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  1. Article: Investigation of the Association Between e-Cigarette Smoking and Oral Mucosal Health Status Among Young People: Protocol for a Case-Control Trial.

    Cheng, Siyuan

    JMIR research protocols

    2024  Volume 13, Page(s) e53644

    Abstract: Background: Given the paucity of current safety studies related to e-cigarettes, there are no definitive studies on whether e-cigarettes cause oral mucosal lesions or even oral cancer. Although it is still undetermined whether e-cigarettes are harmless, ...

    Abstract Background: Given the paucity of current safety studies related to e-cigarettes, there are no definitive studies on whether e-cigarettes cause oral mucosal lesions or even oral cancer. Although it is still undetermined whether e-cigarettes are harmless, an increasing number of teenagers choose to smoke e-cigarettes and believe that they are not harmful to the human body.
    Objective: This aims to determine whether e-cigarettes cause damage to the oral mucosa. This study also aims to evaluate the association between e-cigarette smoking and oral mucous membrane lesions in young adults. The objectives are to (1) compare the oral mucosal conditions in participants with and without e-cigarette smoking habits, (2) assess the effect of the amount of e-cigarette smoking on oral mucosal conditions, and (3) assess the effect of the duration of e-cigarette smoking on oral mucosal conditions.
    Methods: In this prospective study, 304 youths aged 15 to 24 years (n=152, 50% who smoke only e-cigarettes and n=152, 50% who do not smoke e-cigarettes or cigarettes) will be divided into 2 groups for a controlled study. Whether e-cigarettes cause oral mucosal lesions will be verified by comparing the odds of oral mucosal lesions in the 2 experimental groups. For this experiment, the predefined power is 80% (P=.04), and the predefined proportions of groups 1 and 2 are 11% and 2.5%, respectively.
    Results: This experiment is at the conceptualization phase and has not yet been carried out. Experimenters have not been recruited and no data have been collected.
    Conclusions: e-Cigarettes are still an unfamiliar topic to the public, and it is still unknown whether they can cause damage to the oral mucosa. This experiment aims to find out whether there is a link between the 2. There are still many limitations in this study, such as the lack of categorization of e-cigarettes and the lack of testing methods for oral mucosal status. These limitations are expected to be addressed in the future as the experiment is formally conducted and further optimized.
    International registered report identifier (irrid): PRR1-10.2196/53644.
    Language English
    Publishing date 2024-01-26
    Publishing country Canada
    Document type Journal Article
    ZDB-ID 2719222-2
    ISSN 1929-0748
    ISSN 1929-0748
    DOI 10.2196/53644
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: PCTA, A PAN-CANCER CELL LINE TRANSCRIPTOME ATLAS.

    Cheng, Siyuan / Li, Lin / Yu, Xiuping

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Background: A substantial volume of RNA sequencing data were generated from cancer cell lines. However, it requires specific bioinformatics skills to compare gene expression levels across cell lines. This has hindered non-bioinformaticians from fully ... ...

    Abstract Background: A substantial volume of RNA sequencing data were generated from cancer cell lines. However, it requires specific bioinformatics skills to compare gene expression levels across cell lines. This has hindered non-bioinformaticians from fully utilizing these valuable datasets in their research. To bridge this gap, we established a curated Pan-cancer Cell Line Transcriptome Atlas (PCTA) dataset. This resource aims to provide a user-friendly platform, allowing researchers without extensive bioinformatics expertise to access and leverage the wealth of information within the dataset for their studies. Importantly, PCTA stands out by offering sufficient sample numbers per cell line in comparison to other pan-cancer datasets.
    Methods: Cell lines' meta data and RNA sequencing data were retrieved from the Cancer Cell Line Encyclopedia (CCLE), SRA and ARCHS4 databases. Utilizing the programming language R, we conducted data retrieval, normalization, and visualization. Only expression data for protein-coding genes and long-non-coding RNAs (LncRNAs) were considered in this study, streamlining the focus to enhance the precision and relevance of the analysis.
    Results: The resulting PCTA dataset encompasses the expression matrix of 24,965 genes, featuring data from 84,385 samples derived from 5,677 studies. This comprehensive compilation spans 535 cell lines, representing a spectrum of 114 cancer types originating from 30 diverse tissue types. On UMAP plots, cell lines originating from the same type of tissue tend to cluster together, illustrating the dataset's ability to capture biological relationships. To unravel molecular signatures, marker genes were identified for each cancer type. Additionally, an interactive and user-friendly web application (https://pcatools.shinyapps.io/PCTA_app/ ) was developed for researchers to explore the PCTA dataset. This platform allows users to examine the expression pattern of their genes of interest across a diverse array of samples. Data are visualized as violin-, box-, and point- plots, enhancing the interpretability of the findings.
    Conclusion: The PCTA stands as a comprehensive resource, offering insights into gene expression patterns across diverse cancer cell lines and providing a valuable tool to explore molecular signatures and potential therapeutic targets in cancer research.
    Language English
    Publishing date 2024-01-12
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.10.575087
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: PCTA, a pan-cancer cell line transcriptome atlas.

    Cheng, Siyuan / Li, Lin / Yu, Xiuping

    Cancer letters

    2024  Volume 588, Page(s) 216808

    Abstract: A substantial volume of RNA sequencing data have been generated from cancer cell lines. However, it requires specific bioinformatics skills to compare gene expression levels across cell lines. This has hindered non-bioinformaticians from fully utilizing ... ...

    Abstract A substantial volume of RNA sequencing data have been generated from cancer cell lines. However, it requires specific bioinformatics skills to compare gene expression levels across cell lines. This has hindered non-bioinformaticians from fully utilizing these valuable datasets in their research. To bridge this gap, we established a curated Pan-cancer Cell Line Transcriptome Atlas (PCTA) dataset. This resource aims to provide a user-friendly platform, allowing researchers without extensive bioinformatics expertise to access and leverage the wealth of information within the dataset for their studies. The PCTA dataset encompasses the expression matrix of 24,965 genes, featuring data from 84,385 samples derived from 5677 studies. This comprehensive compilation spans 535 cell lines, representing a spectrum of 114 cancer types originating from 30 diverse tissue types. On UMAP plots, cell lines originating from the same type of tissue tend to cluster together, illustrating the dataset's ability to capture biological relationships. Additionally, an interactive and user-friendly web application (https://pcatools.shinyapps.io/PCTA_app/) was developed for researchers to explore the PCTA dataset. This platform allows users to examine the expression of their genes of interest across a diverse array of samples.
    MeSH term(s) Humans ; Transcriptome ; Gene Expression Profiling ; Neoplasms/genetics ; Software ; Cell Line
    Language English
    Publishing date 2024-03-09
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 195674-7
    ISSN 1872-7980 ; 0304-3835
    ISSN (online) 1872-7980
    ISSN 0304-3835
    DOI 10.1016/j.canlet.2024.216808
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: CTPC, a combined transcriptome data set of human prostate cancer cell lines.

    Cheng, Siyuan / Yu, Xiuping

    The Prostate

    2022  Volume 83, Issue 2, Page(s) 158–161

    Abstract: Background: Cell lines are the most used model system in cancer research. The transcriptomic data of established prostate cancer (PCa) cell lines help researchers explore differential gene expressions across the various PCa cell lines.: Methods: ... ...

    Abstract Background: Cell lines are the most used model system in cancer research. The transcriptomic data of established prostate cancer (PCa) cell lines help researchers explore differential gene expressions across the various PCa cell lines.
    Methods: Through large scale datamining, we established a curated Combined Transcriptome dataset of PCa Cell lines (CTPC) which contains the transcriptomic data of 1840 samples of 9 commonly used PCa cell lines including LNCaP, LNCaP-95, LNCaP-abl, C4-2, VCaP, 22Rv1, PC3, DU145, and NCI-H660.
    Results: The CTPC dataset provides an opportunity for researchers to not only compare gene expression across different PCa cell lines but also retrieve the experiment information and associate the differential gene expression data with meta data, such as gene manipulation and drug treatment information. Additionally, based on the CTPC dataset, we built a platform for users to visualize the data (https://pcatools.shinyapps.io/CTPC_V2/).
    Conclusions: It is our hope that the combined CTPC dataset and the user-friendly platform are of great service to the PCa research community.
    MeSH term(s) Male ; Humans ; Transcriptome ; Cell Line, Tumor ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/metabolism ; Gene Expression Profiling
    Language English
    Publishing date 2022-10-07
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 604707-5
    ISSN 1097-0045 ; 0270-4137
    ISSN (online) 1097-0045
    ISSN 0270-4137
    DOI 10.1002/pros.24448
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A fast matching method of coastline changes using single-chain numbering

    CHENG Siyuan / ZHANG Ying / ZHAI Liang

    Acta Geodaetica et Cartographica Sinica, Vol 51, Iss 8, Pp 1817-

    2022  Volume 1825

    Abstract: Affected by natural environment changes and human development activities in the coastal zone, coastline continues to change dramatically. Detecting coastline changes and matching the coastline change segments before and after changing are critical for ... ...

    Abstract Affected by natural environment changes and human development activities in the coastal zone, coastline continues to change dramatically. Detecting coastline changes and matching the coastline change segments before and after changing are critical for analyzing coastline changes. As the traditional tools of spatial analysis lack of direct and effective matching function, this article introduced the single-chain numbering idea to match the coastline change segments quickly. The matching relationships of the coastline change segments were grouped into "one-to-one" and "multi-to-multi". Besides, we also put forward a set of formula for determining the coastline change types such as position change, type change, disappearance and appearance.The matching and recording method of the coastline changes based on single-chain numbering has been designed and packed using python language. Experiments showed that the method proposed realized coastline changes matching quickly and accurately, which has solved the problem of matching the multi-to-multi coastline change segments.
    Keywords single-chain numbering ; coastline changes ; matching method ; change types ; Mathematical geography. Cartography ; GA1-1776
    Language Chinese
    Publishing date 2022-08-01T00:00:00Z
    Publisher Surveying and Mapping Press
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: The spectrum of neuroendocrine differentiation in prostate cancer.

    Cheng, Siyuan / Yu, Xiuping

    Prostate cancer and prostatic diseases

    2021  Volume 24, Issue 4, Page(s) 1214–1215

    MeSH term(s) Cell Line, Tumor ; Humans ; Male ; Prostatic Neoplasms
    Language English
    Publishing date 2021-05-18
    Publishing country England
    Document type Letter ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 1419277-9
    ISSN 1476-5608 ; 1365-7852
    ISSN (online) 1476-5608
    ISSN 1365-7852
    DOI 10.1038/s41391-021-00386-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Hepatic perivascular epithelioid cell tumor resembling hepatic adenoma and hepatocellular carcinoma on preoperative imaging: a case report.

    Zhu, Dongling / Song, Shuang / Wang, Dongdong / Kuang, Dong / Cheng, Siyuan / Zhou, Jianyuan / Zou, Sijuan

    Frontiers in oncology

    2024  Volume 14, Page(s) 1292313

    Abstract: Perivascular epithelioid cell tumor (PEComa), an uncommon mesenchymal neoplasm, arises from specialized perivascular epithelioid cells exhibiting distinct features of smooth muscle and melanocytic differentiation with unpredictable behavior. PEComa tends ...

    Abstract Perivascular epithelioid cell tumor (PEComa), an uncommon mesenchymal neoplasm, arises from specialized perivascular epithelioid cells exhibiting distinct features of smooth muscle and melanocytic differentiation with unpredictable behavior. PEComa tends to occur more commonly in the uterus and kidneys; its occurrence in the liver is exceedingly rare. We presented a case of a 29-year-old woman with hepatic PEComa and evaluated the tumor with MRI, integrated
    Language English
    Publishing date 2024-02-01
    Publishing country Switzerland
    Document type Case Reports
    ZDB-ID 2649216-7
    ISSN 2234-943X
    ISSN 2234-943X
    DOI 10.3389/fonc.2024.1292313
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Hemodynamics regulate spatiotemporal artery muscularization in the developing circle of Willis.

    Cheng, Siyuan / Xia, Ivan Fan / Wanner, Renate / Abello, Javier / Stratman, Amber N / Nicoli, Stefania

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Vascular smooth muscle cells (VSMCs) envelop vertebrate brain arteries, playing a crucial role in regulating cerebral blood flow and neurovascular coupling. The dedifferentiation of VSMCs is implicated in cerebrovascular diseases and neurodegeneration. ... ...

    Abstract Vascular smooth muscle cells (VSMCs) envelop vertebrate brain arteries, playing a crucial role in regulating cerebral blood flow and neurovascular coupling. The dedifferentiation of VSMCs is implicated in cerebrovascular diseases and neurodegeneration. Despite its importance, the process of VSMC differentiation on brain arteries during development remains inadequately characterized. Understanding this process could aid in reprogramming and regenerating differentiated VSMCs in cerebrovascular diseases. In this study, we investigated VSMC differentiation on the zebrafish circle of Willis (CoW), comprising major arteries that supply blood to the vertebrate brain. We observed that the arterial expression of CoW endothelial cells (ECs) occurs after their migration from the cranial venous plexus to form CoW arteries. Subsequently, acta2+ VSMCs differentiate from pdgfrb+ mural cell progenitors upon recruitment to CoW arteries. The progression of VSMC differentiation exhibits a spatiotemporal pattern, advancing from anterior to posterior CoW arteries. Analysis of blood flow suggests that earlier VSMC differentiation in anterior CoW arteries correlates with higher red blood cell velocity wall shear stress. Furthermore, pulsatile blood flow is required for differentiation of human brain pdgfrb+ mural cells into VSMCs as well as VSMC differentiation on zebrafish CoW arteries. Consistently, the flow-responsive transcription factor klf2a is activated in ECs of CoW arteries prior to VSMC differentiation, and
    Language English
    Publishing date 2024-04-12
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.12.01.569622
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Unveiling Novel Double-Negative Prostate Cancer Subtypes Through Single-Cell RNA Sequencing Analysis.

    Cheng, Siyuan / Li, Lin / Yeh, Yunshin / Shi, Yingli / Franco, Omar / Corey, Eva / Yu, Xiuping

    bioRxiv : the preprint server for biology

    2024  

    Language English
    Publishing date 2024-05-02
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.08.11.553009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Industrial agglomeration and haze pollution: Evidence from China

    Chen, Yufeng / Zhu, Zhitao / Cheng, Siyuan

    Science of the total environment. 2022 Nov. 01, v. 845

    2022  

    Abstract: The rapid industrialization has contributed to the miracle of economic growth in China, while also caused a series of environmental problems. As one of the most concerning urban disease in China, the aggravation of haze pollution is closely related to ... ...

    Abstract The rapid industrialization has contributed to the miracle of economic growth in China, while also caused a series of environmental problems. As one of the most concerning urban disease in China, the aggravation of haze pollution is closely related to the accelerating urbanization and industrialization process in recent years, and the strong spatial diffusion makes the negative externality of haze pollution more harmful. This characteristic of haze pollution is closely related to the spatial structure of industrial sectors, especially the agglomeration of industrial sectors. This paper established a spatial economic framework to investigate the spillover effect of industrial agglomeration on haze pollution based on satellite raster map data of PM₂.₅ and location entropy index, and further discuss the question that whether industrial agglomeration can achieve a balanced development for both economic growth and environmental quality. The results indicated that there is an inverted U-shaped relationship between industrial agglomeration and haze pollution, and the indirect effect from spatial spillover dominated this impact. Industrial agglomeration has a single threshold effect on the knowledge spillover and the utilization of pollution disposal infrastructure of industrial sectors. Only when the agglomeration level reaches the threshold value, the scale effect can be realized to promote the air quality. The resource allocation efficiency and knowledge spillovers of industrial agglomeration need to be promoted in order to reach the inflection point and realize the win-win situation.
    Keywords air quality ; entropy ; environment ; industrialization ; infrastructure ; pollution ; resource allocation ; satellites ; urbanization ; China
    Language English
    Dates of publication 2022-1101
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2022.157392
    Database NAL-Catalogue (AGRICOLA)

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