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  1. Article: Value of imaging examinations in diagnosing lumbar disc herniation: A systematic review and meta-analysis.

    Huang, Zhihao / Zhao, Pengfei / Zhang, Chengming / Wu, Jingtao / Liu, Ruidong

    Frontiers in surgery

    2023  Volume 9, Page(s) 1020766

    Abstract: Purpose: To systematically review the clinical value of three imaging examinations (Magnetic Resonance Imaging, Computed Tomography, and myelography) in the diagnosis of Lumbar Disc Herniation.: Methods: Databases including PubMed, Embase, The ... ...

    Abstract Purpose: To systematically review the clinical value of three imaging examinations (Magnetic Resonance Imaging, Computed Tomography, and myelography) in the diagnosis of Lumbar Disc Herniation.
    Methods: Databases including PubMed, Embase, The Cochrane Library, Web of Science, CBM, CNKI, WanFang Data, and VIP were electronically searched to collect relevant studies on three imaging examinations in the diagnosis of Lumbar Disc Herniation from inception to July 1, 2021. Two reviewers using the Quality Assessment of Diagnostic Accuracy Studies-2 tool independently screened the literature, extracted the data, and assessed the risk of bias of included studies. Then, meta-analysis was performed by using Meta-DiSc 1.4 software and Stata 15.0 software.
    Results: A total of 38 studies from 19 articles were included, involving 1,875 patients. The results showed that the pooled Sensitivity, pooled Specificity, pooled Positive Likelihood Ratio, pooled Negative Likelihood Ratio, pooled Diagnostic Odds Ratio, Area Under the Curve of Summary Receiver Operating Characteristic, and Q* were 0.89 (95%CI: 0.87-0.91), 0.83 (95%CI: 0.78-0.87), 4.57 (95%CI: 2.95-7.08), 0.14 (95%CI: 0.09-0.22), 39.80 (95%CI: 18.35-86.32), 0.934, and 0.870, respectively, for Magnetic Resonance Imaging. The pooled Sensitivity, pooled Specificity, pooled Positive Likelihood Ratio, pooled Negative Likelihood Ratio, pooled Diagnostic Odds Ratio, Area Under the Curve of Summary Receiver Operating Characteristic, and Q* were 0.82 (95%CI: 0.79-0.85), 0.78 (95%CI: 0.73-0.82), 3.54 (95%CI: 2.86-4.39), 0.19 (95%CI: 0.12-0.30), 20.47 (95%CI: 10.31-40.65), 0.835, and 0.792, respectively, for Computed Tomography. The pooled Sensitivity, pooled Specificity, pooled Positive Likelihood Ratio, pooled Negative Likelihood Ratio, pooled Diagnostic Odds Ratio, Area Under the Curve of Summary Receiver Operating Characteristic, and Q* were 0.79 (95%CI: 0.75-0.82), 0.75 (95%CI: 0.70-0.80), 2.94 (95%CI: 2.43-3.56), 0.29 (95%CI: 0.21-0.42), 9.59 (95%CI: 7.05-13.04), 0.834, and 0.767 respectively, for myelography.
    Conclusion: Three imaging examinations had high diagnostic value. In addition, compared with myelography, Magnetic Resonance Imaging had a higher diagnostic value.
    Language English
    Publishing date 2023-01-06
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2773823-1
    ISSN 2296-875X
    ISSN 2296-875X
    DOI 10.3389/fsurg.2022.1020766
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Deep latent space fusion for adaptive representation of heterogeneous multi-omics data.

    Zhang, Chengming / Chen, Yabin / Zeng, Tao / Zhang, Chuanchao / Chen, Luonan

    Briefings in bioinformatics

    2022  Volume 23, Issue 2

    Abstract: The integration of multi-omics data makes it possible to understand complex biological organisms at the system level. Numerous integration approaches have been developed by assuming a common underlying data space. Due to the noise and heterogeneity of ... ...

    Abstract The integration of multi-omics data makes it possible to understand complex biological organisms at the system level. Numerous integration approaches have been developed by assuming a common underlying data space. Due to the noise and heterogeneity of biological data, the performance of these approaches is greatly affected. In this work, we propose a novel deep neural network architecture, named Deep Latent Space Fusion (DLSF), which integrates the multi-omics data by learning consistent manifold in the sample latent space for disease subtypes identification. DLSF is built upon a cycle autoencoder with a shared self-expressive layer, which can naturally and adaptively merge nonlinear features at each omics level into one unified sample manifold and produce adaptive representation of heterogeneous samples at the multi-omics level. We have assessed DLSF on various biological and biomedical datasets to validate its effectiveness. DLSF can efficiently and accurately capture the intrinsic manifold of the sample structures or sample clusters compared with other state-of-the-art methods, and DLSF yielded more significant outcomes for biological significance, survival prognosis and clinical relevance in application of cancer study in The Cancer Genome Atlas. Notably, as a deep case study, we determined a new molecular subtype of kidney renal clear cell carcinoma that may benefit immunotherapy in the viewpoint of multi-omics, and we further found potential subtype-specific biomarkers from multiple omics data, which were validated by independent datasets. In addition, we applied DLSF to identify potential therapeutic agents of different molecular subtypes of chronic lymphocytic leukemia, demonstrating the scalability of DLSF in diverse omics data types and application scenarios.
    MeSH term(s) Humans ; Neoplasms/genetics
    Language English
    Publishing date 2022-01-25
    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/bbab600
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Contrastively generative self-expression model for single-cell and spatial multimodal data.

    Zhang, Chengming / Yang, Yiwen / Tang, Shijie / Aihara, Kazuyuki / Zhang, Chuanchao / Chen, Luonan

    Briefings in bioinformatics

    2023  Volume 24, Issue 5

    Abstract: Advances in single-cell multi-omics technology provide an unprecedented opportunity to fully understand cellular heterogeneity. However, integrating omics data from multiple modalities is challenging due to the individual characteristics of each ... ...

    Abstract Advances in single-cell multi-omics technology provide an unprecedented opportunity to fully understand cellular heterogeneity. However, integrating omics data from multiple modalities is challenging due to the individual characteristics of each measurement. Here, to solve such a problem, we propose a contrastive and generative deep self-expression model, called single-cell multimodal self-expressive integration (scMSI), which integrates the heterogeneous multimodal data into a unified manifold space. Specifically, scMSI first learns each omics-specific latent representation and self-expression relationship to consider the characteristics of different omics data by deep self-expressive generative model. Then, scMSI combines these omics-specific self-expression relations through contrastive learning. In such a way, scMSI provides a paradigm to integrate multiple omics data even with weak relation, which effectively achieves the representation learning and data integration into a unified framework. We demonstrate that scMSI provides a cohesive solution for a variety of analysis tasks, such as integration analysis, data denoising, batch correction and spatial domain detection. We have applied scMSI on various single-cell and spatial multimodal datasets to validate its high effectiveness and robustness in diverse data types and application scenarios.
    MeSH term(s) Learning ; Multiomics
    Language English
    Publishing date 2023-07-28
    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/bbad265
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Different nitrogen acquirement and utilization strategies might determine the ecological competition between ferns and angiosperms.

    Zhang, Chengming / Zhang, Chaoqun / Azuma, Takayuki / Maruyama, Hayato / Shinano, Takuro / Watanabe, Toshihiro

    Annals of botany

    2023  Volume 131, Issue 7, Page(s) 1097–1106

    Abstract: Background and aims: The abundance or decline of fern populations in response to environmental change has been found to be largely dependent on specific physiological properties that distinguish ferns from angiosperms. Many studies have focused on water ...

    Abstract Background and aims: The abundance or decline of fern populations in response to environmental change has been found to be largely dependent on specific physiological properties that distinguish ferns from angiosperms. Many studies have focused on water use efficiency and stomatal behaviours, but the effects of nutrition acquirement and utilization strategies on niche competition between ferns and flowering plants are rarely reported.
    Methods: We collected 34 ferns and 42 angiosperms from the Botanic Garden of Hokkaido University for nitrogen (N), sulphur (S), NO3- and SO42- analysis. We then used a hydroponic system to compare the different N and S utilization strategies between ferns and angiosperms under N deficiency conditions.
    Key results: Ferns had a significantly higher NO3--N concentration and NO3--N/N ratio than angiosperms, although the total N concentration in ferns was remarkably lower than that in the angiosperms. Meanwhile, a positive correlation between N and S was found, indicating that nutrient concentration is involved in assimilation. Pteris cretica, a fern species subjected to further study, maintained a slow growth rate and lower N requirement in response to low N stress, while both the biomass and N concentration in wheat (Triticum aestivum) responded quickly to N deficiency conditions.
    Conclusions: The different nutritional strategies employed by ferns and angiosperms depended mainly on the effects of phylogenetic and evolutionary diversity. Ferns tend to adopt an opportunistic strategy of limiting growth rate to reduce N demand and store more pooled nitrate, whereas angiosperms probably utilize N nutrition to ensure as much development as possible under low N stress. Identifying the effects of mineral nutrition on the evolutionary results of ecological competition between plant species remains a challenge.
    MeSH term(s) Magnoliopsida/physiology ; Phylogeny ; Ferns/physiology ; Biological Evolution ; Triticum
    Language English
    Publishing date 2023-01-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1461328-1
    ISSN 1095-8290 ; 0305-7364
    ISSN (online) 1095-8290
    ISSN 0305-7364
    DOI 10.1093/aob/mcad009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: A spectral index for winter wheat mapping using multi-temporal Landsat NDVI data of key growth stages

    Qu, Chang / Li, Peijun / Zhang, Chengming

    International Society for Photogrammetry and Remote Sensing, Inc. (ISPRS) ISPRS journal of photogrammetry and remote sensing. 2021 May, v. 175

    2021  

    Abstract: Winter wheat is one of the most important staple crops in the world. Accurate and timely information on the spatial distribution and temporal change of winter wheat is critical for food security and environmental sustainability. Multi-temporal images and ...

    Abstract Winter wheat is one of the most important staple crops in the world. Accurate and timely information on the spatial distribution and temporal change of winter wheat is critical for food security and environmental sustainability. Multi-temporal images and time series data of medium resolution are widely used in winter wheat mapping. However, relatively long revisit times and image noise often result in a deficiency in full time series data. In this paper, a new spectral index, called the winter wheat index (WWI), using multi-temporal Landsat normalized difference vegetation index (NDVI) data of four key growth stages of winter wheat, was proposed to highlight and map winter wheat. Two distinctive NDVI contrasts, each consisting of an NDVI peak and trough, were identified and used in the WWI. The proposed index was evaluated through qualitative and quantitative analyses as well as winter wheat mapping, and compared with three state-of-the-art methods. To map winter wheat using WWI, a Monte Carlo cross validation procedure was adopted to determine the optimal thresholds of the WWI. Visual comparison showed that winter wheat was highlighted by higher WWI values, whereas other land cover types had lower WWI values. The experimental results from quantitative analysis indicated that WWI achieved better separability between winter wheat and other land cover types than the other comparative indices. The proposed WWI also produced more accurate winter wheat mapping results, compared with the state-of-art methods. Therefore, the proposed WWI provides a useful variable for winter wheat mapping, which reduced the dependence on full time series data and the use of noise images, and can be applied in other study areas.
    Keywords Landsat ; environmental sustainability ; food security ; land cover ; photogrammetry ; quantitative analysis ; temporal variation ; time series analysis ; winter wheat
    Language English
    Dates of publication 2021-05
    Size p. 431-447.
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1007774-1
    ISSN 0924-2716
    ISSN 0924-2716
    DOI 10.1016/j.isprsjprs.2021.03.015
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Optimal N management improves crop yields and soil carbon, nitrogen sequestration in Chinese cabbage-maize rotation

    Xie, Jun / Wang, Jie / Hu, Qijuan / Zhang, Yu / Wan, Yu / Zhang, Chengming / Zhang, Yueqiang / Shi, Xiaojun

    Archives of Agronomy and Soil Science. 2023 June 07, v. 69, no. 7 p.1071-1084

    2023  

    Abstract: Appropriate nitrogen (N) fertilization in vegetable-maize rotations is effective in improving agricultural production and mitigating environmental impacts to ensure sustainable food security. The dynamic and sustainability of crop yields, crop root ... ...

    Abstract Appropriate nitrogen (N) fertilization in vegetable-maize rotations is effective in improving agricultural production and mitigating environmental impacts to ensure sustainable food security. The dynamic and sustainability of crop yields, crop root biomasses, and accumulations and sequestration rates of soil organic C (SOC) and total N (STN) were explored and analyzed under four N application rates (kg N ha⁻¹ year⁻¹): 0 (Control), 285 (Low-N), 480 (Medium-N), and 720 (High-N). The Low-N and Medium-N applications increased Chinese cabbage yield by 22% and 20.7% than the High-N application, respectively. The Medium-N application gained the highest grain yield and root biomass in the maize season when compared with the Low-N application. The sustainable yield index had no difference between Low-N and Medium-N treatments in Chinese cabbage-maize rotation. Compared to the Low-N application, the Medium-N application improved the storage and sequestration rates of SOC and STN. Simultaneously, the Medium-N application significantly enhanced the soil C:N ratio than the High-N application. In conclusion, the Medium-N application is a promising fertilization strategy in the Chinese cabbage-maize cropping system as it increases the yield and root biomass of crops, improves the accumulation and sequestration rates of SOC and STN, and maintains a high soil C:N ratio.
    Keywords Chinese cabbage ; agronomy ; biomass ; carbon nitrogen ratio ; corn ; food security ; grain yield ; nitrogen ; soil ; soil organic carbon ; total nitrogen ; N application rates ; sustainable yield index ; root biomass ; soil total nitrogen
    Language English
    Dates of publication 2023-0607
    Size p. 1071-1084.
    Publishing place Taylor & Francis
    Document type Article ; Online
    ZDB-ID 1132910-5
    ISSN 1476-3567 ; 0365-0340
    ISSN (online) 1476-3567
    ISSN 0365-0340
    DOI 10.1080/03650340.2022.2053113
    Database NAL-Catalogue (AGRICOLA)

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  7. Article: Rapid ultracapacitor life prediction with a convolutional neural network

    Wang, Chenxu / Xiong, Rui / Tian, Jinpeng / Lu, Jiahuan / Zhang, Chengming

    Applied energy. 2022 Jan. 01, v. 305

    2022  

    Abstract: Accurate and rapid prediction of the lifetime is essential for accelerating the application of ultracapacitors. To overcome the large inconsistencies in the lifetime of ultracapacitors, an end-to-end remaining useful life (RUL) prediction method based on ...

    Abstract Accurate and rapid prediction of the lifetime is essential for accelerating the application of ultracapacitors. To overcome the large inconsistencies in the lifetime of ultracapacitors, an end-to-end remaining useful life (RUL) prediction method based on the convolutional neural network (CNN) is proposed. It directly establishes the mapping between the charging and discharging data collected within a few consecutive cycles and the corresponding remaining useful life. It learns many ageing features from limited raw data without any expert knowledge. While improving the prediction accuracy of the RUL, the required test time drops greatly. Validation results based on 113 ultracapacitors demonstrate that our method can accurately predict RUL by using the data within 5 consecutive cycles collected at any ageing stage, and the root mean square error is 501 cycles. Our method demonstrates higher accuracy compared with conventional feature-based prediction methods, while required input data are sharply reduced. Such 5-cycle testing can be conducted within 15 min to collect enough data for RUL prediction. Our work highlights the promise of data-driven approaches to predict the degradation of energy storage devices.
    Keywords electrochemical capacitors ; energy ; expert opinion ; neural networks ; prediction
    Language English
    Dates of publication 2022-0101
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 2000772-3
    ISSN 0306-2619
    ISSN 0306-2619
    DOI 10.1016/j.apenergy.2021.117819
    Database NAL-Catalogue (AGRICOLA)

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  8. Article: Influence of financial development on energy intensity subject to technological innovation: Evidence from panel threshold regression

    Uddin, Md. Kamal / Pan, Xiongfeng / Saima, Umme / Zhang, Chengming

    Energy. 2022 Jan. 15, v. 239

    2022  

    Abstract: Controlling energy intensity has become a prime objective of present time as energy consumption is the main source of about three-fourth of the world's green house gas emissions. Therefore, scholars have been trying to detect the ways that can ensure ... ...

    Abstract Controlling energy intensity has become a prime objective of present time as energy consumption is the main source of about three-fourth of the world's green house gas emissions. Therefore, scholars have been trying to detect the ways that can ensure efficient utilization of energy with minimal degradation of environment. Consequently, studies have been conducted to explore the linkages between financial development and energy consumption to see whether financial development can help reduce energy intensity. Nonetheless, this study considers technological innovation as a crucial dimension of socio-economic changes and explores the technology dependency of the influence of financial development on energy intensity. To do so, a panel threshold regression model is applied in a panel of 23 European Union (EU) countries. The results corroborate that the inhibiting effects of banking sector development, stock market development and overall financial development on energy intensity depend on the levels of technological innovation. Thus, policymakers need to consider the matter carefully when they devise policy decisions.
    Keywords European Union ; economic development ; energy ; issues and policy ; market development ; regression analysis ; socioeconomics ; stock exchange ; technology
    Language English
    Dates of publication 2022-0115
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 2019804-8
    ISSN 0360-5442 ; 0360-5442
    ISSN (online) 0360-5442
    ISSN 0360-5442
    DOI 10.1016/j.energy.2021.122337
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Research progress and hotspots on macrophages in osteoarthritis: A bibliometric analysis from 2009 to 2022.

    Liu, Yang / Liu, Pei-Dong / Zhang, Cheng-Ming / Liu, Meng-Rou / Wang, Gui-Shan / Li, Peng-Cui / Yang, Zi-Quan

    Medicine

    2023  Volume 102, Issue 34, Page(s) e34642

    Abstract: Background: Macrophages in the synovium, as immune cells, can be polarized into different phenotypes to play an anti-inflammatory role in the treatment of osteoarthritis. In this study, bibliometric methods were used to search the relevant literature to ...

    Abstract Background: Macrophages in the synovium, as immune cells, can be polarized into different phenotypes to play an anti-inflammatory role in the treatment of osteoarthritis. In this study, bibliometric methods were used to search the relevant literature to find valuable research directions for researchers and provide new targets for osteoarthritis prevention and early treatment.
    Methods: Studies about the application of macrophages in the treatment of osteoarthritis were searched through the Web of Science core database from 2009 to 2022. Microsoft Excel 2019, VOSviewer, CiteSpace, R software, and 2 online websites were used to analyze the research status and predict the future development of the trend in research on macrophages in osteoarthritis.
    Results: The number of publications identified with the search strategy was 1304. China and the United States ranked first in the number of publications. Shanghai Jiao Tong University ranked first in the world with 37 papers. Osteoarthritis and Cartilage was the journal with the most publications, and "exosomes," "stem cells," "macrophage polarization," "regeneration," and "innate immunity" may remain the research hotspots and frontiers in the future.
    Conclusion: The findings from the global trend analysis indicate that research on macrophages in the treatment of osteoarthritis is gradually deepening, and the number of studies is increasing. Exosomes may become a research trend and hotspot in the future.
    MeSH term(s) Humans ; China/epidemiology ; Macrophages ; Immunity, Innate ; Bibliometrics ; Osteoarthritis/therapy
    Language English
    Publishing date 2023-08-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 80184-7
    ISSN 1536-5964 ; 0025-7974
    ISSN (online) 1536-5964
    ISSN 0025-7974
    DOI 10.1097/MD.0000000000034642
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: The silencing of NREP aggravates OA cartilage damage through the TGF-β1/Smad2/3 pathway in chondrocytes.

    Liu, Yang / Liu, Mengrou / Zhang, Chengming / Li, Xiaoke / Zheng, Siyu / Wen, Le / Liu, Peidong / Li, Pengcui / Yang, Ziquan

    Journal of orthopaedic translation

    2023  Volume 44, Page(s) 26–34

    Abstract: Background: Osteoarthritis (OA) is a common chronic degenerative joint disease. Due to the limited understanding of its complex pathological mechanism, there is currently no effective treatment that can alleviate or even reverse cartilage damage ... ...

    Abstract Background: Osteoarthritis (OA) is a common chronic degenerative joint disease. Due to the limited understanding of its complex pathological mechanism, there is currently no effective treatment that can alleviate or even reverse cartilage damage associated with OA. With improvement in public databases, researchers have successfully identified the key factors involved in the occurrence and development of OA through bioinformatics analysis. The aim of this study was to screen for the differentially expressed genes (DEGs) between the normal and OA cartilage through bioinformatics, and validate the function of the TGF-β1/Smad2/3 pathway-related neuron regeneration related protein (NREP) in the articular cartilage.
    Methods: The DEGs between the cartilage tissues of OA patients and healthy controls were screened by bioinformatics, and functionally annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The expression levels of the DEG in human and murine OA cartilage was verified by reverse transcription-quantitative PCR (RT-qPCR), Western blotting and immunohistochemistry (IHC). RT-qPCR, Western-blotting, Cell Counting Kit-8(CCK8) and EdU assays were used to evaluate the effects of knocking down NREP in normal chondrocytes, and the molecular mechanisms were investigated by RT-qPCR, Western blotting and IHC.
    Results: In this study, we identified NREP as a DEG in OA through bioinformatics analysis, and found that NREP was downregulated in the damaged articular cartilage of OA patients and mouse model with surgically-induced OA. In addition, knockdown of NREP in normal chondrocytes reduced their proliferative capacity, which is the pathological basis of OA. At the molecular level, knock-down of NREP inactivated the TGF-β1/Smad2/3 pathway, resulting in the downregulation of the anabolic markers Col2a1 and Sox9, and an increase in the expression of the catabolic markers MMP3 and MMP13.
    Conclusion: NREP plays a key role in the progression of OA by regulating the TGF-β1/Smad2/3 pathway in chondrocytes, and warrants further study as a potential therapeutic target.
    Language English
    Publishing date 2023-12-27
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2747531-1
    ISSN 2214-031X
    ISSN 2214-031X
    DOI 10.1016/j.jot.2023.11.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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