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  1. Article ; Online: Combining a glycolysis‑related prognostic model based on scRNA‑Seq with experimental verification identifies ZFP41 as a potential prognostic biomarker for HCC.

    Teng, Yu / Xu, Jianrong / Wang, Yaoqun / Wen, Ningyuan / Ye, Hui / Li, Bei

    Molecular medicine reports

    2024  Volume 29, Issue 5

    Abstract: Hepatocellular carcinoma (HCC) is a common malignancy with a poor prognosis, and its heterogeneity affects the response to clinical treatments. Glycolysis is highly associated with HCC therapy and prognosis. The present study aimed to identify a novel ... ...

    Abstract Hepatocellular carcinoma (HCC) is a common malignancy with a poor prognosis, and its heterogeneity affects the response to clinical treatments. Glycolysis is highly associated with HCC therapy and prognosis. The present study aimed to identify a novel biomarker for HCC by exploring the heterogeneity of glycolysis in HCC. The intersection of both marker genes of glycolysis‑related cell clusters from single‑cell RNA sequencing analysis and mRNA data of liver HCC from The Cancer Genome Atlas were used to construct a prognostic model through Cox proportional hazard regression and the least absolute shrinkage and selection operator Cox regression. Data from the International Cancer Genome Consortium were used to validate the results of the analysis. Immune status analysis was then conducted. A significant gene in the prognostic model was identified as a potential biomarker and was verified through
    MeSH term(s) Humans ; Carcinoma, Hepatocellular/diagnosis ; Carcinoma, Hepatocellular/genetics ; Glycolysis/genetics ; Liver Neoplasms/diagnosis ; Liver Neoplasms/genetics ; Prognosis ; RNA, Messenger ; Single-Cell Gene Expression Analysis ; Kruppel-Like Transcription Factors/genetics ; Kruppel-Like Transcription Factors/metabolism ; Biomarkers
    Chemical Substances RNA, Messenger ; ZNF41 protein, human ; Kruppel-Like Transcription Factors ; Biomarkers
    Language English
    Publishing date 2024-03-22
    Publishing country Greece
    Document type Journal Article
    ZDB-ID 2469505-1
    ISSN 1791-3004 ; 1791-2997
    ISSN (online) 1791-3004
    ISSN 1791-2997
    DOI 10.3892/mmr.2024.13203
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Corrigendum to "Correlation between hypertension and high homocysteine levels caused by the MTHFR C677T gene polymorphisms" [Asian J Surg 45(4) (2022) 1039-1040].

    Xu, Jian-Rong / Zhang, Xia-Ying / Zhao, Li / Han, Qing-Hua

    Asian journal of surgery

    2022  Volume 45, Issue 6, Page(s) 1373

    Language English
    Publishing date 2022-04-03
    Publishing country China
    Document type Published Erratum
    ZDB-ID 1068461-x
    ISSN 0219-3108 ; 1015-9584
    ISSN (online) 0219-3108
    ISSN 1015-9584
    DOI 10.1016/j.asjsur.2022.03.071
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  3. Article ; Online: HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention.

    Zhu, Weimin / Zhang, Yi / Zhao, Duancheng / Xu, Jianrong / Wang, Ling

    Journal of chemical information and modeling

    2022  Volume 63, Issue 1, Page(s) 43–55

    Abstract: Elucidating and accurately predicting the druggability and bioactivities of molecules plays a pivotal role in drug design and discovery and remains an open challenge. Recently, graph neural networks (GNNs) have made remarkable advancements in graph-based ...

    Abstract Elucidating and accurately predicting the druggability and bioactivities of molecules plays a pivotal role in drug design and discovery and remains an open challenge. Recently, graph neural networks (GNNs) have made remarkable advancements in graph-based molecular property prediction. However, current graph-based deep learning methods neglect the hierarchical information of molecules and the relationships between feature channels. In this study, we propose a well-designed hierarchical informative graph neural network (termed HiGNN) framework for predicting molecular property by utilizing a corepresentation learning of molecular graphs and chemically synthesizable breaking of retrosynthetically interesting chemical substructure (BRICS) fragments. Furthermore, a plug-and-play feature-wise attention block is first designed in HiGNN architecture to adaptively recalibrate atomic features after the message passing phase. Extensive experiments demonstrate that HiGNN achieves state-of-the-art predictive performance on many challenging drug discovery-associated benchmark data sets. In addition, we devise a molecule-fragment similarity mechanism to comprehensively investigate the interpretability of the HiGNN model at the subgraph level, indicating that HiGNN as a powerful deep learning tool can help chemists and pharmacists identify the key components of molecules for designing better molecules with desired properties or functions. The source code is publicly available at https://github.com/idruglab/hignn.
    MeSH term(s) Benchmarking ; Drug Design ; Drug Discovery ; Neural Networks, Computer ; Software
    Language English
    Publishing date 2022-12-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.2c01099
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A Comparative Study on Visual Health and Physical Activity of Chinese and Japanese Children Aged 6-12 Years.

    Yang, Ganfeng / Zhang, Meng / Ujihara, Hiroshi / Xu, Jianrong / Zhou, Sheng

    American journal of health behavior

    2022  Volume 46, Issue 5, Page(s) 567–575

    Abstract: Objectives: In this study, we compare the visual acuity levels and physical activity participation of Chinese and Japanese children.: Methods: We collected data on static visual acuity, kinetic visual acuity, axial length, intensity, frequency, ... ...

    Abstract Objectives: In this study, we compare the visual acuity levels and physical activity participation of Chinese and Japanese children.
    Methods: We collected data on static visual acuity, kinetic visual acuity, axial length, intensity, frequency, duration, amount, and physical activity items of 431 children aged 6-12 years from Chinese and Japanese schools in the same city. Our analysis examined the relationships involving age, visual function indicators, ocular biometric parameters, and extracurricular physical activity.
    Results: We found the myopia rate higher in Chinese children than in Japanese children, increasing with age except in grade 4; kinetic visual acuity in Chinese children was lower than in Japanese children (p<.01). The axial length becomes longer with age in both groups, with Chinese children having a longer axial length than Japanese children. The amount of physical activity in Chinese and Japanese children aged 6-12 years fluctuates. The frequency, duration, and physical activity items are lower in Chinese children than Japanese (p<.01).
    Conclusions: Chinese and Japanese children's overall static visual acuity development level shows a decreasing trend, and Japanese children have better kinetic visual acuity and physical activity participation than Chinese children. Physical activity could have an impact on visual acuity.
    MeSH term(s) Child ; Humans ; Japan ; Myopia ; Visual Acuity ; Exercise ; China
    Language English
    Publishing date 2022-11-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1312417-1
    ISSN 1945-7359 ; 1087-3244 ; 0147-0353
    ISSN (online) 1945-7359
    ISSN 1087-3244 ; 0147-0353
    DOI 10.5993/AJHB.46.5.7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Correlation between hypertension and high homocysteine levels caused by the MTHFR C677T gene polymorphisms.

    Xu, Jian-Rong / Zhang, Xia-Ying / Zhao, Li / Han, Qing-Hua

    Asian journal of surgery

    2022  Volume 45, Issue 4, Page(s) 1039–1040

    MeSH term(s) Homocysteine/genetics ; Humans ; Hypertension/genetics ; Methylenetetrahydrofolate Reductase (NADPH2)/genetics ; Polymorphism, Genetic
    Chemical Substances Homocysteine (0LVT1QZ0BA) ; MTHFR protein, human (EC 1.5.1.20) ; Methylenetetrahydrofolate Reductase (NADPH2) (EC 1.5.1.20)
    Language English
    Publishing date 2022-02-27
    Publishing country China
    Document type Letter
    ZDB-ID 1068461-x
    ISSN 0219-3108 ; 1015-9584
    ISSN (online) 0219-3108
    ISSN 1015-9584
    DOI 10.1016/j.asjsur.2022.01.028
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  6. Article ; Online: METTL3-mediated m

    Li, Bei / Xiong, Xianze / Xu, Jianrong / Peng, Dingzhong / Nie, Guilin / Wen, Ningyuan / Wang, Yaoqun / Lu, Jiong

    Oncogene

    2024  Volume 43, Issue 14, Page(s) 1050–1062

    Abstract: In a previous study, we discovered that the level of lnc-TSPAN12 was significantly elevated in hepatocellular carcinoma (HCC) and correlated with a low survival rate. However, the function and mechanism of lnc-TSPAN12 in modulating epithelial-mesenchymal ...

    Abstract In a previous study, we discovered that the level of lnc-TSPAN12 was significantly elevated in hepatocellular carcinoma (HCC) and correlated with a low survival rate. However, the function and mechanism of lnc-TSPAN12 in modulating epithelial-mesenchymal transition (EMT) and metastasis in HCC remains poorly understood. This study demonstrates that lnc-TSPAN12 positively influences migration, invasion, and EMT of HCC cells in vitro and promotes hepatic metastasis in vivo. The modification of N6-methyladenosine, driven by METTL3, is essential for the stability of lnc-TSPAN12, which may partially contribute to the upregulation of lnc-TSPAN12. Mechanistically, lnc-TSPAN12 exhibits direct interactions with EIF3I and SENP1, acting as a scaffold to enhance the SENP1-EIF3I interaction. As a result, the SUMOylation of EIF3I is inhibited, preventing its ubiquitin-mediated degradation. Ultimately, this activates the Wnt/β-catenin signaling pathway, stimulating EMT and metastasis in HCC. Our findings shed light on the regulatory mechanism of lnc-TSPAN12 in HCC metastasis and identify the lnc-TSPAN12-EIF3I/SENP1 axis as a novel therapeutic target for HCC.
    MeSH term(s) Humans ; Carcinoma, Hepatocellular/metabolism ; Carcinoma, Hepatocellular/pathology ; Cell Line, Tumor ; Cell Movement ; Cysteine Endopeptidases/genetics ; Cysteine Endopeptidases/metabolism ; Epithelial-Mesenchymal Transition ; Eukaryotic Initiation Factor-3/genetics ; Eukaryotic Initiation Factor-3/metabolism ; Gene Expression Regulation, Neoplastic ; Liver Neoplasms/pathology ; Methyltransferases/genetics ; Methyltransferases/metabolism ; RNA, Long Noncoding/genetics ; Tetraspanins ; Wnt Signaling Pathway
    Chemical Substances Cysteine Endopeptidases (EC 3.4.22.-) ; EIF3I protein, human (171601-26-6) ; Eukaryotic Initiation Factor-3 ; Methyltransferases (EC 2.1.1.-) ; METTL3 protein, human (EC 2.1.1.62) ; RNA, Long Noncoding ; SENP1 protein, human (EC 3.4.-) ; Tetraspanins ; TSPAN12 protein, human
    Language English
    Publishing date 2024-02-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 639046-8
    ISSN 1476-5594 ; 0950-9232
    ISSN (online) 1476-5594
    ISSN 0950-9232
    DOI 10.1038/s41388-024-02970-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: A comprehensive comparative assessment of 3D molecular similarity tools in ligand-based virtual screening.

    Jiang, Zhenla / Xu, Jianrong / Yan, Aixia / Wang, Ling

    Briefings in bioinformatics

    2021  Volume 22, Issue 6

    Abstract: Three-dimensional (3D) molecular similarity, one major ligand-based virtual screening (VS) method, has been widely used in the drug discovery process. A variety of 3D molecular similarity tools have been developed in recent decades. In this study, we ... ...

    Abstract Three-dimensional (3D) molecular similarity, one major ligand-based virtual screening (VS) method, has been widely used in the drug discovery process. A variety of 3D molecular similarity tools have been developed in recent decades. In this study, we assessed a panel of 15 3D molecular similarity programs against the DUD-E and LIT-PCBA datasets, including commercial ROCS and Phase, in terms of screening power and scaffold-hopping power. The results revealed that (1) SHAFTS, LS-align, Phase Shape_Pharm and LIGSIFT showed the best VS capability in terms of screening power. Some 3D similarity tools available to academia can yield relatively better VS performance than commercial ROCS and Phase software. (2) Current 3D similarity VS tools exhibit a considerable ability to capture actives with new chemotypes in terms of scaffold hopping. (3) Multiple conformers relative to single conformations will generally improve VS performance for most 3D similarity tools, with marginal improvement observed in area under the receiving operator characteristic curve values, enrichment factor in the top 1% and hit rate in the top 1% values showed larger improvement. Moreover, redundancy and complementarity analyses of hit lists from different query seeds and different 3D similarity VS tools showed that the combination of different query seeds and/or different 3D similarity tools in VS campaigns retrieved more (and more diverse) active molecules. These findings provide useful information for guiding choices of the optimal 3D molecular similarity tools for VS practices and designing possible combination strategies to discover more diverse active compounds.
    MeSH term(s) Area Under Curve ; Benchmarking ; Databases, Pharmaceutical ; Drug Design ; Drug Discovery/methods ; Drug Evaluation, Preclinical/methods ; Ligands ; Models, Molecular ; Molecular Conformation ; Molecular Structure ; ROC Curve ; Software ; Web Browser
    Chemical Substances Ligands
    Language English
    Publishing date 2021-03-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbab231
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Investigation of clear cell renal cell carcinoma grades using diffusion-relaxation correlation spectroscopic imaging with optimized spatial-spectrum analysis.

    Luo, Yuansheng / Zhu, Mengying / Wei, Xiaobin / Xu, Jianrong / Pan, Shihang / Liu, Guiqin / Song, Yang / Hu, Wentao / Dai, Yongming / Wu, Guangyu

    The British journal of radiology

    2024  Volume 97, Issue 1153, Page(s) 135–141

    Abstract: Objectives: To differentiate high-grade from low-grade clear cell renal cell carcinoma (ccRCC) using diffusion-relaxation correlation spectroscopic imaging (DR-CSI) spectra in an equal separating analysis.: Methods: Eighty patients with 86 ... ...

    Abstract Objectives: To differentiate high-grade from low-grade clear cell renal cell carcinoma (ccRCC) using diffusion-relaxation correlation spectroscopic imaging (DR-CSI) spectra in an equal separating analysis.
    Methods: Eighty patients with 86 pathologically confirmed ccRCCs who underwent DR-CSI were enrolled. Two radiologists delineated the region of interest. The spectrum was derived based on DR-CSI and was further segmented into multiple equal subregions from 2*2 to 9*9. The agreement between the 2 radiologists was assessed by the intraclass correlation coefficient (ICC). Logistic regression was used to establish the regression model for differentiation, and 5-fold cross-validation was used to evaluate its accuracy. McNemar's test was used to compare the diagnostic performance between equipartition models and the traditional parameters, including the apparent diffusion coefficient (ADC) and T2 value.
    Results: The inter-reader agreement decreased as the divisions in the equipartition model increased (overall ICC ranged from 0.859 to 0.920). The accuracy increased from the 2*2 to 9*9 equipartition model (0.68 for 2*2, 0.69 for 3*3 and 4*4, 0.70 for 5*5, 0.71 for 6*6, 0.78 for 7*7, and 0.75 for 8*8 and 9*9). The equipartition models with divisions >7*7 were significantly better than ADC and T2 (vs ADC: P = .002-.008; vs T2: P = .001-.004).
    Conclusions: The equipartition method has the potential to analyse the DR-CSI spectrum and discriminate between low-grade and high-grade ccRCC.
    Advances in knowledge: The evaluation of DR-CSI relies on prior knowledge, and how to assess the spectrum derived from DR-CSI without prior knowledge has not been well studied.
    MeSH term(s) Humans ; Carcinoma, Renal Cell ; Spectrum Analysis ; Diagnostic Imaging ; Cell Differentiation ; Kidney Neoplasms
    Language English
    Publishing date 2024-01-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 2982-8
    ISSN 1748-880X ; 0007-1285
    ISSN (online) 1748-880X
    ISSN 0007-1285
    DOI 10.1093/bjr/tqad003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Effect of physical activity combined with extra ciliary-muscle training on visual acuity of children aged 10-11.

    Yin, Rongbin / Xu, Jianrong / Wang, Hongyun / Zhou, Sheng / Zhang, Meng / Cai, Geng

    Frontiers in public health

    2022  Volume 10, Page(s) 949130

    Abstract: This study is intended for exploring the effects of the physical activity combined with extra ciliary-muscle training with different frequencies on children's kinetic visual acuity and uncorrected distance visual acuity, and eventually figuring out the ... ...

    Abstract This study is intended for exploring the effects of the physical activity combined with extra ciliary-muscle training with different frequencies on children's kinetic visual acuity and uncorrected distance visual acuity, and eventually figuring out the optimal frequency of ciliary-muscle training for each physical education class. To do the present research, A total of 160 students aged 10-11 from a school in Suzhou (a major city located in southeastern Jiangsu Province, East China) were randomly selected and divided into control group (
    MeSH term(s) Child ; Exercise ; Humans ; Muscles ; Schools ; Students ; Visual Acuity
    Language English
    Publishing date 2022-08-30
    Publishing country Switzerland
    Document type Journal Article ; Randomized Controlled Trial ; Research Support, Non-U.S. Gov't
    ZDB-ID 2711781-9
    ISSN 2296-2565 ; 2296-2565
    ISSN (online) 2296-2565
    ISSN 2296-2565
    DOI 10.3389/fpubh.2022.949130
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Anti-biofilm activities of coumarin as quorum sensing inhibitor for

    He, Zhiyan / Jiang, Wei / Jiang, Yiting / Dong, Jiachen / Song, Zhongchen / Xu, Jianrong / Zhou, Wei

    Journal of oral microbiology

    2022  Volume 14, Issue 1, Page(s) 2055523

    Abstract: Porphyromonas ... ...

    Abstract Porphyromonas gingivalis
    Language English
    Publishing date 2022-03-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2523919-3
    ISSN 2000-2297
    ISSN 2000-2297
    DOI 10.1080/20002297.2022.2055523
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