38 results on '"Yijing Lu"'
Search Results
2. Transcriptome analysis of sugarcane reveals rapid defense response of SES208 to Xanthomonas albilineans in early infection
- Author
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Yaying Ma, Hongying Yu, Yijing Lu, Sanji Gao, Mahpara Fatima, Ray Ming, and Jingjing Yue
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Saccharum spp. ,Xanthomonas albilineans ,Leaf scald ,RNA-Seq ,Disease resistance ,Botany ,QK1-989 - Abstract
Abstract Background Diseases are the major factor affecting the quality and yield of sugarcane during its growth and development. However, our knowledge about the factors regulating disease responses remain limited. The present study focuses on identifying genes regulating transcriptional mechanisms responsible for resistance to leaf scald caused by Xanthomonas albilineans in S. spontaneum and S. officinarum. Results After inoculation of the two sugarcane varieties SES208 (S. spontaneum) and LA Purple (S. officinarum) with Xanthomonas albilineans, SES208 exhibited significantly greater resistance to leaf scald caused by X. albilineans than did LA Purple. Using transcriptome analysis, we identified a total of 4323 and 1755 differentially expressed genes (DEGs) in inoculated samples of SES208 and LA Purple, respectively. Significantly, 262 DEGs were specifically identified in SES208 that were enriched for KEGG pathway terms such as plant-pathogen interaction, MAPK signaling pathway, and plant hormone signal transduction. Furthermore, we built a transcriptional regulatory co-expression network that specifically identified 16 and 25 hub genes in SES208 that were enriched for putative functions in plant-pathogen interactions, MAPK signaling, and plant hormone signal transduction. All of these essential genes might be significantly involved in resistance-regulating responses in SES208 after X. albilineans inoculation. In addition, we found allele-specific expression in SES208 that was associated with the resistance phenotype of SES208 when infected by X. albilineans. After infection with X. albilineans, a great number of DEGs associated with the KEGG pathways ‘phenylpropanoid biosynthesis’ and ‘flavonoid biosynthesis’ exhibited significant expression changes in SES208 compared to LA Purple that might contribute to superior leaf scald resistance in SES208. Conclusions We provided the first systematical transcriptome map that the higher resistance of SES208 is associated with and elicited by the rapid activation of multiple clusters of defense response genes after infection by X. albilineans and not merely due to changes in the expression of genes generically associated with stress resistance. These results will serve as the foundation for further understanding of the molecular mechanisms of resistance against X. albilineans in S. spontaneum.
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- 2023
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3. Transcriptome analyses shed light on floral organ morphogenesis and bract color formation in Bougainvillea
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Wenping Zhang, Qun Zhou, Jishan Lin, Xinyi Ma, Fei Dong, Hansong Yan, Weimin Zhong, Yijing Lu, Yuan Yao, Xueting Shen, Lixian Huang, Wanqi Zhang, and Ray Ming
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Gene annotation ,Floral organ identity genes ,Betalain ,Co-expression ,Botany ,QK1-989 - Abstract
Abstract Background Bougainvillea is a popular ornamental plant with brilliant color and long flowering periods. It is widely distributed in the tropics and subtropics. The primary ornamental part of the plant is its colorful and unusual bracts, rich in the stable pigment betalain. The developmental mechanism of the bracts is not clear, and the pathway of betalain biosynthesis is well characterized in Bougainvillea. Results At the whole-genome level, we found 23,469 protein-coding genes by assembling the RNA-Seq and Iso-Seq data of floral and leaf tissues. Genome evolution analysis revealed that Bougainvillea is related to spinach; the two diverged approximately 52.7 million years ago (MYA). Transcriptome analysis of floral organs revealed that flower development of Bougainvillea was regulated by the ABCE flower development genes; A-class, B-class, and E-class genes exhibited high expression levels in bracts. Eight key genes of the betalain biosynthetic pathway were identified by homologous alignment, all of which were upregulated concurrently with bract development and betalain accumulation during the bract initiation stage of development. We found 47 genes specifically expressed in stamens, including seven highly expressed genes belonging to the pentose and glucuronate interconversion pathways. BgSEP2b, BgSWEET11, and BgRD22 are hub genes and interacted with many transcription factors and genes in the carpel co-expression network. Conclusions We assembled protein-coding genes of Bougainvilea, identified the floral development genes, and constructed the gene co-expression network of petal, stamens, and carpel. Our results provide fundamental information about the mechanism of flower development and pigment accumulation in Bougainvillea, and will facilitate breeding of cultivars with high ornamental value.
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- 2022
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4. Testing and Analysis of Surrounding Buildings during the Operation of Seismic Simulation Shaking Table
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Wenbo Xie, Huiqi Liang, Zhiqiang Zhang, Peizi Wei, and Yijing Lu
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shaking table ,vibration comfort ,dynamic test ,structural vibration ,Building construction ,TH1-9745 - Abstract
This paper focuses on the transmission of vibration response of the seismic simulation shaking table system at Southeast University, and analyzes the effect of this response on the surrounding building. The location of the building is less than 10 m away from the laboratory where the shaking table is located, and during the maximum load test, a student reported that the vibration caused him a sense of discomfort, as well as the shaking of office objects on desktops on high floors, which caused panic. For these reasons, multiple three-directional vibration sensors were placed around the shaking table system and on the 1st, 8th, and 16th floors of the building. Test the vibration response transfer and the vibration response of the building floor while the exercise table is in operation. The test results show that the vibration-weighted acceleration levels of some floors exceed the code limits under sinusoidal wave conditions, which was the cause of the discomfort. The floors will have an amplifying effect on the lateral vibration. For seismic wave excitation, all measurement points of the building meet the limit values required by the GB 50868-2013 Standard for allowable vibration of building engineering. This study can provide a data reference for future shaking table system commissioning and operation.
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- 2023
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5. Expression profiling of the Dof gene family under abiotic stresses in spinach
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Hongying Yu, Yaying Ma, Yijing Lu, Jingjing Yue, and Ray Ming
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Medicine ,Science - Abstract
Abstract DNA-binding with one finger (Dof) are plant-specific transcription factors involved in numerous pathways of plant development, such as abiotic stresses responses. Although genome-wide analysis of Dof genes has been performed in many species, but these genes in spinach have not been analyzed yet. We performed a genome-wide analysis and characterization of Dof gene family in spinach (Spinacia oleracea L.). Twenty-two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purifying selection. Using cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones, and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.
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- 2021
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6. Three-Dimensional Nonlinear Seismic Response of Shield Tunnel Spatial End Structure
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Yijing Lu, Yongsheng Song, Yanzhen Wang, and Jiale Yuan
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Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
The stiffness mutation of shield tunnel-shaft junction makes the tunnel structure affected by the differential displacement and forms a complex spatial effect. Taking the subsea shield tunnel crossing under the Shantou Gulf, China, as a case study, a three-dimensional finite element global model and a refined local spatial end submodel are established. The nonlinear dynamic behaviors of the seabed soil and concrete, the simulation of the bolt joints between ring segments by using cohesive models and the SMA shape memory alloy flexible joints, and the input ground motions produced by scaling from the high-level earthquake records are considered in detail. The results show that the shield tunnel spatial end structure increases nonlinearly in response to the increase of seismic motion intensity. The opening width and the deformation between ring segments at the vault and the outside spandrel are larger, and serious seismic damage and stress concentration exist at the conjugate 45° directions of shaft. The seismic responses of the tunnel-shaft junction subjected to the seismic motions with rich low-frequency components are much stronger than those of seismic motions with rich high-frequency components. Adding SMA flexible joints, the structural deformation caused by seismic motion propagation can be induced to the preset flexible joint, and the structural damage and stress concentration can be effectively reduced. The seismic response characteristics of shield tunnel spatial end structure calculated by the global model are consistent with those calculated by the submodel, while the seismic response of the submodel is greater than that of the global model.
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- 2021
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7. SIRT5 deficiency enhances the proliferative and therapeutic capacities of adipose‐derived mesenchymal stem cells via metabolic switching
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Tiantong Ou, Wenlong Yang, Wenjia Li, Yijing Lu, Zheng Dong, Hongming Zhu, Xiaolei Sun, Zhen Dong, Xinyu Weng, Suchi Chang, Hua Li, Yufan Li, Zhiwei Qiu, Kai Hu, Aijun Sun, and Junbo Ge
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adipose‐derived mesenchymal stem cells ,cell proliferation ,hind limb ischemia ,metabolic switching ,SIRT5 ,Medicine (General) ,R5-920 - Abstract
Abstract Background Mesenchymal stem cells (MSCs) have therapeutic potential for multiple ischemic diseases. However, in vitro expansion of MSCs before clinical application leads to metabolic reprogramming from glycolysis to oxidative phosphorylation, drastically impairing their proliferative and therapeutic capacities. This study aimed to define the regulatory effects of Sirtuin 5 (SIRT5) on the proliferative and therapeutic functions of adipose‐derived MSCs (ADMSCs) during in vitro expansion. Methods ADMSCs were isolated from wild‐type (WT) and Sirt5‐knockout (Sirt5−/−) mice. Cell counting assay was used to investigate the proliferative capacities of the ADMSCs. Dihydroethidium and senescence‐associated β‐galactosidase stainings were used to measure intracellular ROS and senescence levels. Mass spectrometry was used to analyze protein succinylation. Oxygen consumption rates and extra cellular acidification rates were measured as indicators of mitochondrial respiration and glycolysis. Metabolic‐related genes expression were verified by quantitative PCR and western blot. Hind limb ischemia mouse model was used to evaluate the therapeutic potentials of WT and Sirt5−/− ADSMCs. Results SIRT5 protein levels were upregulated in ADMCs during in vitro expansion. Sirt5−/− ADMSCs exhibited a higher proliferation rate, delayed senescence, and reduced ROS accumulation. Furthermore, elevated protein succinylation levels were observed in Sirt5−/− ADMSCs, leading to the reduced activity of tricarboxylic acid cycle‐related enzymes and attenuated mitochondrial respiration. Glucose uptake, glycolysis, and pentose phosphate pathway were elevated in Sirt5−/− ADMSCs. Inhibition of succinylation by glycine or re‐expression of Sirt5 reversed the metabolic alterations in Sirt5−/‐ ADMSCs, thus abolishing their enhanced proliferative capacities. In the hind limb ischemia mouse model, SIRT5−/− ADMSCs transplantation enhanced blood flow recovery and angiogenesis compared with WT ADMSCs. Conclusions Our results indicate that SIRT5 deficiency during ADMSC culture expansion leads to reversed metabolic pattern, enhanced proliferative capacities, and improved therapeutic outcomes. These data suggest SIRT5 as a potential target to enhance the functional properties of MSCs for clinical application.
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- 2020
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8. Short-Chained Platinum Complex Catalyzed Hydrosilylation under Thermomorphic Conditions: Heterogeneous Phase Separation at Ice Temperature
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Chiao-Fan Chiu, Jinn-Hsuan Ho, Eskedar Tessema, Yijing Lu, Chia-Rui Shen, Chang-Wei Lin, and Norman Lu
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heterogeneous separation ,catalyst ,fluorous ,hydrosilylation ,platinum ,thermomorphic ,Organic chemistry ,QD241-441 - Abstract
Homogeneous catalysts PtCl2[5,5′-bis-(n-ClCF2(CF2)3CH2OCH2)-2,2′-bpy] (2A) and PtCl2[5,5′-bis-(n-HCF2(CF2)3CH2OCH2)-2,2′-bpy] (2B), which contained short fluorous chains, were synthesized and used in catalysis of hydrosilylation of alkynes. In these reactions the thermomorphic mode was effectively used to recover these catalysts from the reaction mixture up to eight cycles by taking advantage of heterogeneous phase separation at ice temperature. This kind of catalysis had previously been observed in fluorous catalysts of platinum containing about 50% F-content, but in this work the percentage of F-content is decreased to only about 30%, by which we termed them as “very light fluorous”. Our new type of catalyst with limited number of F-content is considered as the important discovery in the fluorous technology field as the reduced number of fluorine atoms will help to be able to comply the EPA 8-carbon rule. The metal leaching after the reaction has been examined by ICP-MS, and the testing results show the leaching of residual metal to be minimal. Additionally, comparing these results to our previous work, fluorous chain assisted selectivity has been observed when different fluorous chain lengths of the catalysts are used. It has been found that there exists fluorous chain assisted better selectivity towards β-(E) form in the Pt-catalyzed hydrosilylation of non-symmetric terminal alkyne when the Pt catalyst contains short fluorous chain (i.e., 4 Cs). Phenyl acetylenes showed the opposite regioselectivity due to pi-pi interaction while using the same catalyst via Markovnikov’s addition to form terminal vinyl silane, which is then a major product for Pt-catalyzed hydrosilylation of terminal aryl acetylene with triethylsilane. Finally, the kinetic studies indicate that the insertion of alkyne into the Pt-H bond is the rate-determining step.
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- 2021
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9. Deep Speech Synthesis from MRI-Based Articulatory Representations.
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Peter Wu, Tingle Li, Yijing Lu, Yubin Zhang, Jiachen Lian, Alan W. Black, Louis Goldstein, Shinji Watanabe 0001, and Gopala Krishna Anumanchipalli
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- 2023
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10. Articulatory Representation Learning via Joint Factor Analysis and Neural Matrix Factorization.
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Jiachen Lian, Alan W. Black, Yijing Lu, Louis Goldstein, Shinji Watanabe 0001, and Gopala Krishna Anumanchipalli
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- 2023
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11. TSGCNeXt: Dynamic-Static Multi-Graph Convolution for Efficient Skeleton-Based Action Recognition with Long-term Learning Potential.
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Dongjingdian Liu, Pengpeng Chen, Miao Yao, Yijing Lu, Zijie Cai, and Yuxin Tian
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- 2023
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12. Articulatory Representation Learning Via Joint Factor Analysis and Neural Matrix Factorization.
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Jiachen Lian, Alan W. Black, Yijing Lu, Louis Goldstein, Shinji Watanabe 0001, and Gopala Krishna Anumanchipalli
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- 2022
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13. Service Package Recommendation for Mashup Development Based on a Multi-level Relational Network.
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Jian Cao 0001, Yijing Lu, and Nengjun Zhu
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- 2016
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14. Study on the mass and heat transfer of gas-liquid two-phase flow in the porous media based on the 3D reconstruction model
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Licheng Wang, Mengya Wang, Yu Qi, and Yijing Lu
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Surface tension ,Contact angle ,Materials science ,business.industry ,General Chemical Engineering ,Mass transfer ,Heat transfer ,3D reconstruction ,Thermodynamics ,Two-phase flow ,Computational fluid dynamics ,Porous medium ,business - Abstract
In the study, carbon fiber as porous medium, polycarbosilane-xylene solution and air as fluid, the heat and mass transfer in porous media was investigated. CT images of micro pores were obtained by applying Micro-CT technology. Based on the reconstruction model, 3D structure reconstruction was carried out. The surface tension model and contact angle model were introduced to establish the CFD model for simulation, which was verified by experiments. The effects of feed pressure P and liquid viscosity μ on the mass and heat transfer were systematically studied. It was found that under different P, the liquid holdup α, average temperature T and heat Q absorbed by liquid phase increase with time until stable. The larger the P, the smaller the stable values of T and Q. When μ was larger, the breakthrough time was longer, and the time for T and Q to reach stable values was longer.
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- 2021
15. Expression profiling of the Dof gene family under abiotic stresses in spinach
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Yijing Lu, Jingjing Yue, Ray Ming, Yaying Ma, and Hongying Yu
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0106 biological sciences ,0301 basic medicine ,Spinacia ,Plant genetics ,Science ,Flowers ,Biology ,01 natural sciences ,Article ,03 medical and health sciences ,Negative selection ,Gene Expression Regulation, Plant ,Spinacia oleracea ,Stress, Physiological ,Genetics ,Gene family ,Gene ,Abiotic component ,Multidisciplinary ,Cold-Shock Response ,food and beverages ,biology.organism_classification ,Gene expression profiling ,Plant Leaves ,030104 developmental biology ,Inflorescence ,Spinach ,Medicine ,010606 plant biology & botany - Abstract
DNA-binding with one finger (Dof) are plant-specific transcription factors involved in numerous pathways of plant development, such as abiotic stresses responses. Although genome-wide analysis of Dof genes has been performed in many species, but these genes in spinach have not been analyzed yet. We performed a genome-wide analysis and characterization of Dof gene family in spinach (Spinacia oleracea L.). Twenty-two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purifying selection. Using cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones, and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.
- Published
- 2021
16. Rectification of a Slanted Box-Girder Bridge Caused by Unbalanced Soil Load
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Yongsheng Song, Yanwen Wang, Yijing Lu, Huijuan Jia, Zhiyuan Chen, and Ruiqi Song
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Civil and Structural Engineering - Abstract
Aims: Rectification of a slanted continuous concrete box-girder bridge is presented in this paper. Background: Several bridge piers slanted due to uneven ground settlement, inducing excessive width of some expansion joints and oversize sliding displacement of some bridge bearings. The uneven ground settlement occured due to the unbalanced soil load on the ground. Methods: In this project, reverse ground loading was first applied to produce opposite-direction deformation of the bending bridge piles, thereby rectifying the slanted bridge piers rigidly connected to the piles. The procedure was accelerated by constructing several stress release holes on the opposite side of the reverse ground loading. Results: To stabilize foundation and prevent landsides of riverbank, combimationn of jet grouting piles and deep mixed piles was apliied to reinforce foundation soil, providing lateral restraint on the bridge piles as well. Finally, a hydraulic power system was used to reset the bridge piers, girders, and expansion joints. A similar system and additional equipment were used to replace the damaged bridge bearings. Conclusion: The recommended rectification techniques are suitable for rectifying bridges with similar geotechnical conditions and structure types and for replacing damaged bridge bearings.
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- 2022
17. The reshaping of medical image by news reports during COVID-19 's epidemic situation
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Yijing Lu, Xinyan Lu, Siyu Le, and Yazheng Li
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Medical Terminology ,History ,Coronavirus disease 2019 (COVID-19) ,education ,Media studies ,humanities ,Medical Assisting and Transcription ,Image (mathematics) - Abstract
Medical image has always been a long-term topic in social life, through questionnaires and personal interviews to investigate the role of news reports on the reconstruction of medical image before and after the epidemic. Through the investigation, it can be found that the media has played a certain intermediary role and positive guiding role in the alleviation of doctor-patient relationship and the shaping of medical portrayals; some metaphorical discourse descriptions in news reports can achieve better communication effect; through a variety of reporting forms and attribute agenda settings, the media enriches the foreground image of doctors and indirectly shapes the social image of doctors.
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- 2021
18. Dietary Cholesterol Exacerbates Statin-Induced Hepatic Toxicity in Syrian Golden Hamsters and in Patients in an Observational Cohort Study
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Junbo Ge, Qiongyang Yu, Zhen Dong, Jian An, Yijing Lu, Xiurui Ma, Xunde Xian, George Liu, Yuhui Wang, Aijun Sun, Haozhe Shi, and Yunan Wang
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Male ,0301 basic medicine ,Statin ,medicine.drug_class ,Atorvastatin ,Hamster ,030204 cardiovascular system & hematology ,Pharmacology ,Cholesterol, Dietary ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Cricetinae ,medicine ,Animals ,Humans ,Pharmacology (medical) ,Rosuvastatin ,Rosuvastatin Calcium ,biology ,Cholesterol ,business.industry ,nutritional and metabolic diseases ,Cytochrome P450 ,General Medicine ,Middle Aged ,Disease Models, Animal ,030104 developmental biology ,chemistry ,LDL receptor ,Toxicity ,biology.protein ,Female ,lipids (amino acids, peptides, and proteins) ,Chemical and Drug Induced Liver Injury ,Hydroxymethylglutaryl-CoA Reductase Inhibitors ,Cardiology and Cardiovascular Medicine ,business ,medicine.drug - Abstract
Statins are inhibitors of 3-hydroxy-3-methyl glutaryl coenzyme A (HMG-CoA) reductase, which is involved in cholesterol synthesis. The major side effects of statins include muscle- and liver-related toxicity. Muscle toxicity is highly associated with polymorphisms in cytochrome P450 proteins (CYPs), as predicted by pharmacogenomics. However, the mechanisms of hepatotoxicity are not well understood. Due to differences in cholesterol metabolism, statins are well tolerated in mice. In contrast, hamsters exhibit metabolic traits similar to humans and are suitable for studying the hepatotoxicity of statins. We investigated the effect of rosuvastatin (RSV) on liver damage in wild-type (WT) hamsters fed a high-cholesterol diet (HCD) and LDLR knockout (LDLR−/−) hamsters that developed spontaneous hypercholesterolemia. Two cohorts of clinical subjects (clinical registry number: 2017001) taking atorvastatin (ATV) were recruited for direct (assessment of cholesterol intake individually, n = 44) and indirect (celebratory meals/holiday season, n = 1993) examination of dietary cholesterol intake and liver damage, as indicated by elevation of alanine aminotransferase (ALT). RSV at a dose of 10 mg/kg caused fatal liver damage only in HCD-fed WT hamsters, while LDLR−/− hamsters with the same cholesterol levels were resistant to this toxic effect. In the human studies, we observed that the incidence of hepatic toxicity in patients receiving long-term ATV treatment was higher in patients with greater dietary cholesterol intake and in patients who consumed more food during Chinese holidays. Our results propose, for the first time, that dietary cholesterol significantly contributes to statin-related hepatotoxicity, providing valuable insight into the clinical use of statins.
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- 2020
19. Person-Based Micro-Simulation Demand Model for National Long-Distance Travel in the U.S.A
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Lei Zhang, Di Yang, Sepehr Ghader, Carlos Carrion, Yijing Lu, and Arash Asadabadi
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Transport engineering ,050210 logistics & transportation ,Mechanical Engineering ,0502 economics and business ,05 social sciences ,Micro simulation ,Business ,010501 environmental sciences ,01 natural sciences ,Transportation infrastructure ,0105 earth and related environmental sciences ,Civil and Structural Engineering - Abstract
As the nation and various states engage in funding transportation infrastructure improvements to meet future long-distance passenger travel demand, it is imperative to develop effective and practical modeling methods for analysis of long-distance passenger travel. Evaluating national-level infrastructure improvements requires a reliable analysis tool to model the demand for long-distance travel. The national travel demand model presented in this paper implements a person-level tour-based micro-simulation approach for modeling individuals’ long-distance or national activities in the U.S.A. This paper reviews the model framework, explains the model calibration, and presents applications of the model for policy evaluation and demand prediction. The model was estimated using the latest long-distance travel survey in the U.S.A., which is the 1995 American Travel Survey. As the estimation data is old, and no new long-distance travel survey with appropriate sample size is available to re-estimate the model, model calibration is the solution used to update the model and make it capable of capturing up-to-date travel patterns. Calibrating such a large-scale model can be challenging, because each calibration iteration is very costly. This paper describes the calibration effort conducted on the national long-distance micro-simulation model to showcase how a large-scale travel demand model can be calibrated efficiently. A fuel price scenario is analyzed to show how the national travel demand will change under a national fuel price increase scenario in the future year 2040. Another scenario analysis corresponding to construction of high-speed rail (HSR) is conducted to observe the effects of adding a HSR system to the northeast corridor on travel demand from a national perspective.
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- 2020
20. Modeling speaker-specific vocal tract kinematics from gestural scores
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Shrikanth S. Narayanan, Yijing Lu, Louis Goldstein, Asterios Toutios, and Justin Ly
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Acoustics and Ultrasonics ,Arts and Humanities (miscellaneous) ,Speech recognition ,Kinematics ,Psychology ,Vocal tract - Published
- 2021
21. Variation in compensatory strategies as a function of target constriction degree in post-glossectomy speech
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Christina, Hagedorn, Yijing, Lu, Asterios, Toutios, Uttam, Sinha, Louis, Goldstein, and Shrikanth, Narayanan
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Pulmonary and Respiratory Medicine ,Pediatrics, Perinatology and Child Health ,cardiovascular system ,circulatory and respiratory physiology - Abstract
Individuals who have undergone treatment for oral cancer oftentimes exhibit compensatory behavior in consonant production. This pilot study investigates whether compensatory mechanisms utilized in the production of speech sounds with a given target constriction location vary systematically depending on target manner of articulation. The data reveal that compensatory strategies used to produce target alveolar segments vary systematically as a function of target manner of articulation in subtle yet meaningful ways. When target constriction degree at a particular constriction location cannot be preserved, individuals may leverage their ability to finely modulate constriction degree at multiple constriction locations along the vocal tract.
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- 2022
22. SIRT5 deficiency enhances the proliferative and therapeutic capacities of adipose‐derived mesenchymal stem cells via metabolic switching
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Wenlong Yang, Zhiwei Qiu, Kai Hu, Yufan Li, Zhen Dong, Hongming Zhu, Aijun Sun, Xinyu Weng, Zheng Dong, Junbo Ge, Suchi Chang, Yijing Lu, Wenjia Li, Hua Li, Tiantong Ou, and Xiaolei Sun
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0301 basic medicine ,Medicine (General) ,Glucose uptake ,metabolic switching ,Medicine (miscellaneous) ,Oxidative phosphorylation ,Pentose phosphate pathway ,03 medical and health sciences ,Protein succinylation ,R5-920 ,0302 clinical medicine ,SIRT5 ,Glycolysis ,Research Articles ,biology ,Chemistry ,Mesenchymal stem cell ,adipose‐derived mesenchymal stem cells ,hind limb ischemia ,Cell biology ,Transplantation ,cell proliferation ,030104 developmental biology ,030220 oncology & carcinogenesis ,Sirtuin ,biology.protein ,Molecular Medicine ,Research Article - Abstract
Background Mesenchymal stem cells (MSCs) have therapeutic potential for multiple ischemic diseases. However, in vitro expansion of MSCs before clinical application leads to metabolic reprogramming from glycolysis to oxidative phosphorylation, drastically impairing their proliferative and therapeutic capacities. This study aimed to define the regulatory effects of Sirtuin 5 (SIRT5) on the proliferative and therapeutic functions of adipose‐derived MSCs (ADMSCs) during in vitro expansion. Methods ADMSCs were isolated from wild‐type (WT) and Sirt5‐knockout (Sirt5−/−) mice. Cell counting assay was used to investigate the proliferative capacities of the ADMSCs. Dihydroethidium and senescence‐associated β‐galactosidase stainings were used to measure intracellular ROS and senescence levels. Mass spectrometry was used to analyze protein succinylation. Oxygen consumption rates and extra cellular acidification rates were measured as indicators of mitochondrial respiration and glycolysis. Metabolic‐related genes expression were verified by quantitative PCR and western blot. Hind limb ischemia mouse model was used to evaluate the therapeutic potentials of WT and Sirt5−/− ADSMCs. Results SIRT5 protein levels were upregulated in ADMCs during in vitro expansion. Sirt5−/− ADMSCs exhibited a higher proliferation rate, delayed senescence, and reduced ROS accumulation. Furthermore, elevated protein succinylation levels were observed in Sirt5−/− ADMSCs, leading to the reduced activity of tricarboxylic acid cycle‐related enzymes and attenuated mitochondrial respiration. Glucose uptake, glycolysis, and pentose phosphate pathway were elevated in Sirt5−/− ADMSCs. Inhibition of succinylation by glycine or re‐expression of Sirt5 reversed the metabolic alterations in Sirt5−/‐ ADMSCs, thus abolishing their enhanced proliferative capacities. In the hind limb ischemia mouse model, SIRT5−/− ADMSCs transplantation enhanced blood flow recovery and angiogenesis compared with WT ADMSCs. Conclusions Our results indicate that SIRT5 deficiency during ADMSC culture expansion leads to reversed metabolic pattern, enhanced proliferative capacities, and improved therapeutic outcomes. These data suggest SIRT5 as a potential target to enhance the functional properties of MSCs for clinical application.
- Published
- 2020
23. Dietary Cholesterol is Responsible for Statin-Induced Hepatic Toxicity in Experimental Hamsters and Chinese Cohort Studies
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Yijing Lu, George Liu, Yuhui Wang, Xunde Xian, Yunan Wang, Haozhe Shi, Junbo Ge, Jian An, Xiurui Ma, Zhen Dong, Aijun Sun, and Qiongyang Yu
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Statin ,Cholesterol ,business.industry ,medicine.drug_class ,Physiology ,Disease ,chemistry.chemical_compound ,chemistry ,Informed consent ,Pharmacogenomics ,LDL receptor ,Toxicity ,Medicine ,lipids (amino acids, peptides, and proteins) ,business ,Cohort study - Abstract
Background: Statins are the inhibitors of HMG-CoA reductase in cholesterol synthesis as widely used lipid-lowering drugs. The major side-effects of statins include muscle- and liver- related toxicity. Muscle-toxicity is highly associated with the polymorphism of CYP predictable by pharmacogenomics. However, the mechanisms of hepatotoxicity is not well understood. Due to the differences in cholesterol metabolism, statins are well tolerated in mice. In contrast, hamsters exhibit metabolic traits close to humans and would be suitable to study hepatotoxicity of statins. Methods: We investigated the effect of statins on liver damage in high cholesterol diet (HCD)-fed wild-type (WT) hamsters, LDLR knockout (LDLR -/- ) hamsters with spontaneous hypercholesterolemia. Two cohorts of clinical subjects (Clinical registry number: 2017001) on statins were recruited for direct (assessment of cholesterol intake individually, n=44) and indirect (party meal times/holiday season, n=1,993) examination of dietary cholesterol intake and liver damage indicated by elevation of ALT. Results: Statins at a dose of 10mg/kg caused fatal liver damage only in HCD-fed WT hamsters, while LDLR -/- hamsters with the same cholesterol levels were resistant to this toxic effect. In human studies, we observed that the incidence of hepatic toxicity in patients with a long-term statin treatment was higher in those who had more dietary cholesterol intake and in those who ate more during a Chinese holiday. Conclusions: Our results for the first time propose a hypothesis that dietary or exogenous, but not endogenous cholesterol, significantly contributes to the statin-related hepatotoxicity, then providing a valuable insight into the clinical use of statins. Funding: This project was supported by NSFC 31520103909 and 91739105 to G.L.; National KeyResearch and Development Program of China (2016YFE0126000), NSFC 81570787 and 81770449 to Y.W. G.L. is a fellow at the Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University. Declaration of Interest: The authors declare no conflict of interest. Ethical Approval: The study protocol was approved by the ethics committee of Shanxi Cardiovascular Hospital (Clinical registry number: 2017001), and the written informed consent was provided by each patient at the time of registration. All experimental procedures were conducted under the guide of Care and Use of Laboratory Animals published by the US National Institutes of Health (No.85Y23, revised 1996) and were approved by the Animal Care Committee of Peking University Health Science Center (LA2010-059)
- Published
- 2020
24. Effect of vocal tract morphology on tongue shaping for American English /ɹ
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Yijing Lu, Haley Hsu, Asterios Toutios, and Louis Goldstein
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medicine.anatomical_structure ,Acoustics and Ultrasonics ,Arts and Humanities (miscellaneous) ,Tongue ,business.industry ,American English ,medicine ,Morphology (biology) ,Anatomy ,business ,Vocal tract - Published
- 2021
25. Amide proton transfer (APT) and magnetization transfer (MT) in predicting short-term therapeutic outcome in nasopharyngeal carcinoma after chemoradiotherapy: a feasibility study of three-dimensional chemical exchange saturation transfer (CEST) MRI
- Author
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Wenguang Liu, Xiao Wang, Simin Xie, Weiyin Vivian Liu, Ismail Bilal Masokano, Yu Bai, Juan Chen, Linhui Zhong, Yijing Luo, Gaofeng Zhou, Wenzheng Li, and Yigang Pei
- Subjects
Chemical exchange saturation transfer ,Magnetization transfer ,Amide proton transfer imaging ,Nasopharyngeal carcinoma ,Chemoradiotherapy ,Medical physics. Medical radiology. Nuclear medicine ,R895-920 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background The three-dimensional chemical exchange saturation transfer (3D CEST) technique is a novel and promising magnetic resonance sequence; however, its application in nasopharyngeal carcinoma (NPC) lacks sufficient evaluation. This study aimed to assess the feasibility of the 3D CEST technique in predicting the short-term treatment outcomes for chemoradiotherapy (CRT) in NPC patients. Methods Forty NPC patients and fourteen healthy volunteers were enrolled and underwent the pre-treatment 3D CEST magnetic resonance imaging and diffusion-weighted imaging (DWI). The reliability of 3D CEST was assessed in healthy volunteers by calculating the intra- and inter-observer correlation coefficient (ICC) for amide proton transfer weighted-signal intensity (APTw-SI) and magnetization transfer ratio (MTR) values. NPC patients were divided into residual and non-residual groups based on short-term treatment outcomes after CRT. Whole-tumor regions of interest (ROIs) were manually drawn to measure APTw-SI, MTR and apparent diffusion coefficient (ADC) values. Multivariate analysis and the receiver operating characteristic curve (ROC) were used to evaluate the prediction performance of clinical characteristics, APTw-SI, MTR, ADC values, and combined models in predicting short-term treatment outcomes in NPC patients. Results For the healthy volunteer group, all APTw-SI and MTR values exhibited good to excellent intra- and inter-observer agreements (0.736–0.910, 0.895–0.981, all P > 0.05). For NPC patients, MTR values showed a significant difference between the non-residual and residual groups (31.24 ± 5.21% vs. 34.74 ± 1.54%, P = 0.003) while no significant differences were observed for APTw-SI and ADC values (P > 0.05). Moreover, the diagnostic power of MTR value was superior to APTw-SI (AUC: 0.818 vs. 0.521, P = 0.017) and comparable to ADC values (AUC: 0.818 vs. 0.649, P > 0.05) in predicting short-term treatment outcomes for NPC patients. The prediction performance did not improve even when combining MTR values with APTw-SI and/or ADC values (P > 0.05). Conclusions The pre-treatment MTR value acquired through 3D CEST demonstrated superior predictive performance for short-term treatment outcomes compared to APTw-SI and ADC values in NPC patients after CRT.
- Published
- 2023
- Full Text
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26. Kaistella flava sp. nov., isolated from Antarctic tundra soil, and emended descriptions of Kaistella yonginensis, Kaistella jeonii, Kaistella antarctica and Kaistella chaponensis
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Lu Lu, Jia Liu, Fang Peng, Kun Qin, Chengjie Kuang, Yijing Lu, Yumin Zhang, Xueyin Zhou, Zhourui Wei, Yulin Sun, Yingchao Geng, and Xiaoya Peng
- Subjects
Kaistella flava ,Phylogenetic tree ,Strain (chemistry) ,Botany ,Family Flavobacteriaceae ,Taxonomy (biology) ,General Medicine ,Biology ,16S ribosomal RNA ,Microbiology ,Ecology, Evolution, Behavior and Systematics ,Antarctic Tundra ,Terpenoid - Abstract
A rod-shaped, yellow-pigmented, Gram-stain-negative, non-motile and aerobic bacterium, designated 7-3AT, was isolated from soil from King George Island, maritime Antarctica, and subjected to a polyphasic taxonomic study. Growth occurred at 4–37 °C (optimum, 20°C) and at pH 5.0–9.0 (optimum, pH 7.0–8.0). Tolerance to NaCl was up to 4 % (w/v) with optimum growth in the absence of NaCl. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 7-3AT represented a member of the family Flavobacteriaceae . Strain 7-3AT showed the highest sequence similarities with Kaistella yonginensis HMD 1043T (96.65 %), Kaistella carnis NCTC 13525T (96.53 %), Kaistella chaponensis DSM 23145T (96.27 %), Kaistella antarctica LMG 24720T (96.13 %) and Kaistella jeonii DSM 17048T (96.06 %). A whole genome-level comparison of 7-3AT with K. jeonii DSM 17048T, K. antarctica LMG 24720T, K. chaponensis DSM 23145T, and Kaistella palustris DSM 21579T revealed average nucleotide identity (ANI) values of 79.03, 82.25, 78.12, and 74.42 %, respectively. The major respiratory isoprenoid quinone was identified as MK-6 and a few ubiquinones Q-10 were identified. In addition, flexirubin-type pigments were absent. The polar lipid profile of 7-3AT was found to contain one phosphatidylethanolamine, six unidentified aminolipids (AL) and two unidentified lipids (L). The G+C content of the genomic DNA was determined to be 34.54 mol%. The main fatty acids were iso-C15 : 0, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl), anteiso-C15 : 0, iso-C13 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). On the basis of the evidence presented in this study, a novel species of the genus Kaistella , Kaistella flava sp. nov., is proposed, with the type strain 7-3AT (=CCTCC AB 2016141T= KCTC 52492T). Emended descriptions of Kaistella yonginensis , Kaistella jeonii , Kaistella antarctica and Kaistella chaponensis are also given.
- Published
- 2019
27. Imputing trip purposes for long-distance travel
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Lei Zhang and Yijing Lu
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Engineering ,Data collection ,business.industry ,Decision tree ,Poison control ,Transportation ,Development ,Transport engineering ,Travel behavior ,Travel survey ,Information model ,Global Positioning System ,Imputation (statistics) ,business ,Civil and Structural Engineering - Abstract
Planning and policy analysis at the national, state and inter-regional corridor levels depends on reliable information and forecasts about long-distance travel. Emerging passive data collection technologies such as GPS, smartphones, and social media provide the opportunity for researchers and practitioners to potentially supplement or replace traditional long-distance travel surveys. However, certain important trip information, such as trip purpose, travel mode, and travelers’ socio-demographic characteristics, is missing from passively collected travel data. One promising solution to this data issue is to impute the missing information based on supplementary data (e.g., land use) and advanced statistical or data mining algorithms. This paper develops machine learning methods, including decision tree and meta-learning, to estimate trip purposes for long-distance passenger travel. A passively collected long-distance trip dataset is simulated from the 1995 American Travel Survey for the development and validation of the machine learning methods. The predictive accuracy of the proposed methods is evaluated for several scenarios varying with trip purposes and the extent of data availability as inputs. This research design will provide not only a practically useful approach for long-distance trip purpose imputation, but also generate valuable insights for future long-distance travel surveys. Results show that the accuracy of the trip purpose imputation methods based on all available data decreases from 95 % with two purposes (business and non-business) to 77 % with four purposes (business, personal business, social visit, and leisure). Based on a two-purpose scheme, the predictive accuracy of the imputation algorithms decreases from 95 % when all input data is used (a full-information model), to 72 % with a minimum information model that only utilizes the passively collected data. If traveler’s socio-demographic characteristics are available (possibly through other imputation models), the predictive accuracy only decreases from 95 to 91 %.
- Published
- 2015
28. Are we successful in reducing vehicle miles traveled in air quality nonattainment areas?
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Lei Zhang, Xiang He, Nick Ferrari, Yijing Lu, and Cory Krause
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education.field_of_study ,Transportation planning ,Short run ,Population ,Transportation ,Management Science and Operations Research ,Structural equation modeling ,Simultaneous equations model ,Transport engineering ,Urbanization ,Vehicle miles of travel ,Environmental science ,education ,Air quality index ,Civil and Structural Engineering - Abstract
An important planning and policy question in the transportation, energy, and environment areas is whether or not air quality control and the associated funding preference and mitigation efforts to attain air quality conformity have indeed led to traveler behavior changes such as reduction in vehicle miles traveled (VMT) or VMT growth rates. In this research, we develop statistical models to analyze the relationship between air quality nonattainment designation and VMT between 1966 and 2004 based on observed data. These models employ different statistical methods, including hypothesis testing and simultaneous equations. Findings from these statistical models and datasets are consistent, and suggest there is a statistically significant negative correlation between nonattainment designation and VMT/VMT growth. For instance, the simultaneous equation model in this research, suggests that if a nonattainment area and an attainment area that are similar in all other aspects (population composition, socio-economics, urbanization, fuel price, vehicle stock, etc.) are compared, the VMT in the nonattainment area will be 1.80% less than that in the attainment area in the short run, and 7.61% less in the long run. While these results show strong statistical evidence that efforts in reducing VMT in nonattainment areas have been successful, future research should be conducted to attribute the VMT reduction effects to specific policy instruments for decision-making (e.g. the Congestion Management and Air Quality Improvement program, the conformity regulation in the transportation planning process, etc.).
- Published
- 2014
29. Retail Fuel Price Stabilization and Revenue Generation of Dynamic Taxation Policy
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Yiwen Zhu, Yijing Lu, Shin-pei Tsay, and Lei Zhang
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Finance ,Solvency ,business.industry ,Mechanical Engineering ,Equity (finance) ,Policy analysis ,Microeconomics ,Econometric model ,Travel behavior ,Revenue model ,Greenhouse gas ,Economics ,Revenue ,business ,Civil and Structural Engineering - Abstract
The Carnegie Endowment for International Peace (CEIP), through its Leadership Initiative for Transportation Solvency, in 2011 released Road to Recovery: Transforming America's Transportation, a report that proposed a new revenue mechanism to fund a reformed transportation program fully. The report recommends that Congress couple a per barrel oil fee with a variable, countercyclical gas tax. This paper discusses the dynamic impacts of CEIP's revenue policy on household travel behavior, revenue generation for the federal trust fund, energy consumption, equity, and greenhouse gas (GHG) emissions and air pollution at the national level from 2008 to 2010. The analysis developed econometric models: a multiple vehicle miles traveled (VMT) regression model and a discrete vehicle ownership model. Model results showed that the CEIP revenue proposal could fill the revenue shortfall regardless of the world oil price. During the historic study period of 2008 to 2010, the CEIP policy would have collected up to more than double the federal revenue. At the same time, households would have increased their VMT by as much as 1.8% when oil prices peaked, and reduced their VMT by up to 8.6% when the crude oil price dropped to the lowest point. It is estimated that, without any investments or revenue recycling, lower-income households would have experienced a 0.45% to 0.5% reduction in consumer surplus changes measured as a percentage of income and higher-income households would have experienced a 0.06% to 0.1% reduction. Finally, it is estimated that the CEIP policy would have reduced air pollution and GHG emissions by an average 4% to 4.35% for different pollutant types.
- Published
- 2013
30. Implementing Marginal-Cost Vehicle Mileage Fees on the Maryland Statewide Road Network
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Yijing Lu and Lei Zhang
- Subjects
Marginal cost ,Truck ,Engineering ,business.industry ,Mechanical Engineering ,User fee ,Transport engineering ,Travel behavior ,Traffic congestion ,Vehicle miles of travel ,Revenue ,business ,Externality ,Civil and Structural Engineering - Abstract
Properly structured vehicle mileage fee systems may help transportation professionals and officials at all levels address prominent issues such as funding gaps, traffic congestion, and emissions. In theory, vehicles should be assessed a user fee equivalent to the full marginal cost not borne by users. The full marginal cost of auto and truck travel in different time periods on all roadways in Maryland was estimated. The study evaluated the impacts of such marginal-cost vehicle miles traveled (VMT) fees on travel behavior, revenue generation, equity, pollution, and greenhouse gas emissions in Maryland and the surrounding states of Delaware, Pennsylvania, Virginia, and West Virginia, and the District of Columbia. Results showed that with consideration of all driving externalities, the marginal-cost VMT fee for travel in Maryland during peak periods ranged from 0.20 to about 12.16 cents/mi and from 3.91 to about 45.33 cents/mi for cars and trucks, respectively. Compared with existing revenue policy, the marginal-cost VMT fee could reduce overall VMT by 7.65% in the multistate region covered by the quantitative model and by 7.81% just in Maryland. Also, air pollution and greenhouse gas emissions in Maryland could be reduced by 7.62% to 9.42% by pollutant type. Total revenue generation would increase by about 168% (including fuel taxes and bridge and roadway tolls). In regard to income equity, the middle-income group would be hurt most (largest consumer surplus decrease), while the highest-income group would be hurt least. Results also indicated that the proposed marginal-cost VMT fee in Maryland could affect neighboring states to varying degrees.
- Published
- 2013
31. Service Package Recommendation for Mashup Development Based on a Multi-level Relational Network
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Nengjun Zhu, Jian Cao, and Yijing Lu
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Service (business) ,Branch and bound ,Database ,Computer science ,Quadratic knapsack problem ,02 engineering and technology ,computer.software_genre ,Development (topology) ,020204 information systems ,0202 electrical engineering, electronic engineering, information engineering ,020201 artificial intelligence & image processing ,Data set (IBM mainframe) ,Mashup ,computer - Abstract
With the number of services growing explosively, it has been a serious problem selecting appropriate services for mashup development. In this paper, we come up with a Multi-level Relational Network (MRN) based approach for service recommendation in mashup development, which captures deep relationships among services on top of latent topic, tag and service network. Specifically, by modeling the correlation among services, representing it as a Quadratic Knapsack Problem and solving it using Branch and Bound algorithm, we are able to recommend a package of services, which are complementary and possible to be used together in a mashup. Experiments on a realistic mashup data set have shown its effectiveness.
- Published
- 2016
32. Marginal-Cost Vehicle Mileage Fee
- Author
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Lei Zhang and Yijing Lu
- Subjects
Marginal cost ,Discrete choice ,Actuarial science ,Mechanical Engineering ,Fuel tax ,Vehicle miles of travel ,Fuel efficiency ,Revenue ,Road pricing ,Business ,Environmental economics ,Civil and Structural Engineering ,Corporate Average Fuel Economy - Abstract
The vehicle mileage fee is a strong candidate to mitigate the funding gap in surface transportation caused by the declining purchasing power of fuel tax revenue, the emergence of hybrid and electric vehicles, and more restrictive corporate average fuel economy standards. This study computes the vehicle mileage fee on the basis of the marginal cost of travel and internalizes various externalities such as congestion, infrastructure deterioration, pollution emissions, and greenhouse gas emissions. Multiple regression models and discrete choice models are developed on the basis of the 2009 National Household Travel Survey data to analyze the impacts of the proposed marginal-cost vehicle mileage fee on vehicle ownership, fuel efficiency, vehicle miles traveled, energy consumption, emissions, and equity. In addition, the sensitivity of these impacts to exogenous fuel price volatility is estimated quantitatively. Results show that with consideration of all aforementioned externalities, the marginal-cost vehicle mileage fee by vehicle make and model would range from 7.7 to 9.1 cents/mi, which is much higher than the per mile equivalent of the current fuel taxes (about 1.2 cents/mi). Household vehicle use behavior is much more sensitive to the marginal-cost vehicle mileage fee than vehicle ownership decisions, with a significant (27.1%) reduction in vehicle miles traveled, but a minor increase in vehicle fuel efficiency (up to 4.2%). Nevertheless, the marginal-cost vehicle mileage fee can reduce energy consumption and pollution or greenhouse gas emissions by about a fourth. These sustainability benefits are even more significant if fuel prices continue to increase. Without consideration of the benefits from revenue redistribution, lower-income households, as expected, would be hurt more than higher-income households (1.3%).
- Published
- 2012
33. Homology Modeling of α-Glucosidase and its Interactions with Andrograpolide Derivatives
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Weizai Shen, Haibin Luo, Yijing Lu, Sichao Huang, Jun Xu, Jiaolin Bao, Shaohui Cai, and Yuqiang Wang
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Stereochemistry ,Chemistry ,α glucosidase ,Drug Discovery ,Pharmaceutical Science ,Molecular Medicine ,Homology modeling - Published
- 2011
34. STAT3-Mediated Promoter-Enhancer Interaction Up-Regulates Inhibitor of DNA Binding 1 (ID1) to Promote Colon Cancer Progression
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Zhike Lin, Ying Liu, Tian Xu, Ting Su, Yingying Yang, Runhua Liang, Songgang Gu, Jie Li, Xuhong Song, Bin Liang, Zhijun Leng, Yangsihan Li, Lele Meng, Yijing Luo, Xiaolan Chang, Dongyang Huang, and Lingzhu Xie
- Subjects
ID1 ,enhancer ,STAT3 ,colon cancer ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Background: High expression of inhibitor of DNA binding 1 (ID1) correlates with poor prognosis in colorectal cancer (CRC). Aberrant enhancer activation in regulating ID1 transcription is limited. Methods: Immunohistochemistry (IHC), quantitative RT-PCR (RT-qPCR) and Western blotting (WB) were used to determine the expression of ID1. CRISPR-Cas9 was used to generate ID1 or enhancer E1 knockout cell lines. Dual-luciferase reporter assay, chromosome conformation capture assay and ChIP-qPCR were used to determine the active enhancers of ID1. Cell Counting Kit 8, colony-forming, transwell assays and tumorigenicity in nude mice were used to investigate the biological functions of ID1 and enhancer E1. Results: Human CRC tissues and cell lines expressed a higher level of ID1 than normal controls. ID1 promoted CRC cell proliferation and colony formation. Enhancer E1 actively regulated ID1 promoter activity. Signal transducer and activator of transcription 3 (STAT3) bound to ID1 promoter and enhancer E1 to regulate their activity. The inhibitor of STAT3 Stattic attenuated ID1 promoter and enhancer E1 activity and the expression of ID1. Enhancer E1 knockout down-regulated ID1 expression level and cell proliferation in vitro and in vivo. Conclusions: Enhancer E1 is positively regulated by STAT3 and contributes to the regulation of ID1 to promote CRC cell progression and might be a potential target for anti-CRC drug studies.
- Published
- 2023
- Full Text
- View/download PDF
35. Analyses on Flavonoids and Transcriptome Reveals Key MYB Gene for Proanthocyanidins Regulation in Onobrychis Viciifolia
- Author
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Zhongzhiyue Jin, Wenbo Jiang, Yijing Luo, Haijun Huang, Dengxia Yi, and Yongzhen Pang
- Subjects
Onobrychis viciifolia ,flavonoids ,proanthocyanidins ,transcriptome ,OvMYBPA2 ,Plant culture ,SB1-1110 - Abstract
Onobrychis viciifolia (sainfoin) is one of the most high-quality legume forages, which is rich in proanthocyanidins that is beneficial for the health and production of animals. In this study, proanthocyanidins and total flavonoids in leaves of 46 different sainfoin germplasm resources were evaluated, and it showed that soluble proanthocyanidin contents varied greatly in these sainfoin germplasm resources, but total flavonoids did not show significant difference. Transcriptome sequencing with high and low proanthocyanidins sainfoin resulted in the identification of totally 52,926 unigenes in sainfoin, and they were classed into different GOC categories. Among them, 1,608 unigenes were differentially expressed in high and low proanthocyanidins sainfoin samples, including 1,160 genes that were upregulated and 448 genes that were downregulated. Analysis on gene enrichment via KEGG annotation revealed that the differentially expressed genes were mainly enriched in the phenylpropanoid biosynthetic pathway and the secondary metabolism pathway. We also analyzed the expression levels of structural genes of the proanthocyanidin/flavonoid pathway in roots, stems, and leaves in the high proanthocyanidin sainfoin via RT-qPCR and found that these genes were differentially expressed in these tissues. Among them, the expression levels of F3'5'H and ANR were higher in leaves than in roots or stems, which is consistent with proanthocyanidins content in these tissues. Among MYB genes that were differentially expressed, the expression of OvMYBPA2 was relatively high in high proanthocyanidin sainfoin. Over-expression level of OvMYBPA2 in alfalfa hairy roots resulted in decreased anthocyanin content but increased proanthocyanidin content. Our study provided transcriptome information for further functional characterization of proanthocyanidin biosynthesis-related genes in sainfoin and candidate key MYB genes for bioengineering of proanthocyanidins in plants.
- Published
- 2022
- Full Text
- View/download PDF
36. The complete chloroplast genome of Agropyron pectinatum (M. Bieb.) P. Beauv.
- Author
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Yijing Luo, Junfeng Yang, Wenxuan Du, and Yongzhen Pang
- Subjects
agropyron pectinatum ,chloroplast genome ,Genetics ,QH426-470 - Abstract
Agropyron pectinatum is a perennial forage widely cultivated in China, and it belongs to the Gramineous family. In this study, we assembled the complete chloroplast genome of A. pectinatum. The whole chloroplast genome of A. pectinatum is 135,041 bp in length, comprising a pair of inverted repeat (IR) regions (20,821 bp) that are separated by a large single copy (LSC) region (80,632 bp) and a small single copy (SSC) region (12,767 bp). The chloroplast genome of A. pectinatum contains 133 genes, and 87 of them are protein-coding genes, 38 are tRNA, and eight are rRNA genes. The chloroplast genome of A. pectinatum could provide valuable information for varieties identification and evolution of the Agropyron Gaertn.
- Published
- 2021
- Full Text
- View/download PDF
37. Identification and Characterization of Salt- and Drought-Responsive AQP Family Genes in Medicagosativa L.
- Author
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Yijing Luo, Lin Ma, Wenxuan Du, Su Yan, Zengyu Wang, and Yongzhen Pang
- Subjects
Medicago sativa ,AQP genes ,salt and drought stresses ,aquaporin ,phylogenetic analysis ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Aquaporins (AQP) are distributed ubiquitously in plants, and they play important roles in multiple aspects of plant growth and development, as well as in plant resistance to various environmental stresses. In this study, 43 MsAQP genes were identified in the forage crop Medicago sativa. All the MsAQP proteins were clustered into four subfamilies based on sequence similarity and phylogenetic relationship, including 17 TIPs, 14 NIPs, 9 PIPs and 3 SIPs. Analyses of gene structure and conserved domains indicated that the majority of the deduced MsAQP proteins contained the signature transmembrane domains and the NPA motifs. Analyses on cis-acting elements in the promoter region of MsAQP genes revealed the presence of multiple and diverse stress-responsive and hormone-responsive cis-acting elements. In addition, by analyzing the available and comprehensive gene expression data of M. truncatula, we screened ten representative MtAQP genes that were responsive to NaCl or drought stress. By analyzing the sequence similarity and phylogenetic relationship, we finally identified the corresponding ten salt- or drought-responsive AQP genes in M. sativa, including three MsTIPs, three MsPIPs and four MsNIPs. The qPCRs showed that the relative expression levels of these ten selected MsAQP genes responded differently to NaCl or drought treatment in M. sativa. Gene expression patterns showed that most MsAQP genes were preferentially expressed in roots or in leaves, which may reflect their tissue-specific functions associated with development. Our results lay an important foundation for the future characterization of the functions of MsAQP genes, and provide candidate genes for stress resistance improvement through genetic breeding in M. sativa.
- Published
- 2022
- Full Text
- View/download PDF
38. Methane production pathway in biogas reservoirs via molecular biological technique
- Author
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Xiaofang WEI, Jishun QIN, Yanhua SHUAI, Keyu LIU, Yijing LUO, Yanyao SHI, and Shuguang ZHANG
- Subjects
Petroleum refining. Petroleum products ,TP690-692.5 - Abstract
In order to investigate the microbes in formation water samples from Well Du 6-3 and Ao-7 in the Alaxin and Aonan gas fields, Songliao Basin, China, 16S rDNA was amplified by using the Polymerase Chain Reaction (PCR) technique with templates of the extracted DNA and primers of bacteria and archaea. The PCR products were also inserted into vectors and then ligated with competent cells for gene sequencing. Based on the obtained gene sequences, bacterial and archaeal libraries were constructed and microbiological phylogeny graphs were obtained for the samples to understand the structure of microbial community and deduce the possible pathways of methanogenesis. The result indicates that there are only a few types of microbes in the samples of the two wells. Pseudomonas and Methanobacterium are the dominant species in the microbial and archaeal libraries, respectively. It is concluded that the indigenous microbial community in Well Du 6-3 probably mainly generated methane by CO2 reduction, but methanogenesis of acetic acid could not be completely excluded. The methane from Well Ao-7 is shown to have been definitely converted from CO2. Therefore, methane generation via indigenous microbial metabolism may be ultimately realized by using the right method under favourable conditions in the two fields. Key words: biogas reservoir, polymerase chain reaction (PCR), methane bio-pathway, 16S rRNA clone library
- Published
- 2012
- Full Text
- View/download PDF
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