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Article ; Online: AXL, along with PROS1, is overexpressed in papillary thyroid carcinoma and regulates its biological behaviour.

Wei, Mingze / Wang, Yizeng / Liu, Yuanchao / Li, Dongyang / He, Xianghui

2022 Volume 20, Issue 1, Page(s) 334

Abstract: Background: AXL, a TAM tyrosine kinase receptor, plays an essential role in the pathogenesis of various solid tumours. This study explores the role of AXL and its ligand PROS1 in the generation and biological behaviour of papillary thyroid cancer (PTC).! ...

Abstract	Background: AXL, a TAM tyrosine kinase receptor, plays an essential role in the pathogenesis of various solid tumours. This study explores the role of AXL and its ligand PROS1 in the generation and biological behaviour of papillary thyroid cancer (PTC). Methods: The expression levels of AXL in PTC cancer tissue were analysed using immunohistochemistry (IHC) staining. The expression levels of AXL in PTC and normal thyroid cell lines were analysed using real-time quantitative polymerase chain reaction (RT-qPCR). CCK-8 was used to assess the proliferation of the PTC cell line with and without the effect of the AXL inhibitor (R428). Scratching assays played a role in evaluating the cell migration rate. Results: PROS1 and AXL were expressed in TPC-1, B-CPAP, and Nthy-Ori 3-1 cells at different levels. Expression was significantly higher in PTC cell lines (TPC-1 and B-CPAP) than in the normal thyroid cell line (Nthy-Ori 3-1) (p < 0.05). In addition, AXL expression in PTC tissues was significantly higher than in adjacent normal tissues (p < 0.05). CCK-8 experiments confirmed that R428 suppresses the proliferation of PTC cell lines in a dose-dependent manner, with an increase in concentration from 0.5 to 4 μM, decreasing the inhibitory effect (p < 0.01). In addition, R428 inhibited PTC cell line migration to different degrees in a range of concentrations from 0.5 to 2 μM compared to control cells (p < 0.01). Conclusion: PROS1 and its downstream receptor AXL expression were significantly higher in PTC than in normal thyroid cells. AXL expression was also higher in human PTC tissues than in normal thyroid tissues. Inhibiting the PROS1-AXL-mediated TAM signaling pathway via the AXL blocker R428 suppressed the proliferation and migration of human PTC cells, highlighting the role of this cascade in human PTC development and progression.
MeSH term(s)	Apoptosis ; Cell Line, Tumor ; Cell Movement ; Cell Proliferation ; Gene Expression Regulation, Neoplastic ; Humans ; Ligands ; Protein S/metabolism ; Proto-Oncogene Proteins/metabolism ; Receptor Protein-Tyrosine Kinases/metabolism ; Sincalide/metabolism ; Thyroid Cancer, Papillary/pathology ; Thyroid Neoplasms/pathology
Chemical Substances	Ligands ; PROS1 protein, human ; Protein S ; Proto-Oncogene Proteins ; Receptor Protein-Tyrosine Kinases (EC 2.7.10.1) ; axl receptor tyrosine kinase (EC 2.7.10.1) ; Sincalide (M03GIQ7Z6P)
Language	English
Publishing date	2022-10-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2118383-1
ISSN	1477-7819 ; 1477-7819
ISSN (online)	1477-7819
ISSN	1477-7819
DOI	10.1186/s12957-022-02801-0
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Article ; Online: BIR: Biomedical Information Retrieval System for Cancer Treatment in Electronic Health Record Using Transformers.

Ahmad, Pir Noman / Liu, Yuanchao / Khan, Khalid / Jiang, Tao / Burhan, Umama

Sensors (Basel, Switzerland)

2023 Volume 23, Issue 23

Abstract: The rapid growth of electronic health records (EHRs) has led to unprecedented biomedical data. Clinician access to the latest patient information can improve the quality of healthcare. However, clinicians have difficulty finding information quickly and ... ...

Abstract	The rapid growth of electronic health records (EHRs) has led to unprecedented biomedical data. Clinician access to the latest patient information can improve the quality of healthcare. However, clinicians have difficulty finding information quickly and easily due to the sheer data mining volume. Biomedical information retrieval (BIR) systems can help clinicians find the information required by automatically searching EHRs and returning relevant results. However, traditional BIR systems cannot understand the complex relationships between EHR entities. Transformers are a new type of neural network that is very effective for natural language processing (NLP) tasks. As a result, transformers are well suited for tasks such as machine translation and text summarization. In this paper, we propose a new BIR system for EHRs that uses transformers for predicting cancer treatment from EHR. Our system can understand the complex relationships between the different entities in an EHR, which allows it to return more relevant results to clinicians. We evaluated our system on a dataset of EHRs and found that it outperformed state-of-the-art BIR systems on various tasks, including medical question answering and information extraction. Our results show that Transformers are a promising approach for BIR in EHRs, reaching an accuracy and an F1-score of 86.46%, and 0.8157, respectively. We believe that our system can help clinicians find the information they need more quickly and easily, leading to improved patient care.
MeSH term(s)	Humans ; Electronic Health Records ; Data Mining/methods ; Natural Language Processing ; Neural Networks, Computer ; Information Systems ; Neoplasms/therapy
Language	English
Publishing date	2023-11-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s23239355
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Article ; Online: Staging classification of omicron variant SARS-CoV-2 infection based on dual-spectrometer LIBS (DS-LIBS) combined with machine learning.

Wang, Weiliang / Shi, Shengqun / Liu, Yuanchao / Hou, Zehai / Qi, Jianwei / Guo, Lianbo

Optics express

2023 Volume 31, Issue 25, Page(s) 42413–42427

Abstract: Effective differentiation of the infection stages of omicron can provide significant assistance in transmission control and treatment strategies. The combination of LIBS serum detection and machine learning methods, as a novel disease auxiliary ... ...

Abstract	Effective differentiation of the infection stages of omicron can provide significant assistance in transmission control and treatment strategies. The combination of LIBS serum detection and machine learning methods, as a novel disease auxiliary diagnostic approach, has a high potential for rapid and accurate staging classification of Omicron infection. However, conventional single-spectrometer LIBS serum detection methods focus on detecting the spectra of major elements, while trace elements are more closely related to the progression of COVID-19. Here, we proposed a rapid analytical method with dual-spectrometer LIBS (DS-LIBS) assisted with machine learning to classify different infection stages of omicron. The DS-LIBS, including a broadband spectrometer and a narrowband spectrometer, enables synchronous collection of major and trace elemental spectra in serum, respectively. By employing the RF machine learning models, the classification accuracy using the spectra data collected from DS-LIBS can reach 0.92, compared to 0.84 and 0.73 when using spectra data collected from single-spectrometer LIBS. This significant improvement in classification accuracy highlights the efficacy of the DS-LIBS approach. Then, the performance of four different models, SVM, RF, IGBT, and ETree, is compared. ETree demonstrates the best, with cross-validation and test set accuracies of 0.94 and 0.93, respectively. Additionally, it achieves classification accuracies of 1.00, 0.92, 0.92, and 0.89 for the four stages B1-acute, B1-post, B2, and B3. Overall, the results demonstrate that DS-LIBS combined with the ETree machine learning model enables effective staging classification of omicron infection.
MeSH term(s)	Humans ; COVID-19/diagnosis ; SARS-CoV-2 ; Machine Learning ; Research Design ; Trace Elements
Chemical Substances	Trace Elements
Language	English
Publishing date	2023-12-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	1491859-6
ISSN	1094-4087 ; 1094-4087
ISSN (online)	1094-4087
ISSN	1094-4087
DOI	10.1364/OE.504640
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Article ; Online: Sensitivity and stability improvement on slippery surface-aggregated substrate for trace heavy metals detection using NELIBS.

Xiao, Siyi / Liu, Yuanchao / Luo, Yawen / Zhu, Yuying / Wang, Weiliang / Nie, Junfei / Huang, Weihua / Niu, Chen / Gong, Aojun / Guo, Lianbo

Talanta

2024 Volume 275, Page(s) 126001

Abstract: The sensitive and stable detection of trace heavy metals in liquid is crucial given its profound impact on various aspects of human life. Currently, nanoparticle-enhanced laser-induced breakdown spectroscopy (NELIBS) with dried droplet method (DDM) is ... ...

Abstract	The sensitive and stable detection of trace heavy metals in liquid is crucial given its profound impact on various aspects of human life. Currently, nanoparticle-enhanced laser-induced breakdown spectroscopy (NELIBS) with dried droplet method (DDM) is widely applied for heavy metals detection. Nevertheless, the coffee ring effect (CRE) in DDM affects the stability, accuracy, and sensitivity of NELIBS. Here, we developed a slippery surface-aggregated substrate (SS substrate) to suppress the CRE and enrich analytes, and form a plasmonic platform for NELIBS detection. The SS substrate was prepared by infiltrating perfluorinated lubricant into the pores of PTFE membrane. The droplet, with targeted elements and gold nanoparticles, was dried on the SS substate to form the plasmonic platform for NELIBS analysis. Then, trace heavy metal elements copper (Cu) and manganese (Mn) were analyzed by NELIBS. The results of Cu (RSD = 5.60%, LoD = 3.72 μg/L) and Mn (RSD = 7.42%, LoD = 6.37 μg/L), illustrated the CRE suppression and analytes enrichment by the SS substrate. The results verified the realization of stable, accurate and sensitive NELIBS detection. And the LoDs succeeded to reach the standard limit of China (GB/T 14848-2017). Furthermore, the results for groundwater detection (relative error: 5.92% (Cu) and 4.74% (Mn)), comparing NELIBS and inductively coupled plasma mass spectrometry (ICP-MS), validated the feasibility of the SS substrate in practical applications. In summary, the SS substrate exhibits immense potential for practical application such as water quality detection and supervision.
Language	English
Publishing date	2024-04-14
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1500969-5
ISSN	1873-3573 ; 0039-9140
ISSN (online)	1873-3573
ISSN	0039-9140
DOI	10.1016/j.talanta.2024.126001
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Article ; Online: Study on the inhibitory effect of fermentation extract of Microporus vernicipes on Candida albicans.

Guo, Huiyang / Liu, Yuanchao / Wu, Xiaoxian / Cai, Manjun / Jiang, Ming / Hu, Huiping

International microbiology : the official journal of the Spanish Society for Microbiology

2023

Abstract: Candida albicans is one of the most common species of Candida, which cause various mucosal and systemic infectious diseases. However, the resistance rate to existing clinical antifungal drugs gradually increases in C. albicans. Therefore, new antifungal ... ...

Abstract	Candida albicans is one of the most common species of Candida, which cause various mucosal and systemic infectious diseases. However, the resistance rate to existing clinical antifungal drugs gradually increases in C. albicans. Therefore, new antifungal drugs must be developed to solve the current problem. This study discovered that the solid fermented ethyl acetate crude extract of Microporus vernicipes had inhibitory activity on C. albicans. This study determined that the Mv5 components had significantly inhibited the activity of C. albicans using column chromatography separation component screening. The components included 23 compounds of fatty acids and their derivatives, alkaloids, phenols, and other classes using ultra-high performance liquid chromatography tandem high-resolution mass spectrometry (UHPLC-HR-MS) analysis, with fatty acids constituting the primary components. The mechanism of action showed that the minimum inhibitory concentration (MIC) of Mv5 components against C. albicans was 15.63 μg/mL, while minimum fungicidal concentration (MFC) was 31.25 μg/mL. Mv5 components can inhibit the early biofilm formation and destroy the mature biofilm structure. It can inhibit the germ tube growth of C. albicans, thereby inhibiting the transformation of yeast morphology to hyphae. We detected 193 differentially expressed genes, including 156 upregulated and 37 downregulated genes in the Mv5 components of the MIC concentration group. We detected 391 differentially expressed genes, including 334 upregulated and 57 downregulated expression genes in the MFC concentration group. Among these differentially expressed genes, the genes related to mycelium and biofilm formation were significantly downregulated. GO enrichment analysis presented that single-organism process metabolic process, and cellular processes were the biological processes with the most gene enrichment. Kyoto Encyclopedia of Genes and Genomes (KEGG)of Mv5 components were mainly enriched in metabolic pathways, such as meiosis yeast and amino acid metabolism. Therefore, it is believed that the fermentation extract of M. vernicipes inhibits C. albicans, which can provide clues for developing effective antifungal drugs.
Language	English
Publishing date	2023-12-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1454951-7
ISSN	1618-1905 ; 1139-6709
ISSN (online)	1618-1905
ISSN	1139-6709
DOI	10.1007/s10123-023-00467-6
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Zs.A 4964: Show issues

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Article ; Online: Selective impact of three homogenous polysaccharides with different structural characteristics from Grifola frondosa on human gut microbial composition and the structure-activity relationship.

Bai, Guangjian / Xie, Yizhen / Gao, Xiong / Xiao, Chun / Yong, Tianqiao / Huang, Longhua / Cai, Manjun / Liu, Yuanchao / Hu, Huiping / Chen, Shaodan

International journal of biological macromolecules

2024 Volume 269, Issue Pt 2, Page(s) 132143

Abstract: Natural polysaccharides interact with gut microbes to enhance human well-being. Grifola frondosa is a polysaccharides-rich edible and medicinal mushroom. The prebiotic potential of G. frondosa polysaccharides has been explored in recent years, however, ... ...

Abstract	Natural polysaccharides interact with gut microbes to enhance human well-being. Grifola frondosa is a polysaccharides-rich edible and medicinal mushroom. The prebiotic potential of G. frondosa polysaccharides has been explored in recent years, however, the relationship between their various structural features and prebiotic activities is poorly understood. In this study, three homogenous polysaccharides GFP10, GFP21 and GFP22 having different molecular weights (M
Language	English
Publishing date	2024-05-08
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.2024.132143
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Article ; Online: Revealing the role of ionic liquids in promoting fuel cell catalysts reactivity and durability.

Avid, Arezoo / Ochoa, Jesus López / Huang, Ying / Liu, Yuanchao / Atanassov, Plamen / Zenyuk, Iryna V

Nature communications

2022 Volume 13, Issue 1, Page(s) 6349

Abstract: Ionic liquids (ILs) have shown to be promising additives to the catalyst layer to enhance oxygen reduction reaction in polymer electrolyte fuel cells. However, fundamental understanding of their role in complex catalyst layers in practically relevant ... ...

Abstract	Ionic liquids (ILs) have shown to be promising additives to the catalyst layer to enhance oxygen reduction reaction in polymer electrolyte fuel cells. However, fundamental understanding of their role in complex catalyst layers in practically relevant membrane electrode assembly environment is needed for rational design of highly durable and active platinum-based catalysts. Here we explore three imidazolium-derived ionic liquids, selected for their high proton conductivity and oxygen solubility, and incorporate them into high surface area carbon black support. Further, we establish a correlation between the physical properties and electrochemical performance of the ionic liquid-modified catalysts by providing direct evidence of ionic liquids role in altering hydrophilic/hydrophobic interactions within the catalyst layer interface. The resulting catalyst with optimized interface design achieved a high mass activity of 347 A g
Language	English
Publishing date	2022-10-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-33895-5
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Article ; Online: Heavy metals high-sensitive detection by laser-induced breakdown spectroscopy based on radial electroosmotic flow-driven enrichment.

Nie, Junfei / Guo, Lianbo / Liu, Yuanchao / Deng, Nan / Hu, ZhenLin / Zheng, Peichao / Lau, Condon

Talanta

2023 Volume 267, Page(s) 125199

Abstract: Heavy metal detection is imperative for human health and environmental sustainability. However, the commonly used liquid sample pretreatment, drying liquid droplet to solid, encounters solute diffusion and nonuniform distribution, thus causing ... ...

Abstract	Heavy metal detection is imperative for human health and environmental sustainability. However, the commonly used liquid sample pretreatment, drying liquid droplet to solid, encounters solute diffusion and nonuniform distribution, thus causing unpromising detection results. Here, we developed a radial electroosmotic flow-driven (REOF) platform to enrich heavy metals in water for high-sensitive detection using laser-induced breakdown spectroscopy (LIBS). Firstly, the electrodes in the substate for REOF were designed and produced by the printed circuit board manufacturer. Different particle deposition patterns were observed by modifying the direction and magnitude of voltage in the evaporated droplets of Cadmium Chloride (CdCl
Language	English
Publishing date	2023-09-14
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1500969-5
ISSN	1873-3573 ; 0039-9140
ISSN (online)	1873-3573
ISSN	0039-9140
DOI	10.1016/j.talanta.2023.125199
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Article ; Online: Polysaccharide isolated from

Li, Xiangmin / Ruan, Qinzhao / Yang, Weining / Tian, Huixiang / Wu, Nan / Qadir, Javeria / Wang, Juan / Hu, Huiping / Liu, Yuanchao / Cai, Manjun / Yang, Burton B / Xie, Yizhen / Wu, Qingping

International journal of biological sciences

2024 Volume 20, Issue 2, Page(s) 664–679

Abstract: Myeloid derived suppressor cells (MDSCs) are known to accumulate in cancer patients and tumor-bearing mice, playing a significant role in promoting tumor growth. Depleting MDSCs has emerged as a potential therapeutic strategy for cancer. Here, we ... ...

Abstract	Myeloid derived suppressor cells (MDSCs) are known to accumulate in cancer patients and tumor-bearing mice, playing a significant role in promoting tumor growth. Depleting MDSCs has emerged as a potential therapeutic strategy for cancer. Here, we demonstrated that a fungal polysaccharide, extracted from
MeSH term(s)	Humans ; Mice ; Animals ; Female ; Myeloid-Derived Suppressor Cells/metabolism ; Grifola ; Breast Neoplasms/metabolism ; CD8-Positive T-Lymphocytes/metabolism ; Polysaccharides/pharmacology
Chemical Substances	Polysaccharides
Language	English
Publishing date	2024-01-01
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2179208-2
ISSN	1449-2288 ; 1449-2288
ISSN (online)	1449-2288
ISSN	1449-2288
DOI	10.7150/ijbs.85276
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Article ; Online: Protocol for rapid ammonia detection via surface-enhanced Raman spectroscopy.

Liu, Yuanchao / Murphy, Eamonn / Potma, Eric O / Matanovic, Ivana / Fishman, Dmitry A / Atanassov, Plamen

STAR protocols

2021 Volume 2, Issue 2, Page(s) 100599

Abstract: As a key industrial nitrogenous product and a critical environmental pollutant, ammonia broadly affects our daily lives. Rapid and sensitive detection of ammonia is essential to both environmental monitoring and process control for industrial ... ...

Abstract	As a key industrial nitrogenous product and a critical environmental pollutant, ammonia broadly affects our daily lives. Rapid and sensitive detection of ammonia is essential to both environmental monitoring and process control for industrial manufacturing. Here, we present a protocol for rapid detection of low amounts of ammonia in the aqueous phase, via surface-enhanced Raman spectroscopy. We believe the mechanism and speed of the approach demonstrate its potential toward applications in
MeSH term(s)	Ammonia/analysis ; Catalysis ; Electrochemical Techniques ; Limit of Detection ; Spectrum Analysis, Raman/methods ; Water/chemistry
Chemical Substances	Water (059QF0KO0R) ; Ammonia (7664-41-7)
Language	English
Publishing date	2021-06-11
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2021.100599
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