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Article ; Online: A prognostic exosome-related long non-coding RNAs risk model related to the immune microenvironment and therapeutic responses for patients with liver hepatocellular carcinoma

Yuan Yue / Jie Tao / Dan An / Lei Shi

Heliyon, Vol 10, Iss 2, Pp e24462- (2024)

2024

Abstract: Background: Liver hepatocellular carcinoma (LIHC) is the third largest cause of cancer mortality. Exosomes are vital regulators in the development of cancer. However, the mechanisms regarding the association of exosome-related long non-coding RNAs ( ... ...

Abstract	Background: Liver hepatocellular carcinoma (LIHC) is the third largest cause of cancer mortality. Exosomes are vital regulators in the development of cancer. However, the mechanisms regarding the association of exosome-related long non-coding RNAs (lncRNAs) in LIHC are not clear. Methods: LIHC RNA sequences and exosome-associated genes were collected according to The Cancer Genome Atlas (TCGA), Hepatocellular Carcinoma Cell DataBase (HCCDB) and ExoBCD databases, and exosome-related lncRNAs with prognostic differential expression were screened as candidate lncRNAs using Spearman's method and univariate Cox regression analysis. Candidate lncRNAs were then used to construct a prognostic model and mRNA-lncRNA co-expression network. Differentially expressed genes (DEGs) in low- and high-risk groups were identified and enrichment analysis was performed for up- and down-regulated DEGs, respectively. The expression of immune checkpoint-related genes, immune escape potential and microsatellite instability among different risk groups were further analyzed. Quantitative real-time polymerase chain reaction (qRT-PCR) and transwell assay were applied for detecting gene expression levels and invasion and migration ability. Results: Based on 17 prognostical exosome-associated lncRNAs, four hub lncRNAs (BACE1_AS, DSTNP2, PLGLA, and SNHG3) were selected for constructing a prognostic model, which was demonstrated to be an independent prognostic variable for LIHC. High risk score was indicative of poorer overall survival, lower anti-tumor immune cells, higher genomic instability, higher immune escape potential, and less benefit for immunotherapy. The qRT-PCR test verified the expression level of the lncRNAs in LIHC cells, and the inhibitory effect of BACE1_AS on immune checkpoint genes levels. BACE1_AS silence also depressed the ability of migration and invasion of LIHC cells. Conclusion: The Risk model constructed by exosome-associated lncRNAs could well predict immunotherapy response and prognostic outcomes for LIHC patients. We ...
Keywords	Liver hepatocellular carcinoma ; Exosome-related lncRNAs ; Risk model ; Immune infiltration ; Immunotherapy response ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	610 ; 616
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The roles of histone methylation in the regulation of abiotic stress responses in plants

Lei Shi / Xiaoyun Cui / Yuan Shen

Plant Stress, Vol 11, Iss , Pp 100303- (2024)

1481

Abstract: Abiotic stress greatly threaten plants’ growth and ultimately impact crop productivity. Plants have evolved sophisticated regulatory mechanisms to cope with stressful conditions, including undergoing physiological changes through genetic and epigenetic ... ...

Abstract	Abiotic stress greatly threaten plants’ growth and ultimately impact crop productivity. Plants have evolved sophisticated regulatory mechanisms to cope with stressful conditions, including undergoing physiological changes through genetic and epigenetic regulation of gene expression. Histone methylation takes an essential part in epigenetic regulation of the expression of numerous genes in plant response to abiotic stresses. In this review, we summarize the recent progress on the regulation of histone methylation in plant response to abiotic stress, including drought, high salinity, high temperature, and cold. We also discuss the roles of histone methylation in the formation of plant stress memory, as well as the metabolic regulation of histone methylation under abiotic stress in plants. We posit that a comprehensive understanding of the molecular mechanisms and functional roles of histone methylation in abiotic stress responses will accelerate plant breeding, improve stress resistance and substantially enhance biomass and crop yield.
Keywords	Abiotic stress ; Histone methylation ; Histone methyltransferase ; Histone demethylase ; Epigenetic memory ; Metabolic regulation ; Plant ecology ; QK900-989
Subject code	580 ; 570
Language	English
Publishing date	2024-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Dynamic analysis and optimal control of a class of SISP respiratory diseases

Lei Shi / Longxing Qi

Journal of Biological Dynamics, Vol 16, Iss 1, Pp 64-

2022 Volume 97

Abstract: In this paper, the actual background of the susceptible population being directly patients after inhaling a certain amount of PM $ _{2.5} $ is taken into account. The concentration response function of PM $ _{2.5} $ is introduced, and the SISP ... ...

Abstract	In this paper, the actual background of the susceptible population being directly patients after inhaling a certain amount of PM $ _{2.5} $ is taken into account. The concentration response function of PM $ _{2.5} $ is introduced, and the SISP respiratory disease model is proposed. Qualitative theoretical analysis proves that the existence, local stability and global stability of the equilibria are all related to the daily emission $ P_{0} $ of PM $ _{2.5} $ and PM $ _{2.5} $ pathogenic threshold K. Based on the sensitivity factor analysis and time-varying sensitivity analysis of parameters on the number of patients, it is found that the conversion rate β and the inhalation rate η has the largest positive correlation. The cure rate γ of infected persons has the greatest negative correlation on the number of patients. The control strategy formulated by the analysis results of optimal control theory is as follows: The first step is to improve the clearance rate of PM $ _{2.5} $ by reducing the PM $ _{2.5} $ emissions and increasing the intensity of dust removal. Moreover, such removal work must be maintained for a long time. The second step is to improve the cure rate of patients by being treated in time. After that, people should be reminded to wear masks and go out less so as to reduce the conversion rate of susceptible people becoming patients.
Keywords	respiratory disease ; pm $ _{2.5} $ emissions ; pm $ _{2.5} $ pathogenic threshold ; sensitivity analysis ; optimal control ; Environmental sciences ; GE1-350 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	Taylor & Francis Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Lycorine weakens tamoxifen resistance of breast cancer via abrogating HAGLR‐mediated epigenetic suppression on VGLL4 by DNMT1

Jing Zhai / Jun‐Feng Jiang / Lei Shi

Kaohsiung Journal of Medical Sciences, Vol 39, Iss 3, Pp 278-

2023 Volume 289

Abstract: Abstract Much is known about the significance of lycorine, a natural alkaloid, in combating various types of cancer, including breast cancer (BC), but whether it participates in regulating tamoxifen (TAM) resistance and its underlying mechanism remain to ...

Abstract	Abstract Much is known about the significance of lycorine, a natural alkaloid, in combating various types of cancer, including breast cancer (BC), but whether it participates in regulating tamoxifen (TAM) resistance and its underlying mechanism remain to be elucidated. Tamoxifen‐resistant (TAMR) BC cells were first established by continuously exposed to increasing concentrations of TAM. Levels of targeted gene including HOXD antisense growth‐associated lncRNA (HAGLR) and Vestigial like family member 4 (VGLL4) were analyzed by qRT‐PCR and western blot, respectively. Cell proliferation ability was assessed by MTT and EdU assays. Flow cytometry was carried out to evaluate the apoptosis. VGLL4 promoter methylation was examined using methylation specific PCR (MSP). The role of HAGLR acting on the expression of VGLL4 via DNA hypermethylation was confirmed by RNA immunoprecipitation (RIP). Here, we reported that lycorine administration reduced the survival ratio of TAMR BC cells, decreased the IC50 of TAM, and strengthened TAM‐induced apoptosis. HAGLR, observed to be highly expressed in TAMR BC cells, was identified to be a downstream effector of lycorine, of which overexpression abolished lycorine‐mediated TAMR inhibition. VGLL4 served as a target of HAGLR in regulating lycorine‐mediated suppression on tamoxifen resistance of TAMR BC cells. Mechanistically, HAGLR epigenetically suppressed VGLL4 expression via DNA methyltransferase 1 (DNMT1)‐mediated DNA hypermethylation. Taken together, our data highlights the pivotal role of lycorine in TAM resistance of BC, which may provide a potential agent for improving the effectiveness and efficacy of BC resistance.
Keywords	DNA hypermethylation ; HAGLR ; lycorine ; tamoxifen resistance ; VGLL4 ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Multi-scenario dynamic prediction of ecological risk assessment in an arid area of northwest China

Lu Gan / Ümüt Halik / Lei Shi / Martin Welp

Ecological Indicators, Vol 154, Iss , Pp 110727- (2023)

2023

Abstract: Ecological security is essential for the development of environmental health and human society. However, the driving mechanisms and spatial non-stationarity of ecological risks are still unknown, particularly in arid areas. Thus, this study constructed ... ...

Abstract	Ecological security is essential for the development of environmental health and human society. However, the driving mechanisms and spatial non-stationarity of ecological risks are still unknown, particularly in arid areas. Thus, this study constructed an ecological risk index (ERI) research framework in arid areas based on land use and socio-economic data from 1980 to 2020 to investigate the spatiotemporal evolution trend, driving mechanisms, and spatial non-stationarity of ecological risk and predict the ecological risk under business-as-usual, economic development, and ecological protection scenarios using a patch-generating land use simulation (PLUS) model. The results show that: (1) cropland and build-up land were expanding, whereas forestland and grassland water bodies were shrinking. Compared with the two development stages from 1980 to 2000 and from 2000 to 2020, cropland increased by 4.73% and 51.52%, respectively, whereas build-up land increased by 12.64% and 106.52%, respectively, indicating rapid development and drastic changes in the past 20 years. (2) With the change in landscape diversity, the regional ecological risks showed an increasing trend, whereas the future ecological risks showed an increasing trend because of the cumulative effect of landscape pattern changes caused by human activities. (3) Moreover, dramatic changes in ecological risk, particularly in areas of intense human activity in build-up land, agricultural land, artificial oases, and mountainous areas. Corresponding to the analysis of driving mechanisms, population, GDP, distance to government, water, and primary roads; have a significant effect on ecological risk, whereas DEM has direct and indirect effect paths. Ultimately, the proposed analysis framework can present the spatiotemporal changes of ecological risks and their influencing mechanisms, which can help develop sustainable development policies.
Keywords	Ecological risk assessment ; Driving factors ; Scenario simulations ; Arid areas ; Ecology ; QH540-549.5
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Mediating Role of Sarcopenia in the Association between Physical Activity and Falls among Chinese Older Adults

Chenyu Liang / Lei Shi / Baocheng Li / Zhiyu He

Healthcare, Vol 11, Iss 24, p

A Cross-Sectional Study

2023 Volume 3146

Abstract: Physical inactivity and sarcopenia are potentially modifiable risk factors for falls in older adults, but the strength of the association between physical activity (PA), sarcopenia, and falls in Chinese older adults is unclear. This study sought to ... ...

Abstract	Physical inactivity and sarcopenia are potentially modifiable risk factors for falls in older adults, but the strength of the association between physical activity (PA), sarcopenia, and falls in Chinese older adults is unclear. This study sought to investigate the potential mediation mechanism relationship in the connection between PA, sarcopenia, including its elements (muscle strength, physical performance, and skeletal muscle mass), and falls among Chinese older people. The subjects were 3592 community-dwelling Chinese aged 60 or over, selected from the China Health and Retirement Longitudinal Study (CHARLS). PA was evaluated through the International Physical Activity Questionnaire (IPAQ), and sarcopenia was determined through the Asian Working Group on Sarcopenia (AWGS) 2019 guidelines. We employed logistic regression to explore the link between physical activity, sarcopenia, and falls. Additionally, we applied Karlson, Holm and Breen’s (KHB) method to estimate two different mediation models. The results demonstrated that PA lowers the risk of falls [odds ratio (OR) 0.54, 95% confidence interval (CI) 0.48–0.61], whereas sarcopenia increases the risk of falls (OR 1.34, 95% CI 1.16–1.55). Sarcopenia mediated the association between PA and falls, explaining a total of 2.69% of the association (indirect effect = −0.02). PA also had a significant mediating effect on the association between sarcopenia and falls, explaining a total of 20.12% of the association (indirect effect = 0.06). The proportion mediated by sarcopenia was 2.69% for PA and falls (indirect effect = −0.02). Our findings suggest that PA and sarcopenia have a direct effect on falls as well as an indirect effect through each other. Enhancing PA levels and preventing sarcopenia may help prevent falls in older adults.
Keywords	physical activity ; falls ; sarcopenia ; mediation analysis ; Medicine ; R
Subject code	796
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Fractal Prediction Method for Contact Stiffness of Helical Gear Considering Asperity Lateral Contact and Interaction

Xiangyang Xu / Lei Shi / Linfang Fan

Lubricants, Vol 11, Iss 12, p

2023 Volume 509

Abstract: The normal contact stiffness (NCS) on rough surfaces has a significant impact on the dynamic characteristics of helical gear. Aiming at the problem of inaccurate calculation of the NCS model under the traditional Hertz theory of smooth surfaces, a ... ...

Abstract	The normal contact stiffness (NCS) on rough surfaces has a significant impact on the dynamic characteristics of helical gear. Aiming at the problem of inaccurate calculation of the NCS model under the traditional Hertz theory of smooth surfaces, a fractal prediction model of helical gear contact stiffness considering asperity lateral contact and interaction between asperities is proposed in this paper. The variation formula of asperity and the correction coefficient of a tooth contact surface under asperity lateral contact and interaction are derived, and the influence of micro-elements on normal load and NCS is qualitatively analyzed. The results show that the NCS of considering the interaction and lateral contact of asperity is closer to the experimental results; the contact surface correction coefficient increases with the increase of curvature radius and load. The NCS of a tooth surface increases with the increase in fractal dimension D or the decrease in roughness amplitude G . The influence of asperity lateral contact and interaction decreases with the increase in D and the decrease in G . The NCS of the helical gear decreases under the lateral contact and interaction of the asperity, which is critical for exact estimation of the NCS of contact surfaces in gear.
Keywords	normal contact stiffness ; helical gear ; fractal theory ; asperity lateral contact ; Science ; Q
Subject code	516
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Environmental information disclosure and corporate performance

Yuhan Ye / Xuan Yang / Lei Shi

Heliyon, Vol 9, Iss 12, Pp e22400- (2023)

Evidence from Chinese listed companies

2023

Abstract: Corporate energy consumption and emissions are major contributors to pollution and greenhouse gas emissions. Therefore, corporate energy conservation and emission reduction are essential for sustainable development and low-carbon transformation in China. ...

Abstract	Corporate energy consumption and emissions are major contributors to pollution and greenhouse gas emissions. Therefore, corporate energy conservation and emission reduction are essential for sustainable development and low-carbon transformation in China. With pressing global environmental issues and the mounting pressure for carbon neutrality, it is increasingly important for firms to disclose environmental information. However, research on the relationship and mechanisms between corporate environmental information disclosure (EID) and corporate performance is insufficient. This study examines the effect of EID on corporate environmental performance (EP) and financial performance (FP) using a two-way fixed-effect model. For this purpose, this study considers the panel data of 1125 Chinese A-share listed companies from 2009 to 2021. Additionally, we explore the underlying mechanisms using mediation models. The results reveal that EID can significantly improve corporate performance through green innovation (GI). Moreover, EID can enhance corporate GI, which improves the financial performance of high-polluting firms and the environmental performance of non-high-polluting firms. According to these results, it is imperative to continuously improve corporate EID systems and encourage GI in enterprises. Thus, firms should take the initiative to disclose environmental information. There is a pressing need to enhance the effectiveness of the capital market, therefore, firms with higher levels of EID and better environmental performance can gain greater benefits.
Keywords	Environmental information disclosure ; Environmental performance ; Financial performance ; Green innovation ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	690
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Visualization Method of Knowledge Graphs for the Computation and Comprehension of Ultrasound Reports

Jiayi Feng / Runtong Zhang / Donghua Chen / Lei Shi

Biomimetics, Vol 8, Iss 8, p

2023 Volume 560

Abstract: Knowledge graph visualization in ultrasound reports is essential for enhancing medical decision making and the efficiency and accuracy of computer-aided analysis tools. This study aims to propose an intelligent method for analyzing ultrasound reports ... ...

Abstract	Knowledge graph visualization in ultrasound reports is essential for enhancing medical decision making and the efficiency and accuracy of computer-aided analysis tools. This study aims to propose an intelligent method for analyzing ultrasound reports through knowledge graph visualization. Firstly, we provide a novel method for extracting key term networks from the narrative text in ultrasound reports with high accuracy, enabling the identification and annotation of clinical concepts within the report. Secondly, a knowledge representation framework based on ultrasound reports is proposed, which enables the structured and intuitive visualization of ultrasound report knowledge. Finally, we propose a knowledge graph completion model to address the lack of entities in physicians’ writing habits and improve the accuracy of visualizing ultrasound knowledge. In comparison to traditional methods, our proposed approach outperforms the extraction of knowledge from complex ultrasound reports, achieving a significantly higher extraction index (η) of 2.69, surpassing the general pattern-matching method (2.12). In comparison to other state-of-the-art methods, our approach achieves the highest P (0.85), R (0.89), and F1 (0.87) across three testing datasets. The proposed method can effectively utilize the knowledge embedded in ultrasound reports to obtain relevant clinical information and improve the accuracy of using ultrasound knowledge.
Keywords	ultrasound report ; knowledge graph ; knowledge representation ; machine learning ; natural language processing ; precision medicine ; Technology ; T
Subject code	004
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Optimization and Matching Scheme of Public Management Resources for Industry 4.0 and Smart City

Jinglin Fan / Lei Shi

Complexity, Vol

2021 Volume 2021

Abstract: With the development of Big Data, Industry 4.0, and other technologies, the concept of smart city has become a new goal, new concept, and new practice of many urban developments. It provides a method to solve the problem that public management cannot ... ...

Abstract	With the development of Big Data, Industry 4.0, and other technologies, the concept of smart city has become a new goal, new concept, and new practice of many urban developments. It provides a method to solve the problem that public management cannot optimize resources in China’s urban development and puts forward a supporting scheme more in line with the optimization of public management resources. Effective use of relevant supporting schemes can improve urban public management capacity, optimize resources, and promote the city to embark on the road of scientific development. This paper starts with the multiobjective optimization algorithm to optimize the matching of public resources and realize the effective utilization of public management resources. Using particle swarm optimization algorithm, the optimal allocation management of 8 kinds of resources in this paper is carried out, and the optimization analysis is carried out from the performance indexes, such as resource allocation time and configuration complexity. Finally, the weights of the eight resources in importance, complexity, and resource demand are 0.4, 0.4, and 0.2, respectively. The proposed method realizes the classification of resources and the optimal matching of resources.
Keywords	Electronic computers. Computer science ; QA75.5-76.95
Subject code	720
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Hindawi-Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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