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  1. Article ; Online: Large-Scale Glass-Transition Temperature Prediction with an Equivariant Neural Network for Screening Polymers.

    Long, Zheng / Lu, Hongmei / Zhang, Zhimin

    ACS omega

    2024  Volume 9, Issue 5, Page(s) 5452–5462

    Abstract: The practically infinite chemical and morphological space of polymers makes them pervasive with applications in materials science but challenges the rational discovery of new materials with favorable properties. Polymer informatics aims to accelerate ... ...

    Abstract The practically infinite chemical and morphological space of polymers makes them pervasive with applications in materials science but challenges the rational discovery of new materials with favorable properties. Polymer informatics aims to accelerate materials design through property prediction and large-scale virtual screening. In this study, a new method (Lieconv-Tg) has been developed to predict glass-transition temperature (Tg) values from repeating units of polymers based on Lieconv, which is equivariant with transformations from any specified Lie group. The introduction of equivariance allows the prediction of molecular properties from their 3D structures, independent of orientation and position. A total of 27,659 homopolymers with Tg values were collected from PolyInfo, and a standard data set containing 7166 polymers (named data set_Tg) was created for training a robust Lieconv-Tg model. Using the 3D coordinates as input, Lieconv-Tg performs better than Edge-Conditioned Convolution (ECC), and the mean absolute error (MAE) is significantly reduced by ∼6 from ∼30 to ∼24 on both the validation set and the test set, and the
    Language English
    Publishing date 2024-01-26
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c06843
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Repurposing FBP1: dephosphorylating IκBα to suppress NFκB.

    Zhang, Gang / Tao, Jingjing / Lin, Liming / Qiu, Wensheng / Lu, Zhimin

    Cell research

    2023  Volume 33, Issue 6, Page(s) 419–420

    Language English
    Publishing date 2023-03-21
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 1319303-x
    ISSN 1748-7838 ; 1001-0602
    ISSN (online) 1748-7838
    ISSN 1001-0602
    DOI 10.1038/s41422-023-00785-4
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  3. Article ; Online: Single cell RNA-sequencing data generated from mouse adipose tissue during the development of obesity.

    Lu, Zhimin / Ding, Ling / Tian, Xuewen / Wang, Qinglu

    Data in brief

    2024  Volume 53, Page(s) 110119

    Abstract: In recent years, the number of obesity has increased rapidly around the world, and it has become a major public health problem endangering global health [1]. Obesity is caused by excessive calorie intake over a long period of time, and high-fat diet (HFD) ...

    Abstract In recent years, the number of obesity has increased rapidly around the world, and it has become a major public health problem endangering global health [1]. Obesity is caused by excessive calorie intake over a long period of time, and high-fat diet (HFD) is one of the important predisposing factors [2], [3], [4]. Adipose tissue (AT) is an important immune and endocrine organ in the body, and plays an important role in the body [5]. Obesity leads to AT dysfunction, AT dilation and cell hypertrophy. Dysfunctional fat cells are the main source of pro-inflammatory cytokines, which aggravate low-grade systemic inflammation and further promote the development of obesity-related diseases [6], [7], [8]. However, whether AT releases pro-inflammatory cytokines in the early stages of obesity development remains unknown. The AT microenvironment is composed of a variety of cells, including fat cells, immune cells, fibroblasts, and endothelial cells. The immune microenvironment (TIME) and its metabolic imbalance can lead to the secretion or regulation of related hormones, which causes inflammation AT [9]. TIME is very important for maintaining AT homeostasis, which is crucial for the occurrence of obesity [10,11]. This data use single-cell RNA sequencing (sNuc-Seq) to analyze the characteristics of TIME changes in the mouse epididymal adipose tissue during the development of obesity, and the changes of cell types and genes in the tissue.
    Language English
    Publishing date 2024-02-01
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2024.110119
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  4. Article ; Online: Hexokinases in cancer and other pathologies.

    Guo, Dong / Meng, Ying / Jiang, Xiaoming / Lu, Zhimin

    Cell insight

    2023  Volume 2, Issue 1, Page(s) 100077

    Abstract: Glucose metabolism is indispensable for cell growth and survival. Hexokinases play pivotal roles in glucose metabolism through canonical functions of hexokinases as well as in immune response, cell stemness, autophagy, and other cellular activities ... ...

    Abstract Glucose metabolism is indispensable for cell growth and survival. Hexokinases play pivotal roles in glucose metabolism through canonical functions of hexokinases as well as in immune response, cell stemness, autophagy, and other cellular activities through noncanonical functions. The aberrant regulation of hexokinases contributes to the development and progression of pathologies, including cancer and immune diseases.
    Language English
    Publishing date 2023-01-03
    Publishing country Netherlands
    Document type Journal Article ; Review
    ISSN 2772-8927
    ISSN (online) 2772-8927
    DOI 10.1016/j.cellin.2023.100077
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: HK2: Gatekeeping microglial activity by tuning glucose metabolism and mitochondrial functions.

    Fang, Jing / Luo, Shudi / Lu, Zhimin

    Molecular cell

    2023  Volume 83, Issue 6, Page(s) 829–831

    Abstract: Hexokinase 2 (HK2) plays a multifaceted role in the regulation of cellular activities. A new study by Hu et al. ...

    Abstract Hexokinase 2 (HK2) plays a multifaceted role in the regulation of cellular activities. A new study by Hu et al.
    MeSH term(s) Hexokinase/genetics ; Hexokinase/metabolism ; Microglia/metabolism ; Gatekeeping ; Mitochondria/metabolism ; Glycolysis/physiology ; Glucose/metabolism
    Chemical Substances Hexokinase (EC 2.7.1.1) ; Glucose (IY9XDZ35W2)
    Language English
    Publishing date 2023-03-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2023.02.022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: A comprehensive pan-cancer analysis of the expression characteristics, prognostic value, and immune characteristics of

    Fei, Lihong / Lu, Zhimin / Xu, Yufen / Hou, Guoxin

    Frontiers in genetics

    2022  Volume 13, Page(s) 920897

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2022-08-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2022.920897
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  7. Article: The Mitochondrial Protein C1QBP Promotes Hepatocellular Carcinoma Progression by Enhancing Cell Survival, Migration and Invasion.

    Hou, Guoxin / Lu, Zhimin / Wang, Zhen / Yang, Xinmei

    Journal of Cancer

    2022  Volume 13, Issue 8, Page(s) 2477–2489

    Abstract: Backgrounds: ...

    Abstract Backgrounds:
    Language English
    Publishing date 2022-05-09
    Publishing country Australia
    Document type Journal Article
    ZDB-ID 2573318-7
    ISSN 1837-9664
    ISSN 1837-9664
    DOI 10.7150/jca.69379
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  8. Article ; Online: GCMSFormer: A Fully Automatic Method for the Resolution of Overlapping Peaks in Gas Chromatography-Mass Spectrometry.

    Guo, Zixuan / Fan, Yingjie / Yu, Chuanxiu / Lu, Hongmei / Zhang, Zhimin

    Analytical chemistry

    2024  Volume 96, Issue 15, Page(s) 5878–5886

    Abstract: Gas chromatography-mass spectrometry (GC-MS) is one of the most important instruments for analyzing volatile organic compounds. However, the complexity of real samples and the limitations of chromatographic separation capabilities lead to coeluting ... ...

    Abstract Gas chromatography-mass spectrometry (GC-MS) is one of the most important instruments for analyzing volatile organic compounds. However, the complexity of real samples and the limitations of chromatographic separation capabilities lead to coeluting compounds without ideal separation. In this study, a Transformer-based automatic resolution method (GCMSFormer) is proposed to resolve mass spectra from GC-MS peaks in an end-to-end manner, predicting the mass spectra of components directly from the raw overlapping peaks data. Furthermore, orthogonal projection resolution (OPR) was integrated into GCMSFormer to resolve minor components. The GCMSFormer model was trained, validated, and tested using 100,000 augmented data. It achieves 99.88% of the bilingual evaluation understudy (BLEU) value on the test set, significantly higher than the 97.68% BLEU value of the baseline sequence-to-sequence model long short-term memory (LSTM). GCMSFormer was also compared with two nondeep learning resolution tools (MZmine and AMDIS) and two deep learning resolution tools (PARAFAC2 with DL and MSHub/GNPS) on a real plant essential oil GC-MS data set. Their resolution results were compared on evaluation metrics, including the number of compounds resolved, mass spectral match score, correlation coefficient, explained variance, and resolution speed. The results demonstrate that GCMSFormer has better resolution performance, higher automation, and faster resolution speed. In summary, GCMSFormer is an end-to-end, fast, fully automatic, and accurate method for analyzing GC-MS data of complex samples.
    Language English
    Publishing date 2024-04-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.3c05772
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    Zs.A 4033: Show issues Location:
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  9. Article ; Online: Efficacy and safety of tyrosine kinase inhibitors for advanced metastatic thyroid cancer: A systematic review and network meta-analysis of randomized controlled trials.

    Zhao, Mingjian / Li, Ruowen / Song, Zhimin / Miao, Chengxu / Lu, Jinghui

    Medicine

    2024  Volume 103, Issue 15, Page(s) e37655

    Abstract: Background: Tyrosine kinase inhibitors (TKIs) have been approved for treating patients with clinically advanced metastatic thyroid cancer. However among the many TKIs, it remains unknown which regimen is the best choice for these patients.: Methods: ... ...

    Abstract Background: Tyrosine kinase inhibitors (TKIs) have been approved for treating patients with clinically advanced metastatic thyroid cancer. However among the many TKIs, it remains unknown which regimen is the best choice for these patients.
    Methods: We conducted a systematic review and network meta-analysis to compare the survival benefits and efficacy of the available first-line regimens. We conducted an active search for phase II, III, or IV randomized controlled trials (RCTs) in the PubMed, Embase, and Cochrane databases to compare the effects of at least 2 drugs in the systemic treatment of advanced or metastatic thyroid cancer up to May 2023. The network meta-analysis model was adjusted using Bayesian Network model. Twelve trials with 2535 patients were included in our meta-analysis. The overall survival (OS), progression-free survival (PFS), and serious adverse events (SAEs) were taken as reference indicators. We also performed subgroup analyses of OS and PFS in medullary thyroid cancer (MTC) and radioiodine-refractory differentiated thyroid cancer (RR-DTC) to explore the variations of TKIs in different groups.
    Results: As a result, apatinib had the best effect on overall survival (OS) (hazards ratio [HR] = 0.42, 95% confidence interval [CI] = 0.18-0.98), lenvatinib 18 mg/d has the best effect on progression-free survival (PFS) (HR = 0.13, 95% CI = 0.064-0.27), and cabozantinib 60 mg/d has the best safety profile.
    Conclusions: Our network meta-analysis showed that we believe that cabozantinib has the potential to become a widely used drug in clinical practice.
    MeSH term(s) Humans ; Tyrosine Kinase Inhibitors ; Network Meta-Analysis ; Randomized Controlled Trials as Topic ; Anilides ; Neoplasms ; Pyridines
    Chemical Substances cabozantinib (1C39JW444G) ; Tyrosine Kinase Inhibitors ; Anilides ; Pyridines
    Language English
    Publishing date 2024-04-12
    Publishing country United States
    Document type Meta-Analysis ; Systematic Review ; Journal Article
    ZDB-ID 80184-7
    ISSN 1536-5964 ; 0025-7974
    ISSN (online) 1536-5964
    ISSN 0025-7974
    DOI 10.1097/MD.0000000000037655
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  10. Article ; Online: [Site-directed mutagenesis enhances the activity of benzylidene acetone synthase of polyketide synthase from

    He, Zhimin / Ma, Wenrui / Yu, Liping / Lü, Heshu / Yang, Mingfeng

    Sheng wu gong cheng xue bao = Chinese journal of biotechnology

    2023  Volume 39, Issue 7, Page(s) 2806–2817

    Abstract: Polygonum ... ...

    Abstract Polygonum cuspidatum
    MeSH term(s) Amino Acid Sequence ; Fallopia japonica/genetics ; Fallopia japonica/metabolism ; Polyketide Synthases/chemistry ; Acetone ; Mutagenesis, Site-Directed ; Flavonoids/chemistry ; Flavonoids/metabolism ; Acyltransferases/metabolism
    Chemical Substances Polyketide Synthases (79956-01-7) ; Acetone (1364PS73AF) ; Flavonoids ; Acyltransferases (EC 2.3.-)
    Language Chinese
    Publishing date 2023-08-02
    Publishing country China
    Document type English Abstract ; Journal Article
    ZDB-ID 1042206-7
    ISSN 1872-2075 ; 1042-749X
    ISSN (online) 1872-2075
    ISSN 1042-749X
    DOI 10.13345/j.cjb.220815
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