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Article: [Mechanism of Zixin Biqiu Granules in treatment of allergic rhinitis based on network pharmacology and molecular docking technology].

Yuan, An-Lei / Ming, Yu / Zhang, Xin-Yi / Shu, Xin-Yang

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica

2022 Volume 47, Issue 19, Page(s) 5344–5352

Abstract: ... exposure triggering IgE-mediated inflammation. With frequent recurrence, it is difficult to be cured. Zixin ... being prepared, but the mechanism is unclear. Therefore, this study explored the mechanism of Zixin ... components and targets of Zixin Biqiu Granules were retrieved from Traditional Chinese Medicine Systems ...

Abstract	Allergic rhinitis(AR) is a chronic inflammatory disorder of nasal mucosa induced by allergen exposure triggering IgE-mediated inflammation. With frequent recurrence, it is difficult to be cured. Zixin Biqiu Granules is developed based on the 60-year clinical experience of CHAO En-xiang, a master of national medicine of China-Japan Friendship Hospital. At present, phase Ⅲ multicenter clinical trial is being prepared, but the mechanism is unclear. Therefore, this study explored the mechanism of Zixin Biqiu Granules against AR based on network pharmacology and molecular docking. First, the chemical components and targets of Zixin Biqiu Granules were retrieved from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP), and the targets of AR from GeneCards and Online Mendelian Inheritance in Man(OMIM). Then the common targets of the two were screened out and the "Chinese medicine-component-target" network was constructed. Afterward, the common targets were imported into the STRING to obtain the interaction of them, and Cytoscape was employed to establish the protein-protein interaction(PPI) network. Through topological analysis, the core targets were obtained. DAVID was used for Gene Ontology(GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment. The "key target-pathway-biological process" network was constructed to explore the anti-AR mechanism of Zixin Biqiu Granules. Finally, the core targets were selected for molecular docking with the key components of Zixin Biqiu Granules to verify the mechanism. The results showed that there were 151 components and 97 targets in the "Chinese medicine-component-target" network. We obtained 20 core targets, 488 biological processes and 147 pathways in topological, GO, and KEGG enrichment analysis of the protein interaction network, and in the comprehensive analysis, it was found that Zixin Biqiu Granules mainly exerted the therapeutic effect through anti-inflammation and immunoregulation. Serine/threonine-protein kinase 1(AKT1) and tumor necrosis factor(TNF) were docked with the key components of Zixin Biqiu Granules, and the results showed that the key components of Zixin Biqiu Granules had high binding affinity to the core targets. This study preliminarily discussed the anti-AR mechanism of Zixin Biqiu Granules, which laid a scientific basis for its clinical application.
Language	Chinese
Publishing date	2022-12-05
Publishing country	China
Document type	English Abstract ; Journal Article
ZDB-ID	1004649-5
ISSN	1001-5302 ; 0254-0029
ISSN	1001-5302 ; 0254-0029
DOI	10.19540/j.cnki.cjcmm.20220524.401
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Article ; Online: Printed flexible mechanical sensors.

Smocot, Samuel / Zhang, Zixin / Zhang, Lingzhi / Guo, Shu / Cao, Changhong

Nanoscale

2022 Volume 14, Issue 46, Page(s) 17134–17156

Abstract: Flexible mechanical sensors ( ...

Abstract	Flexible mechanical sensors (
Language	English
Publishing date	2022-12-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/d2nr04015h
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Article ; Online: A novel nano-cerium oxide functionalized biochar composite for degradation of organic dye: insight of the photocatalysis mechanism.

Luo, Kun / Jiang, Shu / Yang, Zixin / Li, Xue / Pang, Ya / Yang, Qi

Environmental science and pollution research international

2024 Volume 31, Issue 19, Page(s) 28658–28670

Abstract: Recently, visible-light-driven photocatalysis attracts much concerns in the remediation of environmental organic pollutants. In this study, the cerium doped biochar was fabricated through the hydrothermal method, and served as an efficient photocatalyst ... ...

Abstract	Recently, visible-light-driven photocatalysis attracts much concerns in the remediation of environmental organic pollutants. In this study, the cerium doped biochar was fabricated through the hydrothermal method, and served as an efficient photocatalyst towards rhodamine B degradation under visible light irradiation. Almost 100% of rhodamine B was removed by 2.0 g·L
MeSH term(s)	Cerium/chemistry ; Charcoal/chemistry ; Catalysis ; Rhodamines/chemistry ; Coloring Agents/chemistry ; Photolysis ; Kinetics ; Light
Chemical Substances	Cerium (30K4522N6T) ; Charcoal (16291-96-6) ; biochar ; ceric oxide (619G5K328Y) ; Rhodamines ; rhodamine B (K7G5SCF8IL) ; Coloring Agents
Language	English
Publishing date	2024-04-01
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-024-32828-7
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Article ; Online: Surface-enhanced Raman database of 24 metabolites: Stable measurement of spectra, extraction and analysis of the main features.

Zhang, Xiaoyu / Fan, Aoran / Shu, Zixin / Ma, Weigang / Zhang, Xing

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy

2023 Volume 306, Page(s) 123587

Abstract: Surface-enhanced Raman spectroscopy (SERS) has been used in Raman-based metabolomics to provide abundant molecular fingerprint information in situ with extremely high sensitivity, without damaging the sample. However, poor reproducibility, caused by the ... ...

Abstract	Surface-enhanced Raman spectroscopy (SERS) has been used in Raman-based metabolomics to provide abundant molecular fingerprint information in situ with extremely high sensitivity, without damaging the sample. However, poor reproducibility, caused by the randomness of the adsorption sites, and the short-range effect of SERS have hindered the development of SERS in metabolomics, resulting in very few SERS reference databases for small-molecule metabolites. In this work, our previously proposed large laser spot-swift mapping SERS method was adopted for the measurement of 24 commercially available metabolite standards, to provide reproducible and reliable references for Raman-based metabolomics study. Among these 24 metabolites, 22 contained no Raman data in PubChem. Other than the SERS spectra data, we extracted and explained the molecular vibration information of these metabolites, and combined with the density functional theory (DFT) calculations, we provided a new possibility for the fast Raman recognition of small-molecule metabolites. Accordingly, a large laser spot-swift mapping SERS database of metabolites in human serum was initially established, which contained not only the original spectral data but also other detailed feature information regarding the Raman peaks. With continuous accumulation, this database could play a promising role in Raman-based metabolomics and other Raman-related research.
MeSH term(s)	Humans ; Reproducibility of Results ; Spectrum Analysis, Raman/methods ; Metabolomics ; Adsorption ; Vibration
Language	English
Publishing date	2023-10-30
Publishing country	England
Document type	Journal Article
ZDB-ID	210413-1
ISSN	1873-3557 ; 0370-8322 ; 0584-8539 ; 1386-1425
ISSN (online)	1873-3557
ISSN	0370-8322 ; 0584-8539 ; 1386-1425
DOI	10.1016/j.saa.2023.123587
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Article ; Online: Bacillus pumilus TS1 alleviates Salmonella Enteritidis-induced intestinal injury in broilers

Yinkun Liu / Zixin Li / Hao Li / Shuangshuang Wan / Shu Tang

BMC Veterinary Research, Vol 19, Iss 1, Pp 1-

2023 Volume 13

Abstract: Abstract Background In the current context of reduced and limited antibiotic use, several pathogens and stressors cause intestinal oxidative stress in poultry, which leads to a reduced feed intake, slow or stagnant growth and development, and even death, ...

Abstract	Abstract Background In the current context of reduced and limited antibiotic use, several pathogens and stressors cause intestinal oxidative stress in poultry, which leads to a reduced feed intake, slow or stagnant growth and development, and even death, resulting in huge economic losses to the poultry breeding industry. Oxidative stress in animals is a non-specific injury for which no targeted drug therapy is available; however, the health of poultry can be improved by adding appropriate feed additives. Bacillus pumilus, as a feed additive, promotes growth and development and reduces intestinal oxidative stress damage in poultry. Heat shock protein 70 (HSP70) senses oxidative damage and repairs unfolded and misfolded proteins; its protective effect has been widely investigated. Mitogen-activated protein kinase/protein kinase C (MAPK/PKC) and hypoxia inducible factor-1 alpha (HIF-1α) are also common proteins associated with inflammatory response induced by several stressors, but there is limited research on these proteins in the context of poultry intestinal Salmonella Enteritidis (SE) infections. In the present study, we isolated a novel strain of Bacillus pumilus with excellent performance from the feces of healthy yaks, named TS1. To investigate the effect of TS1 on SE-induced enteritis in broilers, 120 6-day-old white-feathered broilers were randomly divided into four groups (con, TS1, SE, TS1 + SE). TS1 and TS1 + SE group chickens were fed with 1.4 × 107 colony-forming units per mL of TS1 for 15 days and intraperitoneally injected with SE to establish the oxidative stress model. Then, we investigated whether TS1 protects the intestine of SE-treated broiler chickens using inflammatory cytokine gene expression analysis, stress protein quantification, antioxidant quantification, and histopathological analysis. Results The TS1 + SE group showed lower MDA and higher GSH-Px, SOD, and T-AOC than the SE group. TS1 alleviated the effects of SE on intestinal villus length and crypt depth. Our results suggest that SE ...
Keywords	Bacillus pumilus ; HIF-1α ; Histopathology ; HSP70 ; Inflammatory cytokines ; Oxidative stress ; Veterinary medicine ; SF600-1100
Subject code	610
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Land Use Change in the Cross-Boundary Regions of a Metropolitan Area

Linlin Dai / Zixin Zhan / Yeshuo Shu / Xiao Rong

Land, Vol 11, Iss 153, p

A Case Study of Tongzhou-Wuqing-Langfang

2022 Volume 153

Abstract: Since the 1980s, metropolitan areas have increased worldwide due to urbanization and regionalization. While the spatial integration of the labor and housing markets has benefitted the development of cities within metropolitan areas, they have also ... ...

Abstract	Since the 1980s, metropolitan areas have increased worldwide due to urbanization and regionalization. While the spatial integration of the labor and housing markets has benefitted the development of cities within metropolitan areas, they have also brought great challenges for land governance; this is particularly evident in cross-boundary regions due to the complex relations between the markets and the regulations and between governments at different levels. Extensive research has been conducted on the city-level analysis of socioeconomic integration, land use development, and urban governance within metropolitan areas; yet, it is insufficient for understanding the intricate interplay between the various forces in such regions. This study aims to reveal the dynamics of land use change from 1990–2020 and its driving forces in the recent decade in the Tongzhou-Wuqing-Langfang (TWL) region—a typical cross-boundary area between Beijing, Tianjin, and the Hebei Metropolitan Area—using Landsat imagery. We employed the land-use dynamic degree, kernel density analysis, principal component analysis, and multiple linear regression to explore the spatiotemporal patterns of land use change and its driving factors at the district/county level. The results show that the general land use changes from cultivated and forest land to urban and rural construction land across the region. The speed of the trend varies considerably over time between different areas as the land use policies and regulations of each local government change. The population growth and the tertiary and secondary industry growth are the main driving factors for the change in construction land across the whole TWL region, while the urbanization rate and fixed asset investment have different impacts across the cross-boundary region. The results suggest that expanding the integration of land use policies and regulations in the cross-boundary region is urgently required.
Keywords	land use change ; metropolitan area ; cross-boundary management ; driving factors ; Agriculture ; S
Subject code	910
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Bacillus pumilus TS1 alleviates Salmonella Enteritidis-induced intestinal injury in broilers.

Liu, Yinkun / Li, Zixin / Li, Hao / Wan, Shuangshuang / Tang, Shu

BMC veterinary research

2023 Volume 19, Issue 1, Page(s) 41

Abstract: Background: In the current context of reduced and limited antibiotic use, several pathogens and stressors cause intestinal oxidative stress in poultry, which leads to a reduced feed intake, slow or stagnant growth and development, and even death, ... ...

Abstract	Background: In the current context of reduced and limited antibiotic use, several pathogens and stressors cause intestinal oxidative stress in poultry, which leads to a reduced feed intake, slow or stagnant growth and development, and even death, resulting in huge economic losses to the poultry breeding industry. Oxidative stress in animals is a non-specific injury for which no targeted drug therapy is available; however, the health of poultry can be improved by adding appropriate feed additives. Bacillus pumilus, as a feed additive, promotes growth and development and reduces intestinal oxidative stress damage in poultry. Heat shock protein 70 (HSP70) senses oxidative damage and repairs unfolded and misfolded proteins; its protective effect has been widely investigated. Mitogen-activated protein kinase/protein kinase C (MAPK/PKC) and hypoxia inducible factor-1 alpha (HIF-1α) are also common proteins associated with inflammatory response induced by several stressors, but there is limited research on these proteins in the context of poultry intestinal Salmonella Enteritidis (SE) infections. In the present study, we isolated a novel strain of Bacillus pumilus with excellent performance from the feces of healthy yaks, named TS1. To investigate the effect of TS1 on SE-induced enteritis in broilers, 120 6-day-old white-feathered broilers were randomly divided into four groups (con, TS1, SE, TS1 + SE). TS1 and TS1 + SE group chickens were fed with 1.4 × 10 Results: The TS1 + SE group showed lower MDA and higher GSH-Px, SOD, and T-AOC than the SE group. TS1 alleviated the effects of SE on intestinal villus length and crypt depth. Our results suggest that SE exposure increased the expression of inflammatory factors (IL-1β, IL-6, TNF-α, IL-4, and MCP-1), p38 MAPK, and PKCβ and decreased the expression of HSP60, HSP70, and HIF-1α, whereas TS1 alleviated these effects. Conclusions: Bacillus pumilus TS1 alleviated oxidative stress damage caused by SE and attenuated the inflammatory response in broilers through MAPK/PKC regulation of HSPs/HIF-1α.
MeSH term(s)	Animals ; Chickens ; Salmonella enteritidis ; Bacillus pumilus ; Intestines ; Intestinal Mucosa/metabolism ; Animal Feed/analysis ; Diet/veterinary ; Dietary Supplements
Language	English
Publishing date	2023-02-10
Publishing country	England
Document type	Randomized Controlled Trial, Veterinary ; Journal Article
ZDB-ID	2191675-5
ISSN	1746-6148 ; 1746-6148
ISSN (online)	1746-6148
ISSN	1746-6148
DOI	10.1186/s12917-023-03598-0
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Article ; Online: KDGene: knowledge graph completion for disease gene prediction using interactional tensor decomposition.

Wang, Xinyan / Yang, Kuo / Jia, Ting / Gu, Fanghui / Wang, Chongyu / Xu, Kuan / Shu, Zixin / Xia, Jianan / Zhu, Qiang / Zhou, Xuezhong

Briefings in bioinformatics

2024 Volume 25, Issue 3

Abstract: The accurate identification of disease-associated genes is crucial for understanding the molecular mechanisms underlying various diseases. Most current methods focus on constructing biological networks and utilizing machine learning, particularly deep ... ...

Abstract	The accurate identification of disease-associated genes is crucial for understanding the molecular mechanisms underlying various diseases. Most current methods focus on constructing biological networks and utilizing machine learning, particularly deep learning, to identify disease genes. However, these methods overlook complex relations among entities in biological knowledge graphs. Such information has been successfully applied in other areas of life science research, demonstrating their effectiveness. Knowledge graph embedding methods can learn the semantic information of different relations within the knowledge graphs. Nonetheless, the performance of existing representation learning techniques, when applied to domain-specific biological data, remains suboptimal. To solve these problems, we construct a biological knowledge graph centered on diseases and genes, and develop an end-to-end knowledge graph completion framework for disease gene prediction using interactional tensor decomposition named KDGene. KDGene incorporates an interaction module that bridges entity and relation embeddings within tensor decomposition, aiming to improve the representation of semantically similar concepts in specific domains and enhance the ability to accurately predict disease genes. Experimental results show that KDGene significantly outperforms state-of-the-art algorithms, whether existing disease gene prediction methods or knowledge graph embedding methods for general domains. Moreover, the comprehensive biological analysis of the predicted results further validates KDGene's capability to accurately identify new candidate genes. This work proposes a scalable knowledge graph completion framework to identify disease candidate genes, from which the results are promising to provide valuable references for further wet experiments. Data and source codes are available at https://github.com/2020MEAI/KDGene.
MeSH term(s)	Pattern Recognition, Automated ; Algorithms ; Biological Science Disciplines ; Machine Learning ; Semantics
Language	English
Publishing date	2024-04-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbae161
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Article ; Online: A screening method based on analytic hierarchy process for closed-loop DBS strategies of Parkinson's disease.

Chen, Huan / Zhao, Dechun / Luo, Zixin / Shen, Lihao / Shu, Yang / Li, Ling

Technology and health care : official journal of the European Society for Engineering and Medicine

2023 Volume 31, Issue 4, Page(s) 1319–1331

Abstract: Background: Closed-loop deep brain stimulation (DBS) is a research hotspot in the treatment of Parkinson's disease. However, a variety of stimulation strategies will increase the selection time and cost in animal experiments and clinical studies. ... ...

Abstract	Background: Closed-loop deep brain stimulation (DBS) is a research hotspot in the treatment of Parkinson's disease. However, a variety of stimulation strategies will increase the selection time and cost in animal experiments and clinical studies. Moreover, the stimulation effect is little difference between similar strategies, so the selection process will be redundant. Objective: The objective was to propose a comprehensive evaluation model based on analytic hierarchy process (AHP) to select the best one among similar strategies. Methods: Two similar strategies, namely, threshold stimulation (CDBS) and threshold stimulus after EMD feature extraction (EDBS), were used for analysis and screening. The values of Similar to Unified Parkinson's Disease Rating Scale estimates (SUE), β power and energy consumption were calculated and analysed. The stimulation threshold with the best improvement effect was selected. The weights of the indices were allocated by AHP. Finally, the weights and index values were combined, and the comprehensive scores of the two strategies were calculated using the evaluation model. Results: The optimal stimulation threshold for CDBS was 52% and for EDBS was 62%. The weights of the indices were 0.45, 0.45 and 0.1, respectively. According to comprehensive scores, different from the situation where either EDBS or CDBS can be called optimal stimulation strategies. But under the same threshold stimulation, the EDBS was better than the CDBS under the optimal level. Conclusion: The evaluation model based on AHP under the optimal stimulation conditions satisfied the screening conditions between the two strategies.
MeSH term(s)	Animals ; Parkinson Disease/therapy ; Analytic Hierarchy Process ; Deep Brain Stimulation/methods ; Treatment Outcome
Language	English
Publishing date	2023-03-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1159961-3
ISSN	1878-7401 ; 0928-7329
ISSN (online)	1878-7401
ISSN	0928-7329
DOI	10.3233/THC-220587
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Article: Land Use Change in the Cross-Boundary Regions of a Metropolitan Area: A Case Study of Tongzhou-Wuqing-Langfang

Dai, Linlin / Zhan, Zixin / Shu, Yeshuo / Rong, Xiao

Land. 2022 Jan. 19, v. 11, no. 2

2022

Abstract	Since the 1980s, metropolitan areas have increased worldwide due to urbanization and regionalization. While the spatial integration of the labor and housing markets has benefitted the development of cities within metropolitan areas, they have also brought great challenges for land governance; this is particularly evident in cross-boundary regions due to the complex relations between the markets and the regulations and between governments at different levels. Extensive research has been conducted on the city-level analysis of socioeconomic integration, land use development, and urban governance within metropolitan areas; yet, it is insufficient for understanding the intricate interplay between the various forces in such regions. This study aims to reveal the dynamics of land use change from 1990–2020 and its driving forces in the recent decade in the Tongzhou-Wuqing-Langfang (TWL) region—a typical cross-boundary area between Beijing, Tianjin, and the Hebei Metropolitan Area—using Landsat imagery. We employed the land-use dynamic degree, kernel density analysis, principal component analysis, and multiple linear regression to explore the spatiotemporal patterns of land use change and its driving factors at the district/county level. The results show that the general land use changes from cultivated and forest land to urban and rural construction land across the region. The speed of the trend varies considerably over time between different areas as the land use policies and regulations of each local government change. The population growth and the tertiary and secondary industry growth are the main driving factors for the change in construction land across the whole TWL region, while the urbanization rate and fixed asset investment have different impacts across the cross-boundary region. The results suggest that expanding the integration of land use policies and regulations in the cross-boundary region is urgently required.
Keywords	Landsat ; assets ; case studies ; forest land ; governance ; industry ; land use change ; local government ; metropolitan areas ; population growth ; principal component analysis ; regression analysis ; urbanization ; China
Language	English
Dates of publication	2022-0119
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2682955-1
ISSN	2073-445X
ISSN	2073-445X
DOI	10.3390/land11020153
Database	NAL-Catalogue (AGRICOLA)

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