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  1. Article: Prediction of early recurrence in patients with colorectal liver metastases.

    Liao, Xingyu / Chi, Jiayu / Xia, Qi / Sun, Lejia

    Journal of gastrointestinal oncology

    2023  Volume 14, Issue 5, Page(s) 2279–2281

    Language English
    Publishing date 2023-10-23
    Publishing country China
    Document type Journal Article ; Comment
    ZDB-ID 2594644-4
    ISSN 2219-679X ; 2078-6891
    ISSN (online) 2219-679X
    ISSN 2078-6891
    DOI 10.21037/jgo-23-653
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  2. Article ; Online: Learning from real world data about combinatorial treatment selection for COVID-19.

    Zhai, Song / Zhang, Zhiwei / Liao, Jiayu / Cui, Xinping

    Frontiers in artificial intelligence

    2023  Volume 6, Page(s) 1123285

    Abstract: COVID-19 is an unprecedented global pandemic with a serious negative impact on virtually every part of the world. Although much progress has been made in preventing and treating the disease, much remains to be learned about how best to treat the disease ... ...

    Abstract COVID-19 is an unprecedented global pandemic with a serious negative impact on virtually every part of the world. Although much progress has been made in preventing and treating the disease, much remains to be learned about how best to treat the disease while considering patient and disease characteristics. This paper reports a case study of combinatorial treatment selection for COVID-19 based on real-world data from a large hospital in Southern China. In this observational study, 417 confirmed COVID-19 patients were treated with various combinations of drugs and followed for four weeks after discharge (or until death). Treatment failure is defined as death during hospitalization or recurrence of COVID-19 within four weeks of discharge. Using a virtual multiple matching method to adjust for confounding, we estimate and compare the failure rates of different combinatorial treatments, both in the whole study population and in subpopulations defined by baseline characteristics. Our analysis reveals that treatment effects are substantial and heterogeneous, and that the optimal combinatorial treatment may depend on baseline age, systolic blood pressure, and c-reactive protein level. Using these three variables to stratify the study population leads to a stratified treatment strategy that involves several different combinations of drugs (for patients in different strata). Our findings are exploratory and require further validation.
    Language English
    Publishing date 2023-04-03
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2624-8212
    ISSN (online) 2624-8212
    DOI 10.3389/frai.2023.1123285
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data.

    Liao, Herui / Shang, Jiayu / Sun, Yanni

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 12

    Abstract: Motivation: With advances in metagenomic sequencing technologies, there are accumulating studies revealing the associations between the human gut microbiome and some human diseases. These associations shed light on using gut microbiome data to ... ...

    Abstract Motivation: With advances in metagenomic sequencing technologies, there are accumulating studies revealing the associations between the human gut microbiome and some human diseases. These associations shed light on using gut microbiome data to distinguish case and control samples of a specific disease, which is also called host disease status classification. Importantly, using learning-based models to distinguish the disease and control samples is expected to identify important biomarkers more accurately than abundance-based statistical analysis. However, available tools have not fully addressed two challenges associated with this task: limited labeled microbiome data and decreased accuracy in cross-studies. The confounding factors, such as the diet, technical biases in sample collection/sequencing across different studies/cohorts often jeopardize the generalization of the learning model.
    Results: To address these challenges, we develop a new tool GDmicro, which combines semi-supervised learning and domain adaptation to achieve a more generalized model using limited labeled samples. We evaluated GDmicro on human gut microbiome data from 11 cohorts covering 5 different diseases. The results show that GDmicro has better performance and robustness than state-of-the-art tools. In particular, it improves the AUC from 0.783 to 0.949 in identifying inflammatory bowel disease. Furthermore, GDmicro can identify potential biomarkers with greater accuracy than abundance-based statistical analysis methods. It also reveals the contribution of these biomarkers to the host's disease status.
    Availability and implementation: https://github.com/liaoherui/GDmicro.
    MeSH term(s) Humans ; Gastrointestinal Microbiome ; Microbiota ; Metagenome ; Inflammatory Bowel Diseases ; Biomarkers
    Chemical Substances Biomarkers
    Language English
    Publishing date 2023-12-12
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad747
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  4. Article ; Online: Learning from real world data about combinatorial treatment selection for COVID-19

    Song Zhai / Zhiwei Zhang / Jiayu Liao / Xinping Cui

    Frontiers in Artificial Intelligence, Vol

    2023  Volume 6

    Abstract: COVID-19 is an unprecedented global pandemic with a serious negative impact on virtually every part of the world. Although much progress has been made in preventing and treating the disease, much remains to be learned about how best to treat the disease ... ...

    Abstract COVID-19 is an unprecedented global pandemic with a serious negative impact on virtually every part of the world. Although much progress has been made in preventing and treating the disease, much remains to be learned about how best to treat the disease while considering patient and disease characteristics. This paper reports a case study of combinatorial treatment selection for COVID-19 based on real-world data from a large hospital in Southern China. In this observational study, 417 confirmed COVID-19 patients were treated with various combinations of drugs and followed for four weeks after discharge (or until death). Treatment failure is defined as death during hospitalization or recurrence of COVID-19 within four weeks of discharge. Using a virtual multiple matching method to adjust for confounding, we estimate and compare the failure rates of different combinatorial treatments, both in the whole study population and in subpopulations defined by baseline characteristics. Our analysis reveals that treatment effects are substantial and heterogeneous, and that the optimal combinatorial treatment may depend on baseline age, systolic blood pressure, and c-reactive protein level. Using these three variables to stratify the study population leads to a stratified treatment strategy that involves several different combinations of drugs (for patients in different strata). Our findings are exploratory and require further validation.
    Keywords G-computation ; virtual multiple matching ; subgroup analysis ; multiple comparisons with the best ; COVID-19 ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 610
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Editorial: Human decision-making behaviors in engineering and management: A neuropsychological perspective.

    Fu, Hanliang / Ye, Gui / Chen, Jiayu / Liao, Pin-Chao

    Frontiers in neuroscience

    2022  Volume 16, Page(s) 1062171

    Language English
    Publishing date 2022-11-11
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2411902-7
    ISSN 1662-453X ; 1662-4548
    ISSN (online) 1662-453X
    ISSN 1662-4548
    DOI 10.3389/fnins.2022.1062171
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  6. Article: Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species.

    Ji, Huiyue / Liu, Junnan / Chen, Yineng / Yu, Xinyi / Luo, Chenlu / Sang, Luxi / Zhou, Jiayu / Liao, Hai

    Plants (Basel, Switzerland)

    2024  Volume 13, Issue 4

    Abstract: Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified ... ...

    Abstract Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified 140
    Language English
    Publishing date 2024-02-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants13040468
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  7. Article ; Online: PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic data.

    Shang, Jiayu / Peng, Cheng / Liao, Herui / Tang, Xubo / Sun, Yanni

    Bioinformatics advances

    2023  Volume 3, Issue 1, Page(s) vbad101

    Abstract: Motivation: There is accumulating evidence showing the important roles of bacteriophages (phages) in regulating the structure and functions of the microbiome. However, lacking an easy-to-use and integrated phage analysis software hampers microbiome- ... ...

    Abstract Motivation: There is accumulating evidence showing the important roles of bacteriophages (phages) in regulating the structure and functions of the microbiome. However, lacking an easy-to-use and integrated phage analysis software hampers microbiome-related research from incorporating phages in the analysis.
    Results: In this work, we developed a web server, PhaBOX, which can comprehensively identify and analyze phage contigs in metagenomic data. It supports integrated phage analysis, including phage contig identification from the metagenomic assembly, lifestyle prediction, taxonomic classification, and host prediction. Instead of treating the algorithms as a black box, PhaBOX also supports visualization of the essential features for making predictions. The web server is designed with a user-friendly graphical interface that enables both informatics-trained and nonspecialist users to analyze phages in microbiome data with ease.
    Availability and implementation: The web server of PhaBOX is available via: https://phage.ee.cityu.edu.hk. The source code of PhaBOX is available at: https://github.com/KennthShang/PhaBOX.
    Language English
    Publishing date 2023-08-02
    Publishing country England
    Document type Journal Article
    ISSN 2635-0041
    ISSN (online) 2635-0041
    DOI 10.1093/bioadv/vbad101
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  8. Article ; Online: Intrathyroid thymic carcinoma: clinicopathological features and whole exome sequencing analysis.

    Li, Jiayu / Xiang, Run / Li, Yunzhu / Liao, Qiong / Liu, Yang

    Virchows Archiv : an international journal of pathology

    2023  Volume 482, Issue 5, Page(s) 813–822

    Abstract: Intrathyroid thymic carcinoma (ITC) is a rare malignant tumour. We present nine cases of ITC that were analysed by immunohistochemical staining, of which five were analysed using whole exome sequencing (WES). These cases included six women and three men ... ...

    Abstract Intrathyroid thymic carcinoma (ITC) is a rare malignant tumour. We present nine cases of ITC that were analysed by immunohistochemical staining, of which five were analysed using whole exome sequencing (WES). These cases included six women and three men with an age range of 31-66 years. The average postoperative follow-up term was 37.8 months (range, 7-95 months), and all patients survived well except for one case with lung metastasis. Microscopically, ITC showed solid islands of tumour cells separated by fibrous connective tissue containing lymphocytes and other inflammatory cells. Tumour cells strongly expressed Ckpan (AE1/AE3), P63, and CD117. And all cases but one were positive for CD5. The median value of Ki-67 was 32% (range 10-60%). We observed partial positivity of Syn and CgA in only one case. ITC shares morphological and immunohistochemical similarities with thymic squamous cell carcinoma. In situ hybridization of EBER showed negative results. All cases were microsatellite stable, and the tumour mutational burden of the 5 cases was all < 1 mutations/Mb. WES showed higher mutation rates for N4BP1 (2/5), and many genetic alterations were related to the NF-kB signalling pathway, which is crucial for insight into the molecular mechanisms of the occurrence and development of ITC.
    MeSH term(s) Male ; Humans ; Female ; Adult ; Middle Aged ; Aged ; Thymoma/genetics ; Thymoma/metabolism ; Exome Sequencing ; Thymus Neoplasms/pathology ; Thyroid Neoplasms/pathology
    Language English
    Publishing date 2023-04-05
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1184867-4
    ISSN 1432-2307 ; 0945-6317
    ISSN (online) 1432-2307
    ISSN 0945-6317
    DOI 10.1007/s00428-023-03536-3
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  9. Article ; Online: Sirtuin 1 in osteoarthritis: Perspectives on regulating glucose metabolism.

    Liao, Zhihao / Cai, Xuepei / Zheng, Yifan / Lin, Jiayu / Yang, Xia / Lin, Weiyin / Zhang, Ying / He, Xin / Liu, Chufeng

    Pharmacological research

    2024  Volume 202, Page(s) 107141

    Abstract: Osteoarthritis (OA) is a degenerative disease characterised by articular cartilage destruction, and its complex aetiology contributes to suboptimal clinical treatment outcomes. A close association exists between glucose metabolism dysregulation and OA ... ...

    Abstract Osteoarthritis (OA) is a degenerative disease characterised by articular cartilage destruction, and its complex aetiology contributes to suboptimal clinical treatment outcomes. A close association exists between glucose metabolism dysregulation and OA pathogenesis. Owing to the unique environment of low oxygen and glucose concentrations, chondrocytes rely heavily on their glycolytic capacity, exhibiting distinct spatiotemporal differences. However, under pathological stimulation, chondrocytes undergo excessive glycolytic activity while mitochondrial respiration and other branches of glucose metabolism are compromised. This metabolic change induces cartilage degeneration by reprogramming the inflammatory responses. Sirtuins, a highly conserved family of nicotinamide adenine dinucleotide (NAD
    MeSH term(s) Animals ; Humans ; Cartilage, Articular/pathology ; Glucose/metabolism ; Osteoarthritis/metabolism ; Sirtuin 1/metabolism ; Sirtuins/metabolism
    Chemical Substances Glucose (IY9XDZ35W2) ; Sirtuin 1 (EC 3.5.1.-) ; Sirtuins (EC 3.5.1.-) ; SIRT1 protein, human (EC 3.5.1.-)
    Language English
    Publishing date 2024-03-14
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 1003347-6
    ISSN 1096-1186 ; 0031-6989 ; 1043-6618
    ISSN (online) 1096-1186
    ISSN 0031-6989 ; 1043-6618
    DOI 10.1016/j.phrs.2024.107141
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    Zs.A 721: Show issues Location:
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  10. Article ; Online: Implementation of micelle-enabled C(sp

    Wu, Bin / Ye, Ning / Zhao, Kangming / Shi, Min / Liao, Jiayu / Zhang, Jing / Chen, Wei / Li, Xianzhong / Han, Yufeng / Cortes-Clerget, Margery / Regnier, Morgan Louis / Parmentier, Michael / Mathes, Christian / Rampf, Florian / Gallou, Fabrice

    Chemical communications (Cambridge, England)

    2024  Volume 60, Issue 17, Page(s) 2349–2352

    Abstract: A sustainable C( ... ...

    Abstract A sustainable C(sp
    MeSH term(s) Micelles ; Solvents ; Water ; Catalysis
    Chemical Substances Micelles ; Solvents ; Water (059QF0KO0R)
    Language English
    Publishing date 2024-02-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d3cc05916b
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