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Article ; Online: Comprehensive analysis of competitive endogenous RNA network in colorectal cancer.

Zhang, Meng-Yi / Guo, Bin-Han

2022 Volume 9, Issue 7, Page(s) 4306–4316

Abstract: Background: Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Growing evidence supports a role for noncoding RNAs (ncRNAs) in CRC. In particular, they form competitive endogenous RNA (ceRNA) networks involved in the ... ...

Abstract	Background: Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Growing evidence supports a role for noncoding RNAs (ncRNAs) in CRC. In particular, they form competitive endogenous RNA (ceRNA) networks involved in the regulation of mRNA expression. However, the role of these networks in the pathogenesis of CRC is not fully understood. The aim of this study was to elucidate the role of circRNA/lncRNA-miRNA-mRNA systems in CRC pathogenesis based on the construction of a ceRNA network. Methods: RNA expression profiles were obtained from public datasets in the Gene Expression Omnibus (GEO) database and used for further analysis by online databases and tools. Results: In total, 245 circRNAs, 1,666 lncRNAs, 5 miRNAs, and 934 mRNAs were differentially expressed in CRC samples. Functional enrichment analysis identified altered biological functions related to the mRNAs in the ceRNA network, and it was found that the oxytocin signaling pathway was significantly enriched (P<0.05) in genes with differential expression in CRC. Additionally, we established a protein-protein interaction (PPI) network and identified 10 hub genes for the construction of circRNA/lncRNA-miRNA-hub gene regulatory modules. Conclusions: We identified several ncRNAs with a possible pathogenetic role in CRC and built a CRC-specific ceRNA network. The results of our study provide novel insights into the molecular events implicated in CRC.
Language	English
Publishing date	2022-01-15
Publishing country	China
Document type	Journal Article
ZDB-ID	2901601-0
ISSN	2219-6803 ; 2218-676X
ISSN (online)	2219-6803
ISSN	2218-676X
DOI	10.21037/tcr-19-2973
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Article ; Online: Nodule-CLIP: Lung nodule classification based on multi-modal contrastive learning.

Sun, Lijing / Zhang, Mengyi / Lu, Yu / Zhu, Wenjun / Yi, Yang / Yan, Fei

Computers in biology and medicine

2024 Volume 175, Page(s) 108505

Abstract: The latest developments in deep learning have demonstrated the importance of CT medical imaging for the classification of pulmonary nodules. However, challenges remain in fully leveraging the relevant medical annotations of pulmonary nodules and ... ...

Abstract	The latest developments in deep learning have demonstrated the importance of CT medical imaging for the classification of pulmonary nodules. However, challenges remain in fully leveraging the relevant medical annotations of pulmonary nodules and distinguishing between the benign and malignant labels of adjacent nodules. Therefore, this paper proposes the Nodule-CLIP model, which deeply mines the potential relationship between CT images, complex attributes of lung nodules, and benign and malignant attributes of lung nodules through a comparative learning method, and optimizes the model in the image feature extraction network by using its similarities and differences to improve its ability to distinguish similar lung nodules. Firstly, we segment the 3D lung nodule information by U-Net to reduce the interference caused by the background of lung nodules and focus on the lung nodule images. Secondly, the image features, class features, and complex attribute features are aligned by contrastive learning and loss function in Nodule-CLIP to achieve lung nodule image optimization and improve classification ability. A series of testing and ablation experiments were conducted on the public dataset LIDC-IDRI, and the final benign and malignant classification rate was 90.6%, and the recall rate was 92.81%. The experimental results show the advantages of this method in terms of lung nodule classification as well as interpretability.
MeSH term(s)	Humans ; Lung Neoplasms/diagnostic imaging ; Lung Neoplasms/classification ; Lung Neoplasms/pathology ; Tomography, X-Ray Computed/methods ; Solitary Pulmonary Nodule/diagnostic imaging ; Deep Learning ; Lung/diagnostic imaging ; Radiographic Image Interpretation, Computer-Assisted/methods ; Databases, Factual
Language	English
Publishing date	2024-04-26
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.2024.108505
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Article ; Online: CRISPR/Cas9-mediated genome editing of gustatory receptor NlugGr23a causes male sterility in the brown planthopper Nilaparvata lugens.

Zhang, Mengyi / Hu, Yutao / Liu, Jiahui / Guan, Zhanwen / Zhang, Wenqing

International journal of biological macromolecules

2023 Volume 241, Page(s) 124612

Abstract: Gustatory receptors (Grs) have an essential role in chemical recognition so as to evaluate food quality. Insect Grs also participate in non-gustatory functions, such as olfaction, temperature sensing, and mating. In this study, we knocked out NlugGr23a, ... ...

Abstract	Gustatory receptors (Grs) have an essential role in chemical recognition so as to evaluate food quality. Insect Grs also participate in non-gustatory functions, such as olfaction, temperature sensing, and mating. In this study, we knocked out NlugGr23a, a putative fecundity-related Gr, using the CRISPR/Cas9 system in the brown planthopper Nilaparvata lugens, a serious insect pest of rice. Surprisingly, homozygous NlugGr23a mutant (NlugGr23a
MeSH term(s)	Male ; Female ; Animals ; Humans ; Gene Editing ; CRISPR-Cas Systems/genetics ; Seeds ; Receptors, Cell Surface/genetics ; Drosophila Proteins ; Hemiptera/genetics ; Infertility, Male
Chemical Substances	Receptors, Cell Surface ; Drosophila Proteins
Language	English
Publishing date	2023-04-28
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.2023.124612
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Article ; Online: Diagnostic model based on bioinformatics and machine learning to distinguish Kawasaki disease using multiple datasets.

Zhang, Mengyi / Ke, Bocuo / Zhuo, Huichuan / Guo, Binhan

BMC pediatrics

2022 Volume 22, Issue 1, Page(s) 512

Abstract: Background: Kawasaki disease (KD), characterized by systemic vasculitis, is the leading cause of acquired heart disease in children. Herein, we developed a diagnostic model, with some prognosis ability, to help distinguish children with KD.: Methods: ...

Abstract	Background: Kawasaki disease (KD), characterized by systemic vasculitis, is the leading cause of acquired heart disease in children. Herein, we developed a diagnostic model, with some prognosis ability, to help distinguish children with KD. Methods: Gene expression datasets were downloaded from Gene Expression Omnibus (GEO), and gene sets with a potential pathogenic mechanism in KD were identified using differential expressed gene (DEG) screening, pathway enrichment analysis, random forest (RF) screening, and artificial neural network (ANN) construction. Results: We extracted 2,017 DEGs (1,130 with upregulated and 887 with downregulated expression) from GEO. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the DEGs were significantly enriched in innate/adaptive immune response-related processes. Subsequently, the results of weighted gene co-expression network analysis and DEG screening were combined and, using RF and ANN, a model with eight genes (VPS9D1, CACNA1E, SH3GLB1, RAB32, ADM, GYG1, PGS1, and HIST2H2AC) was constructed. Classification results of the new model for KD diagnosis showed excellent performance for different datasets, including those of patients with KD, convalescents, and healthy individuals, with area under the curve values of 1, 0.945, and 0.95, respectively. Conclusions: We used machine learning methods to construct and validate a diagnostic model using multiple bioinformatic datasets, and identified molecules expected to serve as new biomarkers for or therapeutic targets in KD.
MeSH term(s)	Child ; Computational Biology/methods ; Gene Expression Profiling/methods ; Gene Ontology ; Humans ; Machine Learning ; Mucocutaneous Lymph Node Syndrome/diagnosis ; Mucocutaneous Lymph Node Syndrome/genetics
Language	English
Publishing date	2022-08-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2041342-7
ISSN	1471-2431 ; 1471-2431
ISSN (online)	1471-2431
ISSN	1471-2431
DOI	10.1186/s12887-022-03557-y
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Article ; Online: Use of bioinformatic analyses in identifying characteristic genes and mechanisms active in the progression of idiopathic thrombocytopenic purpura in individuals with different phenotypes.

Zhang, Mengyi / Guo, Binhan

The Journal of international medical research

2020 Volume 48, Issue 11, Page(s) 300060520971437

Abstract: Objective: To explore the mechanism underlying the progression of newly diagnosed idiopathic thrombocytopenic purpura (ITP) to its chronic or remission state using bioinformatic methods.: Methods: GSE56232 and GSE46922 gene expression profile ... ...

Abstract	Objective: To explore the mechanism underlying the progression of newly diagnosed idiopathic thrombocytopenic purpura (ITP) to its chronic or remission state using bioinformatic methods. Methods: GSE56232 and GSE46922 gene expression profile datasets were downloaded from Gene Expression Omnibus (GEO). Differentially expressed genes were identified and characteristic genes were screened by weighted gene co-expression network analysis. These genes were used for function enrichment analysis and construction of a protein-protein interaction network. Finally, characteristic genes were verified to determine potential molecular mechanisms underlying ITP progression. Results: We found that characteristic genes in the chronic ITP group were mainly involved in intracellular processes and ion binding, while characteristic genes in the remission ITP group were involved in intracellular processes and nuclear physiological activities. We identified a sub-network of characteristic genes, Conclusion: Our findings improve the understanding of the pathogenesis and progression of ITP, and may provide new directions for the development of treatment strategies.
MeSH term(s)	Computational Biology ; Humans ; Phenotype ; Purpura, Thrombocytopenic, Idiopathic/diagnosis ; Purpura, Thrombocytopenic, Idiopathic/genetics ; Transcriptome
Language	English
Publishing date	2020-11-12
Publishing country	England
Document type	Journal Article
ZDB-ID	184023-x
ISSN	1473-2300 ; 0300-0605 ; 0142-2596
ISSN (online)	1473-2300
ISSN	0300-0605 ; 0142-2596
DOI	10.1177/0300060520971437
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Article: COVID-19 and employee job performance trajectories: The moderating effect of different sources of status.

Liu, Xin / Zheng, Xiaoming / Lee, Byron Y / Yu, Yu / Zhang, Mengyi

Journal of vocational behavior

2023 Volume 142, Page(s) 103862

Abstract: This study investigates the impact of the COVID-19 pandemic on employee job performance trajectories, and further examines the moderating effects of different sources of status. Drawing from event system theory (EST), we propose that employee job ... ...

Abstract	This study investigates the impact of the COVID-19 pandemic on employee job performance trajectories, and further examines the moderating effects of different sources of status. Drawing from event system theory (EST), we propose that employee job performance decreases upon COVID-19 onset, but gradually increases during the postonset period. Furthermore, we argue that status from society, occupation, and workplace functions to moderate such performance trajectories. We test our hypotheses with a unique dataset of 708 employees that combines survey responses and job performance archival data over 21 consecutive months (10,808 observations) spanning the preonset, onset, and postonset periods of the initial encounter with COVID-19 in China. Utilizing discontinuous growth modeling (DGM), our findings indicate that the onset of COVID-19 created an immediate decrease in job performance, but such decrease was weakened by higher occupation and/or workplace status. However, the postonset period resulted in a positive employee job performance trajectory, which was strengthened for employees with lower occupational status. These findings enrich our understanding of COVID-19's impact on employee job performance trajectories, highlight the role of status in moderating such changes over time, and also provide practical implications to understand employee performance when facing such a crisis.
Language	English
Publishing date	2023-02-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	1470972-7
ISSN	1095-9084 ; 0001-8791
ISSN (online)	1095-9084
ISSN	0001-8791
DOI	10.1016/j.jvb.2023.103862
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Article ; Online: An overview of Twist1 in glioma progression and recurrence.

Li, Cong / Li, Zixuan / Zhang, Mengyi / Dai, Jiaxuan / Wang, Yunmin / Zhang, Zhiqiang

International review of neurobiology

2023 Volume 172, Page(s) 285–301

Abstract: Glioma cells are characterized by high migration ability, resulting in the aggressive growth of the tumors and poor prognosis of patients. Epithelial-to-mesenchymal transition (EMT) is one of the most important steps for tumor migration and metastasis ... ...

Abstract	Glioma cells are characterized by high migration ability, resulting in the aggressive growth of the tumors and poor prognosis of patients. Epithelial-to-mesenchymal transition (EMT) is one of the most important steps for tumor migration and metastasis and be elevated during glioma progression and recurrence. Twist1 is a basic helix-loop-helix transcription factor and a key transcription factor involved in the process of EMT. Twist1 is related to glioma mesenchymal change, invasion, heterogeneity, self-renewal of tumor stem cells, angiogenesis, etc., and may be used as a prognostic indicator and therapeutic target for glioma patients. This paper mainly reviews the structural characteristics, regulatory mechanisms, and apparent regulation of Twist1, as well as the roles of Twist1 during glioma progression and recurrence, providing new revelations for its use as a potential drug target and glioma treatment research.
MeSH term(s)	Humans ; Glioma ; Neoplasm Invasiveness ; Transcription Factors ; Twist-Related Protein 1/genetics ; Twist-Related Protein 1/metabolism
Chemical Substances	Transcription Factors ; Twist-Related Protein 1
Language	English
Publishing date	2023-09-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209876-3
ISSN	2162-5514 ; 0074-7742
ISSN (online)	2162-5514
ISSN	0074-7742
DOI	10.1016/bs.irn.2023.07.003
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Article ; Online: A new record of Squalus montalbani (Chondrichthyes: Squaliformes: Squalidae) from the Nansha (Spratly) Islands, South China Sea

Zhang, Mengyi / Shan, Binbin / Liu, Yan / Wang, Liangming / Yang, Changping / Liu, Manting / Xie, Qijian / Sun, Dianrong

Acta Ichthyologica et Piscatoria. 2023 May 09, v. 53 p.51-57

2023

Abstract: AbstractThe Indonesian greeneye spurdog (or a dogfish shark), Squalus montalbani Whitley, 1931, is widely distributed in the warm temperate to tropical waters of Indonesia, Philippines, the island of Taiwan, and Australia. Previous studies suggested ... ...

Abstract	AbstractThe Indonesian greeneye spurdog (or a dogfish shark), Squalus montalbani Whitley, 1931, is widely distributed in the warm temperate to tropical waters of Indonesia, Philippines, the island of Taiwan, and Australia. Previous studies suggested that the distribution of dogfish shark species in the South China Sea is composed of two species, Squalus mitsukurii Jordan et Snyder, 1903 and Squalus brevirostris Tanaka, 1917. In March 2020 a dogfish shark specimen was collected from the Nansha (Spratly) Islands, South China Sea. We identified it as S. montalbani based on morphology and mitochondrial DNA barcoding. Our results confirmed the presence of S. montalbani in the South China Sea, leading us to conclude that it represents a new species record of the genus Squalus in the region. Furthermore, our findings demonstrate that the combined approach is highly effective in identifying Squalus species that share similar morphological characteristics.
Keywords	DNA barcoding ; Philippines ; Squalus ; mitochondrial DNA ; sharks ; Australia ; Indonesia ; South China Sea ; Taiwan ; fish taxonomy ; mitochondrial DNA barcoding ; new record ; Squalusmontalbani
Language	English
Dates of publication	2023-0509
Size	p. 51-57.
Publishing place	Pensoft Publishers
Document type	Article ; Online
ZDB-ID	441372-6
ISSN	1734-1515 ; 0137-1592 ; 0860-8962
ISSN (online)	1734-1515
ISSN	0137-1592 ; 0860-8962
DOI	10.3897/aiep.53.103579
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Article: Carbon emission accounting and spatial distribution of industrial entities in Beijing—Combining nighttime light data and urban functional areas

Wang, Xiaoyu / Cai, Ying / Liu, Gang / Zhang, Mengyi / Bai, Yuping / Zhang, Fan

Ecological informatics. 2022 Sept., v. 70

2022

Abstract: Quantifying current carbon emissions their fine scale spatial distribution is necessary to improve carbon emission management, requirements, and emission reduction strategies of key industries. This study established an entity-level model to estimate ... ...

Abstract	Quantifying current carbon emissions their fine scale spatial distribution is necessary to improve carbon emission management, requirements, and emission reduction strategies of key industries. This study established an entity-level model to estimate carbon emissions by combining geographic information of points of interest (POIs) and nighttime light data from Beijing in 2018. The model accounted for the carbon emissions of Beijing's key entities and industries and simulated their spatial distribution. The results showed a good fit between the carbon emissions of the entities and nighttime light brightness values. The 130-m resolution of the urban carbon emission distribution data had a higher spatial simulation accuracy than that of the 1-km Open-Data inventory for anthropogenic carbon dioxide (ODIAC) data. Through the lens of urban functional areas, the average value of carbon emissions was highest in commercial areas and lowest in public management and service areas, at 78,840.11 tC/km² and 6844.79 tC/km², respectively. In terms of the industrial sector, the transportation industry had the highest carbon emissions, with a total of 31.86 Mt., while non-metal mining and oil and gas extraction had almost no energy consumption, with total carbon emissions of 1.38 Mt. The spatial clustering results showed that the distribution of carbon emissions in Beijing had a significant positive spatial correlation; forming high-high aggregation clusters dominated by the city center and major business districts and a low-low aggregation clusters dominated by the city's suburban areas. The simulation model clearly reflected the fine scale characteristics of carbon emissions, in terms of their quantity and spatial distribution. Results obtained in this study can aid relevant departments to formulate appropriate strategies for collectively guiding industrial enterprises towards carbon neutrality.
Keywords	carbon ; carbon dioxide ; energy ; inventories ; oils ; simulation models ; spatial data ; transportation industry ; China
Language	English
Dates of publication	2022-09
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2212016-6
ISSN	1878-0512 ; 1574-9541
ISSN (online)	1878-0512
ISSN	1574-9541
DOI	10.1016/j.ecoinf.2022.101759
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Article ; Online: Adaptive Discrete Vector Field in Sensor Networks.

Zhang, Mengyi / Goupil, Alban

Sensors (Basel, Switzerland)

2018 Volume 18, Issue 8

Abstract: Homology groups are a prime tool for measuring the connectivity of a network, and their computation in a distributed and adaptive way is mandatory for their use in sensor networks. In this paper, we propose a solution based on the construction of an ... ...

Abstract	Homology groups are a prime tool for measuring the connectivity of a network, and their computation in a distributed and adaptive way is mandatory for their use in sensor networks. In this paper, we propose a solution based on the construction of an adaptive discrete vector field from where, thanks to the discrete Morse theory, the generators of the homology groups are extracted. The efficiency and the adaptability of our approach are tested against two applications: the detection and the localization of the holes in the coverage, and the selection of active sensors ensuring complete coverage.
Language	English
Publishing date	2018-08-12
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/s18082642
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