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  1. Article: Covariates distributions balancing for continuous treatment

    Jiang, Qingshan / Xu, Li / Huang, Can

    Economics letters. 2022 Aug., v. 217

    2022  

    Abstract: We define a different weighted sample distance covariance and incorporate it into a weighting method optimizing covariates balancing with continuous treatment. The balancing weights are identified with the assistance of the weighted sample energy ... ...

    Abstract We define a different weighted sample distance covariance and incorporate it into a weighting method optimizing covariates balancing with continuous treatment. The balancing weights are identified with the assistance of the weighted sample energy distance.
    Keywords covariance ; economics ; energy
    Language English
    Dates of publication 2022-08
    Publishing place Elsevier B.V.
    Document type Article
    ISSN 0165-1765
    DOI 10.1016/j.econlet.2022.110644
    Database NAL-Catalogue (AGRICOLA)

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  2. Article: Role of CD23 Activated ERK Signaling Pathway in the Pathogenesis of Eosinophilic Chronic Sinusitis with Nasal Polyps.

    Xu, Ming / Chen, Zuyao / Jiang, Qingshan / Gong, Yongqian / Tang, Hongbo

    Alternative therapies in health and medicine

    2023  Volume 29, Issue 8, Page(s) 638–643

    Abstract: Objective: In the context of the rising prevalence of eosinophilic chronic sinusitis accompanied by nasal polyps, this study aims toinvestigate the role of CD23 in the pathogenesis of eosinophilic chronic sinusitis with nasal polyps.: Methods: The ... ...

    Abstract Objective: In the context of the rising prevalence of eosinophilic chronic sinusitis accompanied by nasal polyps, this study aims toinvestigate the role of CD23 in the pathogenesis of eosinophilic chronic sinusitis with nasal polyps.
    Methods: The cross-sectional study was conducted, 75 patients with chronic sinusitis and nasal polyps treated in our hospital from January 2019 to May 2021 were selected, including 40 cases of eosinophilic patients with the average age of 29.92 years and 35 cases of non-eosinophilic patients with the average age of 30.05 years and 30 patients with the average age of 30.14 years who underwent skull base benign tumor resection in our hospital were selected as the control group, the expression of CD23 in polyp tissue was detected by immunohistochemistry, and the expression of CD23, p-ERK and CCL20 in polyp tissue were detected by Western blot. Specifically, tissue samples were processed and subjected to staining using specific antibodies targeting CD23. The stained sections were then visualized under a microscope to determine the expression levels of CD23. CD23, p-ERK, and CCL20 expressions in polyp tissue were evaluated via Western blot. Total protein was extracted, separated on a gel, transferred to a membrane, and probed with specific antibodies. Chemiluminescence allowed visualization and quantification of protein expressions.
    Results: Immunohistochemistry showed that CD23 expression was high in the eosinophilic group but low in the non-eosinophilic and control groups. The relative expression levels of CD23 protein, p-ERK protein, and CCL20 protein in polyp tissue s of the eosinophilic group were (0.892 ± 0.092), (0.733 ± 0.101) and (0.813 ± 0.106), respectively, which were significantly higher than those in non-eosinophilic group and control group (P < .05). The relative expression levels of CD23 protein, p-ERK protein, and CCL20 protein in the non-eosinophilic group were (0.461 ± 0.087), 0.412 ± 0.096) and (0.424 ± 0.098), which were significantly higher than those in the control group (P < .05). The relative expression level of CD23 protein in the eosinophilic group was positively correlated with the relative expression levels of p-ERK protein and CCL20 protein (P < .05). The Lund-Kennedy score in the eosinophilic group was (6.10 ± 1.01), which was significantly higher than that in the non-eosinophilic group (P < .05). The relative expression level of CD23 protein in the eosinophilic group was positively correlated with Lund-Kennedy score (P < .05).
    Conclusion: Eosinophilic chronic sinusitis with nasal polyp mucosal tissue CD23 expression is up-regulated, which is positively correlated with the ERK signaling pathway and disease severity. This study provides valuable insights into potential therapeutic targets that could be explored to develop future treatment modalities. The potential clinical significance of the study is to reveal the important role of CD23 in the pathogenesis of chronic sinusitis with nasal polyps. The upward adjustment of CD23 is positively related to the severity of the disease, which provides valuable guidance for future treatment strategies. This discovery may provide new ways for the development of CD23 treatment methods, so as to better control the progress of the disease of eosinophilic chronic sinusitis with nasal polyps. Further research can explore the molecular mechanism of CD23 regulation, further verify the feasibility of CD23 as the treatment target, and evaluate the potential value of CD23 as a prognostic logo.
    MeSH term(s) Humans ; Adult ; Rhinitis/complications ; Nasal Polyps/complications ; Nasal Polyps/pathology ; Cross-Sectional Studies ; Sinusitis/complications ; Sinusitis/pathology ; Signal Transduction ; Chronic Disease
    Language English
    Publishing date 2023-09-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1225073-9
    ISSN 1078-6791
    ISSN 1078-6791
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: BO-DNA: Biologically optimized encoding model for a highly-reliable DNA data storage.

    Rasool, Abdur / Hong, Jingwei / Jiang, Qingshan / Chen, Hui / Qu, Qiang

    Computers in biology and medicine

    2023  Volume 165, Page(s) 107404

    Abstract: DNA data storage is a promising technology that utilizes computer simulation, and synthetic biology, offering high-density and reliable digital information storage. It is challenging to store massive data in a small amount of DNA without losing the ... ...

    Abstract DNA data storage is a promising technology that utilizes computer simulation, and synthetic biology, offering high-density and reliable digital information storage. It is challenging to store massive data in a small amount of DNA without losing the original data since nonspecific hybridization errors occur frequently and severely affect the reliability of stored data. This study proposes a novel biologically optimized encoding model for DNA data storage (BO-DNA) to overcome the reliability problem. BO-DNA model is developed by a new rule-based mapping method to avoid data drop during the transcoding of binary data to premier nucleotides. A customized optimization algorithm based on a tent chaotic map is applied to maximize the lower bounds that help to minimize the nonspecific hybridization errors. The robustness of BO-DNA is computed by four bio-constraints to confirm the reliability of newly generated DNA sequences. Experimentally, different medical images are encoded and decoded successfully with 12%-59% improved lower bounds and optimally constrained-based DNA sequences reported with 1.77bit/nt average density. BO-DNA's results demonstrate substantial advantages in constructing reliable DNA data storage.
    MeSH term(s) Computer Simulation ; Reproducibility of Results ; DNA/genetics ; Algorithms
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2023-08-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2023.107404
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Contrastive variational information bottleneck for aspect-based sentiment analysis

    Chang, Mingshan / Yang, Min / Jiang, Qingshan / Xu, Ruifeng

    2023  

    Abstract: Deep learning techniques have dominated the literature on aspect-based sentiment analysis (ABSA), achieving state-of-the-art performance. However, deep models generally suffer from spurious correlations between input features and output labels, which ... ...

    Abstract Deep learning techniques have dominated the literature on aspect-based sentiment analysis (ABSA), achieving state-of-the-art performance. However, deep models generally suffer from spurious correlations between input features and output labels, which hurts the robustness and generalization capability by a large margin. In this paper, we propose to reduce spurious correlations for ABSA, via a novel Contrastive Variational Information Bottleneck framework (called CVIB). The proposed CVIB framework is composed of an original network and a self-pruned network, and these two networks are optimized simultaneously via contrastive learning. Concretely, we employ the Variational Information Bottleneck (VIB) principle to learn an informative and compressed network (self-pruned network) from the original network, which discards the superfluous patterns or spurious correlations between input features and prediction labels. Then, self-pruning contrastive learning is devised to pull together semantically similar positive pairs and push away dissimilar pairs, where the representations of the anchor learned by the original and self-pruned networks respectively are regarded as a positive pair while the representations of two different sentences within a mini-batch are treated as a negative pair. To verify the effectiveness of our CVIB method, we conduct extensive experiments on five benchmark ABSA datasets and the experimental results show that our approach achieves better performance than the strong competitors in terms of overall prediction performance, robustness, and generalization. Code and data to reproduce the results in this paper is available at: https://github.com/shesshan/CVIB.

    Comment: Accepted by Knowledge-Based Systems (KBS)
    Keywords Computer Science - Computation and Language ; Computer Science - Artificial Intelligence
    Subject code 006
    Publishing date 2023-03-05
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Evolutionary approach to construct robust codes for DNA-based data storage.

    Rasool, Abdur / Jiang, Qingshan / Wang, Yang / Huang, Xiaoluo / Qu, Qiang / Dai, Junbiao

    Frontiers in genetics

    2023  Volume 14, Page(s) 1158337

    Abstract: DNA is a practical storage medium with high density, durability, and capacity to accommodate exponentially growing data volumes. A DNA sequence structure is a biocomputing problem that requires satisfying bioconstraints to design robust sequences. ... ...

    Abstract DNA is a practical storage medium with high density, durability, and capacity to accommodate exponentially growing data volumes. A DNA sequence structure is a biocomputing problem that requires satisfying bioconstraints to design robust sequences. Existing evolutionary approaches to DNA sequences result in errors during the encoding process that reduces the lower bounds of DNA coding sets used for molecular hybridization. Additionally, the disordered DNA strand forms a secondary structure, which is susceptible to errors during decoding. This paper proposes a computational evolutionary approach based on a synergistic moth-flame optimizer by Levy flight and opposition-based learning mutation strategies to optimize these problems by constructing reverse-complement constraints. The MFOS aims to attain optimal global solutions with robust convergence and balanced search capabilities to improve DNA code lower bounds and coding rates for DNA storage. The ability of the MFOS to construct DNA coding sets is demonstrated through various experiments that use 19 state-of-the-art functions. Compared with the existing studies, the proposed approach with three different bioconstraints substantially improves the lower bounds of the DNA codes by 12-28% and significantly reduces errors.
    Language English
    Publishing date 2023-03-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1158337
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A Micro-Topography Measurement and Compensation Method for the Key Component Surface Based on White-Light Interferometry.

    Chen, Junying / Wang, Boxuan / Chen, Xiuyu / Jiang, Qingshan / Feng, Wei / Xu, Zhilong / Zhao, Zhenye

    Sensors (Basel, Switzerland)

    2023  Volume 23, Issue 19

    Abstract: The grinding grooves of material removal machining and the residues of a machining tool on the key component surface cause surface stress concentration. Thus, it is critical to carry out precise measurements on the key component surface to evaluate the ... ...

    Abstract The grinding grooves of material removal machining and the residues of a machining tool on the key component surface cause surface stress concentration. Thus, it is critical to carry out precise measurements on the key component surface to evaluate the stress concentration. Based on white-light interferometry (WLI), we studied the measurement distortion caused by the reflected light from the steep side of the grinding groove being unable to return to the optical system for imaging. A threshold value was set to eliminate the distorted measurement points, and the cubic spline algorithm was used to interpolate the eliminated points for compensation. The compensation result agrees well with the atomic force microscope (AFM) measurement result. However, for residues on the surface, a practical method was established to obtain a microscopic 3D micro-topography point cloud and a super-depth-of-field fusion image simultaneously. Afterward, the semantic segmentation network U-net was adopted to identify the residues in the super-depth-of-field fusion image and achieved a recognition accuracy of 91.06% for residual identification. Residual feature information, including height, position, and size, was obtained by integrating the information from point clouds and super-depth-of-field fusion images. This work can provide foundational data to study surface stress concentration.
    Language English
    Publishing date 2023-10-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s23198307
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Isoquercitrin promotes ferroptosis and oxidative stress in nasopharyngeal carcinoma via the AMPK/NF-κB pathway.

    Luo, Xinggu / Gong, Yongqian / Jiang, Qingshan / Wang, Qin / Li, Songtao / Liu, Lijun

    Journal of biochemical and molecular toxicology

    2023  Volume 38, Issue 1, Page(s) e23542

    Abstract: Isoquercitrin has been discovered with various biological properties, including anticancer, anti-inflammation, antioxidation, and neuroprotection. The aim of this study is to explore the efficacy of isoquercitrin in nasopharyngeal carcinoma (NPC) and to ... ...

    Abstract Isoquercitrin has been discovered with various biological properties, including anticancer, anti-inflammation, antioxidation, and neuroprotection. The aim of this study is to explore the efficacy of isoquercitrin in nasopharyngeal carcinoma (NPC) and to disclose its potential regulating mechanisms. CNE1 and HNE1 cells were treated with various concentrations of isoquercitrin. Ferrostatin-1 (Fer-1, a ferroptosis inhibitor) and alpha-lipoic acid (ALA, an activator of the AMP-activated protein kinase [AMPK] pathway) treatments were conducted to verify the effects of isoquercitrin, respectively. Cell viability, proliferation, reactive oxygen species (ROS) generation, and lipid peroxidation were determined, respectively. GPX4 expression and ferroptosis- and pathway-related protein expression were measured. A xenograft tumor model was constructed by subcutaneously inoculating CNE1 cells into the middle groin of each mouse. We found that the IC50 values of CNE1 and HNE1 cells were 392.45 and 411.38 μM, respectively. CNE1 and HNE1 viability and proliferation were both markedly reduced with the increasing concentration of isoquercitrin. ROS generation and lipid peroxidation were both enhanced with declined ferroptosis-related markers under isoquercitrin treatment. The nuclear factor kappa B (NF-κB) pathway, the AMPK pathway, and the interleukin (IL)-1β expression were all markedly suppressed by isoquercitrin. Moreover, isoquercitrin restrained the tumor growth and enhanced lipid peroxidation and ferroptosis in vivo. Interestingly, both Fer-1 and ALA treatments distinctly offset isoquercitrin-induced effects in vitro and in vivo. These findings indicated that isoquercitrin might enhance oxidative stress and ferroptosis in NPC via AMPK/NF-κB p65 inhibition.
    MeSH term(s) Humans ; Mice ; Animals ; NF-kappa B/metabolism ; AMP-Activated Protein Kinases/metabolism ; Nasopharyngeal Carcinoma/drug therapy ; Signal Transduction ; Reactive Oxygen Species/metabolism ; Ferroptosis ; Oxidative Stress ; Disease Models, Animal ; Nasopharyngeal Neoplasms ; Quercetin/analogs & derivatives
    Chemical Substances NF-kappa B ; AMP-Activated Protein Kinases (EC 2.7.11.31) ; isoquercitrin (0YX10VRV6J) ; Reactive Oxygen Species ; Quercetin (9IKM0I5T1E)
    Language English
    Publishing date 2023-09-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1410020-4
    ISSN 1099-0461 ; 1095-6670
    ISSN (online) 1099-0461
    ISSN 1095-6670
    DOI 10.1002/jbt.23542
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: EIF4A3-induced circFIP1L1 represses miR-1253 and promotes radiosensitivity of nasopharyngeal carcinoma

    Zhou, Xiangqi / Yuan, Guangjin / Wu, Yangjie / Yan, Sijia / Jiang, Qingshan / Tang, Sanyuan

    Cellular and molecular life sciences. 2022 July, v. 79, no. 7

    2022  

    Abstract: BACKGROUND: Radiation is currently used to be a mainstay of salvage therapy for nasopharyngeal carcinoma (NPC), however, development of radioresistance largely limits the radiation efficacy. Circular RNAs (circRNAs) have been shown to affect NPC ... ...

    Abstract BACKGROUND: Radiation is currently used to be a mainstay of salvage therapy for nasopharyngeal carcinoma (NPC), however, development of radioresistance largely limits the radiation efficacy. Circular RNAs (circRNAs) have been shown to affect NPC progression, but its role in radioresistance remain unclear. METHODS: The circular structure of circFIP1L1(circ_0069740) was verified by RNA-sequencing, RT-PCR based on gDNA or cDNA, RNase R treatment, and actinomycin D treatment. Cellular localization of circFIP1L1 and miR-1253 was detected by nucleoplasmic separation and/or fluorescence in situ hybridization. Expression of non-coding RNAs and mRNAs was detected by qRT-PCR, protein expression was detected by Western blot. Functionally, EdU, CCK-8, and colony formation experiments were employed to assess cell proliferation, flow cytometry was adopted to estimate cell cycle and apoptosis. Xenograft tumor growth was performed to detect the role of circFIP1L1 in vivo. Mechanistically, we examined the interplay between miR-1253 and circFIP1L1 or EIF4A3 through dual-luciferase reporter assay. The potential regulatory impacts of EIF4A3 on circFIP1L1 or PTEN was examined by RNA immunoprecipitation and RNA pull-down assays. RESULTS: CircFIP1L1 overexpression and miR-1253 knockdown repressed NPC cell proliferation, facilitated NPC cell apoptosis, and enhanced NPC radiosensitivity. Mechanistically, circFIP1L1 was revealed to repress miR-1253 by binding to it, and EIF4A3 is a target gene of miR-1253. CircFIP1L1 regulated NPC proliferation, apoptosis, and radiosensitivity through miR-1253/EIF4A3. Moreover, we found that EIF4A3 bound to FIP1L1 mRNA transcript and induced circFIP1L1 formation, and thus stabilizing PTEN mRNA. CONCLUSION: Our findings suggested that EIF4A3-induced circFIP1L1 repressed NPC cell proliferation, facilitated NPC cell apoptosis, and enhanced NPC radiosensitivity by miR-1253.
    Keywords Western blotting ; apoptosis ; bioluminescence assay ; carcinoma ; cell cycle ; cell proliferation ; flow cytometry ; fluorescence ; genes ; hybridization ; precipitin tests ; protein synthesis ; radiation resistance ; ribonucleases ; sequence analysis ; xenotransplantation
    Language English
    Dates of publication 2022-07
    Size p. 357.
    Publishing place Springer International Publishing
    Document type Article
    ZDB-ID 1358415-7
    ISSN 1420-9071 ; 1420-682X
    ISSN (online) 1420-9071
    ISSN 1420-682X
    DOI 10.1007/s00018-022-04350-x
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: PFBNet: a priori-fused boosting method for gene regulatory network inference.

    Che, Dandan / Guo, Shun / Jiang, Qingshan / Chen, Lifei

    BMC bioinformatics

    2020  Volume 21, Issue 1, Page(s) 308

    Abstract: Background: Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data ... ...

    Abstract Background: Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of potential interactions.
    Results: We present a novel method, namely priori-fused boosting network inference method (PFBNet), to infer GRNs from time-series expression data by using the non-linear model of Boosting and the prior information (e.g., the knockout data) fusion scheme. Specifically, PFBNet first calculates the confidences of the regulation relationships using the boosting-based model, where the information about the accumulation impact of the gene expressions at previous time points is taken into account. Then, a newly defined strategy is applied to fuse the information from the prior data by elevating the confidences of the regulation relationships from the corresponding regulators.
    Conclusions: The experiments on the benchmark datasets from DREAM challenge as well as the E.coli datasets show that PFBNet achieves significantly better performance than other state-of-the-art methods (Jump3, GEINE3-lag, HiDi, iRafNet and BiXGBoost).
    MeSH term(s) Algorithms ; Area Under Curve ; Computational Biology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Gene Regulatory Networks ; ROC Curve
    Language English
    Publishing date 2020-07-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-020-03639-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Clinical Significance of an m6A Reader Gene,

    Deng, Xiaoli / Jiang, Qingshan / Liu, Zhifeng / Chen, Wen

    Frontiers in molecular biosciences

    2020  Volume 7, Page(s) 68

    Abstract: The importance of N6-methyladenosine (m6A) in tumor recurrence and prognosis has been recognized in recent years. The role of m6A readers, such as insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2), in regulating head and neck squamous cell ... ...

    Abstract The importance of N6-methyladenosine (m6A) in tumor recurrence and prognosis has been recognized in recent years. The role of m6A readers, such as insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2), in regulating head and neck squamous cell carcinoma (HNSCC) remains unclear. We, therefore, assessed the prognostic role of IGF2BP2 in HNSCC using openly available data from The Cancer Genome Atlas (TCGA) in conjunction with HNSCC patient sample immunohistochemistry (
    Language English
    Publishing date 2020-04-24
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2020.00068
    Database MEDical Literature Analysis and Retrieval System OnLINE

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