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  1. Article: The need for masked genomes in gymnosperms.

    Zhu, Pengkai / He, Tianyou / Zheng, Yushan / Chen, Lingyan

    Frontiers in plant science

    2023  Volume 14, Page(s) 1309744

    Language English
    Publishing date 2023-12-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1309744
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A Key-Points Based Anchor-Free Cervical Cell Detector.

    Shu, Tong / Shi, Jun / Zheng, Yushan / Jiang, Zhiguo / Yu, Lanlan

    Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

    2023  Volume 2023, Page(s) 1–5

    Abstract: Cervical cell detection is crucial to cervical cytology screening at early stage. Currently most cervical cell detection methods use anchor-based pipeline to achieve the localization and classification of cells, e.g. faster R-CNN and YOLOv3. However, the ...

    Abstract Cervical cell detection is crucial to cervical cytology screening at early stage. Currently most cervical cell detection methods use anchor-based pipeline to achieve the localization and classification of cells, e.g. faster R-CNN and YOLOv3. However, the anchors generally need to be pre-defined before training and the detection performance is inevitably sensitive to these pre-defined hyperparameters (e.g. number of anchors, anchor size and aspect ratios). More importantly, these preset anchors fail to conform to the cells with different morphology at inference phase. In this paper, we present a key-points based anchor-free cervical cell detector based on YOLOv3. Compared with the conventional YOLOv3, the proposed method applies a key-points based anchor-free strategy to represent the cells in the initial prediction phase instead of the preset anchors. Therefore, it can generate more desirable cell localization effect through refinement. Furthermore, PAFPN is applied to enhance the feature hierarchy. GIoU loss is also introduced to optimize the small cell localization in addition to focal loss and smooth L1 loss. Experimental results on cervical cytology ROI datasets demonstrate the effectiveness of our method for cervical cell detection and the robustness to different liquid-based preparation styles (i.e. drop-slide, membrane-based and sedimentation).
    MeSH term(s) Humans ; Female ; Cervix Uteri ; Vaginal Smears/methods ; Uterine Cervical Neoplasms/diagnosis
    Language English
    Publishing date 2023-12-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2694-0604
    ISSN (online) 2694-0604
    DOI 10.1109/EMBC40787.2023.10341092
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Responses of Planting Modes to Photosynthetic Characteristics and Fluorescence Parameters of Fokienia hodginsii Seedlings in a Heterogeneous Nutrient Environment

    Li, Bingjun / Deng, Mi / Pan, Yanmei / Rong, Jundong / He, Tianyou / Chen, Liguang / Zheng, Yushan

    Forests. 2023 May 10, v. 14, no. 5

    2023  

    Abstract: Fokienia hodginsii seedlings tend to vary significantly in response to differences in the surrounding environment, especially when the nutrient environment is heterogeneous and neighboring plants are in competition. Plant physiological differences occur ... ...

    Abstract Fokienia hodginsii seedlings tend to vary significantly in response to differences in the surrounding environment, especially when the nutrient environment is heterogeneous and neighboring plants are in competition. Plant physiological differences occur not only in the root system, but also in the photosynthetic characteristics and fluorescence parameters of the leaves. Therefore, in this experiment, three planting modes (single planting, pure planting of F. hodginsii and mixed planting of F. hodginsii and Cunninghamia lanceolata) were set up to simulate different competition patterns. Three heterogeneous nutrient environments (N, P, K heterogeneous nutrient environment) were planted in this experiment, and the homogeneous environments were used as controls to determine the differences in photosynthetic characteristics, fluorescence parameters and the interaction of different environmental factors on each index in different heterogeneous nutrient and planting environments. The interactions of different environmental factors with various indicators were measured. In addition, all treatment combinations were evaluated and ranked by principal components analysis. The results showed that the net photosynthetic rate (Pₙ) was on average 28.8% and 22.3% higher under monoculture treatment compared to pure and mixed planting in each nutrient environment. Transpiration rate (Tᵣ) and stomatal conductance (Gₛ) were the lowest under pure planting mode, and the overall mean of Tr was 27.2% and 5.5% lower than monoculture and mixed planting, respectively, and the overall mean of Gs was 36.5% and 14.7% lower, respectively. Intercellular CO₂ concentration (Cᵢ) was higher under mixed and pure planting mode than monoculture, but their overall increments were not significant. Pₙ, Tᵣ and Gₛ values of F. hodginsii in the N and P patches were significantly higher than those in the homogeneous patches, whereas the average values of Pₙ, Tᵣ and Gₛ in the K patches were slightly higher than those in the homogeneous patches. The average values of leaf Fₒ, Fᵥ/Fₘ and qP in each nutrient patch under single planting were higher than those under pure and mixed planting, but most of the differences were not significant. The actual photochemical efficiency (yield), photosynthetic electron transfer rate (ETR) and Fᵥ/Fₘ in N and P patches were significantly higher than those in the homogeneous patches, whereas qP and NPQ in N and P patches differed due to different planting patterns. Most fluorescence parameters in the K patches were lower than those in the homogeneous patches. Planting patterns and nutrient heterogeneity showed significant interaction effects on Pₙ, Gₛ, Yield, ETR, Fᵥ/Fₘ and NPQ. The highest scores for photosynthetic characteristics and fluorescence parameters of F. hodginsii single planting were in N and P nutrient patches.
    Keywords Cunninghamia lanceolata ; Fokienia hodginsii ; carbon dioxide ; electron transfer ; fluorescence ; leaves ; photochemistry ; photosynthesis ; planting ; root systems ; stomatal conductance
    Language English
    Dates of publication 2023-0510
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527081-3
    ISSN 1999-4907
    ISSN 1999-4907
    DOI 10.3390/f14050984
    Database NAL-Catalogue (AGRICOLA)

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  4. Article: Response of the root morphological structure of

    Li, Bingjun / Deng, Mi / Pan, Yanmei / Chen, Wenchen / He, Tianyou / Chen, Liguang / Zheng, Yushan / Rong, Jundong

    Frontiers in plant science

    2024  Volume 14, Page(s) 1327322

    Abstract: Introduction: Critical changes often occur in : Methods: In this study, we selected one-year-old, high-quality : Results: Heterogeneous nutrient environments, compared with a homogeneous environment, significantly increased the dry matter ... ...

    Abstract Introduction: Critical changes often occur in
    Methods: In this study, we selected one-year-old, high-quality
    Results: Heterogeneous nutrient environments, compared with a homogeneous environment, significantly increased the dry matter accumulation and root morphology indexes of the root system of
    Discussion: The root dry matter accumulation, root morphology, and anatomical structure of
    Language English
    Publishing date 2024-01-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1327322
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Variability in Leaf Color Induced by Chlorophyll Deficiency: Transcriptional Changes in Bamboo Leaves.

    Zhu, Peng-Kai / Zeng, Mei-Yin / Lin, Yu-Han / Tang, Yu / He, Tian-You / Zheng, Yu-Shan / Chen, Ling-Yan

    Current issues in molecular biology

    2024  Volume 46, Issue 2, Page(s) 1503–1515

    Abstract: The diversity of leaf characteristics, particularly leaf color, underscores a pivotal area of inquiry within plant science. The synthesis and functionality of chlorophyll, crucial for photosynthesis, largely dictate leaf coloration, with varying ... ...

    Abstract The diversity of leaf characteristics, particularly leaf color, underscores a pivotal area of inquiry within plant science. The synthesis and functionality of chlorophyll, crucial for photosynthesis, largely dictate leaf coloration, with varying concentrations imparting different shades of green. Complex gene interactions regulate the synthesis and degradation of chlorophyll, and disruptions in these pathways can result in abnormal chlorophyll production, thereby affecting leaf pigmentation. This study focuses on
    Language English
    Publishing date 2024-02-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2000024-8
    ISSN 1467-3045 ; 1467-3037
    ISSN (online) 1467-3045
    ISSN 1467-3037
    DOI 10.3390/cimb46020097
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Histopathology language-image representation learning for fine-grained digital pathology cross-modal retrieval.

    Hu, Dingyi / Jiang, Zhiguo / Shi, Jun / Xie, Fengying / Wu, Kun / Tang, Kunming / Cao, Ming / Huai, Jianguo / Zheng, Yushan

    Medical image analysis

    2024  Volume 95, Page(s) 103163

    Abstract: Large-scale digital whole slide image (WSI) datasets analysis have gained significant attention in computer-aided cancer diagnosis. Content-based histopathological image retrieval (CBHIR) is a technique that searches a large database for data samples ... ...

    Abstract Large-scale digital whole slide image (WSI) datasets analysis have gained significant attention in computer-aided cancer diagnosis. Content-based histopathological image retrieval (CBHIR) is a technique that searches a large database for data samples matching input objects in both details and semantics, offering relevant diagnostic information to pathologists. However, the current methods are limited by the difficulty of gigapixels, the variable size of WSIs, and the dependence on manual annotations. In this work, we propose a novel histopathology language-image representation learning framework for fine-grained digital pathology cross-modal retrieval, which utilizes paired diagnosis reports to learn fine-grained semantics from the WSI. An anchor-based WSI encoder is built to extract hierarchical region features and a prompt-based text encoder is introduced to learn fine-grained semantics from the diagnosis reports. The proposed framework is trained with a multivariate cross-modal loss function to learn semantic information from the diagnosis report at both the instance level and region level. After training, it can perform four types of retrieval tasks based on the multi-modal database to support diagnostic requirements. We conducted experiments on an in-house dataset and a public dataset to evaluate the proposed method. Extensive experiments have demonstrated the effectiveness of the proposed method and its advantages to the present histopathology retrieval methods. The code is available at https://github.com/hudingyi/FGCR.
    Language English
    Publishing date 2024-04-09
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1356436-5
    ISSN 1361-8423 ; 1361-8431 ; 1361-8415
    ISSN (online) 1361-8423 ; 1361-8431
    ISSN 1361-8415
    DOI 10.1016/j.media.2024.103163
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Association between serum 25-hydroxy vitamin D level and metabolic associated fatty liver disease (MAFLD)-a population-based study.

    Wan, Bo / Gao, Yuan / Zheng, Yushan / Chen, Ruanqin

    Endocrine journal

    2021  Volume 68, Issue 6, Page(s) 631–637

    Abstract: Metabolic associated fatty liver disease (MAFLD) is a new concept proposed in 2020. This study aimed to explore the relationship between serum 25-hydroxy vitamin D (25(OH)D) level and MAFLD based on a population survey dataset (the third National Health ... ...

    Abstract Metabolic associated fatty liver disease (MAFLD) is a new concept proposed in 2020. This study aimed to explore the relationship between serum 25-hydroxy vitamin D (25(OH)D) level and MAFLD based on a population survey dataset (the third National Health and Nutrition Examination Surveys of the United States). Multivariate logistic regression was used to estimate the odds ratio (OR) of serum 25(OH)D level for MAFLD. A total of 12,878 participants were included in this analysis. Among them, 4,027 (31.27%) cases were diagnosed with MAFLD and 8,851 (66.40%) were without MAFLD (non-MAFLD). Patients with vitamin D sufficiency and insufficiency totaled 6,983 (54.22%) and 5,895 (45.78%), respectively. The incidence of MAFLD and the grade of hepatic steatosis were both significantly higher in vitamin D insufficiency group. Multivariate analysis showed that vitamin D insufficiency was an independent risk factor for MAFLD after adjusted for other confounders (OR: 1.130, 95%CI: 1.035 to 1.234). In MAFLD population, the average serum 25(OH)D level decreased with the numbers of metabolic risks in MAFLD cases. Serum 25(OH)D level was not associated with the severity of fibrosis or steatosis in MAFLD group. In Conclusion, lower serum 25(OH)D level is associated with higher prevalence of MAFLD in general population. No relationship was found between serum 25(OH)D level and the severity of hepatic steatosis or fibrosis in MAFLD.
    MeSH term(s) Adult ; Female ; Humans ; Insulin Resistance ; Male ; Middle Aged ; Non-alcoholic Fatty Liver Disease/blood ; Non-alcoholic Fatty Liver Disease/epidemiology ; Nutrition Surveys ; Prevalence ; Sex Factors ; United States ; Vitamin D/analogs & derivatives ; Vitamin D/blood ; Vitamin D Deficiency/blood ; Vitamin D Deficiency/epidemiology
    Chemical Substances Vitamin D (1406-16-2) ; 25-hydroxyvitamin D (A288AR3C9H)
    Language English
    Publishing date 2021-03-04
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 1151918-6
    ISSN 1348-4540 ; 0918-8959
    ISSN (online) 1348-4540
    ISSN 0918-8959
    DOI 10.1507/endocrj.EJ20-0758
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Kernel Attention Transformer for Histopathology Whole Slide Image Analysis and Assistant Cancer Diagnosis.

    Zheng, Yushan / Li, Jun / Shi, Jun / Xie, Fengying / Huai, Jianguo / Cao, Ming / Jiang, Zhiguo

    IEEE transactions on medical imaging

    2023  Volume 42, Issue 9, Page(s) 2726–2739

    Abstract: Transformer has been widely used in histopathology whole slide image analysis. However, the design of token-wise self-attention and positional embedding strategy in the common Transformer limits its effectiveness and efficiency when applied to gigapixel ... ...

    Abstract Transformer has been widely used in histopathology whole slide image analysis. However, the design of token-wise self-attention and positional embedding strategy in the common Transformer limits its effectiveness and efficiency when applied to gigapixel histopathology images. In this paper, we propose a novel kernel attention Transformer (KAT) for histopathology WSI analysis and assistant cancer diagnosis. The information transmission in KAT is achieved by cross-attention between the patch features and a set of kernels related to the spatial relationship of the patches on the whole slide images. Compared to the common Transformer structure, KAT can extract the hierarchical context information of the local regions of the WSI and provide diversified diagnosis information. Meanwhile, the kernel-based cross-attention paradigm significantly reduces the computational amount. The proposed method was evaluated on three large-scale datasets and was compared with 8 state-of-the-art methods. The experimental results have demonstrated the proposed KAT is effective and efficient in the task of histopathology WSI analysis and is superior to the state-of-the-art methods.
    MeSH term(s) Humans ; Neoplasms/diagnostic imaging ; Image Processing, Computer-Assisted
    Language English
    Publishing date 2023-08-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 622531-7
    ISSN 1558-254X ; 0278-0062
    ISSN (online) 1558-254X
    ISSN 0278-0062
    DOI 10.1109/TMI.2023.3264781
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Toward ultra-tough and heat-resistant biodegradable polylactide/core-shell rubber blends by regulating the distribution of rubber particles with stereocomplex crystallites.

    Liu, Huili / Zhao, Yaling / Zheng, Yushan / Chen, Jianyang / Wang, Jianchuan / Gao, Guangyong / Bai, Dongyu

    International journal of biological macromolecules

    2023  Volume 232, Page(s) 123422

    Abstract: Ultra-tough and heat-resistant poly(l-lactide)/core-shell rubber (PLLA/CSR) blends were fabricated by utilizing stereocomplex (SC) crystallites to effectively regulate the CSR distribution in PLLA matrix. Linear and 3-11 armed poly(d-lactide)s (PDLAs) ... ...

    Abstract Ultra-tough and heat-resistant poly(l-lactide)/core-shell rubber (PLLA/CSR) blends were fabricated by utilizing stereocomplex (SC) crystallites to effectively regulate the CSR distribution in PLLA matrix. Linear and 3-11 armed poly(d-lactide)s (PDLAs) were synthesized and then melt-mixed with PLLA/CSR blend. Interestingly, the incorporated PDLA chains could collaborate with PLLA chains to form dense SC crystallites network in PLLA/PDLA/CSR blends, thus inducing the CSR particles to transform from uniform distribution structure to network-like structure. With increasing the PDLA arm numbers, the size of CSR clusters in the network-like structure first increased and then decreased, and the continuity of the network-like structure first remained at a high level and then decreased obviously. The formation of CSR network-like structure could remarkably improve the impact strength of PLLA/PDLA/CSR blends without deteriorating their strength and modulus (compared with PLLA/CSR blend), and the CSR network-like structure with larger-sized CSR clusters and higher continuity could help obtain higher impact strength (78.3 kJ/m
    MeSH term(s) Hot Temperature ; Crystallization ; Stereoisomerism ; Polyesters/chemistry
    Chemical Substances poly(lactide) (459TN2L5F5) ; Polyesters
    Language English
    Publishing date 2023-01-25
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2023.123422
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Toward ultra-tough and heat-resistant biodegradable polylactide/core-shell rubber blends by regulating the distribution of rubber particles with stereocomplex crystallites

    Liu, Huili / Zhao, Yaling / Zheng, Yushan / Chen, Jianyang / Wang, Chien-chuan / Gao, Guangyong / Bai, Dongyu

    International Journal of Biological Macromolecules. 2023 Mar., v. 232 p.123422-

    2023  

    Abstract: Ultra-tough and heat-resistant poly(l-lactide)/core-shell rubber (PLLA/CSR) blends were fabricated by utilizing stereocomplex (SC) crystallites to effectively regulate the CSR distribution in PLLA matrix. Linear and 3–11 armed poly(d-lactide)s (PDLAs) ... ...

    Abstract Ultra-tough and heat-resistant poly(l-lactide)/core-shell rubber (PLLA/CSR) blends were fabricated by utilizing stereocomplex (SC) crystallites to effectively regulate the CSR distribution in PLLA matrix. Linear and 3–11 armed poly(d-lactide)s (PDLAs) were synthesized and then melt-mixed with PLLA/CSR blend. Interestingly, the incorporated PDLA chains could collaborate with PLLA chains to form dense SC crystallites network in PLLA/PDLA/CSR blends, thus inducing the CSR particles to transform from uniform distribution structure to network-like structure. With increasing the PDLA arm numbers, the size of CSR clusters in the network-like structure first increased and then decreased, and the continuity of the network-like structure first remained at a high level and then decreased obviously. The formation of CSR network-like structure could remarkably improve the impact strength of PLLA/PDLA/CSR blends without deteriorating their strength and modulus (compared with PLLA/CSR blend), and the CSR network-like structure with larger-sized CSR clusters and higher continuity could help obtain higher impact strength (78.3 kJ/m²). Moreover, the heat resistance of PLLA/PDLA/CSR blends could also be significantly improved (the highest Vicat softening temperature was 131 °C) by the SC crystallites network and CSR network-like structure. This work provides an effective strategy for controlling the rubber network-like morphology and thereby preparing high-performance PLLA materials.
    Keywords biodegradability ; heat tolerance ; impact strength ; rubber ; temperature ; Polylactide ; Core-shell rubber ; Stereocomplex crystallites ; Network morphology ; Toughening
    Language English
    Dates of publication 2023-03
    Publishing place Elsevier B.V.
    Document type Article ; Online
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2023.123422
    Database NAL-Catalogue (AGRICOLA)

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