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Simplex Initialization: A Survey of Techniques and Trends [article]

Mengyu Huang, Yuxing Zhong, Huiwen Yang, Jiazheng Wang, Fan Zhang, Bo Bai, Ling Shi
2021 arXiv   pre-print
The simplex method is one of the most fundamental technologies for solving linear programming (LP) problems and has been widely applied to different practical applications. In the past literature, how to improve and accelerate the simplex method has attracted plenty of research. One important way to achieve this goal is to find a better initialization method for the simplex. In this survey, we aim to provide an overview about the initialization methods in the primal and dual simplex,
more » ... y. We also propose several potential future directions about how to improve the existing initialization methods with the help of advanced learning technologies.
arXiv:2111.03376v1 fatcat:6cddy34m6bed5hmx4kvnuiap4i

Concentric Circular Grating Generated by the Patterning Trapping of Nanoparticles in an Optofluidic Chip

Hailang Dai, Zhuangqi Cao, Yuxing Wang, Honggen Li, Minghuang Sang, Wen Yuan, Fan Chen, Xianfeng Chen
2016 Scientific Reports  
Due to the field enhancement effect of the hollow-core metal-cladded optical waveguide chip, massive nanoparticles in a solvent are effectively trapped via exciting ultrahigh order modes. A concentric ring structure of the trapped nanoparticles is obtained since the excited modes are omnidirectional at small incident angle. During the process of solvent evaporation, the nanoparticles remain well trapped since the excitation condition of the optical modes is still valid, and a concentric
more » ... grating consisting of deposited nanoparticles can be produced by this approach. Experiments via scanning electron microscopy, atomic force microscopy and diffraction of a probe laser confirmed the above hypothesis. This technique provides an alternative strategy to enable effective trapping of dielectric particles with low-intensity nonfocused illumination, and a better understanding of the correlation between the guided modes in an optical waveguide and the nanoparticles in a solvent. Optical micromanipulation, with its capability to non-invasively move or trap micro-or nano-objects, has attracted much attention in the past decade and contributed to the development of many fields, such as biology, colloidal dynamics, particle sorting, and lab-on-a-chip technology 1 . Several exciting developments have occurred recently. The optical trapping of small objects such as dielectric spheres 2 , carbon nanotubes 3 , semiconductor nanowires 4 , metal nanoparticles 5-7 and even bio-particles 8-10 has already been experimentally demonstrated 11 . Despite their different configurations, the key to realize effective optical trapping is to achieve a very strong electric field gradient, since the competition between the gradient and scattering force determines the trapping efficiency. Among these trapping techniques, optical tweezers are widely used for various optical micromanipulation applications. Optical tweezers usually consist of a single-beam optical trap based on a standard microscope using a laser as its light source. The three-dimensional confinement can be achieved at the focal point through gradients. To achieve a tightly focused laser beam, high numerical aperture (NA) lenses are usually indispensable, and relatively high laser power is also required to obtain large gradients near the focal point. Consequently, the corresponding system is rather expensive. Near-field trap is another major type of optical-trapping technique based on the near-field optical schemes, such as whispering gallery mode-based micro-resonators 12 , plasmonic nano-antennas 13 , slot waveguides 14 and photonic crystal cavities 15 . These methods can overcome the free space diffraction limit imposed by conventional optics, and trap particles whose sizes are smaller than the wavelength. Owing to the near-field enhancement effect in nano-scale structures, low incident power is enough to achieve effective trapping. However, to realize a near-field trap, rather complicated nanofabrication processes are required to produce micro-or nano-scale features. Furthermore, although substantial work has been conducted on the optical trapping issue, most has been focused on trapping and manipulating a single particle. Few research has been devoted on the issue of trapping many particles simultaneously, which may find wider application in particle stacking, sorting and filtering. K. Dholakia et al. performed pioneering work to demonstrate the optical trapping
doi:10.1038/srep32018 pmid:27550743 pmcid:PMC4994086 fatcat:kypckuwknncu3b6g7tylpq3ufa

CUL4B contributes to cancer stemness by repressing tumor suppressor miR34a in colorectal cancer

Yanjun Li, Huili Hu, Yuxing Wang, Yujia Fan, Yang Yang, Beibei Guo, Xueyong Xie, Jiabei Lian, Baichun Jiang, Bo Han, Yanlei Wang, Changshun Shao (+1 others)
2020 Oncogenesis  
Given that colorectal cancer stem cells (CCSCs) play key roles in the tumor dormancy, metastasis, and relapse, targeting CCSCs is a promising strategy in cancer therapy. Here, we aimed to identify the new regulators of CCSCs and found that Cullin 4B (CUL4B), which possesses oncogenic properties in multiple solid tumors, drives the development and metastasis of colon cancer by sustaining cancer stem-like features. Elevated expression of CUL4B was confirmed in colon tumors and was associated with
more » ... poor overall survival. Inhibition of CUL4B in cancer cell lines and patient-derived tumor organoids led to reduced sphere formation, proliferation and metastasis capacity. Mechanistically, CUL4B coordinates with PRC2 complex to repress miR34a expression, thus upregulates oncogenes including MYCN and NOTCH1, which are targeted by miR34a. Furthermore, we found that elevated CUL4B expression is associated with miR34a downregulation and upregulation of miR34a target genes in colon cancer specimens. Collectively, our findings demonstrate that CUL4B functions to repress miR34a in maintaining cancer stemness in CRC and provides a potential therapeutic target.
doi:10.1038/s41389-020-0206-3 pmid:32054830 fatcat:eyyiajogh5hr3cnkjgp7mijgku

Prestress-loading effect on the current–voltage characteristics of a piezoelectric p–n junction together with the corresponding mechanical tuning laws

Wanli Yang, Shuaiqi Fan, Yuxing Liang, Yuantai Hu
2019 Beilstein Journal of Nanotechnology  
Acknowledgements ORCID ® iDs Wanli Yang - Yuxing Liang -  ...  Fan et al.  ...  Recently, Fan et al. [21] and Zhang et al. [22] revisited the bending behavior of a cantilevered ZnO nanowire based on the linear phenomenological theory of piezoelectric semiconductors.  ... 
doi:10.3762/bjnano.10.178 pmid:31579080 pmcid:PMC6753683 fatcat:b7peck635ne4vdwh5gh4fa4h4m

Nonlinear effect of carrier drift on the performance of an n-type ZnO nanowire nanogenerator by coupling piezoelectric effect and semiconduction

Yuxing Liang, Shuaiqi Fan, Xuedong Chen, Yuantai Hu
2018 Beilstein Journal of Nanotechnology  
ORCID ® iDs Yuxing Liang -  ...  Recently, Fan et al. studied the linear solutions of electromechanical quantities in a bent ZNW under the assumption of a small fluctuation of the carrier concentration [31] .  ... 
doi:10.3762/bjnano.9.183 pmid:30013885 pmcid:PMC6037001 fatcat:7k5va7k555au5paxhplloffz3m

Copper salt-catalyzed formation of a novel series of triazole–spirodienone conjugates with potent anticancer activity

Linghui Gu, Peng Wang, Qiu Zhong, Yuxing Deng, Jiangping Xie, Fei Liu, Fan Xiao, Shilong Zheng, Yue Chen, Guangdi Wang, Ling He
2017 RSC Advances  
Copper salt-catalyzed oxidative amination resulted in the formation of a novel series of triazole–spirodienone conjugates, 4-triazolyl-1-oxa-4-azaspiro[4,5]deca-6,9-dien-3,8-diones and 4-triazolyl-1-oxa-4-azaspiro[4,5]deca-6,9-dien-8-ones.
doi:10.1039/c6ra24764d pmid:30740218 pmcid:PMC6364840 fatcat:skrmsbflujce5phtcrfmeq6udi

In Silico Prediction of O6-Methylguanine-DNA Methyltransferase Inhibitory Potency of Base Analogs with QSAR and Machine Learning Methods

Guohui Sun, Tengjiao Fan, Xiaodong Sun, Yuxing Hao, Xin Cui, Lijiao Zhao, Ting Ren, Yue Zhou, Rugang Zhong, Yongzhen Peng
2018 Molecules  
O6-methylguanine-DNA methyltransferase (MGMT), a unique DNA repair enzyme, can confer resistance to DNA anticancer alkylating agents that modify the O6-position of guanine. Thus, inhibition of MGMT activity in tumors has a great interest for cancer researchers because it can significantly improve the anticancer efficacy of such alkylating agents. In this study, we performed a quantitative structure activity relationship (QSAR) and classification study based on a total of 134 base analogs
more » ... to their ED50 values (50% inhibitory concentration) against MGMT. Molecular information of all compounds were described by quantum chemical descriptors and Dragon descriptors. Genetic algorithm (GA) and multiple linear regression (MLR) analysis were combined to develop QSAR models. Classification models were generated by seven machine-learning methods based on six types of molecular fingerprints. Performances of all developed models were assessed by internal and external validation techniques. The best QSAR model was obtained with Q2Loo = 0.83, R2 = 0.87, Q2ext = 0.67, and R2ext = 0.69 based on 84 compounds. The results from QSAR studies indicated topological charge indices, polarizability, ionization potential (IP), and number of primary aromatic amines are main contributors for MGMT inhibition of base analogs. For classification studies, the accuracies of 10-fold cross-validation ranged from 0.750 to 0.885 for top ten models. The range of accuracy for the external test set ranged from 0.800 to 0.880 except for PubChem-Tree model, suggesting a satisfactory predictive ability. Three models (Ext-SVM, Ext-Tree and Graph-RF) showed high and reliable predictive accuracy for both training and external test sets. In addition, several representative substructures for characterizing MGMT inhibitors were identified by information gain and substructure frequency analysis method. Our studies might be useful for further study to design and rapidly identify potential MGMT inhibitors.
doi:10.3390/molecules23112892 pmid:30404161 fatcat:2qpdbkiikjaubpzh7mwzkclfgm

Cryo-electron Microscopy Structure and Transport Mechanism of a Wall Teichoic Acid ABC Transporter

Li Chen, Wen-Tao Hou, Tao Fan, Banghui Liu, Ting Pan, Yu-Hui Li, Yong-Liang Jiang, Wen Wen, Zhi-Peng Chen, Linfeng Sun, Cong-Zhao Zhou, Yuxing Chen (+2 others)
2020 mBio  
The wall teichoic acid (WTA) is a major cell wall component of Gram-positive bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), a common cause of fatal clinical infections in humans. Thus, the indispensable ABC transporter TarGH, which flips WTA from cytoplasm to extracellular space, becomes a promising target of anti-MRSA drugs. Here, we report the 3.9-Å cryo-electron microscopy (cryo-EM) structure of a 50% sequence-identical homolog of TarGH from Alicyclobacillus herbarius
more » ... t an ATP-free and inward-facing conformation. Structural analysis combined with activity assays enables us to clearly decode the binding site and inhibitory mechanism of the anti-MRSA inhibitor Targocil, which targets TarGH. Moreover, we propose a "crankshaft conrod" mechanism utilized by TarGH, which can be applied to similar ABC transporters that translocate a rather big substrate through relatively subtle conformational changes. These findings provide a structural basis for the rational design and optimization of antibiotics against MRSA. IMPORTANCE The wall teichoic acid (WTA) is a major component of cell wall and a pathogenic factor in methicillin-resistant Staphylococcus aureus (MRSA). The ABC transporter TarGH is indispensable for flipping WTA precursor from cytoplasm to the extracellular space, thus making it a promising drug target for anti-MRSA agents. The 3.9-Å cryo-EM structure of a TarGH homolog helps us to decode the binding site and inhibitory mechanism of a recently reported inhibitor, Targocil, and provides a structural platform for rational design and optimization of potential antibiotics. Moreover, we propose a "crankshaft conrod" mechanism to explain how a big substrate is translocated through subtle conformational changes of type II exporters. These findings advance our understanding of anti-MRSA drug design and ABC transporters.
doi:10.1128/mbio.02749-19 pmid:32184247 fatcat:f2mxasvc2vgt3ndsszvmtobelu

PNUTS mediates ionizing radiation-induced CNE-2 nasopharyngeal carcinoma cell migration, invasion, and epithelial–mesenchymal transition via the PI3K/AKT signaling pathway

Dan Yu, Xiang An, Wanlin Fan, Xin Wang, Yuxing He, Bing Li
2019 OncoTargets and Therapy  
Ionizing radiation (IR) is widely used for treating nasopharyngeal carcinoma (NPC). However, recent studies indicate that IR can also promote the migration and invasion of malignant tumors. Phosphatase 1 nuclear-targeting subunit (PNUTS), a novel interacting protein, was recently demonstrated to be involved in tumorigenesis and metastasis formation. This protein was hypothesized to take part in IR-induced migration and invasion in NPC cells in this study. Western blotting was used to detect how
more » ... PNUTS was expressed in NPC cells with or without IR treatment. Wound-healing and Transwell assays were used to measure cell migration and invasion. Quantitative real-time PCR and Western blotting were used to determine the expression levels of PNUTS and epithelial-mesenchymal transition (EMT) proteins, respectively, after CNE-2 cells were infected with an adenovirus vector, ad-PNUTS, or transfected with PNUTS-specific siRNA. Finally, the expression levels of PI3K/AKT signaling-related proteins were detected by Western blotting. IR significantly promoted PNUTS expression and the migration and invasion in CNE-2 cells. Moreover, after exposure to IR, expression of the mesenchymal markers N-cadherin and vimentin increased, while that of the epithelial marker E-cadherin decreased. Silencing PNUTS remarkably attenuated IR-induced increases in cell migration and invasion and reversed the EMT process. Additionally, the overexpression of PNUTS restored the mobility and invasiveness of CNE-2 cells, which regained EMT characteristics. Furthermore, we found that PNUTS regulated IR-induced EMT via the PI3K/AKT signaling pathway. Our research illustrates a relationship between PNUTS and IR-induced cell migration and invasion and provides a novel therapeutic target for preventing radiotherapy-induced metastasis in NPC patients.
doi:10.2147/ott.s188571 pmid:30863088 pmcid:PMC6388972 fatcat:fnw2kq5s6fdqzdsevclfwt2hya

Silencing the Girdin gene enhances radio-sensitivity of hepatocellular carcinoma via suppression of glycolytic metabolism

Li Yu, Yifan Sun, Jingjing Li, Yan Wang, Yuxing Zhu, Yong Shi, Xiaojun Fan, Jianda Zhou, Ying Bao, Jie Xiao, Ke Cao, Peiguo Cao
2017 Journal of Experimental & Clinical Cancer Research  
Radiotherapy has been used increasingly to treat primary hepatocellular carcinoma. Clinically, the main cause of radiotherapy failure is cellular radioresistance, conferred via glycolytic metabolism. Our previous study demonstrated that Girdin is upregulated in primary hepatocellular carcinoma and promotes the invasion and metastasis of tumor cells. However, whether Girdin underlies the radio-sensitivity of hepatocellular carcinoma remains unclear. Methods: A short hairpin RNA (shRNA) was used
more » ... o silence CCDC88A (encoding Girdin), and real-time PCR was performed to determine CCDC88A mRNA expression. Then, cell proliferation, colony formation, flow cytometric, scratch, and transwell assays were to examine the influence of Girdin silencing on cellular radiosensitivity. Glycolysis assays were conducted to exam cell glycolysis process. Western blotting was performed to explore the signaling pathway downstream of Girdin. Finally, animal experiments were performed to demonstrate the effect of CCDC88A silencing on the radiosensitivity of hepatoma in vivo. Results: shRNA-induced Girdin silencing suppressed glycolysis and enhanced the radio-sensitivity of hepatic cell lines, HepG2 and Huh-7. Furthermore, silencing of Girdin inhibited the PI3K/AKT/HIF-1α signaling pathway, which is a central regulator of glycolysis. Conclusion: Girdin can regulate glycolysis in hepatocellular carcinoma cells through the PI3K/AKT/HIF-1α signaling pathway, which decreases the sensitivity of tumor cells to radiotherapy.
doi:10.1186/s13046-017-0580-7 pmid:28810896 pmcid:PMC5558715 fatcat:fgccpuxz7reo3dg2gpve43i37a

The Controlling of the Subtropical High Leading Modes on the Spatial Pattern of Tropical Cyclone Genesis in the Western North Pacific and Tracks Landing on the East Coast of China

Tingting Fan, Yuxing Yang, Shibin Xu
2022 Atmosphere  
As a prime circulation system, the western Pacific subtropical high (WPSH) significantly impacts tropical cyclone (TC) activities over the western North Pacific (WNP), especially TCs landing on the east coast of China; however, the associated mechanism is not firmly established. This study investigates the underlying dynamic impact of the first two empirical orthogonal function (EOF) modes of the WPSH on the interannual variability in the genesis and number of TCs landing over the WNP. The
more » ... ts show that these two dominant modes control the WNP TC activity over different subregions via different environmental factors. The first mode (EOF1) affects the TC genesis number over region I (105°–128° E, 5°–30° N) (r = −0.49) and region II (130°–175° E, 17°–30° N) (r = −0.5) and controls the TCs landing on the east coast of China, while the second mode (EOF2) affects the TC genesis number over region III (128°–175° E, 5°–17° N) (r = −0.69). The EOF1 mode, a southwest-northeast-oriented enhanced pattern, causes the WPSH to expand (retreat) along the southwest-northeast direction, which makes both mid-low-level relative humidity and low-level vorticity unfavorable (favorable) for TC genesis in region I and region II and steers fewer (more) TC tracks to land on the coast of China. The EOF2 mode features a strengthened WPSH over the southeast quarter of the WNP region. The active (inactive) phases of this mode control the low-level vorticity and vertical wind shear in region III, which lead to less (more) TC genesis over this region. The prediction equations combining the two modes of the WPSH for the total number of TCs and TCs that make landfall show high correlation coefficients. Our findings verify the high prediction skill of the WPSH on WNP TC activities, provide a new way to predict TCs that will make landfall on the east coast of China, and help to improve the future projection of WNP TC activity.
doi:10.3390/atmos13010079 fatcat:aqcf3ap3srgpflx6rir67goebu

Inhibition of REDD1 Sensitizes Bladder Urothelial Carcinoma to Paclitaxel by Inhibiting Autophagy

Qinghai Zeng, Jianye Liu, Peiguo Cao, Jingjing Li, Xiaoming Liu, Xiaojun Fan, Ling Liu, Yan Cheng, Wei Xiong, Jigang Li, Hao Bo, Yuxing Zhu (+7 others)
2017 Clinical Cancer Research  
Purpose: Regulated in development and DNA damage response-1 (REDD1) is a stress-related protein and is involved in the progression of cancer. The role and regulatory mechanism of REDD1 in bladder urothelial carcinoma (BUC), however, is yet unidentified. Experimental Design: The expression of REDD1 in BUC was detected by Western blot analysis and immunohistochemistry (IHC). The correlation between REDD1 expression and clinical features in patients with BUC were assessed. The effects of REDD1 on
more » ... ellular proliferation, apoptosis, autophagy, and paclitaxel sensitivity were determined both in vitro and in vivo. Then the targeted-regulating mechanism of REDD1 by miRNAs was explored. Results: Here the significant increase of REDD1 expression is detected in BUC tissue, and REDD1 is first reported as an independent prognostic factor in patients with BUC. Silencing REDD1 expression in T24 and EJ cells decreased cell proliferation, increased apoptosis, and decreased autophagy, whereas the ectopic expression of REDD1 in RT4 and BIU87 cells had the opposite effect. In addition, the REDD1-mediated proliferation, apoptosis, and autophagy are found to be negatively regulated by miR-22 in vitro, which intensify the paclitaxel sensitivity via inhibition of the well-acknowledged REDD1-EEF2Kautophagy axis. AKT/mTOR signaling initially activated or inhibited in response to silencing or enhancing REDD1 expression and then recovered rapidly. Finally, the inhibited REDD1 expression by either RNAi or miR-22 sensitizes BUC tumor cells to paclitaxel in a subcutaneous transplant carcinoma model in vivo. Conclusions: REDD1 is confirmed as an oncogene in BUC, and antagonizing REDD1 could be a potential therapeutic strategy to sensitize BUC cells to paclitaxel.
doi:10.1158/1078-0432.ccr-17-0419 pmid:29084921 fatcat:ibonjisesjeehi52fcdw36qr7u

A multicenter real-world study of tumor-derived DNA from pleural effusion supernatant in genomic profiling of advanced lung cancer

Shidai Jin, Chengzhi Zhou, Xue Hou, Zaiwen Fan, Jun Zhao, Xinghao Ai, Yuxing Chu, Rongrong Chen, Renhua Guo, Likun Chen
2020 Translational Lung Cancer Research  
Pleural effusion (PE) is commonly observed in advanced lung cancer. Research has suggested that molecular profiling of PE could be used to detect tumor driver mutations, thus informing clinical decision-making. However, the performance of PE samples in a real-world setting has yet to be examined. A total of 678 metastatic lung cancer patients with pleural effusion were enrolled in this study. Cohort 1 included 22 patients whose PE and matched plasma samples were simultaneously collected as a
more » ... ot study. Cohort 2 comprised 656 patients, from whom 734 samples were collected in a real world setting. These samples were subjected to targeted next-generation sequencing (NGS) of 1,021 cancer-related genes. PE supernatant was the preferred choice for genetic profiling. While the maximal somatic allele frequency (MSAF) of plasma in patients with M1a stage was significantly lower than that in patients with M1b/c stages (4.4%±9.6% vs. 9.0%±14.1%, P<0.01), the MSAF of PE supernatant was similar between M1a and M1b/c stages. PE supernatant demonstrated higher sensitivity than plasma in detecting actionable mutations in cohort 1 (81.8% vs. 45.5%, P=0.01) as well as in M1a disease (84.7% vs. 42.1%, P<0.01), but not in M1b/c disease, in cohort 2. Known resistant mutations were identified in 72 of the 117 patients who were resistant to first- or second-generation EGFR-TKIs, 22 of the 42 patients who were resistant to osimertinib, and 9 of the 13 patients who were resistant to crizotinib. Remarkably, PE supernatant outperformed plasma in identifying mutations that confer resistance to first- and second-generation EGFR-TKIs (75.4% vs. 29.8%, P<0.001). This real-world large cohort study verified that PE supernatant had higher sensitivity than plasma for identifying actionable mutations, including resistance mutations. PE supernatant would be preferred by physicians for assessing tumor genomics in advanced lung cancer when tumor tissue is not available.
doi:10.21037/tlcr-20-882 pmid:32953522 pmcid:PMC7481626 fatcat:k6grjlcgjfgidbnw34vegme4ki

Night-Warming Priming at the Vegetative Stage Alleviates Damage to the Flag Leaf Caused by Post-anthesis Warming in Winter Wheat (Triticum aestivum L.)

Yonghui Fan, Zhaoyan Lv, Ting Ge, Yuxing Li, Wei Yang, Wenjing Zhang, Shangyu Ma, Tingbo Dai, Zhenglai Huang
2021 Frontiers in Plant Science  
compared with the damage observed in non-primed plants, heat priming during the stemelongation stage and booting significantly prevented the grainyield damage caused by heat stress during grain-filling (Fan  ... 
doi:10.3389/fpls.2021.706567 pmid:34691092 pmcid:PMC8526553 fatcat:f4e4p3uiejellnzixvth4puhay

Comparison of Spray Deposition, Control Efficacy on Wheat Aphids and Working Efficiency in the Wheat Field of the Unmanned Aerial Vehicle with Boom Sprayer and Two Conventional Knapsack Sprayers

Guobin Wang, Yubin Lan, Huizhu Yuan, Haixia Qi, Pengchao Chen, Fan Ouyang, Yuxing Han
2019 Applied Sciences  
As a new low volume application technology, unmanned aerial vehicle (UAV) application is developing quickly in China. The aim of this study was to compare the droplet deposition, control efficacy and working efficiency of a six-rotor UAV with a self-propelled boom sprayer and two conventional knapsack sprayers on the wheat crop. The total deposition of UAV and other sprayers were not statistically significant, but significantly lower for run-off. The deposition uniformity and droplets
more » ... ity of the UAV were poor. The deposition variation coefficient of the UAV was 87.2%, which was higher than the boom sprayer of 31.2%. The deposition on the third top leaf was only 50.0% compared to the boom sprayer. The area of coverage of the UAV was 2.2% under the spray volume of 10 L/ha. The control efficacy on wheat aphids of UAV was 70.9%, which was comparable to other sprayers. The working efficiency of UAV was 4.11 ha/h, which was roughly 1.7–20.0 times higher than the three other sprayers. Comparable control efficacy results suggest that UAV application could be a viable strategy to control pests with higher efficiency. Further improvement on deposition uniformity and penetrability are needed.
doi:10.3390/app9020218 fatcat:zj6j2n5azvambnclf5fkfqrlqy
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