied Mathematics ,Modeling and Simulation ,Humans ,Uterine Cervical Neoplasms ,Female ,General Medicine ,Prognosis ,General Biochemistry, Genetics and Molecular Biology ,Neoplasm Staging ,Retrospective Studies - Abstract
Background. Cervical cancer ranks as the 4th most common female cancer worldwide. Early stage cervical cancer patients can be treated with operation, but clinical staging system is not a good predictor of patients’ survival. We aimed to develop a novel prognostic model to predict the prognosis for operable cervical cancer patients with better accuracy than clinical staging system. Methods. A total of 13,952 operable cervical cancer patients were retrospectively enrolled in this study. The whole dataset was randomly split into a training set ( n = 9,068 , 65%), validation set ( n = 2,442 , 17.5%), and testing set ( n = 2,442 , 17.5%). Cox proportional hazard (CPH) model and random survival forest (RSF) model were used as baseline models for the prediction of overall survival (OS). Then, a deep survival learning model (DSLM) was developed for OS prediction. Finally, a novel prognostic model was explored based on this DSLM. Results. The C-indexes for the CPH and RSF model were 0.731 and 0.753, respectively. DSLM, which had four layers that had 50 neurons in each layer, achieved a C-index of 0.782 in the validation set and a C-index of 0.758 in the testing set. The novel prognostic model based on DSLM showed better performances than the conventional clinical staging system (area under receiver operating curves were 0.826 and 0.689, respectively). Personalized survival curves for individual patient using this novel model also showed notably different survival slopes. Conclusions. Our study developed a novel, practical, personalized prognostic model for operable cervical cancer patients. This novel prognostic model may have the potential to provide a more prognostic information to oncologists.
- Published
- 2022
31. Monitoring Electron Flow in Nickel Single-Atom Catalysts during Nitrogen Photofixation
- Author
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Qingyu Wang, Yu Xiao, Shaokang Yang, Yida Zhang, Lihui Wu, Haibin Pan, Dewei Rao, Tao Chen, Zhihu Sun, Gongming Wang, Junfa Zhu, Jie Zeng, Shiqiang Wei, and Xusheng Zheng
- Subjects
Mechanical Engineering ,General Materials Science ,Bioengineering ,General Chemistry ,Condensed Matter Physics - Abstract
An efficient catalytic system for nitrogen (N
- Published
- 2022
32. Regulating local charges of atomically dispersed Mo+ sites by nitrogen coordination on cobalt nanosheets to trigger water dissociation for boosted hydrogen evolution in alkaline media
- Author
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Maoqi Cao, Kang Liu, Yao Song, Chao Ma, Yiyang Lin, Huangjingwei Li, Kejun Chen, Junwei Fu, Hongmei Li, Jun Luo, Yida Zhang, Xusheng Zheng, Junhua Hu, and Min Liu
- Subjects
Fuel Technology ,Electrochemistry ,Energy Engineering and Power Technology ,Energy (miscellaneous) - Published
- 2022
33. Metabolomics Reveals Process of Allergic Rhinitis Patients with Single- and Double-Species Mite Subcutaneous Immunotherapy
- Author
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Peiyan Zheng, Guanyu Yan, Yida Zhang, Huimin Huang, Wenting Luo, Mingshan Xue, Na Li, Jian-Lin Wu, and Baoqing Sun
- Subjects
allergic rhinitis ,allergen immunotherapy ,hydroxyeicosatetraenoic acid ,Microbiology ,QR1-502 - Abstract
Allergen immunotherapy (AIT) is the only treatment that can change the course of allergic diseases. However, there has not been any research on metabolic reactions in relation to AIT with single or mixed allergens. In this study, patients with allergic rhinitis caused by Dermatophagoides pteronyssinus (Der p) and Dermatophagoides farinae (Der f) were treated with single-mite (Der p) and double-mite (Der p:Der f = 1:1) subcutaneous immunotherapy (SCIT), respectively. To compare the efficacy and the dynamic changes of inflammation-related single- and double-species mite subcutaneous immunotherapy (SM-SCIT and DM-SCIT), we performed visual analogue scale (VAS) score, rhinoconjunctivitis quality of life questionnaire (RQLQ) score and serum metabolomics in allergic rhinitis patients during SCIT. VAS and RQLQ score showed no significant difference in efficacy between the two treatments. A total of 57 metabolites were identified, among which downstream metabolites (5(S)-HETE (Hydroxyeicosatetraenoic acid), 8(S)-HETE, 11(S)-HETE, 15(S)-HETE and 11-hydro TXB2) in the ω-6-related arachidonic acid and linoleic acid pathway showed significant differences after approximately one year of treatment in SM-SCIT or DM-SCIT, and the changes of the above serum metabolic components were correlated with the magnitude of RQLQ improvement, respectively. Notably, 11(S)-HETE decreased more with SM-SCIT, and thus it could be used as a potential biomarker to distinguish the two treatment schemes. Both SM-SCIT and DM-SCIT have therapeutic effects on patients with allergic rhinitis, but there is no significant difference in efficacy between them. The reduction of inflammation-related metabolites proved the therapeutic effect, and potential biomarkers (arachidonic acid and its downstream metabolites) may distinguish the options of SCIT.
- Published
- 2021
- Full Text
- View/download PDF
34. The promoting effect of interstitial hydrogen on the oxygen reduction performance of PtPd alloy nanotubes for fuel cells
- Author
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Tingting Chao, Xuan Luo, Mengzhao Zhu, Yanmin Hu, Yida Zhang, Yunteng Qu, Hantao Peng, Xiaoshuang Shen, Xusheng Zheng, Liang Zhang, and Xun Hong
- Subjects
General Materials Science ,Electrical and Electronic Engineering ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics - Published
- 2022
35. Support Amorphization Engineering Regulates Single-Atom Ru as an Electron Pump for Nitrogen Photofixation
- Author
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Peigen Liu, Zixiang Huang, Shaokang Yang, Junyi Du, Yida Zhang, Rui Cao, Cai Chen, Lei Li, Tao Chen, Gongming Wang, Dewei Rao, Xusheng Zheng, and Xun Hong
- Subjects
General Chemistry ,Catalysis - Published
- 2022
36. Metabolomics of Clinical Poisoning by Aconitum Alkaloids Using Derivatization LC-MS
- Author
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Yida Zhang, Xiqing Bian, Jing Yang, Haiying Wu, Jian-Lin Wu, and Na Li
- Subjects
metabolomics ,clinical poisoning ,Aconitum kusnezoffii ,derivatization ,carboxyl-containing metabolites ,metabolic pathway ,Therapeutics. Pharmacology ,RM1-950 - Abstract
The root of Aconitum kusnezoffii (Caowu in Chinese, CW) is not only commonly used as a traditional Chinese medicine (TCM), but also served as a tonic in China. Due to its high toxicity, clinical poisoning cases induced by CW have frequently been reported. However, the mechanism is still unclear. In this study, Aconitum alkaloids and altered endogenous metabolites in CW poisoning patients were investigated to elucidate the possible intoxication mechanism. Eighteen alkaloids, including 6 toxic diester diterpenoid alkaloids (DDAs), were determined from the sera of patients. At the same time, 5-(diisopropylamino)amylamine (DIAAA) derivatization-ultrahigh performance liquid chromatography- quadrupole-time of flight mass spectrometry (UHPLC-Q-TOF/MS) approach was applied in the metabolomics analysis to find much more carboxyl-containing metabolites (CCMs), which are the essential components for life and critical to elucidate the mechanism of toxicity. As a result, 32 altered metabolites after poisoning were identified. Among them, hydroxyeicosatetraenoic acids (HETEs) and some dicarboxylic acids were first found to be related to Aconitum alkaloids toxicity. Finally, biological pathway analysis indicated that the significantly changed metabolites were primarily involved in amino acid metabolism, TCA cycle, fatty acid metabolism, pyruvate metabolism, arachidonic acid metabolism, sphingolipid metabolism and so on. These results can not only provide more information on the mechanism of CW intoxication but also help the clinical diagnosis of CW poisoning.
- Published
- 2019
- Full Text
- View/download PDF
37. Gene panel selection for targeted spatial transcriptomics
- Author
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Yida Zhang, Viktor Petukhov, Evan Biederstedt, Richard Que, Kun Zhang, and Peter V. Kharchenko
- Subjects
Article - Abstract
Targeted spatial transcriptomics hold particular promise in analysis of complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types or processes being studied. A limitation of existing gene selection methods is that they rely on scRNA-seq data, ignoring platform effects between technologies. Here we describe gpsFISH, a computational method to perform gene selection through optimizing detection of known cell types. By modeling and adjusting for platform effects, gpsFISH outperforms other methods. Furthermore, gpsFISH can incorporate cell type hierarchies and custom gene preferences to accommodate diverse design requirements.
- Published
- 2023
38. A directional microcrack damage theory for brittle solids based on continuous hyperplasticity
- Author
-
Mitul Sisodiya and Yida Zhang
- Subjects
Mechanics of Materials ,Mechanical Engineering ,Computational Mechanics ,General Materials Science - Abstract
We present a novel microcrack-damage theory for brittle solids under compression. Instead of using internal variables like zeroth, second or fourth rank damage tensors, the state of material damage is represented by an internal function that encapsulates the information of direction, density and size of microcracks. Just like other internal variables, the evolution of this state function must obey the second law of thermodynamics for arbitrary loading paths. This is done by casting the model in the framework of continuous hyperplasticity and enforcing a non-negative dissipation rate functional. The proposed framework offers predictions on the continuous evolution of microcrack density and the induced material anisotropy along with the macroscopic stress-strain curves. The use of continuous damage function grants the model significantly enhanced resolution in characterizing the direction-dependent response of cracked solids compared to classical models that are based on damage tensors. Two scenarios are considered in developing the theory, one assumes frictionless cracks and the other incorporates friction between crack surfaces. The results highlight that inelasticity, pressure dependence, and loading-unloading hysteresis exhibited by brittle solids are natural consequences of frictional microcracks. The proposed theory offers a generic and versatile framework to upscale micromechanical processes operating at individual crack scale to explain the macroscopic behavior of cracked solids.
- Published
- 2022
39. Urinary Catheterization Induces Delirium-Like Behavior Through Glucose Metabolism Impairment in Mice
- Author
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Zhangjie, Jiang, Feng, Liang, Yida, Zhang, Yuanlin, Dong, Annie, Song, Xiaoping, Zhu, Yiying, Zhang, and Zhongcong, Xie
- Subjects
Vascular Endothelial Growth Factor A ,Glucose Transporter Type 1 ,Adenosine Triphosphate ,Glucose ,Anesthesiology and Pain Medicine ,Animals ,Delirium ,Female ,Urinary Catheterization - Abstract
Delirium, an acute confusion status, is associated with adverse effects, including the development of Alzheimer's disease. However, the etiology and underlying mechanisms of delirium remain largely to be determined. Many patients have urinary catheterization (UC), and UC is associated with delirium. However, the cause effects of UC-associated delirium and the underlying mechanisms remain largely unknown. We, therefore, established an animal model of UC, without urinary tract infection, in mice and determined whether UC could induce delirium-like behavior in the mice and the underlying mechanism of these effects.Adult female mice (16 weeks old) had UC placement under brief isoflurane anesthesia. The delirium-like behavior was determined using our established mice model at 3, 6, 9, and 24 hours after UC placement. We measured the amounts of glucose in both blood and brain interstitial fluid, adenosine triphosphate (ATP) concentration in the cortex, and glucose transporter 1 in the cortex of mice using western blot, immunohistochemistry imaging, reverse transcriptase-polymerase chain reaction (RT-PCR), and fluorescence at 6 hours after the UC placement. Finally, we used vascular endothelial growth factor (VEGF) in the interaction studies.We found that UC induced delirium-like behavior in mice at 3, 6, 9, but not 24 hours after the UC placement. UC decreased glucose amounts in brain interstitial fluid (86.38% ± 4.99% vs 100% ± 6.26%, P = .003), but not blood of mice and reduced ATP amounts (84.49% ± 8.85% vs 100% ± 10.64%, P = .031) in the cortex of mice. Finally, UC reduced both protein amount (85.49% ± 6.83% vs 100% ± 11.93%, P = .040) and messenger ribonucleic acid (mRNA) expression (41.95% ± 6.48% vs 100% ± 19.80%, P = .017) of glucose transporter 1 in the cortex of mice. VEGF attenuated these UC-induced changes.These data demonstrated that UC decreased brain glucose and energy amounts via impairing the glucose transport from blood to brain, leading to delirium-like behavior in mice. These findings will promote more research to identify the etiologies and underlying mechanisms of delirium.
- Published
- 2022
40. Relation between void ratio and contact fabric of granular soils
- Author
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Yuxuan Wen and Yida Zhang
- Subjects
Earth and Planetary Sciences (miscellaneous) ,Geotechnical Engineering and Engineering Geology - Published
- 2022
41. Molecular insights into the temperature and pressure dependence of mechanical behavior and dynamics of Na-montmorillonite clay.
- Author
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Ghazanfari, Sarah, Alesadi, Amirhadi, Yangchao Liao, Yida Zhang, and Wenjie Xia
- Published
- 2023
- Full Text
- View/download PDF
42. A Convex Hull-Based Feature Descriptor for Learning Tree Species Classification From ALS Point Clouds
- Author
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Li Zhengrong, Dong Suying, Yanxing Lv, Shaojun Hu, Zhiyi Zhang, Long Yang, and Yida Zhang
- Subjects
Convex hull ,Computer science ,business.industry ,Deep learning ,Point cloud ,Pattern recognition ,Geotechnical Engineering and Engineering Geology ,Tree (data structure) ,Feature (computer vision) ,Face (geometry) ,Point (geometry) ,Artificial intelligence ,Electrical and Electronic Engineering ,business ,Alpha shape - Abstract
Classifying tree species from point clouds acquired by light detection and ranging (LiDAR) scanning systems is important in many applications, including remote sensing, virtual reality, and forestry inventory. Compared with terrestrial laser scanning systems, airborne laser scanning (ALS) systems can acquire large-scale tree point clouds from only a single scan. However, ALS point clouds have the disadvantages of low density, uneven distribution, and unclear branch structure, making the classification of tree species from ALS point clouds a challenging task. Recently, deep learning-based classification approaches, such as PointNet++, which can operate directly on 3-D point sets, have been intensively studied in scene classification. However, the classification precision of learning-based approaches for point clouds relies on point coordinates and features, such as normals. Unlike the face normals of regular objects, trees have complex branch structures and detailed leaves, which are difficult to capture using ALS systems. Hence, it might be inappropriate to use the normals of ALS tree points for classification. In this letter, we propose a novel convex hull-based feature descriptor for tree species classification using the deep learning network PointNet++. To evaluate the effectiveness of our approach, three additional feature descriptors (normal descriptor, alpha shape-based descriptor, and covariance descriptor) are also investigated with PointNet++. The results show that the convex hull-based feature descriptor can achieve 86.6% overall accuracy in tree species classification, which is notably higher than the other three descriptors.
- Published
- 2022
43. Stressed target cancer cells drive nongenetic reprogramming of CAR T cells and tumor microenvironment, overcoming multiple obstacles of CAR T therapy for solid tumors
- Author
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Yufeng Wang, David L. Drum, Ruochuan Sun, Yida Zhang, Ling Yu, Lin Jia, Steven J Isakoff, Allison M Kehlmann, Ali Emre Dal, Gianpietro Dotti, Hui Zheng, Cristina R Ferrone, Alphonse G Taghian, Albert B DeLeo, Hanyu Zhang, Youssef Jounaidi, Song Fan, Peigen Huang, Cheng Wang, Jibing Yang, Genevieve M Boland, Ruslan I Sadreyev, LaiPing Wong, Soldano Ferrone, and Xinhui Wang
- Abstract
The poor efficacy of chimeric antigen receptor T-cell therapy (CAR T) for solid tumor is due to insufficient CAR T cell tumor infiltration, in vivo expansion, persistence, and effector function, as well as exhaustion, intrinsic target antigen heterogeneity or antigen loss of target cancer cells, and immunosuppressive tumor microenvironment (TME). Here we describe a broadly applicable nongenetic approach that simultaneously addresses the multiple challenges of CAR T as a therapy for solid tumors. The approach massively reprograms CAR T cells by exposing them to stressed target cancer cells which have been exposed to the cell stress inducer disulfiram (DSF) and copper (Cu)(DSF/Cu) plus ionizing irradiation (IR). The reprogrammed CAR T cells acquired early memory-like characteristics, potent cytotoxicity, enhanced in vivo expansion, persistence, and decreased exhaustion. Tumors stressed by DSF/Cu and IR also reprogrammed and reversed immunosuppressive TME in humanized mice. The reprogrammed CAR T cells, derived from peripheral blood mononuclear cells (PBMC) of healthy or metastatic breast cancer patients, induced robust, sustained memory and curative anti-solid tumor responses in multiple xenograft mouse models, establishing proof of concept for empowering CAR T by stressing tumor as a novel therapy for solid tumor.
- Published
- 2023
44. Combination of chemical profiling and network pharmacology analysis to investigate the potential mechanism of Li‐Zhong‐Xiao‐Pi granules in the treatment of gastric precancerous lesions
- Author
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Chenchen Liu, Huiling Chen, Yida Zhang, Meng Li, Qiyao Jiang, Zhendong Wang, Liangwen Yu, Qi Wang, Huafeng Pan, and Yue Zhuo
- Subjects
Pharmacology ,Clinical Biochemistry ,Drug Discovery ,General Medicine ,Molecular Biology ,Biochemistry ,Analytical Chemistry - Published
- 2023
45. RoboCup 2013 Humanoid Kidsize League Winner.
- Author
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Daniel D. Lee, Seung-Joon Yi, Stephen G. McGill, Yida Zhang, Larry Vadakedathu, Samarth Brahmbhatt, Richa Agrawal, and Vibhavari Dasagi
- Published
- 2013
- Full Text
- View/download PDF
46. Extensions of a RoboCup Soccer Software Framework.
- Author
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Stephen G. McGill, Seung-Joon Yi, Yida Zhang, and Daniel D. Lee
- Published
- 2013
- Full Text
- View/download PDF
47. Research on position inverse solution of electric-driven Stewart platform based on Simulink
- Author
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Guangzheng Jia, Guangxu Pan, Qian Gao, and Yida Zhang
- Subjects
robot kinematics ,electric actuators ,graphical user interfaces ,motion control ,position control ,matrix algebra ,control engineering computing ,mechanical engineering computing ,electric-driven Stewart platform ,Simulink ,structural characteristics ,position inverse solution ,electric cylinders ,coordinate transformation ,rotation matrix ,homogeneous transformation ,mathematical model ,input-output signal simulation model ,GUI module ,motion simulation curves ,motion state control ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
The structural characteristics and modes of the Stewart platform driven by electric cylinders are briefly introduced. Based on Simulink, the modelling method of the platform is analysed. To obtain the coordinate transformation of Stewart platform, the rotation matrix and homogeneous transformation are resolved, and the mathematical model of the electric-driven Stewart platform is established related to the structural characteristics. The simulation model of input and output signals is constructed by using graphical user interface (GUI) module provided by Simulink. The motion simulation curves of six electric actuators under different position and posture are obtained, which gives benefit to understand and control the different motion states of the electric-driven Stewart platform.
- Published
- 2018
- Full Text
- View/download PDF
48. SDTIOA: Modeling the Timed Privacy Requirements of IoT Service Composition: A User Interaction Perspective for Automatic Transformation from BPEL to Timed Automata
- Author
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Huaikou Miao, Yida Zhang, Ramón J. Durán Barroso, Honghao Gao, and Xiaoxian Yang
- Subjects
Computer Networks and Communications ,business.industry ,computer.internet_protocol ,Computer science ,Perspective (graphical) ,Service composition ,Transformation (music) ,Automaton ,Business Process Execution Language ,Hardware and Architecture ,Internet of Things ,business ,Software engineering ,computer ,Software ,Information Systems - Published
- 2021
49. Compressive Strain Modulation of Single Iron Sites on Helical Carbon Support Boosts Electrocatalytic Oxygen Reduction
- Author
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Xusheng Zheng, Li-Ming Yang, C.H. Chen, Lingxiao Wang, Xiao Zhou, Chun-Xiang Huang, Huang Zhou, Qinghua Zhang, Yuen Wu, Yida Zhang, Junyi Du, Ying Zhang, Jia Yang, Lin Gu, and Zhiyuan Wang
- Subjects
Materials science ,Strain (chemistry) ,Carbonization ,chemistry.chemical_element ,General Medicine ,General Chemistry ,Polypyrrole ,Catalysis ,Metal ,chemistry.chemical_compound ,Strain engineering ,Chemical engineering ,chemistry ,visual_art ,visual_art.visual_art_medium ,Selectivity ,Carbon - Abstract
Designing and modulating the local structure of metal sites is the key to gain the unique selectivity and high activity of single metal site catalysts. Herein, we report strain engineering of curved single atomic iron-nitrogen sites to boost electrocatalytic activity. First, a helical carbon structure with abundant high-curvature surface is realized by carbonization of helical polypyrrole that is templated from self-assembled chiral surfactants. The high-curvature surface introduces compressive strain on the supported Fe-N4 sites. Consequently, the curved Fe-N4 sites with 1.5 % compressed Fe-N bonds exhibit downshifted d-band center than the planar sites. Such a change can weaken the bonding strength between the oxygenated intermediates and metal sites, resulting a much smaller energy barrier for oxygen reduction. Catalytic tests further demonstrate that a kinetic current density of 7.922 mA cm-2 at 0.9 V vs. RHE is obtained in alkaline media for curved Fe-N4 sites, which is 31 times higher than that for planar ones. Our findings shed light on modulating the local three-dimensional structure of single metal sites and boosting the catalytic activity via strain engineering.
- Published
- 2021
50. Constructing directional component distribution in a bifunctional catalyst to boost the tandem reaction of syngas conversion
- Author
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Chuanming Wang, Yiqing Lu, Yangdong Wang, Liu Chang, Su Liu, Xiao Yu, Zaiku Xie, Yingchun Ye, Jiao Wenqian, Su Junjie, Yida Zhang, Jian Zhou, Xusheng Zheng, Zhang Lin, and Haibo Zhou
- Subjects
Materials science ,Recrystallization (geology) ,Diffusion ,Oxide ,Catalysis ,Bifunctional catalyst ,chemistry.chemical_compound ,Chemical engineering ,Cascade reaction ,chemistry ,General Earth and Planetary Sciences ,Zeolite ,General Environmental Science ,Syngas - Abstract
Summary Controlling the formation, diffusion, and conversion of bridging intermediate is important for improving the performance of a tandem reaction over a multi-component catalyst. However, it remains highly challenging because the random distribution of catalytic components via conventional mechanical combination usually endows nondirectional diffusion, resulting in an obvious decrease in catalytic performance. Here, we report a recrystallization methodology dealing with the extruded Cr2O3/ZSM-5 bifunctional catalyst to distribute the oxide on zeolite in an oriented manner. It is confirmed that Cr2O3 preferentially locates on the (100) and (101) surfaces of plate-like ZSM-5 and that the (010) surface is highly exposed. Hence, the diffusion of the bridging intermediate and products is modulated in a directional way, boosting the tandem reaction of CO conversion to aromatics. A 2.99 mmol g−1 h−1 formation rate of aromatic rings (on carbon base) at a 49.4% CO conversion is achieved over the recrystallized catalyst, which is the highest performance data yet reported.
- Published
- 2021
Catalog
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