68 results on '"Linhua Wang"'
Search Results
2. Endoscopic-Assisted Trans-Lateral Ventricular Transchoroidal Fissure Trans-Aqueductal Approach for Evacuation of Severe Intraventricular Hemorrhage
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Huaiyu Sun, Yue Wang, Linhua Wang, Huachao Li, and Tingzhong Wang
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Surgery ,Neurology (clinical) - Abstract
Intraventricular hemorrhage (IVH) is one of the most fatal types of intracerebral hemorrhage (ICH), especially when the third and the fourth ventricles are involved. The use of external ventricular drainage is limited for evacuation of hemorrhage in the lateral ventricles. Endoscopic surgery can provide visualized evacuation of the hemorrhage in the lateral and third ventricles. However, it is usually challenging to access the fourth ventricle using a routine endoscopic approach.We have reported 3 cases of severe IVH with cast fourth ventricles treated using an endoscopic-assisted trans-lateral ventricular transchoroidal fissure trans-aqueductal approach.The average preoperative Graeb score was 11, and the average IVH volume was 75.12 mL. The IVH evacuation rate was 97.5%-100%. The average Glasgow coma scale score had increased to 12 at discharge from 6.6 at admission. At 3 months after surgery, the average modified Rankin scale score was 3. No cerebrospinal fluid shunt had been required and no surgery-related complication had occurred in any patient.Our results have shown that the endoscopic-assisted trans-lateral ventricular transchoroidal fissure trans-aqueductal approach is a feasible and safe endoscopic option that can achieve one-off complete removal of clots in all 4 ventricles in patients with severe IVH.
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- 2022
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3. Erosion and covered zones altered by surface coverage effects on soil nitrogen and carbon loss from an agricultural slope under laboratory-simulated rainfall events
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Linhua Wang, Haw Yen, Chi-hua Huang, and Yafeng Wang
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Soil Science ,Agronomy and Crop Science ,Nature and Landscape Conservation ,Water Science and Technology - Published
- 2022
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4. Planar Tetraindolodipleiadiene via Zirconium-Promoted Intramolecular Indolyl C4–H Homocoupling
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Xuesong Zheng, Zhenmei Huang, Qinze Zheng, Linhua Wang, Cheng Zhang, and Ge Gao
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Organic Chemistry ,Physical and Theoretical Chemistry ,Biochemistry - Abstract
A novel N-rimmed PAH molecule containing a dipleiadiene core (
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- 2022
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5. Thioether-Assisted Cu-Catalyzed C5–H Arylation of Imidazo[1,5-a]pyridines
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Linhua Wang, Xuesong Zheng, Qinze Zheng, Zhenlong Li, Jian Wu, and Ge Gao
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Organic Chemistry ,Physical and Theoretical Chemistry ,Biochemistry - Published
- 2022
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6. A prototype of benzobis(imidazolium)-embedded conjugated polyelectrolyte: Synthesis by direct C‒H arylation and fluorescent responses to anions
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Ge Gao, Linhua Wang, Tianbao Wang, Qinze Zheng, Xuesong Zheng, and Chuangui Yu
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Conjugated polyelectrolyte ,Bisulfite ,chemistry.chemical_compound ,Monomer ,chemistry ,Comonomer ,Cationic polymerization ,General Chemistry ,Naked eye ,Conjugated system ,Photochemistry ,Fluorescence - Abstract
We report the convenient synthesis of a benzobis(imidazolium)-embedded conjugated polyelectrolyte pBBI by a Cu-catalyzed direct C‒H arylation of a cationic benzobis(imidazolium) monomer with a diiodide comonomer. pBBI shows weak fluorescence in solution due to rotation of the repeat units in the conjugated backbone, and enhanced fluorescence when electrostatically interacting with a variety of anions to form aggregates. Specially, pBBI responds to the bisulfite anion with intensified unique deep-blue fluorescence easily discriminated by naked eye.
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- 2022
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7. Comparison of the Diagnostic Accuracy of Xpert MTB/RIF and CapitalBio Mycobacterium RT-PCR Detection Assay for Tuberculous Pericarditis
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Guocan Yu, Linhua Wang, Yanqin Shen, Likui Fang, Jun Yang, Bo Ye, Kan Xu, and Fangming Zhong
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Pharmacology ,Infectious Diseases ,Infection and Drug Resistance ,Pharmacology (medical) - Abstract
Guocan Yu,1,* Linhua Wang,2 Yanqin Shen,1 Likui Fang,1 Jun Yang,1 Bo Ye,1 Kan Xu,1 Fangming Zhong1,* 1Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, Peopleâs Republic of China; 2Department of Hospital Infection, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, Peopleâs Republic of China*These authors contributed equally to this workCorrespondence: Guocan Yu; Fangming Zhong, Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, Peopleâs Republic of China, Email dabaitwo@163.com; zhongfangm@126.comPurpose: We evaluated CapitalBio Mycobacterium RT-PCR assay diagnosing tuberculous pericarditis (TBP), performed a head-to-head comparison with Xpert MTB/RIF, and assessed the impact of a parallel test (positive result for either of these two tests).Methods: We reviewed suspected TBP patients with Xpert MTB/RIF, CapitalBio Mycobacterium RT-PCR assay, and Mycobacterium tuberculosis (MTB) culture. We analyzed sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the curve (AUC).Results: Seventy-four patients were included. Overall sensitivity, specificity, PPV, NPV, and AUC of CapitalBio Mycobacterium RT-PCR assay compared with culture were 50%, 91.1%, 64.3%, 85%, and 0.71, respectively. Overall sensitivity, specificity, PPV, NPV, and AUC of Xpert MTB/RIF for TBP were 61.1%, 91.1%, 68.8%, 87.9%, and 0.76. Parallel test values were 72.2%, 91.1%, 72.2%, 91.1%, and 0.82. The diagnostic accuracy of Xpert MTB/RIF was higher than CapitalBio Mycobacterium RT-PCR assay but was not significant (P > 0.05). The parallel test could improve diagnostic accuracy, but it was not significant compared to single tests (P > 0.05).Conclusion: CapitalBio Mycobacterium RT-PCR assay had a moderate diagnostic accuracy, similar to Xpert MTB/RIF. The parallel test maximized diagnostic efficacy, but differences were not significant. CapitalBio Mycobacterium RT-PCR assay and Xpert MTB/RIF for TBP could be an initial option for early diagnosis.Keywords: tuberculosis pericarditis, polymerase chain reaction, Xpert MTB/RIF, CapitalBio, accuracy
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- 2022
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8. Correction: Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss
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Chaozhong Liu, Linhua Wang, and Zhandong Liu
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Structural Biology ,Applied Mathematics ,Molecular Biology ,Biochemistry ,Computer Science Applications - Published
- 2023
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9. Automatic Classification of Mass Shape and Margin on Mammography with Artificial Intelligence: Deep CNN Versus Radiomics
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Longxiu Qi, Xing Lu, Hailin Shen, Qilei Gao, Zhigang Han, Jianguo Zhu, You Meng, Linhua Wang, Shuangqing Chen, and Yonggang Li
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Radiological and Ultrasound Technology ,Radiology, Nuclear Medicine and imaging ,Computer Science Applications - Published
- 2023
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10. Synthesis of cationic π-extended imidazolium salts by sequential Cu-catalyzed arylation/annulation and photocyclization
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Tianbao Wang, Qinze Zheng, Linhua Wang, Zhenmei Huang, Huaxing Zhang, Yuming Zhang, Cheng Zhang, and Ge Gao
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Materials Chemistry ,Metals and Alloys ,Ceramics and Composites ,General Chemistry ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials - Abstract
A series of cationic π-extended imidazolium salts were synthesized by a sequential Cu-catalyzed arylation/annulation and photocyclization strategy in a simple but efficient way. Among them, a nine-fused-ring compound with a doubly aza[5]helical geometry is by far the largest cationic polycyclic heteroaromatic with a central imidazolium core.
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- 2022
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11. scGREAT: Graph-based regulatory element analysis tool for single-cell multi-omics data
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Chaozhong Liu, Linhua Wang, and Zhandong Liu
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Article - Abstract
MotivationWith the development in single-cell multi-omics sequencing technology and data integration algorithms, we have entered the single-cell multi-omics era. Current multi-omics analysis algorithms failed to systematically dissect the heterogeneity within the datasets when inferring cis-regulatory events. Thus, there is a need for cis-regulatory element inferring algorithms that considers the cellular heterogeneity.ResultsHere, we propose scGREAT, a single-cell multi-omics regulatory state analysis Python package with a rapid graph-based correlation measurementL. The graph-based correlation method assigns each cell a localLindex, pinpointing specific cell groups of certain regulatory states. Such single-cell resolved regulatory state information enables the heterogeneity analysis equipped in the package. Applying scGREAT to the 10X Multiome PBMC dataset, we demonstrated how it could help subcluster cell types, infer regulation-based pseudo-time trajectory, discover feature modules, and find cluster-specific regulatory gene-peak pairs. Besides, we showed that global L index, which is the average of all local L values, is a better replacement for Pearson’s r in ruling out confounding regulatory relationships that are not of research interests.Availabilityhttps://github.com/ChaozhongLiu/scGREAT
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- 2023
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12. Study on the treatment of postmenopausal osteoporosis with quercetin in Liuwei Dihuang Pill based on network pharmacology
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Fuping Zhu, Wuping Li, Linhua Wang, Bing Dai, Zongyi Liu, Hang Wu, and Ting Deng
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Orthopedics and Sports Medicine ,Surgery - Abstract
Background Liuwei Dihuang Pill (LP) was verified to alleviate postmenopausal osteoporosis (PMOP) development. Nevertheless, the major constituent of LP and the related network pharmacology study remain unexplored. Methods Protein–protein interaction was established to identify the downstream target of LP in PMOP, and the related signaling pathway was investigated by bioinformatics analysis. MC3T3-E1 cells were added to ferric ammonium citrate (FAC) to mimic osteoporosis in vitro. The osteoblasts were identified by Alizarin red staining. Western blot was applied to evaluate protein levels. In addition, Cell Counting Kit-8 (CCK8) assay was applied to assess cell viability, and cell apoptosis was assessed by flow cytometry. Results Quercetin was the major constituent of LP. In addition, quercetin significantly reversed FAC-induced inhibition of osteogenic differentiation in MC3T3-E1 cells. In addition, quercetin notably abolished the FAC-induced upregulation of Bax, Caspase-3, FOS, JUN, TGFB1 and PPARD. In contrast, Bcl-2, p-mTOR/mTOR, p-AKT/AKT and p-PI3K/PI3K levels in MC3T3-E1 cells were reduced by FAC, which was restored by quercetin. Meanwhile, FAC notably inhibited the viability of MC3T3-E1 cells via inducing apoptosis, but this impact was abolished by quercetin. Furthermore, quercetin could reverse pcDNA3.1-FOS-mediated growth of FAC-treated osteoblasts by mediating PI3K/AKT/mTOR signaling. Conclusion Quercetin alleviated the progression of PMOP via activation of PI3K/AKT/mTOR signaling. Hence, this study would shed novel insights into discovering new methods against PMOP.
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- 2023
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13. Accurate cell type deconvolution in spatial transcriptomics using a batch effect-free strategy
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Linhua Wang, Ling Wu, Chaozhong Liu, Wanli Wang, Xiang H.-F. Zhang, and Zhandong Liu
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Sequencing-based spatial transcriptomics (ST) techniques have been groundbreaking in dissecting cell-cell communications within tissues by profiling positional gene expression. However, the most widely used ST technique, Visium Spatial Gene Expression by 10x Genomics (Visium), does not provide single-cell resolution, making it difficult to profile cell type-level information. Many reference-based deconvolution methods have been developed to increase its resolution, but the platform and batch effects between the reference and ST data compromise their accuracy. Here, we propose a new approach,Region-based cellSorting (ReSort), that generates a pseudo-internal-reference to reduce these platform effects. By simulating ST datasets under various scenarios, we demonstrate that ReSort significantly improves the accuracy of six state-of-the-art reference-based deconvolution methods. Moreover, applying ReSort to a mouse breast cancer tumor bearing both epithelial and mesenchymal clones identifies the spatial differences of immune cells between the clones, providing important insights for understanding the relationship between epithelial-mesenchymal transition and immune infiltration in breast cancer.
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- 2022
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14. Latent factor in Brain RNA-seq studies reflects cell type and clinical heterogeneity
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Rami Al-Ouran, Chaozhong Liu, Linhua Wang, Ying-Wooi Wan, Xiqi Li, Aleksandar Milosavljevic, Joshua M. Shulman, and Zhandong Liu
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With the growing availability of Alzheimer’s disease (AD) transcriptomic data, several studies have nominated new therapeutic targets. However, a major challenge is accounting for latent (hidden) factors which affect the discovery of therapeutic targets. Using unsupervised machine learning, we identified a latent factor in brain tissue, and we validated the factor in AD and normal samples, across multiple studies, and different brain tissues. Moreover, significant metabolic differences were observed due to the latent factor. The latent factor was found to reflect cell-type heterogeneity in the brain and after adjusting for it, we were able to identify new biological pathways. The changes observed at both transcriptomic and metabolomic levels support the importance of identifying any latent factors before pursuing downstream analysis to accurately identify biomarkers.
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- 2022
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15. Nodakenin attenuates cartilage degradation and inflammatory responses in a mice model of knee osteoarthritis by regulating mitochondrial Drp1/ROS/NLRP3 axis
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Nanxing Yi, Yilin Mi, Xiaotong Xu, Naping Li, Baiyi Chen, Ke Yan, Kaiyun Tan, Bo Zhang, Linhua Wang, Gaoyan Kuang, and Min Lu
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Pharmacology ,Cartilage, Articular ,Dynamins ,Immunology ,Osteoarthritis, Knee ,Mitochondria ,Mice ,Disease Models, Animal ,Chondrocytes ,Coumarins ,NLR Family, Pyrin Domain-Containing 3 Protein ,Immunology and Allergy ,Animals ,Reactive Oxygen Species - Abstract
Osteoarthritis (OA) is a common degenerative disease with few treatments. In traditional Chinese medicine (TCM), Radix Angelicae biseratae (RAB) is commonly used to treat OA. Nodakenin (Nod) is one main coumarin active component in RAB and exhibits anti-inflammatory, anti-oxidative, and anti-apoptotic effects. Reactive oxygen species (ROS) produced by mitochondria play a vital role in the pathogenesis of OA. We hypothesized that Nod might ameliorate cartilage degradation and inflammatory responses by regulating the mitochondrial Drp1/ROS/NLRP3 axis. With this, the effects of Nod on a mouse model of knee OA and activated primary chondrocytes were assessed. The results showed that Nod intervention improved bone volume, lowered trabecular separation, and increased trabecular number in the subchondral bone. Nod decreased the Osteoarthritis Research Society International (OARSI) scores and increased collagen II-positive areas in the articular cartilage of the tibial plateau. Compared with OA mice, Nod-treated animals exhibited lower levels of inflammatory factors in the serum and synovitis of the knee joint. In vitro results indicated that Nod suppressed dynamin-related protein 1 (Drp1) phosphorylation and massive ROS production by Drp1-dependent mitochondrial fission in lipopolysaccharide-stimulated chondrocytes. Moreover, Nod inhibited the mRNA levels of inflammatory cytokines (COX 2, IL-1β, and TNF-α), nod-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome, and matrix metalloproteinase 13 expression in activated chondrocytes. In conclusion, Nod attenuates cartilage degradation and inflammatory responses in mice with OA by regulating the mitochondrial Drp1/ROS/NLRP3 axis, suggesting its potential for OA therapy.
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- 2022
16. Integrating multimodal data through interpretable heterogeneous ensembles
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Yan Chak Li, Linhua Wang, Jeffrey N. Law, T. M. Murali, and Gaurav Pandey
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Computer science ,business.industry ,Leverage (statistics) ,Protein function prediction ,Artificial intelligence ,General Medicine ,Machine learning ,computer.software_genre ,business ,computer ,Article ,Data integration - Abstract
Motivation Integrating multimodal data represents an effective approach to predicting biomedical characteristics, such as protein functions and disease outcomes. However, existing data integration approaches do not sufficiently address the heterogeneous semantics of multimodal data. In particular, early and intermediate approaches that rely on a uniform integrated representation reinforce the consensus among the modalities but may lose exclusive local information. The alternative late integration approach that can address this challenge has not been systematically studied for biomedical problems. Results We propose Ensemble Integration (EI) as a novel systematic implementation of the late integration approach. EI infers local predictive models from the individual data modalities using appropriate algorithms and uses heterogeneous ensemble algorithms to integrate these local models into a global predictive model. We also propose a novel interpretation method for EI models. We tested EI on the problems of predicting protein function from multimodal STRING data and mortality due to coronavirus disease 2019 (COVID-19) from multimodal data in electronic health records. We found that EI accomplished its goal of producing significantly more accurate predictions than each individual modality. It also performed better than several established early integration methods for each of these problems. The interpretation of a representative EI model for COVID-19 mortality prediction identified several disease-relevant features, such as laboratory test (blood urea nitrogen and calcium) and vital sign measurements (minimum oxygen saturation) and demographics (age). These results demonstrated the effectiveness of the EI framework for biomedical data integration and predictive modeling. Availability and implementation Code and data are available at https://github.com/GauravPandeyLab/ensemble_integration. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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- 2022
17. Responses of soil erosion to land‐use changes in the largest tableland of the Loess Plateau
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Aiping Hu, Yafeng Wang, Linhua Wang, Junhe Chen, Naiang Wang, Xianbao Su, Jianxiang Zhang, and Duoyong Zhang
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Hydrology ,Land use ,Soil Science ,Environmental Chemistry ,Environmental science ,Land use, land-use change and forestry ,Loess plateau ,Development ,General Environmental Science - Published
- 2021
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18. Adjusting hydrophilicity of g-C3N4 based heterojunction photocatalyst through sulfur-impregnation to enhancing degradation effect of tetracycline
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Shirong Kang, Hongjie Zhu, Linhua Wang, Xiaoyan Zhao, Xianqiang Huang, Hua Yang, Mingyu Dou, Dacheng Li, and Jianmin Dou
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Mechanics of Materials ,Mechanical Engineering ,General Materials Science ,Condensed Matter Physics - Published
- 2023
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19. Synthesis of π-extended dibenzo[d,k]ullazines by a palladium-catalyzed double annulation using arynes
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Ge Gao, Yan Liu, Yuming Zhang, Linhua Wang, Deping Wang, and Hu Cheng
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Annulation ,Materials science ,chemistry.chemical_element ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Aryne ,0104 chemical sciences ,Catalysis ,Core (optical fiber) ,chemistry ,Polymer chemistry ,0210 nano-technology ,Palladium - Abstract
An efficient Pd-catalyzed double annulation reaction of 1-(2,6-dibromophenyl)-1H-pyrroles with arynes is developed to synthesize π-extended dibenzo[d,k]ullazines in good to excellent yields. For the first time, the parent dibenzo[d,k]ullazine core is obtained and characterized.
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- 2021
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20. Single-cell Multi-omics Integration for Unpaired Data by a Siamese Network with Graph-based Contrastive Loss
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Chaozhong Liu, Linhua Wang, and Zhandong Liu
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Structural Biology ,Applied Mathematics ,Humans ,COVID-19 ,Neural Networks, Computer ,Single-Cell Analysis ,Multiomics ,Transcriptome ,Molecular Biology ,Biochemistry ,Computer Science Applications - Abstract
Background Single-cell omics technology is rapidly developing to measure the epigenome, genome, and transcriptome across a range of cell types. However, it is still challenging to integrate omics data from different modalities. Here, we propose a variation of the Siamese neural network framework called MinNet, which is trained to integrate multi-omics data on the single-cell resolution by using graph-based contrastive loss. Results By training the model and testing it on several benchmark datasets, we showed its accuracy and generalizability in integrating scRNA-seq with scATAC-seq, and scRNA-seq with epitope data. Further evaluation demonstrated our model's unique ability to remove the batch effect, a common problem in actual practice. To show how the integration impacts downstream analysis, we established model-based smoothing and cis-regulatory element-inferring method and validated it with external pcHi-C evidence. Finally, we applied the framework to a COVID-19 dataset to bolster the original work with integration-based analysis, showing its necessity in single-cell multi-omics research. Conclusions MinNet is a novel deep-learning framework for single-cell multi-omics sequencing data integration. It ranked top among other methods in benchmarking and is especially suitable for integrating datasets with batch and biological variances. With the single-cell resolution integration results, analysis of the interplay between genome and transcriptome can be done to help researchers understand their data and question.
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- 2022
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21. Thioether-Assisted Cu-Catalyzed C5-H Arylation of Imidazo[1,5
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Linhua, Wang, Xuesong, Zheng, Qinze, Zheng, Zhenlong, Li, Jian, Wu, and Ge, Gao
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A Cu-catalyzed regioselective C5-H arylation of imidazo[1,5
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- 2022
22. Targeting the TXNIP‐NLRP3 interaction with PSSM1443 to suppress inflammation in sepsis‐induced myocardial dysfunction
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Huifen Xu, Qingyun Peng, Xiangxin Liu, Mingbing Xiao, Xinlong Chen, Linhua Wang, and Hongsheng Zhao
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0301 basic medicine ,Heart Diseases ,Inflammasomes ,Physiology ,Interleukin-1beta ,Clinical Biochemistry ,Anti-Inflammatory Agents ,Inflammation ,Exosomes ,Systemic inflammation ,Exosome ,Pyrin domain ,Monocytes ,Proinflammatory cytokine ,Pathogenesis ,Mice ,03 medical and health sciences ,Thioredoxins ,0302 clinical medicine ,Sepsis ,NLR Family, Pyrin Domain-Containing 3 Protein ,medicine ,Animals ,Tetraspanin 30 ,Chemistry ,Macrophages ,Interleukin-18 ,Cell Biology ,Macrophage Activation ,Coculture Techniques ,Microvesicles ,Mice, Inbred C57BL ,Disease Models, Animal ,Oxidative Stress ,RAW 264.7 Cells ,030104 developmental biology ,030220 oncology & carcinogenesis ,Cancer research ,Inflammation Mediators ,medicine.symptom ,Carrier Proteins ,TXNIP - Abstract
Sepsis-induced myocardial dysfunction (SIMD), a deadly symptom in sepsis patients, is mainly caused by cardiovascular inflammation. However, it remains unclear how systemic inflammation triggers and aggravates cardiovascular inflammation in the pathogenesis of SIMD. This study found that proinflammatory cytokines and H2 O2 concentrations were significantly induced in SIMD-mice. In particular, a microarray analysis of CD63+ exosomes isolated from sham- and SIMD-monocytes revealed a significant induction of thioredoxin-interacting protein (TXNIP) and NLR family pyrin domain-containing 3 (NLRP3). We proved that oxidative stress caused the disassociation of the TXNIP-TRX2 (thioredoxin 2) complex and the assembly of the TXNIP-NLRP3 complex. In addition, this finding showed that the latter complex could be embedded into CD63+ exosomes and traffic from monocytes to the resident heart macrophages, where it activated caspase-1 and cleaved inactive interleukin 1β (IL-1β) and IL-18. Furthermore, using an amplified luminescent proximity homogeneous assay (Alpha) with GST-TXNIP and His-NLRP3, we obtained a small molecule named PSSM1443 that could disrupt the TXNIP-NLRP3 interaction in vitro, impairing NLRP3 downstream events. Of note, after administering PSSM1443 to the SIMD-mice, we found the small molecule could significantly suppress the activation of caspase-1 and the cleavage of pro-IL-1β and pro-IL-18, reducing inflammation in the SIMD-mice. Collectively, our results reveal that monocyte-derived exosomes harbor the overexpressed TXNIP-NLRP3 complex, which traffics from circulating monocytes to local macrophages and promotes the cleavage of inactive IL-1β and IL-18 in the macrophages, aggravating cardiovascular inflammation. PSSM1443 functions as an inhibitor of the TXNIP-NLRP3 complex and its administration can decrease inflammation in SIMD-mice.
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- 2021
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23. Ni(II)-catalyzed C-H hydroarylation of diarylacetylenes with imidazolium salts
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Tianbao Wang, Xuesong Zheng, Qinze Zheng, Fulin Zhou, Linhua Wang, and Ge Gao
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Materials Chemistry ,Metals and Alloys ,Ceramics and Composites ,General Chemistry ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials - Abstract
A Ni(ii)-catalyzed C–H hydroarylation of diarylacetylenes with imidazolium salts without adding any ligand was developed. It provides an easy and efficient access to (E)-2-(1,2-diarylvinyl)imidazolium salts.
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- 2022
24. Clinical application of Mycobacterium RT-PCR assay using various specimens for the rapid detection of lymph node tuberculosis: A diagnostic accuracy study
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Fangming Zhong, Wuchen Zhao, Linhua Wang, and Yi Shen
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General Medicine - Published
- 2023
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25. Comparison of the Diagnostic Accuracy of Xpert MTB/RIF and CapitalBio
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Guocan, Yu, Linhua, Wang, Yanqin, Shen, Likui, Fang, Jun, Yang, Bo, Ye, Kan, Xu, and Fangming, Zhong
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We evaluated CapitalBioWe reviewed suspected TBP patients with Xpert MTB/RIF, CapitalBioSeventy-four patients were included. Overall sensitivity, specificity, PPV, NPV, and AUC of CapitalBioCapitalBio
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- 2022
26. The NCOA1-CBP-NF-κB transcriptional complex induces inflammation response and triggers endotoxin-induced myocardial dysfunction
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Qingyun Peng, Yun Hua, Haixia Xu, Xinlong Chen, Huifen Xu, Linhua Wang, and Hongsheng Zhao
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Endotoxins ,Inflammation ,Lipopolysaccharides ,Mice ,Nuclear Receptor Coactivator 1 ,NF-kappa B ,Animals ,Cytokines ,Heart ,Cell Biology ,CREB-Binding Protein - Abstract
Inflammatory pathways represented by TLR4/NF-κB (Toll-like receptor 4/Nuclear factor-κB) axis signaling are activated in the pathogenesis of endotoxin-induced myocardial dysfunction (EIMD). However, the underlying mechanism by which NF-κB coordinates with other transcriptional coactivators/corepressors to regulate the expression of proinflammatory cytokine genes remains unclear. We established an EIMD-mouse model by intraperitoneal injection of lipopolysaccharides (LPS), and we discovered that NCOA1 (nuclear receptor coactivator 1) assembled with CBP (CREB binding protein) and NF-κB subunits to form a transcriptional complex that specifically bound to promoters of proinflammatory cytokine genes to activate their expression. LPS treatment also inhibited DNMT1 (DNA methyltransferase 1) expression, thereby decreasing DNA methylation of a CpG island located on the promoter of NCOA1 and causing NCOA1 overexpression. Screening small molecules that abolished NCOA1-CBP interaction in a yeast system identified a compound PSSM2126 that effectively blocked the NCOA1-CBP interaction in vitro and in vivo. Administration of PSSM2126 to EIMD mice significantly alleviated the inflammation response and improved cardiac function. Collectively, our results reveal that an NCOA1-dependent transactivation mechanism can regulate proinflammatory cytokine expression, thereby improving our understanding of the activation of NF-κB targets. The promising inhibition of the NCOA1-CBP interaction by PSSM2126 may provide a new therapeutic option for EIMD.
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- 2022
27. Identification of spatial co-expression patterns and intra-tissue heterogeneity in spatially resolved transcriptomics by region-specific denoising
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Zhandong Liu and Linhua Wang
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Transcriptome ,Tissue heterogeneity ,Region specific ,Spatially resolved ,Identification (biology) ,Computational biology ,Biology ,Expression (mathematics) - Abstract
We are pleased to introduce a first-of-its-kind tool that combines in-silico region detection and missing value estimation for spatially resolved transcriptomics. Spatial transcriptomics by 10X Visium (ST) is a new technology used to dissect gene and cell spatial organization. Analyzing this new type of data has two main challenges: automatically annotating the major tissue regions and excessive zero values of gene expression due to high dropout rates. We developed a computational tool—MIST—that addresses both challenges by automatically identifying tissue regions and estimating missing gene-expression values for each detected region. We validated MIST detected regions across multiple datasets using manual annotation on the histological staining images as references. We also demonstrated that MIST can accurately recover ST’s missing values through hold-out experiments. Furthermore, we showed that MIST could identify intra-tissue heterogeneity and recover spatial gene-gene co-expression signals. We therefore strongly encourage using MIST before downstream ST analysis because it provides unbiased region annotations and enables accurately denoised spatial gene-expression profiles.
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- 2021
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28. Region-specific denoising identifies spatial co-expression patterns and intra-tissue heterogeneity in spatially resolved transcriptomics data
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Linhua Wang, Mirjana Maletic-Savatic, and Zhandong Liu
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Multidisciplinary ,General Physics and Astronomy ,General Chemistry ,Transcriptome ,General Biochemistry, Genetics and Molecular Biology - Abstract
Spatially resolved transcriptomics is a relatively new technique that maps transcriptional information within a tissue. Analysis of these datasets is challenging because gene expression values are highly sparse due to dropout events, and there is a lack of tools to facilitate in silico detection and annotation of regions based on their molecular content. Therefore, we develop a computational tool for detecting molecular regions and region-based Missing value Imputation for Spatially Transcriptomics (MIST). We validate MIST-identified regions across multiple datasets produced by 10x Visium Spatial Transcriptomics, using manually annotated histological images as references. We benchmark MIST against a spatial k-nearest neighboring baseline and other imputation methods designed for single-cell RNA sequencing. We use holdout experiments to demonstrate that MIST accurately recovers spatial transcriptomics missing values. MIST facilitates identifying intra-tissue heterogeneity and recovering spatial gene-gene co-expression signals. Using MIST before downstream analysis thus provides unbiased region detections to facilitate annotations with the associated functional analyses and produces accurately denoised spatial gene expression profiles.
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- 2021
29. Missing-value imputation and in-silico region detection for spatially resolved transcriptomics
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Linhua Wang and Zhandong Liu
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Computer science ,business.industry ,In silico ,Spatially resolved ,Missing value imputation ,Region detection ,Pattern recognition ,Artificial intelligence ,Imputation (statistics) ,Missing data ,business ,Spatial organization ,Dropout (neural networks) - Abstract
We are pleased to introduce a first-of-its-kind algorithm that combines in-silico region detection and spatial gene-expression imputation. Spatial transcriptomics by 10X Visium (ST) is a new technology used to dissect gene and cell spatial organization. Analyzing this new type of data has two main challenges: automatically annotating the major tissue regions and excessive zero values of gene-expression due to high dropout rates. We developed a computational tool—MIST—that addresses both challenges by automatically identifying tissue regions and estimating missing gene-expression values for individual tissue regions. We validated MIST detected regions across multiple datasets using manual annotation on the histological staining images as references. We also demonstrated that MIST can accurately recover ST’s missing values through hold-out experiments. Furthermore, we showed that MIST could identify subtle intra-tissue heterogeneity and recover spatial gene-gene interaction signals. We therefore strongly encourage using MIST prior to downstream ST analysis because it provides unbiased region annotations and enables accurately de-noised spatial gene-expression profiles.
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- 2021
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30. Computational performance of heterogeneous ensemble frameworks on high-performance computing platforms
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Gaurav Pandey, Linhua Wang, and Prem Timsina
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0301 basic medicine ,Source code ,Computer science ,business.industry ,media_common.quotation_subject ,Distributed computing ,Big data ,02 engineering and technology ,Supercomputer ,computer.software_genre ,Software framework ,03 medical and health sciences ,030104 developmental biology ,Memory management ,Software ,Analytics ,020204 information systems ,0202 electrical engineering, electronic engineering, information engineering ,Data analysis ,business ,computer ,media_common - Abstract
To enable efficient computations on rapidly growing big data, a variety of high-performance computing (HPC) platforms, such as traditional multi-processor systems, Hadoop and cloud computing systems, have been developed. On the analytics side of big data, several innovative machine learning methods have been developed to enable the extraction of accurate and actionable knowledge from large datasets. In particular, heterogeneous ensemble algorithms, which are designed to aggregate an unrestricted variety and number of analytical models, have performed well for a variety of prediction problems. However, the performance of these algorithms in terms of computational metrics, such as time requirement, disk space consumption and memory usage, on these HPC platforms has not been systematically examined yet. Here, we address this gap in knowledge by implementing these algorithms and systematically assessing their computational performance on traditional HPC and Hadoop platforms. Our results show that these implementations used the resources, especially disk space and memory, consistent with the respective designs of the platforms. Furthermore, due to the iterative nature of the heterogeneous ensemble computations, the traditional HPC system executed them faster than Hadoop, since an in-memory design is better suited for them than a disk-based one. Overall, our study sheds new light on the computational performance of ensemble algorithms and software frameworks on two prominent HPC platforms, and offers a systematic methodology for conducting similar assessments for other data analytics methods as well. Basic source code of our heterogeneous ensemble implementations, as well as the HPC performance assessments, are available at https://github.com/GauravPandeyLab/HPC-Ensemble.
- Published
- 2020
- Full Text
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31. Isotopic biogeochemical indicators of evapotranspiration and nitrogen flows in a check‐dam catchment in the Loess Plateau, China
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Shibo Chen, Weiliang Chen, Yong Huang, Yang Gao, Linhua Wang, and Yafeng Wang
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Biogeochemical cycle ,Baseflow ,010504 meteorology & atmospheric sciences ,Soil Science ,010501 environmental sciences ,Development ,01 natural sciences ,Manure ,Deposition (aerosol physics) ,Evapotranspiration ,Environmental chemistry ,Kinetic fractionation ,Meteoric water ,Environmental Chemistry ,Environmental science ,Surface runoff ,0105 earth and related environmental sciences ,General Environmental Science - Abstract
The increasingly fragile environment and associative nitrogen (N) biogeochemical cycle have become critical environmental and ecological issues in China's Loess Plateau. However, N flow and N source for typical catchments remain poorly understood in the Loess Plateau. In this study, we measured concentrations and isotopic signatures of N, hydrogen (H), and oxygen (O) in both rainfall and river water. Results showed that baseflow variation in total nitrogen (TN) concentrations ranged from 0.16 to 32.70 mg L⁻¹. The monthly TN deposition flux and monthly TN wet deposition concentration to river water were shown significant variations between rainy and dry seasons. The range of variation in δ²H values for rainfall and baseflow was from −90.0‰ to 19.8‰ and from −67.2‰ to −38.4‰, respectively, whereas δ¹⁸O–H₂O values ranged from −12.1‰ to +2.7‰ and from −9.3‰ to −3.6‰, respectively. The Local Meteoric Water Line in the check‐dam catchment was δ²H = 7.35 δ¹⁸O + 2.29 (R² = 0.93). Furthermore, NO₃⁻ δ¹⁵N and δ¹⁸O values in baseflow ranged from −2.0‰ to +20.5‰ and from +8.0‰ to +15.6‰, respectively. The results indicated that rainfall was affected by below‐cloud secondary evaporation and caused strong isotopic kinetic fractionation to occur during the precipitation process. The NO₃⁻ in runoff was mainly derived from the nitrification of soil organic matter and manure or sewage, for which the proportion of manure or sewage was from 50.5% to 83%.
- Published
- 2018
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32. Analysis of gas discharge characteristics across micro-gap under different pressures
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Yining Sun, Yanzhou Sun, Linhua Wang, Yun Chen, Yansen Li, and Bin Jia
- Subjects
Field electron emission ,Materials science ,Physics and Astronomy (miscellaneous) ,General Engineering ,General Physics and Astronomy ,Micro gap ,Engineering physics ,Electric discharge in gases - Published
- 2021
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33. Effects of different spatial distributions of physical soil crusts on runoff and erosion on the Loess Plateau in China
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Faqi Wu, Pei Lu, Linhua Wang, and Xinli Xie
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Sediment yield ,0208 environmental biotechnology ,Geography, Planning and Development ,Sediment ,Crust ,Soil science ,04 agricultural and veterinary sciences ,02 engineering and technology ,Loess plateau ,Spatial distribution ,020801 environmental engineering ,Sedimentary depositional environment ,040103 agronomy & agriculture ,Earth and Planetary Sciences (miscellaneous) ,Erosion ,0401 agriculture, forestry, and fisheries ,Surface runoff ,Geology ,Earth-Surface Processes - Abstract
The response of runoff and erosion to soil crusts has been extensively investigated in recent decades. However, there have been few attempts to look at the effects of spatial configuration of different soil crusts on erosion processes. Here we investigated the effects of different spatial distributions of physical soil crusts on runoff and erosion in the semi-arid Loess Plateau region. Soil boxes (1.5 m long × 0.2 m wide) were set to a slope of 17.6% (10°) and simulated rainfall of 120 mm h−1 (60 minutes). The runoff generation and erosion rates were determined for three crust area ratios (depositional crust for 20%, 33%, and 50% of the total slope) and five spatial distribution patterns (depositional crust on the lower, lower-middle, middle, mid-upper, and upper slope) of soil crusts. The reduction in sediment loss (‘sediment reduction’) was calculated to evaluate the effects of different spatial distributions of soil crusts on erosion. Sediment yield was influenced by the area ratio and spatial position of different soil crusts. The runoff rate reached a steady state after an initial trend of unsteadily increasing with increasing rainfall duration. Sediment yield was controlled by detachment limitation and then transport limitation under rainfall. The shifting time of erosion from a transport to detachment-limiting regime decreased with increasing area of depositional crust. No significant differences were observed in the total runoff among treatments, while the total sediment yield varied under different spatial distributions. At the same area ratio, total sediment yield was the largest when the depositional crust was on the upper slope, and it was smallest when the crust was deposited on the lower slope. The sediment reduction of structural crust (42.5–66.5%) was greater than that of depositional crust (16.7–34.3%). These results provide a mechanistic understanding of how different spatial distributions of soil crusts affect runoff and sediment production. Copyright © 2017 John Wiley & Sons, Ltd.
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- 2017
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34. Effects of wheat stubble on runoff, infiltration, and erosion of farmland on the Loess Plateau, China, subjected to simulated rainfall
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Faqi Wu, Linhua Wang, and Bo Ma
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business.product_category ,Stratigraphy ,0208 environmental biotechnology ,Soil Science ,02 engineering and technology ,Rainwater harvesting ,Summer fallow ,Plough ,lcsh:Stratigraphy ,Simulated rainfall ,Geochemistry and Petrology ,lcsh:QE640-699 ,Earth-Surface Processes ,Hydrology ,lcsh:QE1-996.5 ,Paleontology ,Geology ,04 agricultural and veterinary sciences ,020801 environmental engineering ,lcsh:Geology ,Water resources ,Infiltration (hydrology) ,Geophysics ,040103 agronomy & agriculture ,Erosion ,0401 agriculture, forestry, and fisheries ,Environmental science ,business ,Surface runoff - Abstract
Soil and water losses in agriculture are major environmental problems worldwide, especially on the Loess Plateau, China. Summer fallow management may help to control soil erosion and conserve water. This study investigated the effects of wheat stubble on runoff, infiltration, and soil loss in laboratory plots under simulated rainfall. The treatments comprised wheat stubble cover (WS) and traditional plowing (TP) in runoff plots (4.0 m × 1.0 m) with three slope gradients (5, 10, and 15°) under simulated rainfall at 80 mm h−1 for 1 h. The runoff volume from WS plots was significantly less than that from TP. The runoff reduction with WS ranged from 91.92 to 92.83 % compared with TP. The runoff rates varied with the runoff volume in the same manner. The infiltration amount was higher with WS (94.8–96.2 % of rainwater infiltrated) than TP (35.4–57.1 %). The sediment concentration was significantly lower with WS than TP. Compared with TP (304.31–731.23 g m−2), the sediment losses were reduced dramatically in WS (2.41–3.78 g m−2) and the sediment loss slightly increased with slope; however, it was greatly increased as slope increased in TP. These results revealed that the stubble cover was the main factor reducing runoff and sediment losses and improving infiltration and that stubble showed a great potential to control erosion and conserve soil and water resources during the summer fallow period in the Loess Plateau region.
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- 2017
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35. Effects of tillage practices and slope on runoff and erosion of soil from the Loess Plateau, China, subjected to simulated rainfall
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Pei Lu, Linhua Wang, Nurmolda Dalabay, and Faqi Wu
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Hydrology ,business.product_category ,010504 meteorology & atmospheric sciences ,Soil Science ,Soil science ,04 agricultural and veterinary sciences ,Loess plateau ,01 natural sciences ,Summer fallow ,Plough ,Tillage ,Digging ,Infiltration (hydrology) ,040103 agronomy & agriculture ,Erosion ,0401 agriculture, forestry, and fisheries ,Environmental science ,business ,Surface runoff ,Agronomy and Crop Science ,0105 earth and related environmental sciences ,Earth-Surface Processes - Abstract
Soil erosion, particularly during summer fallow period, in sloped farmland has been identified as a critical threat to sustainable agricultural development in the Loess Plateau of China. However, the effects of varying tillage practices during the summer fallow period have not been fully investigated. The objective of this study was to determine the effects of tillage practices on runoff and sediment loss under plot (4.0 m in length and 1.0 m in width) rainfall simulations. Runoff initiation time, runoff amount, sediment loss and cumulative infiltration amount were recorded. One rainfall intensity (90 mm h −1 , 40 min), three slopes (5°, 10°, and 15°) and four prevalent tillage practices (Artificial Digging, AD; Artificial Hoeing, AH; Contour Plow, CP; and Traditional Plow, TP) were studied. Two indices, runoff reduction benefits (RRB) and sediment reduction benefits (SRB), were selected to evaluate the effect of the practice on controlling runoff and sediment. Compared to TP treatment, the AD, AH and CP were more effective in reducing the magnitude of runoff amount and sediment loss as well as increasing the rain water infiltration amount. CP with a 15° slope was an exception in which the sediment loss increased. In general, the SRB was greater than the RRB for a given tillage practice under the same slope, suggesting that the benefits from sediment reduction were more effective than the benefits from runoff reduction. RRB and SRB were the largest for AD, followed by AH and CP, irrespective of slopes. The capacity of the three tillage practices to reduce runoff and sediment decreased as the slope increased. In particular, AD at a 5° slope had the best performance in reducing runoff and sediment loss; however, SRB and RRB were −57% and 1%, respectively, for a CP plot with a 15° slope. This finding suggested that CP had a higher sediment loss and a similar runoff amount compared to those of TP. These results of plot simulated rainfall will contribute to our knowledge about the effects of different tillage practices on soil erosion from sloped farmland.
- Published
- 2017
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36. Revised manuscript HESS201908
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Linhua Wang
- Published
- 2019
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37. Response to HESS-2019-8-RC3
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Linhua Wang
- Published
- 2019
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38. Response to HESS-2019-8-RC1
- Author
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Linhua Wang
- Published
- 2019
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39. Response to HESS-2019-8-RC2
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Linhua Wang
- Published
- 2019
- Full Text
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40. Effects of structural and depositional crusts on soil erosion on the Loess Plateau of China
- Author
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Faqi Wu, Qiuju Wu, and Linhua Wang
- Subjects
Soil Science ,Storm ,Soil science ,04 agricultural and veterinary sciences ,010501 environmental sciences ,Soil type ,01 natural sciences ,Tillage ,Sedimentary depositional environment ,Digging ,Soil crust ,040103 agronomy & agriculture ,Erosion ,0401 agriculture, forestry, and fisheries ,Surface runoff ,Geology ,0105 earth and related environmental sciences - Abstract
Conventional tillage practices used on the Loess Plateau lead to different soil surface micro-topography which results in forming two types of soil crusts. The objective of this study was to explore the formation position, properties and erosion characteristics of structural crusts and depositional crusts under the influences of the microtopography in the rainfall experiments. Two simulated rainstorms were applied in the experiments. The first rainfall event was used for soil crust formation, then the following simulated rainfall storms at 40 mm h−1, 60 mm h−1, and 80 mm h−1 rates were applied to the soil boxes set to a 17.6% (10°) slope under three tillage types (contour tillage, artificial digging, and straight slope conditions) to investigate the resulting runoff discharge rate and sediment yield on crusted soil surface. Results show that: (1) structural crusts formed on the mounds, and depositional crusts formed in the depressions after the first rainfall events; structural crusts exhibit a lo...
- Published
- 2016
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41. Deposition- and transport-dominated erosion regime effects on the loss of dissolved and sediment-bound organic carbon: Evaluation in a cultivated soil with laboratory rainfall simulations
- Author
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Jiamei Sun, Xiang Wang, Ashley Hammac, Chi-hua Huang, Haw Yen, Linhua Wang, and Yafeng Wang
- Subjects
Total organic carbon ,Environmental Engineering ,Watershed ,010504 meteorology & atmospheric sciences ,chemistry.chemical_element ,Sediment ,Soil science ,Soil carbon ,010501 environmental sciences ,01 natural sciences ,Pollution ,Deposition (geology) ,chemistry ,Erosion ,Environmental Chemistry ,Environmental science ,Surface runoff ,Waste Management and Disposal ,Carbon ,0105 earth and related environmental sciences - Abstract
Erosion-induced soil carbon loss has been identified as a critical process in the global carbon (C) cycle. Surface coverage substantially alters the soil erosion process and the effects of net loss or deposition on soil organic C (SOC). However, information on SOC loss induced by soil erosion at the process level is limited. The aim of this study was to investigate how runoff and erosion regimes affect dissolved and sediment-bound organic C (DOC and SBOC) loss. Thus, six simulated rainfall events were conducted on two laboratory plots (9.75 m × 1.83 m) with different surface coverages (17–83%) and coverage distributions (upslope vs. downslope) using polypropylene geotextiles. The results showed that the variability in the process of runoff and sediment yield existed as a result of altered surface coverage over the erosion zone (SSerosion zone) and covered zone (SScovered zone) on the slope. Thus, the erosion regimes can be identified as deposition- and transport-dominated processes, which were the main soil erosion subprocesses. The surface coverage located downslope (SCtop-bottom slope) can more efficiently reduce runoff (21.9–85.7%) and sediment (67.6–98.3%) than the SCbottom-top slope (runoff: 20.1–83.0%; sediment: 35.0–93.3%), which has the surface coverage located upslope. DOC (8.0–11.3 mg L−1) and SBOC (0.3–0.5 mg g−1) in the deposition-dominated process on the SCtop-bottom slope were higher than in the transport-dominated process on the SCbottom-top slope (DOC: 6.8–10.2 mg L−1; SBOC: 0.2–0.3 mg g−1). The loading of DOC and SBOC was largely dependent on runoff and sediment yield, and DOC load contributed 83.9–89.7% of the SOC loss. Overall, laboratory results highlighted the soil C loss at different hydrological and erosion regimes (deposition- vs. transport-dominated process). This study provides important information that can be used to facilitate further implementations such as watershed modeling of soil C dynamics and the corresponding decision-making processes.
- Published
- 2021
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42. Research on Ion Enhancement Effect in Micro-gap Gas Discharge
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Linhua Wang, Xuguang Liu, Yanzhou Sun, and Keliang Dong
- Subjects
Materials science ,Atmospheric pressure ,0103 physical sciences ,Electrode ,Analytical chemistry ,General Physics and Astronomy ,Micro gap ,010306 general physics ,01 natural sciences ,010305 fluids & plasmas ,Ion ,Electric discharge in gases - Abstract
To study the deviation from the Paschen curve under the micro-gap, the DC breakdown experiment with the electrode distance of 1–100 µm was carried out under atmospheric pressure in air. By deriving...
- Published
- 2020
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43. Large-scale protein function prediction using heterogeneous ensembles
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T. M. Murali, Gaurav Pandey, Jeffrey N. Law, Shiv D. Kale, and Linhua Wang
- Subjects
0301 basic medicine ,Computer science ,Logistic regression ,Machine learning ,computer.software_genre ,Data type ,protein function prediction,heterogeneous ensembles,machine learning, high-performance computing, performance evaluation ,General Biochemistry, Genetics and Molecular Biology ,Machine Learning ,03 medical and health sciences ,Bacterial Proteins ,Protein function prediction ,General Pharmacology, Toxicology and Pharmaceutics ,General Immunology and Microbiology ,business.industry ,Gene ontology ,Scale (chemistry) ,high-performance computing ,heterogeneous ensembles ,Articles ,General Medicine ,Method Article ,Supercomputer ,Ensemble learning ,performance evaluation ,030104 developmental biology ,Gene Ontology ,Logistic Models ,Artificial intelligence ,business ,computer ,protein function prediction - Abstract
Heterogeneous ensembles are an effective approach in scenarios where the ideal data type and/or individual predictor are unclear for a given problem. These ensembles have shown promise for protein function prediction (PFP), but their ability to improve PFP at a large scale is unclear. The overall goal of this study is to critically assess this ability of a variety of heterogeneous ensemble methods across a multitude of functional terms, proteins and organisms. Our results show that these methods, especially Stacking using Logistic Regression, indeed produce more accurate predictions for a variety of Gene Ontology terms differing in size and specificity. To enable the application of these methods to other related problems, we have publicly shared the HPC-enabled code underlying this work as LargeGOPred (https://github.com/GauravPandeyLab/LargeGOPred). This work was supported in part by National Institutes of Health [R01GM114434] and by an IBM faculty award to GP. It was also partially supported by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), via the Army Research Office (ARO) under Cooperative Agreement Number [W911NF-17-2-0105].
- Published
- 2018
44. Structural Alteration of Gut Microbiota during the Amelioration of Human Type 2 Diabetes with Hyperlipidemia by Metformin and a Traditional Chinese Herbal Formula: a Multicenter, Randomized, Open Label Clinical Trial
- Author
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Zhiping Peng, Qiang Zhou, Xiaotong Yu, Xiyan Zhao, Fengmei Lian, Menghui Zhang, Shengping Wu, Liping Zhao, Linhua Wang, Jian Shen, Jing Wang, Feng Chen, Zhong Zhen, Chenhong Zhang, Jia Xu, Xiaoyan Pang, Lipeng Xu, Chao Fang, Min Li, Limei Chen, Bing Pang, Yufeng Zhao, Jiaxing Tian, and Xiaolin Tong
- Subjects
0301 basic medicine ,Blood Glucose ,Male ,endocrine system diseases ,Type 2 diabetes ,Gut flora ,Pharmacology ,traditional Chinese medicine ,Hyperlipidemia ,hyperlipidemia ,Letter to the Editor ,biology ,clinical trial ,Middle Aged ,QR1-502 ,Metformin ,herbal ,Female ,type 2 diabetes ,medicine.drug ,Adult ,HbA1c ,Adolescent ,Hyperlipidemias ,digestive system ,Microbiology ,03 medical and health sciences ,Young Adult ,Insulin resistance ,Virology ,Diabetes mellitus ,medicine ,Humans ,Triglycerides ,Aged ,Bacteria ,gut microbiota ,business.industry ,Type 2 Diabetes Mellitus ,nutritional and metabolic diseases ,medicine.disease ,biology.organism_classification ,Obesity ,Gastrointestinal Microbiome ,030104 developmental biology ,Diabetes Mellitus, Type 2 ,Anti-Obesity Agents ,business ,Drugs, Chinese Herbal - Abstract
Accumulating evidence implicates gut microbiota as promising targets for the treatment of type 2 diabetes mellitus (T2DM). With a randomized clinical trial, we tested the hypothesis that alteration of gut microbiota may be involved in the alleviation of T2DM with hyperlipidemia by metformin and a specifically designed herbal formula (AMC). Four hundred fifty patients with T2DM and hyperlipidemia were randomly assigned to either the metformin- or AMC-treated group. After 12 weeks of treatment, 100 patients were randomly selected from each group and assessed for clinical improvement. The effects of the two drugs on the intestinal microbiota were evaluated by analyzing the V3 and V4 regions of the 16S rRNA gene by Illumina sequencing and multivariate statistical methods. Both metformin and AMC significantly alleviated hyperglycemia and hyperlipidemia and shifted gut microbiota structure in diabetic patients. They significantly increased a coabundant group represented by Blautia spp., which significantly correlated with the improvements in glucose and lipid homeostasis. However, AMC showed better efficacies in improving homeostasis model assessment of insulin resistance (HOMA-IR) and plasma triglyceride and also exerted a larger effect on gut microbiota. Furthermore, only AMC increased the coabundant group represented by Faecalibacterium spp., which was previously reported to be associated with the alleviation of T2DM in a randomized clinical trial. Metformin and the Chinese herbal formula may ameliorate type 2 diabetes with hyperlipidemia via enriching beneficial bacteria, such as Blautia and Faecalibacterium spp. IMPORTANCE Metabolic diseases such as T2DM and obesity have become a worldwide public health threat. Accumulating evidence indicates that gut microbiota can causatively arouse metabolic diseases, and thus the gut microbiota serves as a promising target for disease control. In this study, we evaluated the role of gut microbiota during improvements in hyperglycemia and hyperlipidemia by two drugs: metformin and a specifically designed Chinese herbal formula (AMC) for diabetic patients with hyperlipidemia. Both drugs significantly ameliorated blood glucose and lipid levels and shifted the gut microbiota. Blautia spp. were identified as being associated with improvements in glucose and lipid homeostasis for both drugs. AMC exerted larger effects on the gut microbiota together with better efficacies in improving HOMA-IR and plasma triglyceride levels, which were associated with the enrichment of Faecalibacterium spp. In brief, these data suggest that gut microbiota might be involved in the alleviation of diabetes with hyperlipidemia by metformin and the AMC herbal formula.
- Published
- 2018
45. Response to bg-2017-488-RC2
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Linhua Wang
- Published
- 2018
- Full Text
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46. Response to bg-2017-488-RC1
- Author
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Linhua Wang
- Published
- 2018
- Full Text
- View/download PDF
47. The revised manuscript
- Author
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Linhua Wang
- Published
- 2018
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48. The revised manuscript
- Author
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Linhua Wang
- Published
- 2018
- Full Text
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49. The Effect of Financing Constraints on China’s Enterprise Export
- Author
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Yonghua Yang and Linhua Wang
- Subjects
Finance ,business.industry ,Process (engineering) ,ComputerApplications_MISCELLANEOUS ,External financing ,business ,China ,Constraint (mathematics) ,Panel data - Abstract
This paper constructs an export model of heterogeneous enterprises with financing constraints and put forward the hypothesis of financing constraints and export. Based on the panel data of China's industry enterprises from 2005 to 2014, this paper establishes a model and estimates the hypothesis. The main conclusions are as follows: the larger the financing constraint, the less export; Compared with domestic financing constraints, export enterprises are more constrained by external financing constraints; In the process of export, the state-owned enterprises are less constrained than the private ones, and the private ones are heavily affected by the financing constraints. Among them, the influence of exogenous financing constraints is the biggest.
- Published
- 2018
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50. The Effect of Financing Constraints on OFDI of China's Enterprise
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Linhua Wang and Yonghua Yang
- Subjects
Financial system ,Business ,China - Published
- 2018
- Full Text
- View/download PDF
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