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  1. Article ; Online: Stacking Ensemble and ECA-EfficientNetV2 Convolutional Neural Networks on Classification of Multiple Chest Diseases Including COVID-19.

    Huang, Mei-Ling / Liao, Yu-Chieh

    Academic radiology

    2022  Volume 30, Issue 9, Page(s) 1915–1935

    Abstract: Rationale and objectives: Early detection and treatment of COVID-19 patients is crucial. Convolutional neural networks have been proven to accurately extract features in medical images, which accelerates time required for testing and increases the ... ...

    Abstract Rationale and objectives: Early detection and treatment of COVID-19 patients is crucial. Convolutional neural networks have been proven to accurately extract features in medical images, which accelerates time required for testing and increases the effectiveness of COVID-19 diagnosis. This study proposes two classification models for multiple chest diseases including COVID-19.
    Materials and methods: The first is Stacking-ensemble model, which stacks six pretrained models including EfficientNetV2-B0, EfficientNetV2-B1, EfficientNetV2-B2, EfficientNetV2-B3, EfficientNetV2-S and EfficientNetV2-M. The second model is self-designed model ECA-EfficientNetV2 based on ECA-Net and EfficientNetV2. Ten-fold cross validation was performed for each model on chest X-ray and CT images. One more dataset, COVID-CT dataset, was tested to verify the performance of the proposed Stacking-ensemble and ECA-EfficientNetV2 models.
    Results: The best performance comes from the proposed ECA-EfficientNetV2 model with the highest Accuracy of 99.21%, Precision of 99.23%, Recall of 99.25%, F1-score of 99.20%, and (area under the curve) AUC of 99.51% on chest X-ray dataset; the best performance comes from the proposed ECA-EfficientNetV2 model with the highest Accuracy of 99.81%, Precision of 99.80%, Recall of 99.80%, F1-score of 99.81%, and AUC of 99.87% on chest CT dataset. The differences for five metrics between Stacking-ensemble and ECA-EfficientNetV2 models are not significant.
    Conclusion: Ensemble model achieves better performance than single pretrained models. Compared to the SOTA, Stacking-ensemble and ECA-EfficientNetV2 models proposed in this study demonstrate promising performance on classification of multiple chest diseases including COVID-19.
    MeSH term(s) Humans ; COVID-19/diagnostic imaging ; COVID-19 Testing ; Thorax ; Benchmarking ; Neural Networks, Computer
    Language English
    Publishing date 2022-11-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1355509-1
    ISSN 1878-4046 ; 1076-6332
    ISSN (online) 1878-4046
    ISSN 1076-6332
    DOI 10.1016/j.acra.2022.11.027
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A lightweight CNN-based network on COVID-19 detection using X-ray and CT images.

    Huang, Mei-Ling / Liao, Yu-Chieh

    Computers in biology and medicine

    2022  Volume 146, Page(s) 105604

    Abstract: Background and objectives: The traditional method of detecting COVID-19 disease mainly rely on the interpretation of computer tomography (CT) or X-ray images (X-ray) by doctors or professional researchers to identify whether it is COVID-19 disease, ... ...

    Abstract Background and objectives: The traditional method of detecting COVID-19 disease mainly rely on the interpretation of computer tomography (CT) or X-ray images (X-ray) by doctors or professional researchers to identify whether it is COVID-19 disease, which is easy to cause identification mistakes. In this study, the technology of convolutional neural network is expected to be able to efficiently and accurately identify the COVID-19 disease.
    Methods: This study uses and fine-tunes seven convolutional neural networks including InceptionV3, ResNet50V2, Xception, DenseNet121, MobileNetV2, EfficientNet-B0, and EfficientNetV2 on COVID-19 detection. In addition, we proposes a lightweight convolutional neural network, LightEfficientNetV2, on small number of chest X-ray and CT images. Five-fold cross-validation was used to evaluate the performance of each model. To confirm the performance of the proposed model, LightEfficientNetV2 was carried out on three different datasets (NIH Chest X-rays, SARS-CoV-2 and COVID-CT).
    Results: On chest X-ray image dataset, the highest accuracy 96.50% was from InceptionV3 before fine-tuning; and the highest accuracy 97.73% was from EfficientNetV2 after fine-tuning. The accuracy of the LightEfficientNetV2 model proposed in this study is 98.33% on chest X-ray image. On CT images, the best transfer learning model before fine-tuning is MobileNetV2, with an accuracy of 94.46%; the best transfer learning model after fine-tuning is Xception, with an accuracy of 96.78%. The accuracy of the LightEfficientNetV2 model proposed in this study is 97.48% on CT image.
    Conclusions: Compared with the SOTA, LightEfficientNetV2 proposed in this study demonstrates promising performance on chest X-ray images, CT images and three different datasets.
    MeSH term(s) COVID-19/diagnostic imaging ; Computers ; Deep Learning ; Humans ; SARS-CoV-2 ; Tomography, X-Ray Computed/methods ; X-Rays
    Language English
    Publishing date 2022-05-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2022.105604
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: DNA oxidation after exercise: a systematic review and meta-analysis.

    Ye, Mengxin / Dewi, Luthfia / Liao, Yu-Chieh / Nicholls, Andrew / Huang, Chih-Yang / Kuo, Chia-Hua

    Frontiers in physiology

    2023  Volume 14, Page(s) 1275867

    Abstract: Purpose: ...

    Abstract Purpose:
    Language English
    Publishing date 2023-10-31
    Publishing country Switzerland
    Document type Systematic Review
    ZDB-ID 2564217-0
    ISSN 1664-042X
    ISSN 1664-042X
    DOI 10.3389/fphys.2023.1275867
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Image dataset on the Chinese medicinal blossoms for classification through convolutional neural network.

    Huang, Mei-Ling / Xu, Yi-Xuan / Liao, Yu-Chieh

    Data in brief

    2021  Volume 39, Page(s) 107655

    Abstract: Tree blossoms have been widely used on the prevention and treatment of a variety of diseases in traditional Chinese medicine for thousand years [1,2]. The growth of flowers is not only for their ornamental value, but also for nutritional, medicinal, ... ...

    Abstract Tree blossoms have been widely used on the prevention and treatment of a variety of diseases in traditional Chinese medicine for thousand years [1,2]. The growth of flowers is not only for their ornamental value, but also for nutritional, medicinal, cooking, cosmetic and aromatic properties. They are a rich source of many compounds, which play an important role in various metabolic processes of the human body [3]. Edible flowers can promote the global demand for more attractive and delicious food, and can improve the nutritional content of gourmet food [4]. Flowers are beneficial for anti-anxiety, anti-cancer, anti-inflammatory, antioxidant, diuretic and immune-modulator, etc. It is very important to identify edible flowers correctly, because only a few are edible [5]. The shapes or colors of different flowers may be very similar. Visual evaluation is one of the classification methods, but it is error-prone and time-consuming [6]. Flowers are divided into flowers from herbaceous plants (flower) and flower trees (blossom). Now there is a public herbaceous flower dataset [7], but lack of dataset for Chinese medicinal blossoms. This article presents and establishes the dataset for twelve most commonly and economically valuable blossoms used in traditional Chinese medicine. The dataset provide a collection of blossom images on traditional Chinese herbs help Chinese pharmacist to classify the categories of Chinese herbs. In addition, the dataset can serve as a resource for researchers who use different algorithms of machine learning or deep learning for image segmentation and image classification.
    Language English
    Publishing date 2021-12-01
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2021.107655
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A predominant genotype of azole-resistant Candida tropicalis clinical strains.

    Tseng, Kuo-Yun / Liao, Yu-Chieh / Chen, Feng-Chi / Chen, Feng-Jui / Lo, Hsiu-Jung

    The Lancet. Microbe

    2022  Volume 3, Issue 9, Page(s) e646

    MeSH term(s) Antifungal Agents/pharmacology ; Azoles/pharmacology ; Candida tropicalis/genetics ; Drug Resistance, Fungal/genetics ; Genotype
    Chemical Substances Antifungal Agents ; Azoles
    Language English
    Publishing date 2022-06-22
    Publishing country England
    Document type Letter
    ISSN 2666-5247
    ISSN (online) 2666-5247
    DOI 10.1016/S2666-5247(22)00179-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes.

    Lin, Hsin-Hung / Liao, Yu-Chieh

    GigaScience

    2017  Volume 6, Issue 2, Page(s) 1–10

    Abstract: Background: Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure ... ...

    Abstract Background: Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data.
    Results: This manuscript presents a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes), for rapid viral read identification, genus-level read partition, read normalization, de novo assembly, sequence annotation, and coverage profiling. The first two procedures and sequence annotation rely on known viral genomes as a reference database. drVM was validated via the analysis of over 300 sequencing runs generated by Illumina and Ion Torrent platforms to provide complete viral genome assemblies for a variety of virus types including DNA viruses, RNA viruses, and retroviruses. drVM is available for free download at: https://sourceforge.net/projects/sb2nhri/files/drVM/ and is also assembled as a Docker container, an Amazon machine image, and a virtual machine to facilitate seamless deployment.
    Conclusions: drVM was compared with other viral detection tools to demonstrate its merits in terms of viral genome completeness and reduced computation time. This substantiates the platform's potential to produce prompt and accurate viral genome sequences from clinical samples.
    MeSH term(s) Computational Biology/methods ; Computer Simulation ; Databases, Nucleic Acid ; Datasets as Topic ; Eukaryotic Cells/virology ; Genome, Viral ; Metagenome ; Metagenomics/methods ; Reproducibility of Results ; Software ; Web Browser
    Keywords covid19
    Language English
    Publishing date 2017-04-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/gix003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Image dataset on the Chinese medicinal blossoms for classification through convolutional neural network

    Huang, Mei-Ling / Xu, Yi-Xuan / Liao, Yu-Chieh

    Data in Brief. 2021 Dec., v. 39

    2021  

    Abstract: Tree blossoms have been widely used on the prevention and treatment of a variety of diseases in traditional Chinese medicine for thousand years [1,2]. The growth of flowers is not only for their ornamental value, but also for nutritional, medicinal, ... ...

    Abstract Tree blossoms have been widely used on the prevention and treatment of a variety of diseases in traditional Chinese medicine for thousand years [1,2]. The growth of flowers is not only for their ornamental value, but also for nutritional, medicinal, cooking, cosmetic and aromatic properties. They are a rich source of many compounds, which play an important role in various metabolic processes of the human body [3]. Edible flowers can promote the global demand for more attractive and delicious food, and can improve the nutritional content of gourmet food [4]. Flowers are beneficial for anti-anxiety, anti-cancer, anti-inflammatory, antioxidant, diuretic and immune-modulator, etc. It is very important to identify edible flowers correctly, because only a few are edible [5]. The shapes or colors of different flowers may be very similar. Visual evaluation is one of the classification methods, but it is error-prone and time-consuming [6]. Flowers are divided into flowers from herbaceous plants (flower) and flower trees (blossom). Now there is a public herbaceous flower dataset [7], but lack of dataset for Chinese medicinal blossoms. This article presents and establishes the dataset for twelve most commonly and economically valuable blossoms used in traditional Chinese medicine. The dataset provide a collection of blossom images on traditional Chinese herbs help Chinese pharmacist to classify the categories of Chinese herbs. In addition, the dataset can serve as a resource for researchers who use different algorithms of machine learning or deep learning for image segmentation and image classification.
    Keywords Oriental traditional medicine ; antioxidants ; data collection ; humans ; image analysis ; immunomodulators ; neural networks ; nutrient content ; ornamental value
    Language English
    Dates of publication 2021-12
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 2786545-9
    ISSN 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2021.107655
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Intestinal dual-specificity phosphatase 6 regulates the cold-induced gut microbiota remodeling to promote white adipose browning.

    Chen, Pei-Chen / Tsai, Tzu-Pei / Liao, Yi-Chu / Liao, Yu-Chieh / Cheng, Hung-Wei / Weng, Yi-Hsiu / Lin, Chiao-Mei / Kao, Cheng-Yuan / Tai, Chih-Cheng / Ruan, Jhen-Wei

    NPJ biofilms and microbiomes

    2024  Volume 10, Issue 1, Page(s) 22

    Abstract: Gut microbiota rearrangement induced by cold temperature is crucial for browning in murine white adipose tissue. This study provides evidence that DUSP6, a host factor, plays a critical role in regulating cold-induced gut microbiota rearrangement. When ... ...

    Abstract Gut microbiota rearrangement induced by cold temperature is crucial for browning in murine white adipose tissue. This study provides evidence that DUSP6, a host factor, plays a critical role in regulating cold-induced gut microbiota rearrangement. When exposed to cold, the downregulation of intestinal DUSP6 increased the capacity of gut microbiota to produce ursodeoxycholic acid (UDCA). The DUSP6-UDCA axis is essential for driving Lachnospiraceae expansion in the cold microbiota. In mice experiencing cold-room temperature (CR) transitions, prolonged DUSP6 inhibition via the DUSP6 inhibitor (E/Z)-BCI maintained increased cecal UDCA levels and cold-like microbiota networks. By analyzing DUSP6-regulated microbiota dynamics in cold-exposed mice, we identified Marvinbryantia as a genus whose abundance increased in response to cold exposure. When inoculated with human-origin Marvinbryantia formatexigens, germ-free recipient mice exhibited significantly enhanced browning phenotypes in white adipose tissue. Moreover, M. formatexigens secreted the methylated amino acid Nε-methyl-L-lysine, an enriched cecal metabolite in Dusp6 knockout mice that reduces adiposity and ameliorates nonalcoholic steatohepatitis in mice. Our work revealed that host-microbiota coadaptation to cold environments is essential for regulating the browning-promoting gut microbiome.
    MeSH term(s) Animals ; Humans ; Mice ; Adiposity ; Cold Temperature ; Dual-Specificity Phosphatases/metabolism ; Gastrointestinal Microbiome/physiology ; Obesity
    Chemical Substances Dual-Specificity Phosphatases (EC 3.1.3.48) ; Dusp6 protein, mouse (EC 3.1.3.48)
    Language English
    Publishing date 2024-03-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2817021-0
    ISSN 2055-5008 ; 2055-5008
    ISSN (online) 2055-5008
    ISSN 2055-5008
    DOI 10.1038/s41522-024-00495-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Cordyceps sinensis

    Dewi, Luthfia / Liao, Yu-Chieh / Jean, Wei-Horng / Huang, Kuo-Chin / Huang, Chih-Yang / Chen, Liang-Kung / Nicholls, Andrew / Lai, Li-Fan / Kuo, Chia-Hua

    Food & function

    2024  Volume 15, Issue 8, Page(s) 4010–4020

    Abstract: Cordyceps ... ...

    Abstract Cordyceps sinensis
    MeSH term(s) Humans ; Cordyceps/chemistry ; Young Adult ; Male ; Exercise/physiology ; Adult ; Muscle, Skeletal/drug effects ; Muscle, Skeletal/metabolism ; Double-Blind Method ; Cross-Over Studies ; Stem Cells/drug effects ; Antigens, CD34/metabolism ; Female ; PAX7 Transcription Factor/metabolism ; PAX7 Transcription Factor/genetics ; Vascular Endothelial Growth Factor A/metabolism ; Vascular Endothelial Growth Factor A/genetics
    Chemical Substances Antigens, CD34 ; PAX7 Transcription Factor ; Vascular Endothelial Growth Factor A
    Language English
    Publishing date 2024-04-22
    Publishing country England
    Document type Randomized Controlled Trial ; Journal Article
    ZDB-ID 2612033-1
    ISSN 2042-650X ; 2042-6496
    ISSN (online) 2042-650X
    ISSN 2042-6496
    DOI 10.1039/d3fo03770c
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Senolytic effects of exercise in human muscles require acute inflammation.

    Jean, Wei-Horng / Lin, Yin-Chou / Ang, Pei-Yao / Goto, Kazushige / Lin, Chao-An / Dewi, Luthfia / Liao, Yu-Chieh / Huang, Chih-Yang / Kuo, Chia-Hua

    Aging

    2024  Volume 16

    Abstract: Higher intensity exercise, despite causing more tissue damage, improved aging conditions. We previously observed decreased ... ...

    Abstract Higher intensity exercise, despite causing more tissue damage, improved aging conditions. We previously observed decreased p16
    Language English
    Publishing date 2024-05-15
    Publishing country United States
    Document type Journal Article
    ISSN 1945-4589
    ISSN (online) 1945-4589
    DOI 10.18632/aging.205827
    Database MEDical Literature Analysis and Retrieval System OnLINE

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