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  1. Article: Correction: Pu et al. Exosome miRNA Expression in Umbilical Cord Blood of High-Parity Sows Regulates Their Reproductive Potential.

    Pu, Qiang / Chai, Jie / Chen, Li / Liu, Changbao / Yang, Changfeng / Huang, Yongfu / Luo, Jia

    Animals : an open access journal from MDPI

    2024  Volume 14, Issue 2

    Abstract: In the original publication [ ... ]. ...

    Abstract In the original publication [...].
    Language English
    Publishing date 2024-01-22
    Publishing country Switzerland
    Document type Published Erratum
    ZDB-ID 2606558-7
    ISSN 2076-2615
    ISSN 2076-2615
    DOI 10.3390/ani14020345
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online: Split-PU

    Xu, Chengming / Liu, Chen / Yang, Siqian / Wang, Yabiao / Zhang, Shijie / Jia, Lijie / Fu, Yanwei

    Hardness-aware Training Strategy for Positive-Unlabeled Learning

    2022  

    Abstract: Positive-Unlabeled (PU) learning aims to learn a model with rare positive samples and abundant ... unlabeled samples. Compared with classical binary classification, the task of PU learning is much more ...

    Abstract Positive-Unlabeled (PU) learning aims to learn a model with rare positive samples and abundant unlabeled samples. Compared with classical binary classification, the task of PU learning is much more challenging due to the existence of many incompletely-annotated data instances. Since only part of the most confident positive samples are available and evidence is not enough to categorize the rest samples, many of these unlabeled data may also be the positive samples. Research on this topic is particularly useful and essential to many real-world tasks which demand very expensive labelling cost. For example, the recognition tasks in disease diagnosis, recommendation system and satellite image recognition may only have few positive samples that can be annotated by the experts. These methods mainly omit the intrinsic hardness of some unlabeled data, which can result in sub-optimal performance as a consequence of fitting the easy noisy data and not sufficiently utilizing the hard data. In this paper, we focus on improving the commonly-used nnPU with a novel training pipeline. We highlight the intrinsic difference of hardness of samples in the dataset and the proper learning strategies for easy and hard data. By considering this fact, we propose first splitting the unlabeled dataset with an early-stop strategy. The samples that have inconsistent predictions between the temporary and base model are considered as hard samples. Then the model utilizes a noise-tolerant Jensen-Shannon divergence loss for easy data; and a dual-source consistency regularization for hard data which includes a cross-consistency between student and base model for low-level features and self-consistency for high-level features and predictions, respectively.
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Subject code 006
    Publishing date 2022-11-30
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Meta-PU

    Ye, Shuquan / Chen, Dongdong / Han, Songfang / Wan, Ziyu / Liao, Jing

    An Arbitrary-Scale Upsampling Network for Point Cloud

    2021  

    Abstract: ... in this work, we propose a novel method called ``Meta-PU" to firstly support point cloud upsampling ... of arbitrary scale factors with a single model. In the Meta-PU method, besides the backbone network consisting ... Together, these two blocks enable our Meta-PU to continuously upsample the point cloud with arbitrary scale ...

    Abstract Point cloud upsampling is vital for the quality of the mesh in three-dimensional reconstruction. Recent research on point cloud upsampling has achieved great success due to the development of deep learning. However, the existing methods regard point cloud upsampling of different scale factors as independent tasks. Thus, the methods need to train a specific model for each scale factor, which is both inefficient and impractical for storage and computation in real applications. To address this limitation, in this work, we propose a novel method called ``Meta-PU" to firstly support point cloud upsampling of arbitrary scale factors with a single model. In the Meta-PU method, besides the backbone network consisting of residual graph convolution (RGC) blocks, a meta-subnetwork is learned to adjust the weights of the RGC blocks dynamically, and a farthest sampling block is adopted to sample different numbers of points. Together, these two blocks enable our Meta-PU to continuously upsample the point cloud with arbitrary scale factors by using only a single model. In addition, the experiments reveal that training on multiple scales simultaneously is beneficial to each other. Thus, Meta-PU even outperforms the existing methods trained for a specific scale factor only.

    Comment: To appear at TVCG
    Keywords Computer Science - Graphics
    Subject code 310
    Publishing date 2021-02-08
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Book ; Online: PC$^2$-PU

    Long, Chen / Zhang, Wenxiao / Li, Ruihui / Wang, Hao / Dong, Zhen / Yang, Bisheng

    Patch Correlation and Point Correlation for Effective Point Cloud Upsampling

    2021  

    Abstract: ... patches. In this paper, we present a novel method PC$^2$-PU, which explores patch-to-patch and point ... at \url{https://github.com/chenlongwhu/PC2-PU.git}. ... Comment: Accepted to ACM MM 2022 ...

    Abstract Point cloud upsampling is to densify a sparse point set acquired from 3D sensors, providing a denser representation for the underlying surface. Existing methods divide the input points into small patches and upsample each patch separately, however, ignoring the global spatial consistency between patches. In this paper, we present a novel method PC$^2$-PU, which explores patch-to-patch and point-to-point correlations for more effective and robust point cloud upsampling. Specifically, our network has two appealing designs: (i) We take adjacent patches as supplementary inputs to compensate the loss structure information within a single patch and introduce a Patch Correlation Module to capture the difference and similarity between patches. (ii) After augmenting each patch's geometry, we further introduce a Point Correlation Module to reveal the relationship of points inside each patch to maintain the local spatial consistency. Extensive experiments on both synthetic and real scanned datasets demonstrate that our method surpasses previous upsampling methods, particularly with the noisy inputs. The code and data are at \url{https://github.com/chenlongwhu/PC2-PU.git}.

    Comment: Accepted to ACM MM 2022
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Subject code 006
    Publishing date 2021-09-20
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Expression profile of PU.1 in CD4

    Xiang, Nan / Fang, Xuan / Sun, Xiao-Ge / Zhou, Ying-Bo / Ma, Yan / Zhu, Chen / Li, Xiang-Pei / Wang, Guo-Sheng / Tao, Jin-Hui / Li, Xiao-Mei

    Clinical and experimental medicine

    2021  Volume 21, Issue 4, Page(s) 621–632

    Abstract: ... predisposing factors involved. PU.1 is an important member of the ETS transcription factors family which has diverse ... cytokines. Previous studies preliminary explored the relation between PU.1 and SLE. To further explain ... the potential role of PU.1 in the pathogenesis of SLE, 40 SLE patients and 20 age-sex matched healthy controls ...

    Abstract Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease with complex genetic predisposing factors involved. PU.1 is an important member of the ETS transcription factors family which has diverse functions such as regulating the proliferation, differentiation of immune cells and multiple inflammatory cytokines. Previous studies preliminary explored the relation between PU.1 and SLE. To further explain the potential role of PU.1 in the pathogenesis of SLE, 40 SLE patients and 20 age-sex matched healthy controls (HC) were recruited in this study. Flow cytometry was used to test the percentages of CD4
    MeSH term(s) CD4-Positive T-Lymphocytes ; Cytokines ; Flow Cytometry ; Humans ; Leukocytes, Mononuclear ; Lupus Erythematosus, Systemic ; Proto-Oncogene Proteins ; T-Lymphocytes ; Trans-Activators
    Chemical Substances Cytokines ; Proto-Oncogene Proteins ; Trans-Activators ; proto-oncogene protein Spi-1
    Language English
    Publishing date 2021-05-08
    Publishing country Italy
    Document type Journal Article
    ZDB-ID 2053018-3
    ISSN 1591-9528 ; 1591-8890
    ISSN (online) 1591-9528
    ISSN 1591-8890
    DOI 10.1007/s10238-021-00717-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online: CAD-PU

    Lin, Jiehong / Shi, Xian / Gao, Yuan / Chen, Ke / Jia, Kui

    A Curvature-Adaptive Deep Learning Solution for Point Set Upsampling

    2020  

    Abstract: ... we propose a novel design of Curvature-ADaptive Point set Upsampling network (CAD-PU), the core of which is ... a module of curvature-adaptive feature expansion. To train CAD-PU, we follow the same motivation and ... curvature minimization objective, which gives a practically effective learning of CAD-PU. We conduct ...

    Abstract Point set is arguably the most direct approximation of an object or scene surface, yet its practical acquisition often suffers from the shortcoming of being noisy, sparse, and possibly incomplete, which restricts its use for a high-quality surface recovery. Point set upsampling aims to increase its density and regularity such that a better surface recovery could be achieved. The problem is severely ill-posed and challenging, considering that the upsampling target itself is only an approximation of the underlying surface. Motivated to improve the surface approximation via point set upsampling, we identify the factors that are critical to the objective, by pairing the surface approximation error bounds of the input and output point sets. It suggests that given a fixed budget of points in the upsampling result, more points should be distributed onto the surface regions where local curvatures are relatively high. To implement the motivation, we propose a novel design of Curvature-ADaptive Point set Upsampling network (CAD-PU), the core of which is a module of curvature-adaptive feature expansion. To train CAD-PU, we follow the same motivation and propose geometrically intuitive surrogates that approximate discrete notions of surface curvature for the upsampled point set. We further integrate the proposed surrogates into an adversarial learning based curvature minimization objective, which gives a practically effective learning of CAD-PU. We conduct thorough experiments that show the efficacy of our contributions and the advantages of our method over existing ones. Our implementation codes are publicly available at https://github.com/JiehongLin/CAD-PU.
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Publishing date 2020-09-10
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Effects of Geographical Origin and Tree Age on the Stable Isotopes and Multi-Elements of Pu-erh Tea.

    Chen, Ming-Ming / Liao, Qiu-Hong / Qian, Li-Li / Zou, Hai-Dan / Li, Yan-Long / Song, Yan / Xia, Yu / Liu, Yi / Liu, Hong-Yan / Liu, Ze-Long

    Foods (Basel, Switzerland)

    2024  Volume 13, Issue 3

    Abstract: Pu-erh tea is a famous tea worldwide, and identification of the geographical origin of Pu-erh tea ... may also influence the fingerprints of Pu-erh tea. In order to study the effects of the geographical origin ... and tree age on the interactions of stable isotopes and multi-elements of Pu-erh tea, 53 Pu-erh tea ...

    Abstract Pu-erh tea is a famous tea worldwide, and identification of the geographical origin of Pu-erh tea can not only protect manufacture's interests, but also boost consumers' confidence. However, tree age may also influence the fingerprints of Pu-erh tea. In order to study the effects of the geographical origin and tree age on the interactions of stable isotopes and multi-elements of Pu-erh tea, 53 Pu-erh tea leaves with three different age stages from three different areas in Yunnan were collected in 2023. The δ
    Language English
    Publishing date 2024-02-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704223-6
    ISSN 2304-8158
    ISSN 2304-8158
    DOI 10.3390/foods13030473
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages.

    Virgilio, Maria C / Ramnani, Barkha / Chen, Thomas / Disbennett, W Miguel / Lubow, Jay / Welch, Joshua D / Collins, Kathleen L

    bioRxiv : the preprint server for biology

    2024  

    Abstract: ... transcriptomic changes by targeting PU.1, a transcription factor necessary for expression of host ... innate immune response genes, including those that target Env. Consistent with this, we find silencing PU.1 in infected ... macrophages lacking Vpr rescues Env. Vpr downmodulates PU.1 through a proteasomal degradation pathway ...

    Abstract HIV-1 Vpr promotes efficient spread of HIV-1 from macrophages to T cells by transcriptionally downmodulating restriction factors that target HIV-1 Envelope protein (Env). Here we find that Vpr induces broad transcriptomic changes by targeting PU.1, a transcription factor necessary for expression of host innate immune response genes, including those that target Env. Consistent with this, we find silencing PU.1 in infected macrophages lacking Vpr rescues Env. Vpr downmodulates PU.1 through a proteasomal degradation pathway that depends on physical interactions with PU.1 and DCAF1, a component of the Cul4A E3 ubiquitin ligase. The capacity for Vpr to target PU.1 is highly conserved across primate lentiviruses. In addition to impacting infected cells, we find that Vpr suppresses expression of innate immune response genes in uninfected bystander cells, and that virion-associated Vpr can degrade PU.1. Together, we demonstrate Vpr counteracts PU.1 in macrophages to blunt antiviral immune responses and promote viral spread.
    Language English
    Publishing date 2024-02-27
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.21.533528
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Metabolites and metagenomic analysis reveals the quality of Pu-erh "tea head".

    He, Shiqiang / Deng, Xinyi / Han, Yuxin / Gong, Zhengli / Wang, Jian / Tao, Xiaoqi / Tong, Huarong / Chen, Yingjuan

    Food chemistry

    2023  Volume 429, Page(s) 136992

    Abstract: Tea head, a derivative product of Pu-erh tea, are tight tea lumps formed during pile-fermentation ... communities between ripened Pu-erh tea (PE-21) and tea heads (CT-21). Compared with PE-21, CT-21 showed a more ... distinct flavor of Pu-erh. ...

    Abstract Tea head, a derivative product of Pu-erh tea, are tight tea lumps formed during pile-fermentation. The aim of this study was to reveal the differences of quality-related metabolites and microbial communities between ripened Pu-erh tea (PE-21) and tea heads (CT-21). Compared with PE-21, CT-21 showed a more mellow and smooth taste with slight bitterness and astringency, and can withstand multiple infusions. Metabolites analysis indicated CT-21 had more abundant water-soluble substances (47.39%) and showed significant differences with PE-21 in the main compositions of amino acids, catechins and saccharides which contributed to the viscosity of tea liquor, mellow taste and the tight tea lumps formation. Microbial communities and COG annotation analysis revealed CT-21 had lower abundance of Bacteria (84.05%), and higher abundance of Eukaryota (15.10%), carbohydrate transport and metabolism (8.28%) and glycoside hydrolases (37.36%) compared with PE-21. The different microbial communities may cause metabolites changes, forming distinct flavor of Pu-erh.
    MeSH term(s) Tea/chemistry ; Microbiota ; Bacteria/genetics ; Catechin ; Fermentation
    Chemical Substances Tea ; Catechin (8R1V1STN48)
    Language English
    Publishing date 2023-07-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 243123-3
    ISSN 1873-7072 ; 0308-8146
    ISSN (online) 1873-7072
    ISSN 0308-8146
    DOI 10.1016/j.foodchem.2023.136992
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: PU.1 induces tumor-associated macrophages promoting glioma progression through BTK-mediated Akt/mTOR pathway activation.

    Song, Gu / Zhang, Zeyu / Chen, Yan / Hou, Weiliang / Zhong, Weiwei / Zhou, Yuhang / Zhang, Anke / Xu, Yuanzhi

    American journal of cancer research

    2024  Volume 14, Issue 3, Page(s) 1139–1156

    Abstract: ... remain elusive. In this study, we investigated the role of PU.1, a crucial transcription factor involved ... and analysis of clinical glioma samples demonstrated a positive correlation between PU.1 expression ... that the expression of PU.1 is increased in glioma cells vs. control cells. Importantly, PU.1-overexpressing ...

    Abstract Glioma, the most common primary malignant brain tumor, is characterized by infiltrating immune cells that contribute to tumor progression and therapeutic resistance. Tumor-associated macrophages (TAMs) constitute a significant proportion of these infiltrating immune cells and have been implicated in glioma progression. However, the underlying molecular mechanisms by which TAMs promote glioma progression remain elusive. In this study, we investigated the role of PU.1, a crucial transcription factor involved in myeloid cell development, in glioma-associated macrophage polarization and activation. First, bioinformatics and analysis of clinical glioma samples demonstrated a positive correlation between PU.1 expression in TAMs and disease severity. Further experiments using in vitro coculture systems revealed that the expression of PU.1 is increased in glioma cells vs. control cells. Importantly, PU.1-overexpressing macrophages exhibited a protumorigenic phenotype characterized by enhanced migration, invasion, and proliferation. Mechanistically, we found that PU.1-induced activation of the Bruton tyrosine kinase (BTK) signaling pathway led to Akt/mTOR pathway activation in macrophages, which further enhanced their protumorigenic functions. Furthermore, pharmacological inhibition of the BTK or Akt/mTOR pathway reversed the protumorigenic effects of macrophages in vitro and impaired their ability to promote glioma progression in vivo. In conclusion, our study elucidates a novel mechanism by which PU.1 induces the polarization and activation of TAMs in the glioma microenvironment. We highlight the significance of BTK-mediated Akt/mTOR pathway activation in driving the protumorigenic functions of TAMs. Targeting PU.1 and its downstream signaling pathways in TAMs may provide a promising therapeutic strategy to suppress glioma progression and improve patient outcomes.
    Language English
    Publishing date 2024-03-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2589522-9
    ISSN 2156-6976
    ISSN 2156-6976
    DOI 10.62347/USAJ2794
    Database MEDical Literature Analysis and Retrieval System OnLINE

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