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Article ; Online: M6A plays a potential role in carotid atherosclerosis by modulating immune cell modification and regulating aging-related genes

Wenpeng Zhao / Yingqi Xu / Jiabao Zhu / Chaoxuan Zhang / Weimin Zhou / Shizhi Wang

Scientific Reports, Vol 14, Iss 1, Pp 1-

2024 Volume 12

Abstract: Abstract RNA N6-methyladenosine (m6A) regulators play essential roles in diverse biological processes, including immune responses. Mounting evidence suggests that their dysregulation is intricately linked to numerous diseases. However, the role of m6A- ... ...

Abstract	Abstract RNA N6-methyladenosine (m6A) regulators play essential roles in diverse biological processes, including immune responses. Mounting evidence suggests that their dysregulation is intricately linked to numerous diseases. However, the role of m6A-associated genes in carotid atherosclerosis and their relationship with aging and immune cells remain unclear. Analyze the expression profiles of m6A-related genes in carotid atherosclerosis-related datasets. Based on the expression patterns of m6A-related genes, perform consistent clustering analysis of carotid atherosclerosis samples and investigate associated immune cell infiltration patterns and aging characteristics. Develop an m6A prediction model specific to carotid atherosclerosis and analyze the relationships between immune cells infiltration and aging features. The m6A methylation modification level exhibited a substantial decrease in early-stage carotid atherosclerosis samples compared to late-stage carotid atherosclerosis samples. Subsequently, two distinct m6A subtypes were defined through consensus clustering analysis, with the lower m6A modification level group showing associations with heightened immune cell infiltration and increased expression of aging-related genes. A model composed of five m6A-related genes was formulated, and the results indicated that this model possesses effective predictive and therapeutic capabilities for carotid atherosclerosis. Furthermore, the downregulation of YTHDC1 expression resulted in elevated expression of inflammatory factors and a decrease in the expression of the aging-related gene RGN. Single-cell data analysis suggests that the reduced expression of YTHDC1 may decrease the degradation of inflammation-related factors in macrophages, leading to a highly inflammatory state in the carotid artery wall. Furthermore, the sustained release of inflammatory factors may increase the expression of the aging-related gene RGN in vascular smooth muscle cells, further exacerbating the progression of atherosclerosis. A ...
Keywords	Medicine ; R ; Science ; Q
Subject code	616 ; 612
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Non-linearity impacts of landscape pattern on ecosystem services and their trade-offs

Rongfang Lyu / Wenpeng Zhao / Xiaolei Tian / Jianming Zhang

Ecological Indicators, Vol 136, Iss , Pp 108608- (2022)

A case study in the City Belt along the Yellow River in Ningxia, China

2022

Abstract: Exploring the impacts of landscape pattern on ecosystem services (ESs) and their trade-offs could provide a new way to improve ESs without largely altering land use types. Using the City Belt along the Yellow River in Ningixa (CBYN) as a case study, we ... ...

Abstract	Exploring the impacts of landscape pattern on ecosystem services (ESs) and their trade-offs could provide a new way to improve ESs without largely altering land use types. Using the City Belt along the Yellow River in Ningixa (CBYN) as a case study, we quantified five critical ESs (one provision service of crop production, three regulating services of carbon sequestration, nutrient retention and sand fixation, and one cultural service of recreational opportunity) in 1989–2019 through CASA model, InVEST model and empirical equations. Then we calculated landscape pattern metrics at landscape and class level through Fragstats 4.3 across multiple scales and quantified their impacts on each ES and ES trade-offs through random forest analysis, self-organizing mapping analysis and multivariable regression tree. The results suggested that 3 km is more suitable for analyzing the impacts of landscape pattern on ESs in the CBYN. The nonlinear relations between landscape pattern metrics and each ES were fitted with adjusted R2 ranging from 0.26 to 0.51, indicating the significant but limited impacts of landscape pattern on ESs. Specially, landscape-level metrics of CONTAG, SHDI and FRACMN have higher impacts on ESs than class-level ones. Significant synergies existed among agricultural production, carbon sequestration and nutrient retention, except in mountain region with higher or lower fragmentation. Sand fixation has synergy relations with the former three ESs, which would be altered in situations with higher or lower diversity. Our results provide a new direction for land use management to achieve high-quality development without largely altering existing land use situation.
Keywords	Ecosystem services ; Trade-off and synergy ; Landscape pattern ; Nonlinearity ; Spatial scale ; Ecology ; QH540-549.5
Subject code	710
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evaluation of daily gridded meteorological datasets for hydrological modeling in data-sparse basins of the largest lake in Southeast Asia

Raksmey Ang / Tsuyoshi Kinouchi / Wenpeng Zhao

Journal of Hydrology: Regional Studies, Vol 42, Iss , Pp 101135- (2022)

2022

Abstract: Study region: Tonle Sap Lake (TSL) Basin in Cambodia. Study focus: The development and application of hydrological models for data-sparse basins are hindered by the limited hydro-meteorological data. Although gridded meteorological products are ... ...

Abstract	Study region: Tonle Sap Lake (TSL) Basin in Cambodia. Study focus: The development and application of hydrological models for data-sparse basins are hindered by the limited hydro-meteorological data. Although gridded meteorological products are alternatively considered in many studies, the validation of the products with limited point observations overlooks the original spatiotemporal characteristics, thus leading to a selection of datasets with high uncertainty. Here, we evaluated seven gridded meteorological datasets of rainfall and air temperature covering the data-sparse Tonle Sap Lake Basin by employing the statistical approach based on the bilinear-interpolation method and hydrological approach using the SWAT model, which ensures the reliable estimates of streamflow and evapotranspiration. New hydrological insights for the region: The results of the statistical approach indicate that APHRODITE, ERA5, TRMM and IMERG-based precipitation and CPC and SA-OBS-based air temperature performed comparably well (R ≥ 0.75) with the gauged data. However, ERA5-based streamflow performed relatively poor, while SWAT driven by APHRODITE underestimated satellite-based evapotranspiration, indicating the underestimation of basin-wide precipitation by APHRODITE. Although TRMM and IMERG provide more reliable estimation of streamflow and evapotranspiration, slightly better performance and a higher spatial resolution of IMERG dataset suggest that IMERG precipitation is superior for basin-wide hydrological modeling and impact assessment. These findings showed that statistical comparisons with gauge-data and hydrological evaluation of streamflow are not enough to justify the reliability of each gridded dataset.
Keywords	The Tonle Sap Lake Basin ; Gridded datasets ; Streamflow ; Evapotranspiration ; SWAT model ; Physical geography ; GB3-5030 ; Geology ; QE1-996.5
Subject code	550
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Circular RNA RBM33 contributes to extracellular matrix degradation via miR-4268/EPHB2 axis in abdominal aortic aneurysm

Shizhi Wang / Qingwen Yuan / Wenpeng Zhao / Weimin Zhou

PeerJ, Vol 9, p e

2021 Volume 12232

Abstract: Background Abdominal aortic aneurysm (AAA) is a complex vascular disease involving expansion of the abdominal aorta. Extracellular matrix (ECM) degradation is crucial to AAA pathogenesis, however, the specific molecular mechanism remains unclear. This ... ...

Abstract	Background Abdominal aortic aneurysm (AAA) is a complex vascular disease involving expansion of the abdominal aorta. Extracellular matrix (ECM) degradation is crucial to AAA pathogenesis, however, the specific molecular mechanism remains unclear. This study aimed to investigate differentially expressed circular RNAs (DEcircRNAs) involved in ECM degradation of AAA. Methods Transcriptome sequencing was used to analyze the DEcircRNAs between the AAA tissues and normal tissues. The expression of circRNAs in tissues and cells was validated using quantitative reverse transcription PCR (RT-qPCR). Overexpression of circRNAs in vascular smooth muscle cells (VSMCs) treated with angiotensin II (Ang II) was employed to explore its effect on ECM degradation of AAA. Bioinformatic technology, luciferase reporter gene assay, RT-qPCR, and rescue experiment were employed to evaluate the regulatory mechanism of circRNA. Results We identified 65 DEcircRNAs in AAA tissues compared with normal abdominal aortic tissues, including 30 up-regulated and 35 down-regulated circRNAs, which were mainly involved in inflammation and ECM-related functions and pathways. Moreover, circRBM33 was significantly increased in AAA tissues and Ang II-induced VSMCs compared with control samples. Overexpression of circRBM33 increased the expression of ECM-related molecule matrix metalloproteinase-2 and reduced the tissue inhibitor of matrix metalloproteinases-1 expression. Mechanistically, miR-4268 targeted binding to circRBM33 and inhibited the luciferase activity of circRBM33. Overexpression of circRBM33 induced the expression of EPH receptor B2 (EPHB2), and this effect was countered by miR-4268 mimics. Conclusions Overall, our data suggest that circRBM33 might be involved in AAA progression by regulating ECM degradation via the miR-4268/EPHB2 axis.
Keywords	Abdominal aortic aneurysm ; Circular RNAs ; circRBM33 ; Extracellular matrix degradation ; EPH receptor B2 ; Matrix metalloproteinase-2 ; Medicine ; R
Subject code	616 ; 570
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Feature Fusion Method for Driving Fatigue of Shield Machine Drivers Based on Multiple Physiological Signals and Auto-Encoder

Kun Liu / Guoqi Feng / Xingyu Jiang / Wenpeng Zhao / Zhiqiang Tian / Rizheng Zhao / Kaihang Bi

Sustainability, Vol 15, Iss 9405, p

2023 Volume 9405

Abstract: The driving fatigue state of shield machine drivers directly affects the safe operation and tunneling efficiency of shield machines during metro construction. To cope with the problem that it is challenging to simulate the working conditions and ... ...

Abstract	The driving fatigue state of shield machine drivers directly affects the safe operation and tunneling efficiency of shield machines during metro construction. To cope with the problem that it is challenging to simulate the working conditions and operation process of shield machine drivers using driving simulation platforms and that the existing fatigue feature fusion methods usually show low recognition accuracy, shield machine drivers at Shenyang metro line 4 in China were taken as the research subjects, and a multi-modal physiological feature fusion method based on an L2-regularized stacked auto-encoder was designed. First, the ErgoLAB cloud platform was used to extract the combined energy feature (E), the reaction time, the HRV (heart rate variability) time-domain SDNN (standard deviation of normal-to-normal intervals) index, the HRV frequency-domain LF/HF (energy ratio of low frequency to high frequency) index and the pupil diameter index from EEG (electroencephalogram) signals, skin signals, pulse signals and eye movement data, respectively. Second, the physiological signal characteristics were extracted based on the WPT (wavelet packet transform) method and time–frequency analysis. Then, a method for driving fatigue feature fusion based on an auto-encoder was designed aiming at the characteristics of the L2-regularization method to solve the over-fitting problem of small sample data sets in the process of model training. The optimal hyper-parameters of the model were verified with the experimental method of the control variable, which reduces the loss of multi-modal feature data in compression fusion and the information loss rate of the fused index. The results show that the method proposed outperforms its competitors in recognition accuracy and can effectively reduce the loss rate of deep features in existing decision-making-level fusion.
Keywords	ErgoLAB ; feature fusion ; driving fatigue ; shield driver ; auto-encoder ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	670
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Land Use Zoning Management to Coordinate the Supply–Demand Imbalance of Ecosystem Services

Rongfang Lyu / Keith C. Clarke / Xiaolei Tian / Wenpeng Zhao / Jili Pang / Jianming Zhang

Frontiers in Environmental Science, Vol

A Case Study in the City Belt Along the Yellow River in Ningxia, China

2022 Volume 10

Abstract: The imbalance between the supply and demand of ecosystem services (ESs) is one of the main reasons for ecological degradation, which significantly impacts human well-being and ecological safety. Spatial heterogeneity of ES supply–demand, ES tradeoffs, ... ...

Abstract	The imbalance between the supply and demand of ecosystem services (ESs) is one of the main reasons for ecological degradation, which significantly impacts human well-being and ecological safety. Spatial heterogeneity of ES supply–demand, ES tradeoffs, and the socioecological environment calls for zoning management, while few studies have combined the above three aspects in dividing management zones and proposed strategies. Using the City Belt along the Yellow River in Ningxia in northwestern China as a case study, this study quantified the supply and demand for five key ESs (crop production, carbon sequestration, nutrient retention, sand fixation, and recreational opportunity), analyzed ES tradeoffs/synergies and bundles through correlation analysis and the self-organizing map (SOM) method, and investigated their socioecological driving mechanisms through a random forest model and the SOM method. Management zones were proposed and differentiated suggestions were provided through overlaying ES bundles and driver clusters. The results suggested that crop production, carbon sequestration, and nutrient retention mostly correlated to the same intrinsic ecological process, resulting in consistent synergies among these three ESs at both supply and demand sides. On the contrary, the variance in interactions between the two ESs of sand fixation and recreational opportunity and the other three ESs is due to the low similarity of their intrinsic ecological processes and external driving mechanisms. Fourteen socioecological factors could effectively explain the spatial heterogeneity of ES supply, demand, and match degree. Fourteen management zones with similar ecological problems and socioecological environments were delineated, and differentiated suggestions were provided for each zone. Adopting both ES characteristics and the socioecological environment into zoning management could effectively detect ecological problems and help to promote management suggestions in different socioecological contexts. This framework could ...
Keywords	ecosystem service ; zoning management ; socioecological environment ; supply and demand ; tradeoff ; Environmental sciences ; GE1-350
Subject code	710
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Bacteriophages isolated from dairy farm mitigated Klebsiella pneumoniae-induced inflammation in bovine mammary epithelial cells cultured in vitro

Yuxiang Shi / Wenpeng Zhao / Gang Liu / Tariq Ali / Peng Chen / Yongxia Liu / John P. Kastelic / Bo Han / Jian Gao

BMC Veterinary Research, Vol 17, Iss 1, Pp 1-

2021 Volume 11

Abstract: Abstract Background Klebsiella pneumoniae, an environmental pathogen causing mastitis in dairy cattle, is often resistant to antibiotics. K. pneumoniae was used as the host bacteria to support bacteriophage replication; 2 bacteriophages, CM8-1 and SJT-2 ... ...

Abstract	Abstract Background Klebsiella pneumoniae, an environmental pathogen causing mastitis in dairy cattle, is often resistant to antibiotics. K. pneumoniae was used as the host bacteria to support bacteriophage replication; 2 bacteriophages, CM8-1 and SJT-2 were isolated and considered to have therapeutic potential. In the present study, we determined the ability of these 2 bacteriophages to mitigate cytotoxicity, pathomorphological changes, inflammatory responses and apoptosis induced by K. pneumoniae (bacteriophage to K. pneumoniae MOI 1:10) in bovine mammary epithelial cells (bMECs) cultured in vitro. Results Bacteriophages reduced bacterial adhesion and invasion and cytotoxicity (lactate dehydrogenase release). Morphological changes in bMECs, including swelling, shrinkage, necrosis and hematoxylin and eosin staining of cytoplasm, were apparent 4 to 8 h after infection with K. pneumoniae, but each bacteriophage significantly suppressed damage and decreased TNF-α and IL-1β concentrations. K. pneumoniae enhanced mRNA expression of TLR4, NF-κB, TNF-α, IL-1β, IL-6, IL-8, caspase-3, caspase-9 and cyt-c in bMECs and increased apoptosis of bMECs, although these effects were mitigated by treatment with either bacteriophage for 8 h. Conclusions Bacteriophages CM8-1 and SJT-2 mitigated K. pneumoniae-induced inflammation in bMECs cultured in vitro. Therefore, the potential of these bacteriophages for treating mastitis in cows should be determined in clinical trials.
Keywords	Klebsiella pneumoniae ; Bovine mastitis ; Bacteriophage ; Inflammation ; Apoptosis ; bMECs ; Veterinary medicine ; SF600-1100
Subject code	610
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparative study on clinical efficacy of different methods for the treatment of intramural aortic hematoma

Junfu Luo / Wenpeng Zhao / Jiasheng Xu / Rui Zou / Kaihua Zhang / Yanhua Wan / Shasha Wan / Riwei Wang / Qingfu Zeng

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 14

Abstract: Abstract To explore the difference of curative effect between different treatment modalities, in order to provide reference for the treatment of aortic intramural hematoma (IMH). 168 patients with aortic intramural hematoma diagnosed and treated from ... ...

Abstract	Abstract To explore the difference of curative effect between different treatment modalities, in order to provide reference for the treatment of aortic intramural hematoma (IMH). 168 patients with aortic intramural hematoma diagnosed and treated from January 2010 to July 2020 were selected in the Second Affiliated Hospital of Nanchang University. Among them, 48 patients were diagnosed with Stanford A aortic intramural hematoma and 120 were diagnosed with Stanford B aortic intramural hematoma. According to the therapeutic methods, patients were divided into conservative treatment group and endovascular treatment group (TEVAR). For endovascular treatment group, according to the different timing of surgery, can be divided into acute phase group (onset within 72 h) and non-acute phase group (time of onset > 72 h).The clinical data and follow-up data were collected and analyzed by variance analysis and χ2 test. There were 168 patients diagnosed with aortic intramural hematoma 39 of them were (81.25%) Stanford A aortic intramural hematoma patients with pleural or pericardial effusion. For patient with Stanford A aortic intramural hematoma, endovascular treatment was performed in 15 patients (31.2%), and 33 cases (68.8%) for conservative treatment. The average follow-up (24.9 ± 13.9) was months. There were 120 patients with Stanford type B aortic intramural hematoma (71.4%), 60 patients received endovascular treatment (50%), and 60 patients (50%) received conservative treatment, with an average follow-up of (27.8 ± 14.6) months. For Stanford A type aortic intramural hematoma patients when the maximum aortic diameter ≥ 50 mm or hematoma thickness ≥ 11 mm, with high morbidity and mortality, positive endovascular treatment can reduce complications and death. For patients with Stanford type B aortic intramural hematoma, when the maximum aortic diameter ≥ 40 mm or hematoma thickness ≥ 10 mm, with high morbidity and mortality, positive endovascular treatment can reduce complications and death. Both Stanford type A and B ...
Keywords	Medicine ; R ; Science ; Q
Subject code	616 ; 610
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: New Autophagy-Ferroptosis Gene Signature Predicts Survival in Glioma

Liwei Zhou / Zhengye Jiang / Zhongjie Shi / Wenpeng Zhao / Zhenwei Lu / Yuanyuan Xie / Bingchang Zhang / Hanwen Lu / Guowei Tan / Zhanxiang Wang

Frontiers in Cell and Developmental Biology, Vol

2021 Volume 9

Abstract: Background: Ferroptosis plays an important role in glioma and significantly affects the prognosis, but the specific mechanism has not yet been elucidated. Recent studies suggest that autophagy regulates the process of ferroptosis. This study aimed to ... ...

Abstract	Background: Ferroptosis plays an important role in glioma and significantly affects the prognosis, but the specific mechanism has not yet been elucidated. Recent studies suggest that autophagy regulates the process of ferroptosis. This study aimed to find potential autophagy-ferroptosis genes and explore the prognostic significance in glioma.Methods: Ferroptosis and autophagy genes were obtained from two online databases (zhounan.org/ferrdb and autophagy.lu/). The RNAseq data and clinical information were obtained from the Chinese Glioma Genome Atlas (CGGA) database (http://www.cgga.org.cn/). Univariate, multivariate, lasso and Cox regression analysis screened out prognosis-related genes, and a risk model was constructed. Receiver operating characteristic (ROC) curve analysis evaluated the predictive efficiency of the model. Finally, a nomogram was constructed to more accurately predict the prognosis of glioma.Results: We developed a Venn diagram showing 23 autophagy-ferroptosis genes. A total of 660 cases (including RNA sequences and complete clinical information) from two different cohorts (training group n = 413, verification group n = 247) of the CGGA database was acquired. Cohorts were screened to include five prognosis-related genes (MTOR, BID, HSPA5, CDKN2A, GABARAPLA2). Kaplan-Meier curves showed that the risk model was a good prognostic indicator (p < 0.001). ROC analysis showed good efficacy of the risk model. Multivariate Cox analysis also revealed that the risk model was suitable for clinical factors related to prognosis, including type of disease (primary, recurrence), grade (III-IV), age, temozolomide treatment, and 1p19q state. Using the five prognosis-related genes and the risk score, we constructed a nomogram assessed by C-index (0.7205) and a calibration plot that could more accurately predict glioma prognosis.Conclusion: Using a current database of autophagy and ferroptosis genes, we confirmed the prognostic significance of autophagy-ferroptosis genes in glioma, and we constructed a ...
Keywords	ferroptosis ; autophagy ; glioma ; prognosis ; risk model ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Imaging features and outcomes in patients with ruptured hepatocellular carcinoma following transcatheter arterial chemoembolization

Wenpeng Zhao / Xiaopu Hou / Honglu Li / Jiang Guo / Liang Cai / Youjia Duan / Hongliu Du / Xihong Shao / Zhenying Diao / Changqing Li

Journal of International Medical Research, Vol

a retrospective clinical study

2021 Volume 49

Abstract: Objective To summarize and analyze the imaging features and outcomes of patients with ruptured hepatocellular carcinoma (HCC) following transcatheter arterial chemoembolization (TACE). Methods We investigated all consecutive patients with HCC who ... ...

Abstract	Objective To summarize and analyze the imaging features and outcomes of patients with ruptured hepatocellular carcinoma (HCC) following transcatheter arterial chemoembolization (TACE). Methods We investigated all consecutive patients with HCC who received standardized TACE based on our hospital database. Ruptured HCCs were divided into three types according to their relationship with the liver capsule, determined by computed tomography or magnetic resonance imaging scans: Type I, portion of tumor cambered outwards ≤30%; Type II, portion of tumor cambered outwards >30% and <50%; and Type III, portion of tumor cambered outwards ≥50%. Results There were 54, 40, and 26 patients with Type I, II, and III HCCs, respectively. Among these, eight patients developed ruptured tumors within 2 weeks after TACE, including one, two, and five patients with type I, II, and III ruptured HCCs, respectively. Patients with type III HCCs had a shorter median survival time than patients with type I–II HCCs. Conclusions Patients with type III HCCs might have a higher re-rupture rate and benefit less from emergency arterial embolization procedures than patients with type I–II HCCs.
Keywords	Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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