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22 pages, 3158 KiB  
Article
Adaptive Strategies and Sustainable Innovations of Chinese Contractors in the Belt and Road Initiative: A Social Network and Supply Chain Integration Perspective
by Jiaxin Huang and Shui Ming Li
Sustainability 2024, 16(20), 8927; https://doi.org/10.3390/su16208927 - 15 Oct 2024
Viewed by 285
Abstract
As global economic integration and rapid technological advancements transform international business, international engineering contracting has become essential for achieving sustainable development goals (SDGs). This paper investigates the significant impact of China’s strategic initiatives, notably the “Going Global” strategy and the Belt and Road [...] Read more.
As global economic integration and rapid technological advancements transform international business, international engineering contracting has become essential for achieving sustainable development goals (SDGs). This paper investigates the significant impact of China’s strategic initiatives, notably the “Going Global” strategy and the Belt and Road Initiative (BRI), on the operational practices of Chinese enterprises involved in overseas investments. Central to this transformation is the Engineering, Procurement, and Construction (EPC) model, which emphasizes the integration of supply chain management and stakeholder collaboration to enhance performance in international EPC projects and underscores the crucial role of these elements in promoting sustainability. Incorporating insights from social network data analysis, this study reveals that contractors collaborating with various stakeholders—such as owners/consulting engineers, domestic and foreign customs departments, and group headquarters/design parties—exhibit a high degree of similarity in personnel profiles. This suggests that the internal organizational structure and personnel allocation of contractors could be optimized to enhance operational efficiency, aligning with the collaborative patterns identified. This study addresses a critical research gap by exploring how effective supply chain management and collaborative stakeholder engagement within multinational EPC projects contribute to sustainable outcomes. Employing advanced social network analysis software, the research examines the complex interactions among stakeholders and their influence on procurement dynamics. Findings indicate that strong relational networks and strategic collaborations significantly enhance procurement efficiency and project success, underscoring the importance of supply chain integration. Ultimately, integrating supply chain management principles into the EPC model not only offers innovative perspectives for advancing sustainability in international projects but also provides actionable insights for improving project outcomes within the BRI framework. This research underscores the pivotal role of supply chain organization and stakeholder cooperation in achieving sustainability objectives, thereby enriching the discourse on sustainable enterprise operation and supply chain management in the context of global initiatives. Full article
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<p>An analysis of the developments in China’s overseas engineering contracting industry from 2003 to 2023. Data Source: Ministry of Commerce, China (2003–2023).</p>
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<p>A network that shows how studies on stakeholder management occur together.</p>
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<p>Co-occurring network for supply chain integration research.</p>
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<p>Network of coauthors on supply chain integration studies.</p>
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<p>Stakeholder collaboration networks.</p>
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<p>Enlarged visualization of stakeholder collaboration.</p>
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<p>Zambian hydroelectric project.</p>
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<p>Procurement management model of internal EPC project from the perspective of supply chain integration.</p>
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16 pages, 3824 KiB  
Article
Comparative Analyses of Dynamic Transcriptome Profile of Heart Highlight the Key Response Genes for Heat Stress in Zhikong Scallop Chlamys farreri
by Xinyuan Wang, Zujing Yang, Cheng Peng, Haitao Yu, Chang Cui, Qiang Xing, Jingjie Hu, Zhenmin Bao and Xiaoting Huang
Antioxidants 2024, 13(10), 1217; https://doi.org/10.3390/antiox13101217 - 10 Oct 2024
Viewed by 357
Abstract
Heat stress resulting from global climate change has been demonstrated to adversely affect growth, development, and reproduction of marine organisms. The Zhikong scallop (Chlamys farreri), an important economical mollusk in China, faces increasing risks of summer mortality due to the prolonged [...] Read more.
Heat stress resulting from global climate change has been demonstrated to adversely affect growth, development, and reproduction of marine organisms. The Zhikong scallop (Chlamys farreri), an important economical mollusk in China, faces increasing risks of summer mortality due to the prolonged heat waves. The heart, responsible for transporting gas and nutrients, is vital in maintaining homeostasis and physiological status in response to environmental changes. In this study, the effect of heat stress on the cardiac function of C. farreri was investigated during the continuous 30-day heat stress at 27 °C. The results showed the heart rate of scallops increased due to stress in the initial phase of high temperature exposure, peaking at 12 h, and then gradually recovered, indicating an acclimatization at the end of the experiment. In addition, the levels of catalase (CAT), superoxide dismutase (SOD), and total antioxidant capacity (T-AOC) exhibited an initial increase followed by recovery in response to heat stress. Furthermore, transcriptome analysis of the heart identified 3541 differentially expressed genes (DEGs) in response to heat stress. Subsequent GO and KEGG enrichment analysis showed that these genes were primarily related to signal transduction and oxidative stress, such as the phosphatidylinositol signaling system, regulation of actin cytoskeleton, MAPK signaling pathway, FoxO signaling pathway, etc. In addition, two modules were identified as significant responsive modules according to the weighted gene co-expression network analysis (WGCNA). The upregulation of key enzymes within the base excision repair and gap junction pathways indicated that the heart of C. farreri under heat stress enhanced DNA repair and maintained cellular integrity. In addition, the variable expression of essential signaling molecules and cytoskeletal regulators suggested that the heart of C. farreri modulated cardiomyocyte contraction, intracellular signaling, and heart rate through complex regulation of phosphorylation and calcium dynamics in response to heat stress. Collectively, this study enhances our understanding of cardiac function and provides novel evidence for unraveling the mechanism underlying the thermal response in mollusks. Full article
(This article belongs to the Special Issue The Role of Oxidative Stress in Aquaculture)
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<p>Heart rate and amplitude of <span class="html-italic">C. farreri</span> under different heat stress time. (<b>A</b>) Heart rate (HR); (<b>B</b>) Heart amplitude (HA). The circle shape represents the mean ± S.D. (<span class="html-italic">n</span> = 3). (* <span class="html-italic">p</span> value <span class="html-italic">&lt;</span> 0.05).</p>
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<p>Antioxidant enzymes activity and total antioxidant capacity in heart of <span class="html-italic">C. farreri</span> under heat stress. (<b>A</b>) CAT activity; (<b>B</b>) SOD activity; (<b>C</b>) T-AOC. The triangular shape represents the mean ± S.D. (<span class="html-italic">n</span> = 3). (* <span class="html-italic">p</span> value &lt; 0.05).</p>
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<p>Numbers of DEGs in heart of <span class="html-italic">C. farreri</span> under heat stress. Red bar represents the number of up-regulated DEGs; blue bar represents the number of down-regulated DEGs.</p>
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<p>Three expression trends of DEGs in heart of <span class="html-italic">C. farreri</span> under heat stress. (<b>A</b>) Expression trend contrary to the trend observed in HR changes; (<b>B</b>) expression trend similar to the trend of HR; (<b>C</b>) expression trend opposite to the trend of HA changes. The <span class="html-italic">X</span>-axis represents the time of heat stress. The <span class="html-italic">Y</span>-axis represents the log<sub>2</sub>FC of gene expression change.</p>
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<p>The expressions of key genes from three trends in heart of <span class="html-italic">C. farreri</span> under heat stress.</p>
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<p>The GO and KEGG analysis of DEGs in heart of <span class="html-italic">C. farreri</span> under heat stress. (<b>A</b>) GO annotation. The <span class="html-italic">X</span>-axis represents the annotated functions. The <span class="html-italic">Y</span>-axis represents the percent of enriched gene numbers. (<b>B</b>) KEGG enrichment. The <span class="html-italic">X</span>-axis represents the rich factor of KEGG terms. The <span class="html-italic">Y</span>-axis represents the enriched pathways. The circle shape represents the number of DGEs in the enriched pathways.</p>
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<p>The WGCNA analysis of scallop heart transcriptome under heat stress. Dendrogram is produced by average linkage hierarchical clustering of genes based on topological overlap. Horizontal color bars represent different co-expression modules that are also numbered. Unassigned genes are labeled in grey.</p>
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<p>Main response modules of WGCNA network of heart after heat treatment. Yellow dots belong to M1 and blue dots belong to M2.</p>
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<p>Quantitative real time-PCR validation. Green line represents RT-qPCR results; red line represents RNA-Seq results.</p>
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27 pages, 3000 KiB  
Article
Effects of Contractual and Relational Governance on Project Performance: The Role of BIM Application Level
by Bing Yi and Nina Lee See Nie
Buildings 2024, 14(10), 3185; https://doi.org/10.3390/buildings14103185 - 7 Oct 2024
Viewed by 478
Abstract
This study aims to explore the moderating role of Building Information Modeling (BIM) between project governance and project performance. The theoretical foundation of this research is rooted in transaction cost economics. The data come from the construction industry in China’s Sichuan province. A [...] Read more.
This study aims to explore the moderating role of Building Information Modeling (BIM) between project governance and project performance. The theoretical foundation of this research is rooted in transaction cost economics. The data come from the construction industry in China’s Sichuan province. A dataset comprising 175 survey responses was subjected to analysis through the Partial Least Squares (PLS) method. The findings confirm that contract completeness and contract flexibility positively influence project performance, and trust in relational governance also has a positive impact on project performance. Additionally, the level of BIM application moderates the relationships between contract flexibility and trust with project performance. However, a significant positive relationship between contract completeness and project performance was not observed. These findings establish a groundwork for transitioning project governance research from a static to a dynamic viewpoint, thereby facilitating the practical implementation of BIM technology. As a result, this study enriches the academic comprehension of governance amidst digital transformation and provides actionable suggestions for fostering efficient governance practices within a technologically progressive landscape. Full article
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<p>The TCT conceptual figure for the construction application process.</p>
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<p>The application of BIM in the whole project life cycle.</p>
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<p>The research framework model.</p>
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<p>The research method of this research.</p>
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<p>Path analysis by PLS.</p>
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<p>The moderating effect of BIM application level on the relationship between contract completeness and project performance.</p>
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<p>The moderating effect of BIM application level on the relationship between contract flexibility and project performance.</p>
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<p>The moderating effect of BIM application level on the relationship between trust and project performance.</p>
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19 pages, 4657 KiB  
Article
Distinct Genomic Expression Signatures after Low-Force Electrically Induced Exercises in Persons with Spinal Cord Injury
by Michael A. Petrie, Manish Suneja and Richard K. Shields
Int. J. Mol. Sci. 2024, 25(18), 10189; https://doi.org/10.3390/ijms251810189 - 23 Sep 2024
Viewed by 537
Abstract
People with a spinal cord injury are at an increased risk of metabolic dysfunction due to skeletal muscle atrophy and the transition of paralyzed muscle to a glycolytic, insulin-resistant phenotype. Providing doses of exercise through electrical muscle stimulation may provide a therapeutic intervention [...] Read more.
People with a spinal cord injury are at an increased risk of metabolic dysfunction due to skeletal muscle atrophy and the transition of paralyzed muscle to a glycolytic, insulin-resistant phenotype. Providing doses of exercise through electrical muscle stimulation may provide a therapeutic intervention to help restore metabolic function for people with a spinal cord injury, but high-frequency and high-force electrically induced muscle contractions increase fracture risk for the underlying osteoporotic skeletal system. Therefore, we investigated the acute molecular responses after a session of either a 3 Hz or 1 Hz electrically induced exercise program. Ten people with a complete spinal cord injury completed a 1 h (3 Hz) or 3 h (1 Hz) unilateral electrically induced exercise session prior to a skeletal muscle biopsy of the vastus lateralis. The number of pulses was held constant. Tissue samples were analyzed for genomic and epigenomic expression profiles. There was a strong acute response after the 3 Hz exercise leading to the upregulation of early response genes (NR4A3, PGC-1α, ABRA, IRS2, EGR1, ANKRD1, and MYC), which have prominent roles in regulating molecular pathways that control mitochondrial biogenesis, contractile protein synthesis, and metabolism. Additionally, these genes, and others, contributed to the enrichment of pathways associated with signal transduction, cellular response to stimuli, gene expression, and metabolism. While there were similar trends observed after the 1 Hz exercise, the magnitude of gene expression changes did not reach our significance thresholds, despite a constant number of stimuli delivered. There were also no robust acute changes in muscle methylation after either form of exercise. Taken together, this study supports that a dose of low-force electrically induced exercise for 1 h using a 3 Hz stimulation frequency is suitable to trigger an acute genomic response in people with chronic paralysis, consistent with an expression signature thought to improve the metabolic and contractile phenotype of paralyzed muscle, if performed on a regular basis. Full article
(This article belongs to the Special Issue Molecular Insights into the Role of Exercise in Disease and Health)
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<p>Gene expression maps. The 25 most increased (red) and 25 most decreased (blue) genes are represented. (<b>A</b>) Heat map of the 50 genes with the largest change in expression (FDR &lt; 0.05) 3 h after the end of the long-duration, low-force exercise with a 3 Hz stimulation frequency in people with SCI. (<b>B</b>) Heat map of the 50 genes with the largest change in expression (<span class="html-italic">p</span> &lt; 0.004) 3 h after the end of the long-duration, low-force exercise with a 1 Hz stimulation frequency in people with SCI. Principal component biplots showing the grouping between the exercised and non-exercised control limbs for the first and second principal components of all genes 3 h after the long-duration, low-force exercise with a 3 Hz stimulation frequency (<b>C</b>) and a 1 Hz stimulation frequency (<b>D</b>).</p>
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<p>EnrichR expression signature after 3 Hz electrically induced exercise. A total of 87 Reactome pathways across 13 domains were found to be positively enriched using the EnrichR algorithm after 3 Hz electrically induced exercise. A total of 18 Reactome pathways across 7 domains were found to be negatively enriched using the GSEA algorithm after 3 Hz electrically induced exercise. A cutoff of 0.05 for the calculated <span class="html-italic">p</span>-value was used. (<b>A</b>) A chord plot showing the relationship between the enriched Reactome domains and the genes that were up-regulated (red) or down-regulated (blue) 3 h after the 3 Hz exercise. (<b>B</b>) A bar plot showing the number of pathways enriched within each domain pathway.</p>
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<p>GSEA expression signature after 3 Hz electrically induced exercise. A total of 168 Reactome pathways across 15 domains were found to be positively enriched using the GSEA algorithm after 3 Hz electrically induced exercise. A total of 57 Reactome pathways across 13 domains were found to be negatively enriched using the GSEA algorithm after 3 Hz electrically induced exercise. A cutoff of 0.05 for the calculated <span class="html-italic">p</span>-value was used. (<b>A</b>) A chord plot showing the relationship between the enriched Reactome domains and the genes that were up-regulated (red) or down-regulated (blue) 3 h after the 3 Hz exercise. (<b>B</b>) A bar plot showing the number of pathways enriched within each domain pathway.</p>
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<p>A priori gene expression fold-change. (<b>A</b>) There was a significant increase in the expression of PGC1α after the 3 Hz exercise (FDR = 0.01) relative to the control (unexercised) limb, but there was not a significant increase of PGC1α after the 1 Hz exercise (FDR = 0.68) relative to the control (unexercised) limb. (<b>B</b>) There was a significant increase in the expression of NR4A3 after the 3 Hz exercise (FDR = 0.0027) relative to the control (unexercised) limb, but there was not a significant increase of NR4A3 after the 1 Hz exercise (FDR = 0.65) relative to the control (unexercised) limb. (<b>C</b>) There was a significant increase in the expression of ABRA after the 3 Hz exercise (FDR = 0.015) relative to the control (unexercised) limb, but there was not a significant increase of ABRA after the 1 Hz exercise (FDR = 0.68) relative to the control (unexercised) limb. (<b>D</b>) There was a significant increase in the expression of IRS2 after the 3 Hz exercise (FDR = 0.0021) relative to the control (unexercised) limb, but there was not a significant increase of IRS2 after the 1 Hz exercise (FDR = 1.0) relative to the control (unexercised) limb. (<b>E</b>) There was a significant decrease in the expression of MSTN after the 3 Hz exercise (FDR = 0.015) relative to the control (unexercised) limb, but there was not a significant decrease of MSTN after the 1 Hz exercise (FDR = 1.0) relative to the control (unexercised) limb.</p>
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<p>Heat map of post-exercise DNA methylation. A heat map of the 25 most hypermethylated (red) and 25 most hypomethylated (blue) CpG probes and corresponding genes 3 h after the end of a long-duration, low-force 3 Hz electrically induced exercise (<b>A</b>) and 1 Hz electrically induced exercise (<b>B</b>) for people with a spinal cord injury. While probes reached a significant differential level using a FDR cutoff of 0.05, these probes did have a differential methylation below an uncorrected <span class="html-italic">p</span>-value of 0.001 between the exercised and non-exercised (control) limbs.</p>
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<p>Epigenetic age correlations. (<b>A</b>) There were strong correlations between the chronological age and estimated epigenetic age for the 3 Hz (R<sup>2</sup> = 0.70, <span class="html-italic">p</span> = 0.010) and the 1 Hz (R<sup>2</sup> = 0.89, <span class="html-italic">p</span> = 0.005) exercise sessions as well as when the exercise sessions were collapsed (R<sup>2</sup> = 0.72, <span class="html-italic">p</span> &lt; 0.001). (<b>B</b>) There were strong correlations between the number of years post injury (YPI) and estimated epigenetic age for the 3 Hz (R<sup>2</sup> = 0.89, <span class="html-italic">p</span> = 0.005) and the 1 Hz (R<sup>2</sup> = 0.50, <span class="html-italic">p</span> = 0.12) exercise sessions as well as when the exercise sessions were collapsed (R<sup>2</sup> = 0.55, <span class="html-italic">p</span> = 0.002).</p>
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<p>Relative methylation levels for a selection of a priori CpG probes. While no probe reached statistical significance using an FDR correction, some probes did demonstrate a subtle difference using the unadjusted <span class="html-italic">p</span>-value. After the 3 Hz electrically induced exercise, the probes for (<b>A</b>) PGC-1α (cg14757717; <span class="html-italic">p</span> = 0.004; FDR = 0.26), (<b>B</b>) NR4A3 (cg04897621; <span class="html-italic">p</span> = 0.007; FDR = 0.27), and (<b>C</b>) ABRA (cg14747011; <span class="html-italic">p</span> = 0.14; FDR = 0.44) were slightly hypermethylated in the exercised limb compared to the control limb, while the probes for (<b>D</b>) IRS2 (cg08510264; <span class="html-italic">p</span> = 0.016; FDR = 0.29) and (<b>E</b>)MSTN (cg2452886; <span class="html-italic">p</span> = 0.08; FDR = 0.38) appeared to be hypomethylated in the exercised limb relative to the control limb. After the 1 Hz electrically induced exercise, none of the a priori probes were found to differ between the exercised and control limbs.</p>
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<p>Study design and example of force response from our previous report [<a href="#B27-ijms-25-10189" class="html-bibr">27</a>]. Note that for every stimulus pulse delivered during the 1 Hz exercise, three stimulus pulses were delivered during the 3 Hz exercise. The number of stimulus pulses delivered to the muscle was kept constant for the 1 Hz and 3 Hz exercise sessions; therefore, the time required to complete the 1 Hz exercise session (~3 h) was three times longer than the time required to complete the 3 Hz exercise session (~1 h).</p>
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25 pages, 6293 KiB  
Article
Activation of GABABR Attenuates Intestinal Inflammation by Reducing Oxidative Stress through Modulating the TLR4/MyD88/NLRP3 Pathway and Gut Microbiota Abundance
by Ziteng Deng, Dan Li, Lu Wang, Jing Lan, Jiaqi Wang and Yunfei Ma
Antioxidants 2024, 13(9), 1141; https://doi.org/10.3390/antiox13091141 - 21 Sep 2024
Viewed by 732
Abstract
Oxidative stress emerges as a prominent factor in the onset and progression of intestinal inflammation, primarily due to its critical role in damaging cells and tissues. GABAergic signaling is important in the occurrence and development of various intestinal disorders, yet its effect on [...] Read more.
Oxidative stress emerges as a prominent factor in the onset and progression of intestinal inflammation, primarily due to its critical role in damaging cells and tissues. GABAergic signaling is important in the occurrence and development of various intestinal disorders, yet its effect on oxidative stress remains unclear. We attempted to assess whether GABAergic signaling participated in the regulation of oxidative stress during enteritis. The results showed that lipopolysaccharide (LPS) significantly decreased γ-aminobutyric acid (GABA) levels in the ileal tissues of mice. Interestingly, the application of GABA significantly repressed the shedding of intestinal mucosal epithelial cells and inflammatory cell infiltration, inhibited the expressions of proinflammatory factors, including granulocyte colony-stimulating factor and granulocyte-macrophage colony stimulating factor, and enhanced the levels of anti-inflammatory cytokines interleukin (IL)-4 and IL-10, indicating that GABA could alleviate enteritis in mice. This observation was further supported by transcriptome sequencing, revealing a total of 271 differentially expressed genes, which exhibited a marked enrichment of inflammatory and immune-related pathways, alongside a prominent enhancement of GABA B receptor (GABABR) signaling following GABA administration. Effectively, Baclofen pretreatment alleviated intestinal mucosal damage in LPS-induced mice, suppressed proinflammatory cytokines IL-1β, IL-6, and tumor necrosis factor alpha expressions, and boosted total antioxidant capacity, superoxide dismutase (SOD), and glutathione (GSH) levels. Moreover, Baclofen notably enhanced the viability of LPS-stimulated IPEC-J2 cells, contracted the proinflammatory secretion factors, and reinforced SOD, GSH, and catalase levels, emphasizing the anti-inflammatory and antioxidant effects associated with GABABR activation. Mechanistically, Baclofen restrained the mRNA and protein levels of toll-like receptor 4 (TLR4), myeloid differentiation factor 88 (MyD88), nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain-containing 3 (NLRP3), and inducible nitric oxide synthase, while elevating nuclear factor erythroid 2-related factor 2 and heme oxygenase-1 in both mice and IPEC-J2 cells, indicating that activating GABABR strengthened antioxidant abilities by interrupting the TLR4/MyD88/NLRP3 pathway. Furthermore, 16S rDNA analysis demonstrated that Baclofen increased the relative abundance of probiotic, particularly Lactobacillus, renowned for its antioxidant properties, while reducing the relative richness of harmful bacteria, predominantly Enterobacteriaceae, suggesting that GABABR signaling may have contributed to reversing intestinal flora imbalances to relieve oxidative stress in LPS-induced mice. Our study identified previously unappreciated roles for GABABR signaling in constricting oxidative stress to attenuate enteritis, thus offering novel insights for the treatment of intestinal inflammation. Full article
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<p>The changes of GABA level during LPS-induced intestinal inflammation. (<b>A</b>) The amount of weight loss was quantified for both the control (CON) and LPS-treated (LPS) groups at various time points. (<b>B</b>) Representative images display H&amp;E-stained cross-sections of the ileum from both the CON and LPS groups at specific time intervals, with a 50 μm scale bar provided. (<b>C</b>–<b>E</b>) The expression levels of IL-1β, IL-6, and TNF-α mRNAs were determined through qRT-PCR analysis of mouse intestinal tissue samples collected at different times. GAPDH served as the reference gene for data normalization, and the relative fold changes in expression compared to the CON group were computed using the 2<sup>−ΔΔCT</sup> method. (<b>F</b>) The levels of GABA in ileal tissue were measured using UHPLC-MS/MS at 3, 6, and 12 h post-treatment. The presented data are the mean ± SD. * indicates that the difference between the CON and the LPS is significant (<span class="html-italic">p</span> &lt; 0.05). ** or *** indicates that the difference between the CON and the LPS is extremely significant (<span class="html-italic">p</span> &lt; 0.01 or <span class="html-italic">p</span> &lt; 0.001).</p>
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<p>GABA attenuates intestinal mucosa injury by improving inflammatory factor expression in LPS-induced mice. (<b>A</b>) To determine weight loss, the body weights of mice were measured and compared to their initial weights at the commencement of LPS treatment. The results are presented for untreated mice (CON), mice subjected to LPS treatment (LPS), and mice treated with GABA following LPS induction (LPS + GABA). (<b>B</b>) Ileal tissues from various groups, including the control (CON), mice treated solely with GABA (GABA), mice treated with LPS, and mice treated with both LPS and GABA, were stained with H&amp;E. The scale bar represents 50 μm. (<b>C</b>–<b>Y</b>) Inflammatory cytokines in ileal tissues were analyzed using Luminex liquid suspension chip detection. The data are presented as the mean ± SD. Statistical significance is denoted as follows: * represents a significant difference between the CON and LPS groups (<span class="html-italic">p</span> &lt; 0.05), while ** or *** signifies an extremely significant difference (<span class="html-italic">p</span> &lt; 0.01 or <span class="html-italic">p</span> &lt; 0.001). Differences between the LPS and LPS + GABA groups are marked with # for significant (<span class="html-italic">p</span> &lt; 0.05) and ## or ### for extremely significant differences (<span class="html-italic">p</span> &lt; 0.01 or <span class="html-italic">p</span> &lt; 0.001).</p>
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<p>Transcriptome analysis of LPS-induced mice after GABA administration. (<b>A</b>) Total number of up- or downregulated genes of significant DEGs. (<b>B</b>,<b>C</b>) Volcano plot illustrating differentially regulated gene expression from RNA-seq analysis between LPS and CON, GABA and LPS, respectively. Genes upregulated and downregulated are shown in red and green, respectively. (<b>D</b>,<b>E</b>) Differential gene expression heat maps of mice between LPS and CON, GABA and LPS, respectively. (<b>F</b>,<b>G</b>) GO analysis showed the top 30 of enriched signaling in ileal tissues between LPS and CON, GABA and LPS, respectively. (<b>H</b>,<b>I</b>) KEGG analysis showed the top 30 of enriched signaling in ileal tissues between LPS and CON, GABA and LPS, respectively. CON: control group; LPS: LPS group; GABA: LPS + GABA treatment group.</p>
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<p>Transcriptome analysis of LPS-induced mice after GABA administration. (<b>A</b>) Total number of up- or downregulated genes of significant DEGs. (<b>B</b>,<b>C</b>) Volcano plot illustrating differentially regulated gene expression from RNA-seq analysis between LPS and CON, GABA and LPS, respectively. Genes upregulated and downregulated are shown in red and green, respectively. (<b>D</b>,<b>E</b>) Differential gene expression heat maps of mice between LPS and CON, GABA and LPS, respectively. (<b>F</b>,<b>G</b>) GO analysis showed the top 30 of enriched signaling in ileal tissues between LPS and CON, GABA and LPS, respectively. (<b>H</b>,<b>I</b>) KEGG analysis showed the top 30 of enriched signaling in ileal tissues between LPS and CON, GABA and LPS, respectively. CON: control group; LPS: LPS group; GABA: LPS + GABA treatment group.</p>
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<p>Transcriptome analysis of LPS-induced mice after GABA administration. (<b>A</b>) Total number of up- or downregulated genes of significant DEGs. (<b>B</b>,<b>C</b>) Volcano plot illustrating differentially regulated gene expression from RNA-seq analysis between LPS and CON, GABA and LPS, respectively. Genes upregulated and downregulated are shown in red and green, respectively. (<b>D</b>,<b>E</b>) Differential gene expression heat maps of mice between LPS and CON, GABA and LPS, respectively. (<b>F</b>,<b>G</b>) GO analysis showed the top 30 of enriched signaling in ileal tissues between LPS and CON, GABA and LPS, respectively. (<b>H</b>,<b>I</b>) KEGG analysis showed the top 30 of enriched signaling in ileal tissues between LPS and CON, GABA and LPS, respectively. CON: control group; LPS: LPS group; GABA: LPS + GABA treatment group.</p>
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<p>GABA<sub>B</sub>R activation could reduce the levels of inflammatory cytokine and oxidative stress in LPS-induced mice. (<b>A</b>) To assess weight loss, the body weights of mice were measured and compared to their weights recorded at the start of LPS treatment. The presented results cover untreated mice (CON), mice treated with LPS, and mice treated with Baclofen following LPS induction (LPS + Baclofen). (<b>B</b>) Ileal tissues from the CON, LPS, and LPS + Baclofen mice groups underwent H&amp;E staining. The scale bar represents 50 μm. (<b>C</b>–<b>E</b>) qRT-PCR was employed to determine the mRNA levels of IL-1β, IL-6, and TNF-α, with GAPDH serving as the reference gene. The average fold changes compared to the CON group were calculated using the 2<sup>−ΔΔCT</sup> method. (<b>F</b>–<b>H</b>) The graphs depict the expression levels of T-AOC, SOD, and GSH in ileal tissues. Data are presented as mean ± SEM. Statistical significance is denoted by asterisks: * for significant differences between CON and LPS (<span class="html-italic">p</span> &lt; 0.05), ** or *** for extremely significant differences (<span class="html-italic">p</span> &lt; 0.01 or <span class="html-italic">p</span> &lt; 0.001). # indicate significant differences between the LPS and LPS + Baclofen groups, with # for significant (<span class="html-italic">p</span> &lt; 0.05) and ## or ### for extremely significant differences (<span class="html-italic">p</span> &lt; 0.01 or <span class="html-italic">p</span> &lt; 0.001).</p>
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<p>GABA<sub>B</sub>R activation could reduce the levels of inflammatory cytokine and oxidative stress in IPEC-J2 cells. (<b>A</b>–<b>C</b>) qRT-PCR was utilized to determine the mRNA levels of IL-1β, IL-6, and TNF-α in IPEC-J2 cells treated with varying concentrations of LPS (0.1, 1, 10, 50 mg/mL). (<b>D</b>–<b>F</b>) The mRNA expression of IL-1β, IL-6, and TNF-α was assessed by qRT-PCR at different time intervals following LPS administration to IPEC-J2 cells. (<b>G</b>) Cultured IPEC-J2 cells were subjected to single immunofluorescence staining for GABA<sub>B</sub>R. The scale bar represents 50 μm. (<b>H</b>,<b>I</b>) Western blot (WB) analysis was conducted to examine the expression of GABA<sub>B</sub>R in IPEC-J2 cells. (<b>J</b>) Cell viability assessments were performed on IPEC-J2 cells in the CON, LPS, and LPS + Baclofen groups. (<b>K</b>–<b>M</b>) The mRNA levels of IL-1β, IL-6, and TNF-α were measured by qRT-PCR in the CON, LPS, and LPS + Baclofen groups. (<b>N</b>–<b>P</b>) The levels of SOD, GSH, and CAT were determined in the same groups. For qRT-PCR, GAPDH was used as the reference gene, and fold changes relative to the CON group were calculated using the 2<sup>−ΔΔCT</sup> method. For WB, protein expression was normalized against β-actin. Data are presented as mean ± SEM. Statistical significance is denoted by asterisks: * for significant differences between CON and LPS (<span class="html-italic">p</span> &lt; 0.05), ** or *** for extremely significant differences (<span class="html-italic">p</span> &lt; 0.01 or <span class="html-italic">p</span> &lt; 0.001). # indicate significant differences between the LPS and LPS + Baclofen groups, with # for significant (<span class="html-italic">p</span> &lt; 0.05) and ## or ### for extremely significant differences (<span class="html-italic">p</span> &lt; 0.01 or <span class="html-italic">p</span> &lt; 0.001).</p>
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<p>GABA<sub>B</sub>R activation could ameliorate oxidative stress by inhibiting TLR4/MyD88/NLRP3 in vivo and in vitro. (<b>A</b>–<b>D</b>) WB analysis of the expression of NRF2, HO-1, and iNOS in ileal tissues of mice. (<b>E</b>–<b>H</b>) WB analysis of the expression of NRF2, HO-1, and iNOS in IPEC-J2 cells. (<b>I</b>–<b>L</b>) WB analysis of the expression of TLR4, MyD88, and NLRP3 in ileal tissues of mice. (<b>M</b>–<b>P</b>) WB analysis of the expression of TLR4, MyD88, and NLRP3 in IPEC-J2 cells. For WB, protein expression was normalized against β-actin. Data are presented as mean ± SEM. Statistical significance is denoted by asterisks: * for significant differences between CON and LPS (<span class="html-italic">p</span> &lt; 0.05), ** or *** for extremely significant differences (<span class="html-italic">p</span> &lt; 0.01 or <span class="html-italic">p</span> &lt; 0.001). # indicate significant differences between the LPS and LPS + Baclofen groups, with # for significant (<span class="html-italic">p</span> &lt; 0.05) and ## or ### for extremely significant differences (<span class="html-italic">p</span> &lt; 0.01 or <span class="html-italic">p</span> &lt; 0.001).</p>
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<p>Diversity indexes of microbiota in the mice intestine. (<b>A</b>) Venn diagram of the number of OTUs. (<b>B</b>) OTU number histogram. (<b>C</b>–<b>F</b>) α-diversity analyzed by ACE, Chao1, Shannon and Simpson indices. (<b>G</b>–<b>J</b>) Principal component, principal coordinates, NMDS and sample clustering heat map analyses of gut microbiota of each group. CON: control group; LPS: LPS group; Baclofen: LPS + Baclofen treatment group.</p>
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<p>Analysis of the microbial composition. (<b>A</b>–<b>F</b>) 16S rDNA sequencing results of relative abundance of intestinal bacteria in mice at phylum, class, order, family, genus, and species levels in each group. (<b>G</b>–<b>L</b>) Cluster heatmap of species abundance in each group. CON: control group; LPS: LPS group; Baclofen: LPS + Baclofen treatment group.</p>
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<p>Analysis of the microbial composition. (<b>A</b>–<b>F</b>) 16S rDNA sequencing results of relative abundance of intestinal bacteria in mice at phylum, class, order, family, genus, and species levels in each group. (<b>G</b>–<b>L</b>) Cluster heatmap of species abundance in each group. CON: control group; LPS: LPS group; Baclofen: LPS + Baclofen treatment group.</p>
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30 pages, 1089 KiB  
Article
Sustainable Operation and Management of a Dynamic Supply Chain under the Framework of a Community with a Shared Future for Mankind
by Lihua Hu, Chengjiu Wang and Tao Fan
Sustainability 2024, 16(17), 7780; https://doi.org/10.3390/su16177780 - 6 Sep 2024
Viewed by 606
Abstract
The values of a community with a shared future for mankind include the views of common interests, sustainable development, and global governance. This article will fully consider introducing the value concept of a community with a shared future into the operation and management [...] Read more.
The values of a community with a shared future for mankind include the views of common interests, sustainable development, and global governance. This article will fully consider introducing the value concept of a community with a shared future into the operation and management of dynamic supply chains. Based on the optimal information fusion mechanism of artificial intelligence, this article aims to examine the operation and management of dynamic supply chains within the framework of a community with a shared future for mankind. The core idea is to consider the common interests among enterprises, establish a global collaborative operation concept for upstream, midstream, and downstream enterprises, and achieve the goal of sustainable development. Firstly, a type of composite dynamic supply chain model is considered, in which the total inventory of each node in the supply chain is further subdivided into raw material inventory and finished product inventory. At the same time, we have considered factors such as the signing of procurement contracts between core enterprises and upstream enterprises, as well as the signing of supply contracts between core enterprises and downstream enterprises. Secondly, the static and dynamic monitoring information of the enterprise has been established. We use steady-state Kalman filtering theory to obtain dynamic reference signals for upstream enterprises, core enterprises, and downstream enterprises. Based on the optimal information fusion processing mechanism of artificial intelligence, the coefficient weighting method is used to obtain the optimal fusion signals of upstream enterprises, core enterprises, and downstream enterprises. Once again, through high-quality switching strategies, enterprises can achieve in-order switching, improve production efficiency, reduce downtime, enhance their competitiveness and responsiveness, and transform the dynamic supply chain, including order switching, into a discrete-time linear switching system for processing. Fourthly, sufficient conditions, robustness analysis results, and inventory control criteria for the solvability of dynamic supply chain H with order switching are provided. Finally, data analysis is conducted using historical order information from three fruit companies to verify the validity and feasibility of the conclusions in this article and to improve the performance of the dynamic supply chain system. The research findings of this article enrich the exploration of the operation and management of dynamic supply chains and the construction of a community with a shared future for mankind. Full article
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<p>The local topology structure of a composite dynamic supply chain network.</p>
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<p>The periodic iteration process of dynamic supply chain networks.</p>
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<p>Artificial intelligence optimal information fusion.</p>
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<p>The operational effectiveness of Chongqing Hongjiu Fruit Co., Ltd.</p>
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<p>The operational effectiveness of Wuhan Golden Orchard Trading Co., Ltd.</p>
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<p>The operational effectiveness of Hangzhou Xianfeng Fruit Co., Ltd.</p>
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12 pages, 309 KiB  
Article
Weak ψ-Contractions on Directed Graphs with Applications to Integral Equations
by Doaa Filali, Mohammad Dilshad and Mohammad Akram
Mathematics 2024, 12(17), 2675; https://doi.org/10.3390/math12172675 - 28 Aug 2024
Viewed by 437
Abstract
This article deals with a few outcomes ensuring the fixed points of a weak (G,ψ)-contraction map of metric spaces comprised with a reflexive and transitive digraph G. To validate our findings, we furnish several examples. The findings [...] Read more.
This article deals with a few outcomes ensuring the fixed points of a weak (G,ψ)-contraction map of metric spaces comprised with a reflexive and transitive digraph G. To validate our findings, we furnish several examples. The findings we obtain enable us to seek out the unique solution of a nonlinear integral equation. The outcomes presented herewith sharpen, subsume, unify, improve, enrich, and compile a number of existing theorems. Full article
15 pages, 8816 KiB  
Article
The Potential Mechanisms of Catechins in Tea for Anti-Hypertension: An Integration of Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation
by Yanming Tuo, Xiaofeng Lu, Fang Tao, Marat Tukhvatshin, Fumin Xiang, Xi Wang, Yutao Shi, Jinke Lin and Yunfei Hu
Foods 2024, 13(17), 2685; https://doi.org/10.3390/foods13172685 - 26 Aug 2024
Viewed by 1111
Abstract
Catechins, a class of polyphenolic compounds found in tea, have attracted significant attention due to their numerous health benefits, particularly for the treatment and protection of hypertension. However, the potential targets and mechanisms of action of catechins in combating hypertension remain unclear. This [...] Read more.
Catechins, a class of polyphenolic compounds found in tea, have attracted significant attention due to their numerous health benefits, particularly for the treatment and protection of hypertension. However, the potential targets and mechanisms of action of catechins in combating hypertension remain unclear. This study systematically investigates the anti-hypertensive mechanisms of tea catechins using network pharmacology, molecular docking, and molecular dynamics simulation techniques. The results indicate that 23 potential anti-hypertensive targets for eight catechin components were predicted through public databases. The analysis of protein–protein interaction (PPI) identified three key targets (MMP9, BCL2, and HIF1A). KEGG pathway and GO enrichment analyses revealed that these key targets play significant roles in regulating vascular smooth muscle contraction, promoting angiogenesis, and mediating vascular endothelial growth factor receptor signaling. The molecular docking results demonstrate that the key targets (MMP9, BCL2, and HIF1A) effectively bind with catechin components (CG, GCG, ECG, and EGCG) through hydrogen bonds and hydrophobic interactions. Molecular dynamics simulations further confirmed the stability of the binding between catechins and the targets. This study systematically elucidates the potential mechanisms by which tea catechins treat anti-hypertension and provides a theoretical basis for the development and application of tea catechins as functional additives for the prevention of hypertension. Full article
(This article belongs to the Collection Advances in Tea Chemistry)
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<p>Network pharmacology regulatory mechanisms of catechins in anti-hypertension.</p>
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<p>Structural formulas of eight catechin components.</p>
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<p>(<b>A</b>) Construction of the tea–catechin–targets network. (<b>B</b>) Venn diagram of predicted catechin targets and hypertension-related targets. (<b>C</b>) PPI network of intersecting targets. (<b>D</b>) tea–catechin–targets–hypertension network diagram.</p>
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<p>(<b>A</b>) KEGG pathway analysis of key targets. (<b>B</b>) GO enrichment analysis of key targets.</p>
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<p>Molecular docking of main catechin components with MMP9, HIF1A, and BCL2. (<b>A</b>) Interaction diagram between MMP9 and gallocatechin gallate (GCG). (<b>B</b>) Interaction diagram between MMP9 and catechin gallate (CG). (<b>C</b>) Interaction diagram between HIF1A and epicatechin gallate (ECG). (<b>D</b>) Interaction diagram between BCL2 and epigallocatechin gallate (EGCG).</p>
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<p>(<b>A</b>) RMSD values of the four complexes. (<b>B</b>) Radius of gyration (Rg) values of the four complexes. (<b>C</b>) Solvent-accessible surface area (SASA) values of the four complexes. (<b>D</b>) Number of hydrogen bonds in the four complexes. (<b>E</b>) Binding free energies (ΔG<sub>bind</sub>) of the four complexes.</p>
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14 pages, 4079 KiB  
Article
Identification and Characterization of Extrachromosomal Circular DNA in Slimming Grass Carp
by Haobin He, Zihan Gao, Zehua Hu, Guanyu Liang, Yanhua Huang, Meng Zhou, Rishen Liang and Kai Zhang
Biomolecules 2024, 14(9), 1045; https://doi.org/10.3390/biom14091045 - 23 Aug 2024
Viewed by 512
Abstract
Slimming grass carp is a commercial variety with good body form and meat quality, which is cultured by starving common grass carp in a clean flowing water environment. Compared to common grass carp, slimming grass carp has a far higher economic value. Until [...] Read more.
Slimming grass carp is a commercial variety with good body form and meat quality, which is cultured by starving common grass carp in a clean flowing water environment. Compared to common grass carp, slimming grass carp has a far higher economic value. Until now, no molecular study has concentrated on the regulation mechanism of the muscle characteristics of slimming grass carp. This study first reported the gene expression profile of the muscle characteristics of slimming grass carp based on the level of extrachromosomal circular DNAs (eccDNAs). EccDNAs are double-stranded circular DNAs derived from genomic DNAs and play crucial roles in the functional regulation of a wide range of biological processes, none of which have been shown to occur in fish. Here, muscle eccDNAs from slimming grass carp and common grass carp were both generally sequenced, and the information, as well as the expression profile of eccDNAs, were compared and analysed. The findings reveal that 82,238 and 25,857 eccDNAs were detected from slimming grass carp and common grass carp, respectively. The length distribution of eccDNAs was in the range of 1~1000 bp, with two peaks at about 200 bp and 400 bp. When the expression profiles of eccDNAs between slimming grass carp and common grass carp were compared, 3523 up-regulated and 175 down-regulated eccDNAs were found. Enrichment analysis showed that these eccDNA genes were correlated with cellular structure and response, cell immunology, enzyme activity, etc. Certain differentially expressed eccDNAs involved in muscle characteristics were detected, which include myosin heavy chain, myosin light chain, muscle segment homeobox C, calsequestrin, calmodulin, etc., among which the majority of genes were linked to muscle structure and contraction. This indicates that during the process of cultivating from common grass carp to slimming grass carp, the treatment primarily affected muscle structure and contraction, making the meat quality of slimming grass carp different from that of common grass carp. This result provides molecular evidence and new insights by which to elucidate the regulating mechanism of muscle phenotypic characterisation in slimming grass carp and other fish. Full article
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<p>Electrophoresis results in the amplification of <span class="html-italic">COX3</span> (<b>A</b>) and <span class="html-italic">Nudt6</span> (<b>B</b>) genes. Numbers 1~5 represent slimming grass carp samples; numbers 6~10 represent common grass carp samples; PC represents the positive control sample.</p>
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<p>Electrophoresis results in the purification of eccDNAs after RCA reaction (<b>A</b>) and enzyme digestion verification (<b>B</b>). Numbers 1~5 represent samples of the slimming grass carp; 6~10 represent samples of the common grass carp.</p>
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<p>The lengths distribution of eccDNAs in slimming grass carp (<b>A</b>) and common grass carp (<b>B</b>).</p>
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<p>The distribution of eccDNAs in different chromosomes.</p>
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<p>The GC content of eccDNA in slimming grass carp (<b>A</b>–<b>C</b>) and common grass carp (<b>D</b>–<b>F</b>).</p>
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<p>GO analysis of differentially expressed eccDNA-associated mRNAs: (<b>A</b>–<b>C</b>) refer to the GO enrichment of up-regulated eccDNAs in slimming grass carp in comparison to common grass carp; (<b>D</b>–<b>F</b>) refer to the GO enrichment of down-regulated genes in slimming grass carp in comparison to common grass carp.</p>
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<p>Pathway analysis of eccDNA-associated mRNAs: (<b>A</b>,<b>B</b>) refer to the down-regulated pathways of eccDNAs; (<b>C</b>,<b>D</b>) refer to the up-regulated pathways of eccDNAs.</p>
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20 pages, 332 KiB  
Article
Enriched Z-Contractions and Fixed-Point Results with Applications to IFS
by Ibrahim Alraddadi, Muhammad Din, Umar Ishtiaq, Mohammad Akram and Ioannis K. Argyros
Axioms 2024, 13(8), 562; https://doi.org/10.3390/axioms13080562 - 19 Aug 2024
Viewed by 420
Abstract
In this manuscript, we initiate a large class of enriched (d,Z)-Z-contractions defined on Banach spaces and prove the existence and uniqueness of the fixed point of these contractions. We also provide an example to support our [...] Read more.
In this manuscript, we initiate a large class of enriched (d,Z)-Z-contractions defined on Banach spaces and prove the existence and uniqueness of the fixed point of these contractions. We also provide an example to support our results and give an existence condition for the uniqueness of the solution to the integral equation. The results provided in the manuscript extend, generalize, and modify the existence results. Our research introduces novel fixed-point results under various contractive conditions. Furthermore, we discuss the iterated function system associated with enriched (d,Z)-Z-contractions in Banach spaces and define the enriched Z-Hutchinson operator. A result regarding the convergence of Krasnoselskii’s iteration method and the uniqueness of the attractor via enriched (d,Z)-Z-contractions is also established. Our discoveries not only confirm but also significantly build upon and broaden several established findings in the current body of literature. Full article
(This article belongs to the Special Issue Trends in Fixed Point Theory and Fractional Calculus)
21 pages, 1827 KiB  
Article
Leader and Employee Behavioral Decision-Making in Construction and Demolition Waste Recycling Projects under Psychological Contract Theory
by Peiao Gao, Sijing Liu, Lianghui Zeng, Jie Peng, Yuhan Wang, Hao Zhang and Xingwei Li
Buildings 2024, 14(8), 2519; https://doi.org/10.3390/buildings14082519 - 15 Aug 2024
Cited by 1 | Viewed by 684
Abstract
Although the beneficial role of enterprises in the management of construction and demolition waste (CDW) should not be overlooked, existing relevant studies have neglected to address the specific effects of the behavioral decisions of leaders and employees within enterprises in CDW recycling projects. [...] Read more.
Although the beneficial role of enterprises in the management of construction and demolition waste (CDW) should not be overlooked, existing relevant studies have neglected to address the specific effects of the behavioral decisions of leaders and employees within enterprises in CDW recycling projects. This study creatively introduces psychological contract theory into the field of CDW management and aims to reveal the mechanism of recycling participation behaviors between leaders and employees in CDW recycling projects. Using the Stackelberg game method, a model consisting of leaders and employees in the construction enterprise was constructed to analyze the optimal decision-making of the enterprise under two cases of whether or not the employees contributed additional effort. The conclusions of this study are as follows: (1) The profits of construction enterprise leaders are always positively correlated with the degree of employee additional effort. Unlike the case of leaders, the effect of additional effort on employee profits hinges on the coefficient of employee additional effort. When the coefficient of employee additional effort is below the threshold, excessive additional effort can negatively impact their own profits. When the additional effort coefficient exceeds the threshold, the employee profits are positively related to the degree of additional effort. (2) Similar to the change in employee profits, the change in the total profit of the construction enterprise with the degree of additional effort is influenced by the additional effort coefficient. However, as the additional effort coefficient increases, the total profit of the enterprise shows a significant increase before employee profits. This study enriches the theoretical study of psychological contracts and provides guidance for decision-making between leaders and employees in the management of CDW recycling projects. Full article
(This article belongs to the Section Construction Management, and Computers & Digitization)
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<p>The research system framework.</p>
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<p>A diagram of the relationships between leaders and employees in construction enterprises.</p>
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<p>The effect of additional effort on leader and employee profits. In particular, subfigures (<b>a</b>,<b>b</b>) represent the change in profits when the additional effort coefficient is below and above the threshold, respectively.</p>
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<p>The effect of additional effort on the profit of a construction enterprise. In particular, subfigures (<b>a</b>,<b>b</b>) represent the change in profits when the additional effort coefficient is below and above the threshold, respectively.</p>
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<p>The effect of key parameters <math display="inline"><semantics> <mi>μ</mi> </semantics></math>, <math display="inline"><semantics> <mi>β</mi> </semantics></math>, <math display="inline"><semantics> <mi>τ</mi> </semantics></math>, <math display="inline"><semantics> <mi>k</mi> </semantics></math> on the profits of leaders and employees. In particular, subfigures (<b>a</b>–<b>d</b>) represent the effect of the recycling rate, the basic effort coefficient, the additional effort coefficient, and the environmental protection sensitivity coefficient on profits, respectively.</p>
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23 pages, 3750 KiB  
Article
Physical Properties of Cellulose Derivative-Based Edible Films Elaborated with Liposomes Encapsulating Grape Seed Tannins
by Constanza Vidal, Johana Lopez-Polo and Fernando A. Osorio
Antioxidants 2024, 13(8), 989; https://doi.org/10.3390/antiox13080989 - 14 Aug 2024
Viewed by 600
Abstract
Combined use of edible films (EF) with nanoencapsulation systems could be an effective alternative for improving the films’ physical properties and maintaining bioactive compounds’ stability. This research work focuses on the combined use of EF of cellulose-derived biopolymers enriched with liposomes that encapsulate [...] Read more.
Combined use of edible films (EF) with nanoencapsulation systems could be an effective alternative for improving the films’ physical properties and maintaining bioactive compounds’ stability. This research work focuses on the combined use of EF of cellulose-derived biopolymers enriched with liposomes that encapsulate grape seed tannins and on the subsequent evaluation of the physical properties and wettability. Tannin-containing liposomal suspensions (TLS) showed 570.8 ± 6.0 nm particle size and 99% encapsulation efficiency. In vitro studies showed that the release of tannins from liposomes was slower than that of free tannins, reaching a maximum release of catechin of 0.13 ± 0.01%, epicatechin of 0.57 ± 0.01%, and gallic acid of 3.90 ± 0.001% over a 144 h period. Adding liposomes to biopolymer matrices resulted in significant decrease (p < 0.05) of density, surface tension, tensile strength, elongation percentage, and elastic modulus in comparison to the control, obtaining films with greater flexibility and lower breaking strength. Incorporating TLS into EF formulations resulted in partially wetting the hydrophobic surface, reducing adhesion and cohesion compared to EF without liposomes. Results indicate that the presence of liposomes improves films’ physical and wettability properties, causing them to extend and not contract when applied to hydrophobic food surfaces. Full article
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<p>Transmission electron microscopy (TEM) microstructure (<b>A</b>,<b>B</b>) of TLS and (<b>C</b>) LS, magnified 17,500×.</p>
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<p>In vitro release of tannins from liposomes TLS (●) and tannins from free suspensions FTS (○) for 144 h by quantifying the cumulative release (%) of (<b>A</b>) catechin, (<b>B</b>) epicatechin and (<b>C</b>) gallic acid.</p>
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<p>Antioxidant activity and total phenolic compounds of TLS (●) and FTS (○) obtained with the (<b>A</b>) ABTS<sup>●+</sup>, (<b>B</b>) DPPH<sup>●</sup> and (<b>C</b>) TPC assays during in vitro tannin release.</p>
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<p>Contact angle between the hydrophobic surface and EF/TLS. (Letters a, b, c, d, and e indicate significant differences in concentrations between EF/TLS. Letters x and y indicate significant differences between HPMC/TLS and CMC/TLS).</p>
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<p>Images of the films produced from EF/TLS (<b>A</b>) and the preparation of EF/TLS formulations after 4 months (<b>B</b>).</p>
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16 pages, 1580 KiB  
Article
Utilizing Deep Neural Networks to Fill Gaps in Small Genomes
by Yu Chen, Gang Wang and Tianjiao Zhang
Int. J. Mol. Sci. 2024, 25(15), 8502; https://doi.org/10.3390/ijms25158502 - 4 Aug 2024
Viewed by 680
Abstract
With the widespread adoption of next-generation sequencing technologies, the speed and convenience of genome sequencing have significantly improved, and many biological genomes have been sequenced. However, during the assembly of small genomes, we still face a series of challenges, including repetitive fragments, inverted [...] Read more.
With the widespread adoption of next-generation sequencing technologies, the speed and convenience of genome sequencing have significantly improved, and many biological genomes have been sequenced. However, during the assembly of small genomes, we still face a series of challenges, including repetitive fragments, inverted repeats, low sequencing coverage, and the limitations of sequencing technologies. These challenges lead to unknown gaps in small genomes, hindering complete genome assembly. Although there are many existing assembly software options, they do not fully utilize the potential of artificial intelligence technologies, resulting in limited improvement in gap filling. Here, we propose a novel method, DLGapCloser, based on deep learning, aimed at assisting traditional tools in further filling gaps in small genomes. Firstly, we created four datasets based on the original genomes of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Neurospora crassa, and Micromonas pusilla. To further extract effective information from the gene sequences, we also added homologous genomes to enrich the datasets. Secondly, we proposed the DGCNet model, which effectively extracts features and learns context from sequences flanking gaps. Addressing issues with early pruning and high memory usage in the Beam Search algorithm, we developed a new prediction algorithm, Wave-Beam Search. This algorithm alternates between expansion and contraction phases, enhancing efficiency and accuracy. Experimental results showed that the Wave-Beam Search algorithm improved the gap-filling performance of assembly tools by 7.35%, 28.57%, 42.85%, and 8.33% on the original results. Finally, we established new gap-filling standards and created and implemented a novel evaluation method. Validation on the genomes of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Neurospora crassa, and Micromonas pusilla showed that DLGapCloser increased the number of filled gaps by 8.05%, 15.3%, 1.4%, and 7% compared to traditional assembly tools. Full article
(This article belongs to the Section Molecular Informatics)
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<p>Gap-filling improvements and effects on the draft assemblies. (<b>A</b>) shows the percentage of filled gaps for three tools across four datasets, evaluated using the Sealer evaluation standard; (<b>B</b>) shows the percentage of filled gaps for three tools across four datasets, evaluated using the DLGapCloser evaluation standard; (<b>C</b>) shows the percentage of completely filled gaps for three tools across four datasets, evaluated using the DLGapCloser evaluation standard; (<b>D</b>) shows the remaining number of N/n on the filled scaffolds after gap filling by the three tools.</p>
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<p>Visualization of various gap-filling results. A–F represent six types of gap-filling categories selected from the filling results. Each filling category is composed of four rows: The first row represents the reference gene sequence, and the remaining three rows represent the gene sequences filled by DLGapCloser, GapPredict, and Sealer, respectively.</p>
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<p>Quality of the gap-filled assemblies of various genomes using various tools. (<b>A</b>) shows the number of mismatches in the filling results of the three tools across four datasets using the QUAST tool; (<b>B</b>) shows the number of indels in the filling results of the three tools across four datasets using the QUAST tool; (<b>C</b>) shows the number of positions in the scaffolds (breakpoints) wherein the flanking sequences are combined at the wrong distance in the scaffold (causing a local misassembly) in the filling results of the three tools across four datasets using the QUAST tool; (<b>D</b>) shows the number of misassemblies at the scaffold level in the filling results of the three tools across four datasets using the QUAST tool.</p>
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<p>Schematic overview of the DLGapCloser algorithm. (<b>A</b>) Data processing; (<b>B</b>) DGCNet network learning and prediction combined with Wave-Beam Search algorithm; (<b>C</b>) Gap filling; (<b>D</b>) Result evaluation.</p>
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<p>A generic architecture of DGCNet. Consists of the encoding sequences part, the network architecture part (Convolutional Layer, Max-Pooling Layer, Bi-LSTM Layer, and Dense Layer), and the prediction part (Wave-Beam Search). The red letters represent newly generated gene sequences.</p>
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<p>Overview of the Wave-Beam search algorithm. The algorithm is divided into the Expand phase (Levels 1–3 and Levels 5–6) and the Shrink phase (Level 4 and Level 7). The two phases alternate, and the algorithm ends the prediction when the predicted length is reached.</p>
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12 pages, 327 KiB  
Article
Nonlinear Contractions Employing Digraphs and Comparison Functions with an Application to Singular Fractional Differential Equations
by Doaa Filali, Mohammad Dilshad and Mohammad Akram
Axioms 2024, 13(7), 477; https://doi.org/10.3390/axioms13070477 - 16 Jul 2024
Viewed by 511
Abstract
After the initiation of Jachymski’s contraction principle via digraph, the area of metric fixed point theory has attracted much attention. A number of outcomes on fixed points in the context of graph metric space employing various types of contractions have been investigated. The [...] Read more.
After the initiation of Jachymski’s contraction principle via digraph, the area of metric fixed point theory has attracted much attention. A number of outcomes on fixed points in the context of graph metric space employing various types of contractions have been investigated. The aim of this paper is to investigate some fixed point theorems for a class of nonlinear contractions in a metric space endued with a transitive digraph. The outcomes presented herewith improve, extend and enrich several existing results. Employing our findings, we describe the existence and uniqueness of a singular fractional boundary value problem. Full article
(This article belongs to the Special Issue Trends in Fixed Point Theory and Fractional Calculus)
15 pages, 647 KiB  
Article
Analyzing Convergence in Sequences of Uncountable Iterated Function Systems—Fractals and Associated Fractal Measures
by Ion Mierluș–Mazilu and Lucian Niță
Mathematics 2024, 12(13), 2106; https://doi.org/10.3390/math12132106 - 4 Jul 2024
Viewed by 461
Abstract
In this paper, we examine a sequence of uncountable iterated function systems (U.I.F.S.), where each term in the sequence is constructed from an uncountable collection of contraction mappings along with a linear and continuous operator. Each U.I.F.S. within the sequence is associated with [...] Read more.
In this paper, we examine a sequence of uncountable iterated function systems (U.I.F.S.), where each term in the sequence is constructed from an uncountable collection of contraction mappings along with a linear and continuous operator. Each U.I.F.S. within the sequence is associated with an attractor, which represents a set towards which the system evolves over time, a Markov-type operator that governs the probabilistic behavior of the system, and a fractal measure that describes the geometric and measure-theoretic properties of the attractor. Our study is centered on analyzing the convergence properties of these systems. Specifically, we investigate how the attractors and fractal measures of successive U.I.F.S. in the sequence approach their respective limits. By understanding the convergence behavior, we aim to provide insights into the stability and long-term behavior of such complex systems. This study contributes to the broader field of dynamical systems and fractal geometry by offering new perspectives on how uncountable iterated function systems evolve and stabilize. In this paper, we undertake a comprehensive examination of a sequence of uncountable iterated function systems (U.I.F.S.), each constructed from an uncountable collection of contraction mappings in conjunction with a linear and continuous operator. These systems are integral to our study as they encapsulate complex dynamical behaviors through their association with attractors, which represent sets towards which the system evolves over time. Each U.I.F.S. within the sequence is governed by a Markov-type operator that dictates its probabilistic behavior and is described by a fractal measure that captures the geometric and measure-theoretic properties of the attractor. The core contributions of our work are presented in the form of several theorems. These theorems tackle key problems and provide novel insights into the study of measures and their properties in Hilbert spaces. The results contribute to advancing the understanding of convergence behaviors, the interaction of Dirac measures, and the applications of Monge–Kantorovich norms. These theorems hold significant potential applications across various domains of functional analysis and measure theory. By establishing new results and proving critical properties, our work extends existing frameworks and opens new avenues for future research. This paper contributes to the broader field of mathematical analysis by offering new perspectives on how uncountable iterated function systems evolve and stabilize. Our findings provide a foundational understanding that can be applied to a wide range of mathematical and real-world problems. By highlighting the interplay between measure theory and functional analysis, our work paves the way for further exploration and discovery in these areas, thereby enriching the theoretical landscape and practical applications of these mathematical concepts. Full article
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