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Search Results (1,042)

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Keywords = change vector analysis

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25 pages, 2038 KiB  
Article
The Path to Sustainable Stability: Can ESG Investing Mitigate the Spillover Effects of Risk in China’s Financial Markets?
by Jiangying Wei, Ridong Hu and Feng Chen
Sustainability 2024, 16(23), 10316; https://doi.org/10.3390/su162310316 - 25 Nov 2024
Viewed by 211
Abstract
In the context of a low-carbon economic transition and escalating uncertainties in financial markets, understanding the relationship between the long-term benefits of ESG (Environmental, Social, and Governance) investments and the stability of China’s financial markets emerges as a critical issue. This paper analyzes [...] Read more.
In the context of a low-carbon economic transition and escalating uncertainties in financial markets, understanding the relationship between the long-term benefits of ESG (Environmental, Social, and Governance) investments and the stability of China’s financial markets emerges as a critical issue. This paper analyzes the risk contagion mechanisms within China’s financial system from the perspective of volatility spillovers associated with ESG investments. Initially, the study employs the Time-Varying Parameter Vector Autoregression (TVP-VAR) model to calculate the variance decomposition spillover index, contrasting the dynamics and risk transmission mechanisms of market volatility between portfolios composed of ESG and conventional stocks. Building upon the analysis of risk spillover relations among financial sub-markets, the study utilizes the generalized forecast error variance decomposition method to construct a complex network of financial system risk spillovers, investigating the risk contagion characteristics within both financial systems through network topology. Empirical findings indicate a significant reduction in the risk and net spillover effects of China’s financial system when ESG stock indices replace conventional stock indices, with a notable mutation in the volatility spillover network structure during extreme risk events and even more substantial changes during the COVID-19 pandemic. Furthermore, based on volatility spillover analysis, the study computes optimal weights and hedging strategies for portfolios incorporating the ESG volatility index and other market volatility indices. The conclusions of this research are instrumental for regulatory authorities in establishing early warning mechanisms and for investors in avoiding financial investment risks. Full article
21 pages, 388 KiB  
Article
From Uncertainty Relations to Quantum Acceleration Limits
by Carlo Cafaro, Christian Corda, Newshaw Bahreyni and Abeer Alanazi
Axioms 2024, 13(12), 817; https://doi.org/10.3390/axioms13120817 - 22 Nov 2024
Viewed by 260
Abstract
The concept of quantum acceleration limit has been recently introduced for any unitary time evolution of quantum systems under arbitrary nonstationary Hamiltonians. While Alsing and Cafaro used the Robertson uncertainty relation in their derivation, employed the Robertson–Schrödinger uncertainty relation to find the upper [...] Read more.
The concept of quantum acceleration limit has been recently introduced for any unitary time evolution of quantum systems under arbitrary nonstationary Hamiltonians. While Alsing and Cafaro used the Robertson uncertainty relation in their derivation, employed the Robertson–Schrödinger uncertainty relation to find the upper bound on the temporal rate of change of the speed of quantum evolutions. In this paper, we provide a comparative analysis of these two alternative derivations for quantum systems specified by an arbitrary finite-dimensional projective Hilbert space. Furthermore, focusing on a geometric description of the quantum evolution of two-level quantum systems on a Bloch sphere under general time-dependent Hamiltonians, we find the most general conditions needed to attain the maximal upper bounds on the acceleration of the quantum evolution. In particular, these conditions are expressed explicitly in terms of two three-dimensional real vectors, the Bloch vector that corresponds to the evolving quantum state and the magnetic field vector that specifies the Hermitian Hamiltonian of the system. For pedagogical reasons, we illustrate our general findings for two-level quantum systems in explicit physical examples characterized by specific time-varying magnetic field configurations. Finally, we briefly comment on the extension of our considerations to higher-dimensional physical systems in both pure and mixed quantum states. Full article
(This article belongs to the Special Issue Mathematical Aspects of Quantum Field Theory and Quantization)
12 pages, 3950 KiB  
Article
Effects of Genetic Polymorphism in the IFI27 Gene on Milk Fat Traits and Relevance to Lipid Metabolism in Bovine Mammary Epithelial Cells
by Xinyi Jiang, Zhihui Zhao, Xuanxu Chen, Fengshuai Miao, Jing Li, Haibin Yu, Ping Jiang and Ziwei Lin
Animals 2024, 14(22), 3284; https://doi.org/10.3390/ani14223284 - 14 Nov 2024
Viewed by 330
Abstract
Milk fat is an important indicator for evaluating milk quality and a symbol of the core competitiveness of the dairy industry. It can be improved through genetic and feed management factors. Interferon alpha-inducible protein 27 (IFI27) was found to be differentially [...] Read more.
Milk fat is an important indicator for evaluating milk quality and a symbol of the core competitiveness of the dairy industry. It can be improved through genetic and feed management factors. Interferon alpha-inducible protein 27 (IFI27) was found to be differentially expressed when comparing the transcriptome in high- and low-fat bovine mammary epithelial cells (bMECs) in our previous research. Therefore, this study aimed to investigate whether the IFI27 gene had a regulatory effect on lipid metabolism.We detected six SNPs in the IFI27 gene (UTR-(-127) C>A, UTR-(-105) T>A, UTR-(-87) G>A, I1-763 G>T, E2-77 G>A, E2-127 G>T) in a Chinese Holstein cow population. Association analysis of the polymorphism of IFI27 and milk quality traits showed that the AG and GG genotype of E2-77 G>A, and the GG and TT genotypes of E2-127 G>T were connected to milk fat (p < 0.05). Haplotype frequency analysis showed that H5H5 was associated with lower milk fat content (p < 0.05), while milk from H5H6 animals had a higher fat content (p < 0.05). Subsequently, IFI27 overexpression vectors (PBI-CMV3-IFI27) and interference vectors (Pb7sk-GFP-shRNA) were constructed. Overexpression of the IFI27 gene in bMECs caused a significant increase in triglycerides (TGs) content (p < 0.05) and decreases in cholesterol (CHOL) and nonestesterified fatty acid (NEFA) content (p < 0.05), while interference with IFI27 expression produced opposing changes (p < 0.05). In summary, IFI27 E2-77 G>A and IFI27 E2-127 G>T may be useful as molecular markers in dairy cattle to measure milk fat, and the IFI27 gene may play an important role in milk lipid metabolism. Full article
(This article belongs to the Topic Advances in Animal-Derived Non-Cow Milk and Milk Products)
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<p>Gel electrophoresis pictures: (<b>A</b>) gel electrophoresis of the first pair of polymorphism primers: lane 1 is the DNA marker; lane 2 to lane 6, UTR-(-127); lane 7 to 11, UTR-(-105); lane 12 to 16, UTR-(-87); (<b>B</b>) gel electrophoresis of the second pair of polymorphism primers: lane 1 is the DNA marker; lane 2 to lane 6, I1-763; lane 7 to 11, E2-77; and lane 12 to 16, E2-127.</p>
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<p>Analysis and sequencing of SNPs in the <span class="html-italic">IFI27</span> gene: (<b>A</b>) identification of SNPs in the key functional domains of the <span class="html-italic">IFI27</span> gene; (<b>B</b>) six SNP sites of <span class="html-italic">IF27</span>.</p>
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<p>Linkage and haplotype analyses of SNPs of <span class="html-italic">IFI27</span> gene. Block1 with red color presents strong linkage between UTR-(-127) C&gt;A(1), UTR-(-105) T&gt;A(2), and UTR-(-87) G&gt;A(3); four haplotypes are shown, with haplotype frequency. Block2 with red color presents strong linkage between I1-763 G&gt;T(4) and E2-77 G&gt;A(5). A total of 9 haplotype combinations with biological repetition significance (number of individuals ≥ 3) were composed.</p>
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<p><span class="html-italic">IFI27</span> gene interference vectors and overexpression vectors: (<b>A</b>) primer sequence and overexpression vectors (pBI-CMV3-<span class="html-italic">IFI27</span>); (<b>B</b>) primer sequence of the RNA interference target sequence and interference vectors (pb7sk-GFP-shRNA4).</p>
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<p>Expression of <span class="html-italic">IFI27</span> in two vector groups: (<b>A</b>) green fluorescence protein expression observation by fluorescent microscope. pBI-CMV3 refers to bMECs transfected with pBI-CMV3 vector; pBI-CMV3-IFI27, bMECs transfected with pBI-CMV3-<span class="html-italic">IFI27</span> vector; pb7sk-GFP-Neo, bMECs transfected with pb7sk-GFP-Neo vector; pb7sk-GFP-shRNA4, bMECs transfected with pBI-CMV3-IFI27vector; (<b>B</b>) mRNA expression of <span class="html-italic">IFI27</span> in bMECs; (<b>C</b>) protein expression of IFI27 in bMECs. <span class="html-italic">** p</span> &lt; 0.01.</p>
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<p>The TGs, CHO, and NEFA contents of each transfected group in bMECs: (<b>A</b>,<b>C</b>,<b>E</b>) The TGs, CHOL, and NEFA contents in the pBI-CMV3-<span class="html-italic">IFI27</span> group; (<b>B</b>,<b>D</b>,<b>F</b>) The TGs, CHO, and NEFA contents in the pb7sk-GFP-shRNA4 group. pBI-CMV3 refers to bMECs transfected with pBI-CMV3 vector; pBI-CMV3-IFI27, bMECs transfected with pBI-CMV3-IFI27 vector; pb7sk-GFP-Neo, bMECs transfected with pb7sk-GFP-Neo vector; pb7sk-GFP-shRNA4, bMECs transfected with pBI-CMV3-IFI27vector. Error bars indicate SEM.* <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01.</p>
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19 pages, 2315 KiB  
Article
Role of the Egr2 Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape
by Margot Martinez Moreno, David Karambizi, Hyeyeon Hwang, Kristen Fregoso, Madison J. Michles, Eduardo Fajardo, Andras Fiser and Nikos Tapinos
Biomedicines 2024, 12(11), 2594; https://doi.org/10.3390/biomedicines12112594 - 13 Nov 2024
Viewed by 445
Abstract
Background: Schwann cells (SCs) and their plasticity contribute to the peripheral nervous system’s capacity for nerve regeneration after injury. The Egr2/Krox20 promoter antisense RNA (Egr2-AS) recruits chromatin remodeling complexes to inhibit Egr2 transcription following peripheral nerve injury. Methods: RNA-seq and ATAC-seq [...] Read more.
Background: Schwann cells (SCs) and their plasticity contribute to the peripheral nervous system’s capacity for nerve regeneration after injury. The Egr2/Krox20 promoter antisense RNA (Egr2-AS) recruits chromatin remodeling complexes to inhibit Egr2 transcription following peripheral nerve injury. Methods: RNA-seq and ATAC-seq were performed on control cells, Lenti-GFP-transduced cells, and cells overexpressing Egr2-AS (Lenti-AS). Egr2 AS-RNA was cloned into the pLVX-DsRed-Express2-N1 lentiviral expression vector (Clontech, Mountain View, CA, USA), and the levels of AS-RNA expression were determined. Ezh2 and Wdr5 were immunoprecipitated from rat SCs and RT-qPCR was performed against AS-Egr2 RNA. ChIP followed by DNA purification columns was used to perform qPCR for relevant promoters. Hi-C, HiC-DC+, R, Bioconductor, and TOBIAS were used for significant and differential loop analysis, identifications of COREs and CORE-promotor loops, comparisons of TF activity at promoter sites, and identification of site-specific TF footprints. OnTAD was used to detect TADs, and Juicer was used to identify A/B compartments. Results: Here we show that a Neuregulin-ErbB2/3 signaling axis mediates binding of the Egr2-AS to YY1Ser184 and regulates its expression. Egr2-AS modulates the chromatin accessibility of Schwann cells and interacts with two distinct histone modification complexes. It binds to EZH2 and WDR5 and enables targeting of H3K27me3 and H3K4me3 to promoters of Egr2 and C-JUN, respectively. Expression of the Egr2-AS results in reorganization of the global chromatin landscape and quantitative changes in the loop formation and contact frequency at domain boundaries exhibiting enrichment for AP-1 genes. In addition, the Egr2-AS induces changes in the hierarchical TADs and increases transcription factor binding scores on an inter-TAD loop between a super-enhancer regulatory hub and the promoter of mTOR. Conclusions: Our results show that Neuregulin-ErbB2/3-YY1 regulates the expression of Egr2-AS, which mediates remodeling of the chromatin landscape in Schwann cells. Full article
(This article belongs to the Special Issue Epigenetic Regulation and Its Impact for Medicine)
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<p>Expression of the EGR2-AS in SCs resulted in gene expression changes. (<b>A</b>) Western blot using total YY1 and phosphoserine antibodies following immunoprecipitation with a total YY1 antibody in non-injured sciatic nerves or 12 h after sciatic nerve transection. An isotype matched IgG was used as control. Sciatic nerve transection inhibits serine phosphorylation of YY1. (<b>B</b>) ELISA using our specific pSer184-YY1 antibody showed significant reduction in pSer184-YY1 12 h after sciatic nerve transection compared to contralateral uninjured nerves. Significance was calculated with a Student’s <span class="html-italic">t</span>-test (N = 4–8, * <span class="html-italic">p</span> &lt; 0.005, dF = 10). (<b>C</b>) Inhibition of pErbB2-Y1248 with PKI-166 for 1 h resulted in significant inhibition of pSer184-YY1. Significance was calculated with a Student’s <span class="html-italic">t</span>-test (N = 4, * <span class="html-italic">p</span> &lt; 0.05, dF = 6). (<b>D</b>) YY1 RIP followed by qPCR for the detection of the Egr2-AS shows increased binding to YY1 after inhibition of ErbB2 with PKI-166. Significance was calculated with a Student’s <span class="html-italic">t</span>-test (N = 4, * <span class="html-italic">p</span> &lt; 0.05, dF = 4). (<b>E</b>) Volcano plot showing log-fold changes in gene expression following expression of the EGR2-AS in SCs. A total of 450 genes were significantly upregulated and 111 downregulated compared to control SCs. (<b>F</b>) Clustering of upregulated and downregulated genes in SCs expressing the EGR2-AS compared to control SCs (n = 2). (<b>G</b>) The downregulated genes were enriched for ERK1/2, ERBB, and MAPK-regulated biological processes, while the upregulated genes were enriched in cell cycle regulators and mTOR-regulated processes.</p>
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<p>The EGR2-AS recruits EZH2 and WDR5 and enables targeting of H3K27me3 and H3K4me3 on <span class="html-italic">EGR2</span> and <span class="html-italic">C-JUN</span> promoters. (<b>A</b>) RIP experiments after the EGR2-AS expression in SCs, with antibodies against EZH2 and WDR5. Significance was calculated with a Student’s <span class="html-italic">t</span>-test (for the WDR5 RIP, N = 13, five biological replicates, * <span class="html-italic">p</span> = 0.040, dF = 27. For the EZH2 RIP, N = 9, three biological replicates, * <span class="html-italic">p</span> = 0.026, dF = 16). (<b>B</b>) ChIP experiments following expression of the EGR2-AS in SCs and its effect on H3K27me3 binding on <span class="html-italic">EGR2</span> promoter and H3K4me3 binding on C-JUN promoter, respectively. Incubation of cells with oligonucleotide GapmeRs against the EGR2-AS inhibits the AS-RNA-induced binding of H3K27me3 and H3K4me3 on the EGR2 and C-JUN promoters. For the H3K27me3 ChIP, N = 13, five biological replicates, and one technical replicate, * <span class="html-italic">p</span> = 0.020, dF = 23, ** <span class="html-italic">p</span> = 0.0094, dF = 22. For the H3K4me3 ChIP, N = 15, five biological replicates and one technical replicate, * <span class="html-italic">p</span> = 0.049, dF = 18, ** <span class="html-italic">p</span> = 0.0012, dF = 23.</p>
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<p>Expression of the EGR2-AS induces chromatin remodeling and increased binding of the AP-1/JUN TF family. (<b>A</b>) Sample correlation analysis based on ATAC-seq peak location and intensity. PCA result of all samples is plotted as a 2D graph with PC1 as <span class="html-italic">X</span>-axis and PC2 as <span class="html-italic">Y</span>-axis. Note that variable 1 is strong (98%) enough to divide into the two hierarchical groups. (<b>B</b>) Scatterplot comparing ATAC-seq signal intensities across all open chromatin sites between the Lenti-AS group compared to the Lenti-GFP group. Significant changes correspond to an FDR-adjusted <span class="html-italic">p</span> value below 0.05 and an absolute log2 fold change above 1.5. The diagonal is shown as a gray area and is a reference indicating regions with no change in chromatin accessibility. Colored dots indicate differences in accessibility. (<b>C</b>) GO analysis among genes located in the vicinity of regions with increased chromatin accessibility after the EGR2-AS overexpression. (<b>D</b>) Volcano plot of differential TF footprint score versus the significance (logpval) revealed that expression of the EGR2-AS induces significant increase in the footprint of AP-1, CTCF, ATF/CREB, CNC, EGR, MiT/FTF, Rfx, and KLF TF families.</p>
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<p>Hi-C following expression of the EGR2-AS in SCs shows 3D genome reorganization. (<b>A</b>–<b>C</b>) Histograms showing the significant total loops via the HiCDCPlus software version 1.0.0. Static loops (not gained or lost) are gray, lost loops are green, and gained loops are red (log2FC cutoff = 1, <span class="html-italic">p</span> &lt; 0.05). (<b>D</b>) Detail of the Hi-C maps on the chromosomes 10 and 5 showing examples of gained and lost loops, respectively. The annotated loop anchors to the promoter of genes are represented by their main pathways (plotted as odds ratios by their corresponding <span class="html-italic">p</span> values).</p>
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<p>Reconstruction of long-range interactions between COREs and associated promoters. (<b>A</b>) Sub-setting of COREs based on transcription factor footprints, with 40% of COREs occupied by at least 1 TF footprint. (<b>B</b>) Hi-C revealed that 157 out of 1563 COREs form long distance interactions with promoters. (<b>C</b>) Pathway enrichment analysis of CORE-interacting genes. (<b>D</b>) Example of CORE–promoter interactions at the mTOR genomic region at chromosome 20. COREs are colored by samples: red and blue for the AS-RNA and GFP control, respectively. Reference genome is color-coded for expressed and non-expressed genes as black and grey, respectively.</p>
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<p>Expression of the EGR2-AS results in changes between the mTOR promoter and its cis-regulatory elements. (<b>A</b>) Change in TF binding scores of all TFs at nearest and mid-distance to TAD boundary loop anchors following expression of the EGR2-AS (farthest to TAD boundary loop anchor could not be analyzed due to very low occupancy). (<b>B</b>) TF families that experienced the greatest increase in binding scores following expression of the AS-RNA. (<b>C</b>) Depiction of changes at mTOR harboring TAD and formation of a new interdomain boundary. (<b>D</b>) Bar-plots of normalized gene expression of mTOR in control and AS-RNA expressing cells (<span class="html-italic">p</span>.adj = 0.03).</p>
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16 pages, 1099 KiB  
Article
Evaluating Enteric Fermentation-Driven Environmental Kuznets Curve Dynamics: A Bayesian Vector Autoregression Comparative Study of the EU and Least Developed Countries
by Eleni Zafeiriou, Spyros Galatsidas, Christina Moulogianni, Spyridon Sofios and Garyfallos Arabatzis
Agriculture 2024, 14(11), 2036; https://doi.org/10.3390/agriculture14112036 - 12 Nov 2024
Viewed by 518
Abstract
Global warming and climate change, primarily driven by human activities, with agriculture playing a significant role, have become central topics of scientific research. Livestock production, especially enteric fermentation, is a major source of greenhouse gas emissions, making it a focal point for both [...] Read more.
Global warming and climate change, primarily driven by human activities, with agriculture playing a significant role, have become central topics of scientific research. Livestock production, especially enteric fermentation, is a major source of greenhouse gas emissions, making it a focal point for both climate change adaptation and mitigation strategies. Both the European Union (EU) and Least Developed Countries (LDCs) are highly dependent on agriculture, particularly livestock, which plays a key role in their economic growth. In developing countries, livestock systems are evolving rapidly due to various factors, while in the EU, the livestock sector remains economically and socially significant, representing 36% of total agricultural activity. This study explores the environmental impact of enteric fermentation in livestock production, alongside the economic value it generates in both the EU and LDCs. The analysis utilizes a Bayesian Vector Autoregression (BVAR) methodology, which provides a more robust performance compared to traditional models like Vector Autoregression (VAR) and the Vector-error Correction Model (VECM). This research identifies significant relationships between the variables studied, with structural breaks quantified to reflect the impact of initiatives undertaken in both regions. Interestingly, the results challenge the environmental Kuznets curve, which hypothesizes an inverted U-shaped relationship between economic growth and environmental degradation, as proposed by Stern. This suggests that stronger economic incentives may be necessary to enhance policy effectiveness and promote eco-efficiency. The distinctive characteristics of livestock production in the EU and LDCs should be carefully considered when shaping agricultural policies, with a strong emphasis on farmer education as a critical factor for success. Additionally, corporate management practices must be tailored to address the unique needs, strengths, and challenges of livestock businesses in these two diverse regions. Full article
(This article belongs to the Section Agricultural Economics, Policies and Rural Management)
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<p>The evolution of the model variables for the time period studied. EMIL denotes CO<sub>2</sub>e for LDCS. EMIEU denotes CO<sub>2</sub>e for EU. VAL denoted value added by agriculture for LDCS. VADL2 denoted the square value added by agriculture for LDCS. VAEU denoted value added by agriculture. VAEU2 denoted value added by agriculture.</p>
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<p>(<b>a</b>) Impulse response analysis of the model variables for a ten-period time horizon or the LDCs. (<b>b</b>) Impulse response analysis of the model variables for a ten-period time horizon or the EU.</p>
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17 pages, 4356 KiB  
Article
Effect of Culture Supernatant of Clostridium butyricum TO-A on Human DNA-Repair-Factor-Encoding Gene Promoters
by Shunsuke Takaoka, Takuro Ishii, Yuriko Umihara, Ryuji Otani, Sota Akazawa, Takahiro Oda, Yoko Ogino, Yoichi Okino, Dian-Sheng Wang and Fumiaki Uchiumi
Int. J. Mol. Sci. 2024, 25(22), 12151; https://doi.org/10.3390/ijms252212151 - 12 Nov 2024
Viewed by 434
Abstract
In this study, Clostridium butyricum TO-A culture supernatant (CBCS) or butyric acid was added to a culture medium of human cervical carcinoma HeLa S3 cells, and changes in DNA-repair-related gene promoter activities were investigated. The HeLa S3 cells were transfected with a luciferase [...] Read more.
In this study, Clostridium butyricum TO-A culture supernatant (CBCS) or butyric acid was added to a culture medium of human cervical carcinoma HeLa S3 cells, and changes in DNA-repair-related gene promoter activities were investigated. The HeLa S3 cells were transfected with a luciferase (Luc) expression vector containing approximately 500 bp of the 5′-upstream region of several human DNA-repair-related genes and cultured with a medium containing the CBCS (10%) or butyric acid (2.5 mM). The cells were harvested after 19 to 42 h of incubation. A Luc assay revealed that the human ATM, PARG, PARP1, and RB1 gene promoter activities were significantly increased. A Western blot analysis showed that the amounts of the proteins encoded by these genes markedly increased. Furthermore, 8, 24, and 48 h after the addition of the CBCS (10%), total RNA was extracted and subjected to RNAseq analysis. The results showed that the expression of several inflammation- and DNA-replication/repair-related genes, including NFKB and the MCM gene groups, decreased markedly after 8 h. However, the expression of the histone genes increased after 24 h. Elucidation of the mechanism by which the CBCS and butyrate affect the expression of genes that encode DNA-repair-associated proteins may contribute to the prevention of carcinogenesis, the risk of which rises in accordance with aging. Full article
(This article belongs to the Section Biochemistry)
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<p>Responses of human gene promoters to bacteria-cultivated supernatants in HeLa S3 cells. (<b>A</b>) Screening of bacteria-cultivated supernatants (BCSs) that could activate human DNA-repair-factor-encoding gene promoters. BSCS: <span class="html-italic">Bacillus subtilis</span> TO-A culture supernatant; EFCS: <span class="html-italic">Enterococcus faecium</span> T-110 culture supernatant; CBCS: <span class="html-italic">Clostridium butyricum</span> TO-A culture supernatant; BACS: <span class="html-italic">Bacillus amyloliquefaciens</span> TOA5001 culture supernatant. (<b>B</b>) Effect of CBCS on human DNA-repair-factor-encoding gene promoters. Three independent experiments were carried out. Results show relative Luc activities compared with those of the pGL4-PIF1-transfected cells untreated with BCS. Asterisks indicate values that were not determined.</p>
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<p>Morphological changes in the HeLa S3 cells after treatment with BCSs. (<b>A</b>) HeLa S3 cells were cultured in a medium containing 10% CBCS or CBCS/BSCS/EFCS mixture (CSM) for 19 h (lower panels). The upper panels indicate HeLa S3 cells that were cultured in a medium with 10% control supernatant for 19 h. (<b>B</b>) HeLa S3 cells were cultured in a medium containing 10% CBCS for 28 and 42 h (lower panels). The upper panels indicate HeLa S3 cells that were cultured in a medium with 10% control supernatant for 28 and 42 h. (<b>C</b>) HeLa S3 cells were cultured in a medium containing 0 (upper left), 1.25 (upper right), 2.5 (lower left), and 5 mM (lower right) of n-butyric acid for 25 h.</p>
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<p>The inhibitory effect of the CBCS on HeLa S3 cell proliferation. HeLa S3 cells (2500 cells/well) were cultivated in a 96-well plate for 24 h. Then, the culture medium was changed to that containing 0 to 20% of the CBCS (orange columns) or a control bacterial culture medium (blue columns), and a CCK-8 assay was carried out after 48 h of incubation at 37 °C with 5% of CO<sub>2</sub>. The results are shown as means ± SD from three independent experiments. Statistical analysis was performed with Student’s <span class="html-italic">t</span>-test, and asterisks (**) indicate a value of ** <span class="html-italic">p</span> &lt; 0.01.</p>
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<p>Responses of the human gene promoters to n-butyric acid in HeLa S3 cells. HeLa S3 cells were transfected with Luc reporter plasmids, including pGL4.10[<span class="html-italic">luc</span>2] and pGL4-PIF1 as negative and positive control vectors, respectively. After 4 h of transfection, the culture medium was changed to that containing 2.5 mM of n-butyric acid. After further incubation, the cells were corrected, and the Luc assay was carried out. Averages from three independent experiments with or without n-butyric acid were calculated. Fold activation indicates the ratio of the results for the average Luc activity of the butyrate-containing culture medium to those for the culture medium that did not contain butyrate.</p>
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<p>Levels of ATM, RB1, and PARP1 proteins in HeLa S3 cells. The HeLa S3 cells (1 × 10<sup>6</sup>) were cultivated with a DMEM containing 10% FBS for 24 h. Then, the culture medium was changed to that containing (<b>A</b>) 10% CBCS or (<b>B</b>) n-butyric acid (2.5 mM). Zero to forty-eight hours after the medium exchange, the cells were corrected, and RIPA buffer extracts were subjected to SDS-PAGE and Western blotting.</p>
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<p>n-Butyric acid response elements in the human <span class="html-italic">RB1</span> and <span class="html-italic">PARP1</span> gene promoters. (<b>A</b>) Deletion experiments on the human <span class="html-italic">RB1</span> and <span class="html-italic">PARP1</span> promoters. HeLa S3 cells were transfected with Luc reporter plasmids. After 4 h of transfection, the culture medium was changed to that containing 5 mM of n-butyric acid, and similar experiments were carried out. Averages from three independent experiments with or without n-butyric acid were calculated. Fold activation indicates the ratio of the results for the average Luc activity of the butyrate-containing culture medium to those for the culture medium that did not contain butyrate. (<b>B</b>) n-Butyric acid-responsive core sequences in the 5′-upstream regions of human <span class="html-italic">RB1</span> and <span class="html-italic">PARP1</span>. The n-butyric acid-responsive sequences in pGL4-RB1Δ3 and pGL4-PARP1Δ 2 were applied in the JASPAR-2020 program (with a threshold &gt; 95%). Restriction sites for <span class="html-italic">Kpn</span>I and <span class="html-italic">Xho</span>I enzymes are highlighted in yellow and pale blue, respectively. The green-highlighted GGAA and TTCC are the core motifs that are recognized by transcription factors, including ETS family proteins.</p>
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<p>Heat map for the RNAseq cluster analysis of differentially expressed genes (DEGs) between samples. HeLa S3 cells that were cultivated with or without CBCS (10%) for 0, 8, 24, and 48 h. Red and green represent up- and down-regulated genes, respectively.</p>
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<p>Classification of genes by protein coding. The up- (<b>left</b>) and down-regulated (<b>right</b>) genes of HeLa S3 cells cultivated for 8 (<b>upper</b>), 24 (<b>middle</b>), and 48 h (<b>lower</b>) were classified further as protein-coding (white pie portions) or non-coding RNAs (black pie portions).</p>
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<p>GO enrichment analysis comparing differential genes between CBCS-treated and non-treated HeLa S3 cells. RNA samples were obtained after (<b>A</b>) 8, (<b>B</b>) 24, and (<b>C</b>) 48 h of cultivation with or without CBCS (10%).</p>
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<p>KEGG enrichment analysis comparing differential genes between CBCS-treated and non-treated HeLa S3 cells. RNA samples were obtained after (<b>A</b>) 8, (<b>B</b>) 24, and (<b>C</b>) 48 h of cultivation with or without CBCS (10%).</p>
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19 pages, 2668 KiB  
Article
Employment Shift in Response to a Technology Shock: An Analysis of Two Rigidities and Two Agents
by Kyuyeon Hwang and Junhee Han
Economies 2024, 12(11), 303; https://doi.org/10.3390/economies12110303 - 10 Nov 2024
Viewed by 388
Abstract
This paper examines the relationship between a technology shock and employment, considering price, wage rigidities, and heterogeneous agents. To explore this relationship, we utilized a Dynamic Stochastic General Equilibrium (DSGE) model, incorporating households with varying savings rates. For empirical validation, we conducted a [...] Read more.
This paper examines the relationship between a technology shock and employment, considering price, wage rigidities, and heterogeneous agents. To explore this relationship, we utilized a Dynamic Stochastic General Equilibrium (DSGE) model, incorporating households with varying savings rates. For empirical validation, we conducted a Structural Vector Autoregression (SVAR) analysis using data from two economies with distinct savings patterns—the United States and China. This approach allowed us to assess the impact of technology shocks on employment dynamics across different savings environments. Under these conditions, we observe that the effect of technology on aggregate employment is initially positive. Still, it gradually decreases in the mid-term, eventually switching to a negative impact before slowly recovering to equilibrium. The reason for this phenomenon depends on (i) the magnitude of fluctuations in price and wage, precisely, which variable’s fluctuations have a greater magnitude, and (ii) which effect, between income effect and substitute effect, is preferred by restricted and unrestricted households. Due to (i), real wages change, and because of (ii), households make different labor supply decisions, leading to fluctuations in employment in response to technology shocks. Full article
(This article belongs to the Section Macroeconomics, Monetary Economics, and Financial Markets)
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<p>Savings rate in the US and China.</p>
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<p>Distribution of standardized variables.</p>
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<p>Impulse response function to TFP shock (structural VAR).</p>
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<p>IRF (Impulse Response Function) of variables to technology shock.</p>
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20 pages, 8075 KiB  
Article
Comparative Analysis of Statistical, Time–Frequency, and SVM Techniques for Change Detection in Nonlinear Biomedical Signals
by Tahmineh Azizi
Signals 2024, 5(4), 736-755; https://doi.org/10.3390/signals5040041 - 7 Nov 2024
Viewed by 426
Abstract
Change detection in biomedical signals is crucial for understanding physiological processes and diagnosing medical conditions. This study evaluates various change detection methods, focusing on synthetic signals that mimic real-world scenarios. We examine the following three methods: classical statistical techniques (thresholding based on mean [...] Read more.
Change detection in biomedical signals is crucial for understanding physiological processes and diagnosing medical conditions. This study evaluates various change detection methods, focusing on synthetic signals that mimic real-world scenarios. We examine the following three methods: classical statistical techniques (thresholding based on mean and standard deviation), Support Vector Machine (SVM) classification, and time–frequency analysis using Continuous Wavelet Transform (CWT). Each method’s performance is assessed using synthetic signals, including nonlinear signals and those with simulated anomalies. We calculated the F1-score to quantify performance, providing a balanced measure of precision and recall. Results showed that SVM classification outperformed both classical techniques and CWT analysis, achieving a higher F1-score in detecting changes. While all methods struggled with synthetic nonlinear signals, classical techniques and SVM successfully detected changes in signals with simulated anomalies, whereas CWT had difficulty with both types of signals. These findings underscore the importance of selecting appropriate change detection methods based on signal characteristics. Future research should explore advanced machine learning and signal processing techniques to improve detection accuracy in biomedical applications. Full article
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<p>Change detection in biomedical signals. This figure illustrates the performance of different change detection methods on a synthetic signal. The original signal contains a known anomaly between time points 100 and 150. The classical statistical method uses mean and standard deviation thresholding to identify changes. The Continuous Wavelet Transform (CWT) method analyzes the signal in both time and frequency domains to detect anomalies. The Support Vector Machine (SVM) classifier is trained on the signal to identify changes based on learned patterns. The figure highlights the detected anomalies by each method, demonstrating their effectiveness in identifying different types of changes in biomedical signals.</p>
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<p>Support Vector Machine (SVM) workflow. An SVM classifies data by finding the optimal hyperplane that separates two classes with maximum margin. Kernel functions map data into a higher-dimensional space to improve separability. The soft margin approach allows for some misclassification, balancing accuracy and generalization. The kernel trick efficiently computes dot products in the transformed space. The SVM training process involves solving a convex optimization problem to learn the hyperplane parameters. Once trained, the SVM can predict class labels for new data points based on their distance from the hyperplane.</p>
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<p>Schematic representation of change detection methods applied to a biomedical signal. The original biomedical signal (blue curve) is analyzed using three methods: classical statistical techniques, Continuous Wavelet Transform (CWT), and Support Vector Machine (SVM). Changes detected by the statistical method are highlighted in the red shaded area, indicating sensitivity to shifts in mean and standard deviation. Changes identified by the CWT method are shown in the green shaded area, demonstrating the method’s ability to capture time–frequency variations. The SVM-detected changes are marked by black arrows, showcasing its capability to recognize subtle and complex patterns in the signal. This visualization underscores the varying effectiveness of each method in different contexts of signal complexity and change characteristics.</p>
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<p>Change detection using mean and standard deviation method. (<b>Top</b>) Synthetic nonlinear signal plotted against time and shown in blue. This signal exhibits complex behavior over time, characterized by variations and fluctuations in amplitude. (<b>Bottom</b>) The red line represents the results of change detection using the mean and standard deviation method.</p>
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<p>Change detection using mean and standard deviation method. (<b>Top</b>) Synthetic nonlinear signal plotted against time and shown in blue. This signal exhibits complex behavior over time, characterized by variations and fluctuations in amplitude. (<b>Bottom</b>) The red line represents the results of change detection using the mean and standard deviation method.</p>
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<p>Change detection using Wavelet Transform. (<b>Top</b>) Synthetic nonlinear signal plotted against time and shown in blue. This signal exhibits complex behavior over time, characterized by variations and fluctuations in amplitude. (<b>Bottom</b>) The bottom subplot displays the results of change detection using the Wavelet Transform method. Changes in the signal are represented by localized regions of high wavelet coefficients, indicating deviations from the background signal.</p>
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<p>Change detection using Wavelet Transform. (<b>Top</b>) Synthetic nonlinear signal plotted against time and shown in blue. This signal exhibits complex behavior over time, characterized by variations and fluctuations in amplitude. (<b>Bottom</b>) The bottom subplot displays the results of change detection using the Wavelet Transform method. Changes in the signal are represented by localized regions of high wavelet coefficients, indicating deviations from the background signal.</p>
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<p>Change detection in synthetic signal using Support Vector Machine (SVM) classification. (<b>Top</b>) Synthetic nonlinear signal plotted against time and shown in blue. This signal exhibits complex behavior over time, characterized by variations and fluctuations in amplitude. (<b>Bottom</b>) Change detection results using Support Vector Machine (SVM) classifier, where red indicates predicted change points based on the trained model.</p>
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<p>Change detection in synthetic signal using Support Vector Machine (SVM) classification. (<b>Top</b>) Synthetic signal with a sinusoidal pattern over a duration of 5 s. Random changes have been introduced into the signal to simulate anomalies, indicated by the red markers. These changes represent potential abnormalities or deviations from the expected signal pattern. (<b>Bottom</b>) The green line represents the true labels indicating the presence of changes in the signal, while the red dashed line represents the predicted labels obtained using a Support Vector Machine (SVM) classifier.</p>
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<p>Change detection in synthetic signal using Support Vector Machine (SVM) classification. (<b>Top</b>) Synthetic signal with complex patterns and amplitude spikes indicating changes (highlighted in red). (<b>Bottom</b>) Detected changes indicated by green (true labels) and red dashed lines (predicted labels) using SVM classification. The accuracy of change detection is shown in the title.</p>
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<p>Analysis of synthetic EEG signal and change detection. (<b>Top</b>) Mean and standard deviation of EEG signal: This subplot displays the mean (red dashed line) and one standard deviation above and below the mean (black dashed lines) of the generated EEG signal over time. The underlying blue line represents the raw EEG-like time series data, showcasing the variations around the average signal level. (<b>Middle</b>) Time–Frequency analysis (Spectrogram): The spectrogram in this subplot illustrates the time–frequency representation of the EEG signal using the short-time Fourier transform (STFT). The x-axis denotes time (in seconds), while the y-axis represents frequency (in Hz). The color intensity indicates the magnitude of the frequency components in decibels (dB), revealing the distribution of power across different frequency bands over time. (<b>Bottom</b>) SVM change detection: This subplot depicts the predicted labels for the EEG signal using a Support Vector Machine (SVM) model. The green line indicates detected changes across the time series, with ‘1’ representing no spike and ‘2’ indicating spike events. The visualization helps demonstrate the effectiveness of the SVM algorithm in identifying significant changes (spikes) in the EEG data.</p>
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<p>Analysis of synthetic sine wave signal and change detection. (<b>Top</b>) Original synthetic sine wave signal with a base frequency of 1 Hz (in blue), along with calculated mean (in green) and standard deviation (in red) lines. The abrupt changes in amplitude are highlighted in the signal plot between the vertical dashed lines. (<b>Middle</b>) Time–Frequency representation of the synthetic sine wave signal obtained via short-time Fourier transform (STFT). The spectrogram illustrates the frequency content over time, showing how the signal’s energy distribution shifts during the introduced changes. (<b>Bottom</b>) Change detection using Support Vector Machine (SVM) classification. The colored regions indicate the predicted states of the signal (baseline vs. changed amplitude), demonstrating the SVM’s ability to identify segments with different characteristics. The SVM was trained using features (mean and standard deviation) extracted from the signal.</p>
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14 pages, 3513 KiB  
Article
Digital Holographic Microscopy in Veterinary Medicine—A Feasibility Study to Analyze Label-Free Leukocytes in Blood and Milk of Dairy Cows
by Sabine Farschtschi, Manuel Lengl, Stefan Röhrl, Christian Klenk, Oliver Hayden, Klaus Diepold and Michael W. Pfaffl
Animals 2024, 14(21), 3156; https://doi.org/10.3390/ani14213156 - 3 Nov 2024
Viewed by 868
Abstract
For several years, the determination of a differential cell count of a raw milk sample has been proposed as a more accurate tool for monitoring the udder health of dairy cows compared with using the absolute somatic cell count. However, the required sample [...] Read more.
For several years, the determination of a differential cell count of a raw milk sample has been proposed as a more accurate tool for monitoring the udder health of dairy cows compared with using the absolute somatic cell count. However, the required sample preparation and staining process can be labor- and cost-intensive. Therefore, the aim of our study was to demonstrate the feasibility of analyzing unlabeled blood and milk leukocytes from dairy cows by means of digital holographic microscopy (DHM). For this, we trained three different machine learning methods, i.e., k-Nearest Neighbor, Random Forests, and Support Vector Machine, on sorted leukocyte populations (granulocytes, lymphocytes, and monocytes/macrophages) isolated from blood and milk samples of three dairy cows by using fluorescence-activated cell sorting. Afterward, those classifiers were applied to differentiate unlabeled blood and milk samples analyzed by DHM. A total of 70 blood and 70 milk samples were used. Those samples were collected from five clinically healthy cows at 14-time points within a study period of 26 days. The outcome was compared with the results of the same samples analyzed by flow cytometry and (in the case of blood samples) also to routine analysis in an external laboratory. Moreover, a standard vaccination was used as an immune stimulus during the study to check for changes in cell morphology or cell counts. When applied to isolated leukocytes, Random Forests performed best, with a specificity of 0.93 for blood and 0.84 for milk cells and a sensitivity of 0.90 and 0.81, respectively. Although the results of the three analytical methods differed, it could be demonstrated that a DHM analysis is applicable for blood and milk leukocyte samples with high reliability. Compared with the flow cytometric results, Random Forests showed an MAE of 0.11 (SD = 0.04), an RMSE of 0.13 (SD = 0.14), and an MRE of 1.00 (SD = 1.11) for all blood leukocyte counts and an MAE of 0.20 (SD = 0.11), an RMSE of 0.21 (SD = 0.11) and an MRE of 1.95 (SD = 2.17) for all milk cell populations. Further studies with larger sample sizes and varying immune cell compositions are required to establish method-specific reference ranges. Full article
(This article belongs to the Section Cattle)
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<p>Schematic overview of the workflow.</p>
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<p>Sampling scheme of blood and milk samples. Blood and milk samples were collected from each of the five cows at 14 time points. All cows were vaccinated on day 8 after sampling.</p>
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<p>Representative false-color phase images of different populations of unlabeled leukocytes, analyzed in DHM. (<b>A</b>) Blood granulocyte; (<b>B</b>) Blood lymphocyte; (<b>C</b>) Blood monocyte; (<b>D</b>) Milk granulocyte; (<b>E</b>) Milk lymphocyte; (<b>F</b>) Milk macrophage.</p>
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<p>Exemplary scatter plots of flow cytometric and digital holographic microscopy analyses. (<b>A</b>) Blood leukocyte populations analyzed by FACS; (<b>B</b>) Blood leukocyte populations analyzed by DHM; (<b>C</b>) Milk leukocyte populations analyzed by FACS; (<b>D</b>) Milk leukocyte populations analyzed by DHM.</p>
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<p>Confusion matrix showing the results of Random Forest classification of sorted blood cells.</p>
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<p>Confusion matrix showing the results of Random Forest classification of sorted milk cells.</p>
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<p>Cell count progression over time, DHM results obtained using k-Nearest Neighbor. (<b>A</b>) Blood cells of cow #963, analyzed by DHM, FACS and external laboratory; (<b>B</b>) Milk cells of cow #963, analyzed by DHM and FACS.</p>
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16 pages, 9480 KiB  
Article
Assessing Climate and Land-Use Change Scenarios on Future Desertification in Northeast Iran: A Data Mining and Google Earth Engine-Based Approach
by Weibo Yin, Qingfeng Hu, Jinping Liu, Peipei He, Dantong Zhu and Abdolhossein Boali
Land 2024, 13(11), 1802; https://doi.org/10.3390/land13111802 - 31 Oct 2024
Viewed by 427
Abstract
Desertification poses a significant threat to dry and semi-arid regions worldwide, including Northeast Iran. This study investigates the impact of future climate and land-use changes on desertification in this region. Six remote sensing indices were selected to model desertification using four machine learning [...] Read more.
Desertification poses a significant threat to dry and semi-arid regions worldwide, including Northeast Iran. This study investigates the impact of future climate and land-use changes on desertification in this region. Six remote sensing indices were selected to model desertification using four machine learning algorithms: Random Forest (RF), Support Vector Machine (SVM), Gradient Boosting Machine (GBM), and Generalized Linear Models (GLM). To enhance the model’s reliability, an ensemble model was employed. Future climate and land-use scenarios were projected using the CNRM-CM6 model and Markov chain analysis, respectively. Results indicate that the RF and SVM models performed best in mapping current desertification patterns. The ensemble model highlights a 2% increase in decertified areas by 2040, primarily in the northwestern regions. The study underscores the importance of land-use change and climate change in driving desertification and emphasizes the need for sustainable land management practices and climate change adaptation strategies to mitigate future impacts. Full article
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<p>Geographical location of the study area in Iran and Golestan province.</p>
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<p>Remote sensing indicators for desertification modeling, (<b>a</b>): NDVI, (<b>b</b>): NDSI, (<b>c</b>): TGSI, (<b>d</b>): Chrips, (<b>e</b>): WEHI, (<b>f</b>): Groundwater and (<b>g</b>): Land use.</p>
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<p>Remote sensing indicators for desertification modeling, (<b>a</b>): NDVI, (<b>b</b>): NDSI, (<b>c</b>): TGSI, (<b>d</b>): Chrips, (<b>e</b>): WEHI, (<b>f</b>): Groundwater and (<b>g</b>): Land use.</p>
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<p>Desertification in northeastern Iran using different models in the SDM package. (<b>a</b>), (<b>b</b>), (<b>c</b>), and (<b>d</b>) are models GBM, GLM, RF, and SVM in 2023, respectively.</p>
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<p>Desertification in northeastern Iran using different models in the SDM package. (<b>a</b>), (<b>b</b>), (<b>c</b>), and (<b>d</b>) are models GBM, GLM, RF, and SVM in 2023, respectively.</p>
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<p>Ensemble model of desertification assessment.</p>
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<p>Importance of variables in the study area in 2023.</p>
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<p>Precipitation prediction in regional stations using different scenarios for the period of 2031–2050.</p>
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<p>Monthly precipitation prediction using different scenarios for the period of 2031–2050 in (<b>a</b>) Gorgan station, (<b>b</b>) Gonbad station, (<b>c</b>) Kalaleh station and (<b>d</b>) Maraveh Tappeh station.</p>
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<p>Predicted land-use change between 2023 and 2040.</p>
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<p>(<b>a</b>) Rainfall scenario in 2040, (<b>b</b>) Land-use scenario in 2040, and (<b>c</b>) Desertification in 2040.</p>
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26 pages, 12380 KiB  
Article
Winch Traction Dynamics for a Carrier-Based Aircraft Under Trajectory Control on a Small Deck in Complex Sea Conditions
by Guofang Nan, Sirui Yang, Yao Li and Yihui Zhou
Aerospace 2024, 11(11), 885; https://doi.org/10.3390/aerospace11110885 - 27 Oct 2024
Viewed by 581
Abstract
When the winch traction system of a carrier-based aircraft works under complex sea conditions, the rope and the tire forces are greatly changed compared with under simple sea conditions, and it poses a potential threat to the safety and stability of the aircraft’s [...] Read more.
When the winch traction system of a carrier-based aircraft works under complex sea conditions, the rope and the tire forces are greatly changed compared with under simple sea conditions, and it poses a potential threat to the safety and stability of the aircraft’s traction system. The accurate calculation of the rope and tire forces of a carrier-based aircraft’s winch traction under complex sea conditions is an arduous problem. A novel method of dynamic analysis of the aircraft-winch-ship whole system under complex sea conditions is proposed. A multiple-frequency excitation is adopted to describe the complex sea conditions and the influences of pitching amplitude, and the rolling frequency on the traction dynamics of a carrier-based aircraft along the setting trajectory under complex sea conditions are studied. The advantages and disadvantages of a winch traction system with trajectory control and without trajectory control in complex sea conditions are analyzed. For realizing the trajectory control of the aircraft, the vector difference between the center of mass for the carrier-based aircraft and the position on the predetermined Bessel curve is calculated, so as to obtain the azimuth vector in the aircraft coordinate system. This research is innovative in the modeling of the whole system and the trajectory control of a carrier-based aircraft’s winch traction system under the complicated sea condition of the multi-frequency excitation. ADAMS (Automatic Dynamic Analysis of Mechanical System) is used to verify the correctness of the theoretical calculation for the winch traction. The results show that the complex sea environment has a certain influence on the winch traction safety of the aircraft; in the range of 10–15 s for the traction, the rope force amplitude of complex sea conditions under the multi-frequency excitation is 29.5% larger than that of the single-frequency amplitude, while the vertical force amplitude of the tire is 201.1% larger than that of the single-frequency amplitude. This research has important guiding significance for the selection of rope and tire models for a carrier-borne aircraft’s winch traction in complex sea conditions. Full article
(This article belongs to the Special Issue Advances in Thermal Fluid, Dynamics and Control)
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<p>Virtual prototyping model of the tractor–aircraft system [<a href="#B20-aerospace-11-00885" class="html-bibr">20</a>].</p>
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<p>Schematic diagram of aircraft winch traction.</p>
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<p>Schematic diagram of the whole system of carrier-based aircraft traction.</p>
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<p>Cardan Angles(The conversion relationships between different coordinate systems).</p>
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<p>The mathematical model of a landing gear-tire system in a <span class="html-italic">z</span>-direction.</p>
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<p>Schematic diagram of wind load.</p>
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<p>Graph of PID control for aircraft speed.</p>
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<p>The generated trajectory diagram (Bessel curve).</p>
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<p>Traveling trajectory diagram of the aircraft with the control (curve) (<b>a</b>) Planar view from <span class="html-italic">z</span> to −<span class="html-italic">z</span>; (<b>b</b>) Three-dimensional view.</p>
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<p>Traveling trajectory diagram of the aircraft without the control (straight line). (<b>a</b>) Planar view from <span class="html-italic">z</span> to <span class="html-italic">−z</span>; (<b>b</b>) Three-dimensional view.</p>
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<p>Curves of rope force changing with time under different pitching amplitudes (<span class="html-italic">θ</span><sub>1</sub> = 5°, 2°, 0.8° and 0.1°, <span class="html-italic">φ</span><sub>1</sub> = 5°).</p>
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<p>Curve of the vertical force of each tire over time (<span class="html-italic">φ</span><sub>1</sub> = 5°, <span class="html-italic">θ</span><sub>1</sub> = 2°).</p>
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<p>Curve of tire force over time in each direction for tire three (<span class="html-italic">φ</span><sub>1</sub> = 5°; <span class="html-italic">θ</span><sub>1</sub> = 2°).</p>
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<p>Curve of the vertical force of tire three over time at different pitching amplitudes (<span class="html-italic">θ</span><sub>1</sub> = 5°, 2°, 0.8° and 0.1°; <span class="html-italic">φ</span><sub>1</sub> = 5°).</p>
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<p>Curve of the force of the front rope over time at different rolling angle frequencies (<span class="html-italic">ω</span><sub>1</sub> = 2π/T<sub>φ1</sub> = 0.93 rad/s, 0.63 rad/s, 0.23 rad/s and 0.1rad/s; <span class="html-italic">φ</span><sub>1</sub> = 5°, <span class="html-italic">θ</span><sub>1</sub> = 2°).</p>
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<p>Curve of the vertical force of tire three changing with time at different rolling angle frequencies (<span class="html-italic">ω</span><sub>1</sub> = 2π/T<sub>φ1</sub> = 0.93 rad/s, 0.63 rad/s, 0.23 rad/s and 0.1 rad/s; <span class="html-italic">φ</span><sub>1</sub> = 5°; <span class="html-italic">θ</span><sub>1</sub> = 2°).</p>
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<p>Curve of the force of the front rope over time at different pitching amplitudes (<span class="html-italic">θ</span><sub>1</sub> = 2°, 0.8°, 0.4° and 0.1°; <span class="html-italic">θ</span><sub>2</sub> = 1°).</p>
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<p>Curve of the vertical force of tire three over time at different pitching amplitudes (<span class="html-italic">θ</span><sub>1</sub> = 2°, 0.8°, 0.4° and 0.1°; <span class="html-italic">θ</span><sub>2</sub> = 1°).</p>
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<p>Curve of the force of the front rope over time at different rolling angle frequencies (<span class="html-italic">ω</span><sub>2</sub> = 2π/T<sub>φ2</sub> = 2 rad/s, 1 rad/s, 0.63 rad/s and 0.23 rad/s).</p>
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<p>Curve of the vertical force of tire three changing with time at different rolling angle frequencies (<span class="html-italic">ω</span><sub>2</sub> = 2π/T<sub>φ2</sub> = 2 rad/s, 1 rad/s, 0.63 rad/s and 0.23 rad/s).</p>
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<p>Curve of the force of the front rope over time at different heaving amplitudes (<span class="html-italic">z</span><sub>1</sub> = 0.19 m, 0.1 m, 0.05 m, and 0.019 m).</p>
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<p>Curve of the vertical force of tire three over time at different heaving amplitudes (<span class="html-italic">z</span><sub>1</sub> = 0.19 m, 0.1 m, 0.05 m, and 0.019 m).</p>
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<p>Curve of the front rope force over time under single-frequency excitation and multi-frequency excitation with trajectory control.</p>
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<p>Curve of the vertical force of tire three over time under single-frequency excitation and multi-frequency excitation with trajectory control.</p>
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<p>Curve of the front rope force over time with trajectory control and without trajectory control under multi-frequency excitation.</p>
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<p>Curve of the vertical force of tire three over time with trajectory control and without trajectory control under multi-frequency excitation.</p>
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<p>Simulation of five-winch traction of aircraft.</p>
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<p>Local amplication view of landing gear in five-winch traction of aircraft.</p>
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<p>Front landing gear model.</p>
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<p>Rear landing gear model.</p>
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<p>Comparison of the front rope forces obtained by ADAMS and MATLAB.</p>
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<p>Comparison of vertical forces for tire three obtained by ADAMS and MATLAB.</p>
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21 pages, 5581 KiB  
Article
Reverse Vaccinology Integrated with Biophysics Techniques for Designing a Peptide-Based Subunit Vaccine for Bourbon Virus
by Taghreed N. Almanaa
Bioengineering 2024, 11(11), 1056; https://doi.org/10.3390/bioengineering11111056 - 23 Oct 2024
Viewed by 688
Abstract
Despite the seriousness of the disease carried by ticks, little is known about the Bourbon virus. Only three US states have recorded human cases of Bourbon virus (BRBV) infection; in all cases, a tick bite was connected with the onset of the illness. [...] Read more.
Despite the seriousness of the disease carried by ticks, little is known about the Bourbon virus. Only three US states have recorded human cases of Bourbon virus (BRBV) infection; in all cases, a tick bite was connected with the onset of the illness. The Bourbon virus (BRBV) belongs to the Orthomyxoviridae family and Thogotovirus genus, originating in the states of the US, i.e., Kansas, Oklahoma and Missouri. The growing rates of BRBV infections in various parts of the US highlight the necessity for a thorough analysis of the virus’s transmission mechanisms, vector types and reservoir hosts. Currently, there are no vaccines or efficient antiviral therapies to stop these infections. It is imperative to produce a vaccination that is both affordable and thermodynamically stable to reduce the likelihood of future pandemics. Various computational techniques and reverse vaccinology methodologies were employed to identify specific B- and T-cell epitopes. After thorough examination, the linker proteins connected the B- and T-cell epitopes, resulting in this painstakingly constructed vaccine candidate. Furthermore, 3D modeling directed the vaccine construct toward molecular docking to determine its binding affinity and interaction with TLR-4. Human beta-defensin was used as an adjuvant and linked to the N-terminus to boost immunogenicity. Furthermore, the C-IMMSIM simulation resulted in high immunogenic activities, with activation of high interferon, interleukins and immunoglobulin. The results of the in silico cloning process for E. coli indicated that the vaccine construct will try its utmost to express itself in the host, with a codon adaptation CAI value of 0.94. A net binding free energy of −677.7 kcal/mol obtained during docking showed that the vaccine has a high binding affinity for immunological receptors. Further validation was achieved via molecular dynamic simulations, inferring the confirmational changes during certain time intervals, but the vaccine remained intact to the binding site for a 100 ns interval. The thermostability determined using an RMSF score predicted certain changes in the mechanistic insights of the loop region with carbon alpha deviations, but no major changes were observed during the simulations. Thus, the results obtained highlight a major concern for researchers to further validate the vaccine’s efficacy using in vitro and in vivo approaches. Full article
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Graphical abstract

Graphical abstract
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<p>Flow chart of the current study depicting the protocol for predicting the multi-epitope vaccine construct.</p>
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<p>There are two distinct ways to view the final MEVC. (<b>A</b>,<b>B</b>) illustrate the arrangement of epitopes throughout the vaccine construct; (<b>C</b>) depicts the 3D model, with each component clearly colored, highlighting the vaccine folding and loop regions at N- and C-terminals.</p>
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<p>(<b>A</b>) depicts the Ramachandran plot with a confidence score; (<b>B</b>) shows the X-ray- and NMR-based prediction of the modeled vaccine construct; and (<b>C</b>) presents the sequence positioning in a 3D vaccine construct.</p>
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<p>A secondary structure diagram illustrating the presence of alpha helices (46.93%), beta strands (2.9%) and coils (51%) in the vaccine design with numerous epitopes.</p>
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<p>(<b>A</b>) depicts the binding pose of epitopes against nucleoprotein HTLs; (<b>B</b>) presents the binding pose of polymerase subunit PA HTLs in complex with epitopes.</p>
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<p>(<b>A</b>) shows the graphical insights of binding free energies for epitopes against nucleoprotein HTLs; (<b>B</b>) illustrates the binding free energies’ calculation of polymerase subunit PA HTLs in complex with the predicted epitopes.</p>
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<p>The red line, surrounded by a black circle, symbolizes the MEV’s restriction cloned into the pET28a(+) transcription vector in silico.</p>
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<p>MEBV in silico cloning and immune simulation investigations. (<b>A</b>) The amount of interleukin and interferon produced in milliliters per nanogram in response to MEBV. (<b>B</b>) The immunoglobulin response measured in microliters in response to the MEBV antigen.</p>
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<p>(<b>A</b>) TLR-4 receptor and vaccine with docked pose. The vaccine construct is shown in cyan and is also encoded by (C)<b>,</b> whereas the TLR-4 receptor networks A, B, C and D are colored green, red, yellow and pink, respectively. (<b>B</b>) shows the receptor’s interaction residues with vaccine construct encoded by (C).</p>
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<p>(<b>A</b>) An examination of the vaccine–TLR4 complexes and vaccine RMSD graphs at 100 ns time intervals. (<b>B</b>) The vaccine–TLR complexes’ RMSF plot. (<b>C</b>) The vaccine–TLR complexes’ H-bonds plot.</p>
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12 pages, 2363 KiB  
Article
Transcriptional Modulation of Plant Defense Genes by a Bipartite Begomovirus Promotes the Performance of Its Whitefly Vector
by Wen-Ze He, Shu-Sheng Liu and Li-Long Pan
Viruses 2024, 16(11), 1654; https://doi.org/10.3390/v16111654 - 23 Oct 2024
Viewed by 551
Abstract
The majority of plant viruses rely on insect vectors for inter-plant transmission. Amid virus transmission, vector-borne viruses such as begomoviruses may significantly modulate host plants in various ways and, in turn, plant palatability to insect vectors. While many case studies on monopartite begomoviruses [...] Read more.
The majority of plant viruses rely on insect vectors for inter-plant transmission. Amid virus transmission, vector-borne viruses such as begomoviruses may significantly modulate host plants in various ways and, in turn, plant palatability to insect vectors. While many case studies on monopartite begomoviruses are available, bipartite begomoviruses are understudied. More importantly, detailed elucidation of the molecular mechanisms involved is limited. Here, we report the mechanisms by which an emerging bipartite begomovirus, the Sri Lankan cassava mosaic virus (SLCMV), modulates plant defenses against whitefly. SLCMV infection of tobacco (Nicotiana tabacum) plants significantly downregulated defenses against whitefly, as whitefly survival and fecundity increased significantly on virus-infected plants when compared to the controls. We then profiled SLCMV-induced transcriptomic changes in plants and identified a repertoire of differentially expressed genes (DEGs). GO enrichment analysis of DEGs demonstrated that the term defense response was significantly enriched. Functional analysis of DEGs associated with defense response revealed that four downregulated DEGs, including putative late blight resistance protein homolog R1B-17 (R1B-17), polygalacturonase inhibitor-like (PGI), serine/threonine protein kinase CDL1-like (CDL1), and Systemin B, directly contributed to plant defenses against whitefly. Taken together, our findings elucidate the role of novel plant factors involved in the modulation of plant defenses against whitefly by a bipartite begomovirus and shed new light on insect vector–virus–host plant tripartite interactions. Full article
(This article belongs to the Special Issue Molecular Virus-Insect Interactions 2nd Edition)
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<p>Effect of SLCMV infection of tobacco plants on plant phenotype and whitefly performance. (<b>A</b>) picture of tobacco plants. Tobacco plants were inoculated with pBINPLUS (empty vector, control) or SLCMV DNA-A+DNA-B. At 25 days post inoculation, plants showing typical symptoms were used for photographing. (<b>B</b>,<b>C</b>) survival and fecundity of Asia II 1 whiteflies on tobacco plants. Ten Asia II 1 whiteflies were released into leaf-clip cages that were placed on tobacco leaves. Whitefly survival and fecundity were recorded seven days post whitefly release. N = 27 for B and C. * <span class="html-italic">p</span> &lt; 0.05 and ** <span class="html-italic">p</span> &lt; 0.01 (independent <span class="html-italic">t</span>-test).</p>
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<p>Pearson’s correlation coefficients of overall gene expression patterns between samples. The coefficient values are presented and indicated by the red color.</p>
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<p>Volcano plot of differentially expressed genes in SLCMV vs. pBINPLUS. The <span class="html-italic">x</span>-axis represents the log fold change, and the <span class="html-italic">y</span>-axis represents the log significance (<span class="html-italic">p</span> value). Blue dots represent downregulated genes, and red dots represent upregulated genes.</p>
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<p>Distribution of the top twenty GO terms in the GO database. The <span class="html-italic">Y</span>-axis represents the name of the GO term, and the <span class="html-italic">X</span>-axis indicates the rich factor. The <span class="html-italic">p</span> value was indicated by the color of the dots, and the number of genes in each term was indicated by the size of the dots.</p>
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<p>Effect of SLCMV infection of tobacco plants on the expression of DEGs. (<b>A</b>,<b>B</b>) expression of DEGs. Tobacco plants were inoculated with pBINPLUS (empty vector) and SLCMV DNA-A+DNA-B. Plants were sampled for gene expression analysis at 25 days post inoculation. The number of replicates was 5–6. * <span class="html-italic">p</span> &lt; 0.05 and ** <span class="html-italic">p</span> &lt; 0.01 (independent <span class="html-italic">t</span>-test).</p>
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<p>Effects of DEG silencing on whitefly performance. (<b>A</b>,<b>D</b>,<b>G</b>,<b>J</b>,<b>M</b>) Silencing efficiency; (<b>B</b>,<b>E</b>,<b>H</b>,<b>K</b>,<b>N</b>) survival rate of whiteflies on control and virus-induced gene silencing (VIGS) plants; (<b>C</b>,<b>F</b>,<b>I</b>,<b>L</b>,<b>O</b>) fecundity of whiteflies on control and VIGS plants. The number of replicates was 7–19 for (<b>A</b>,<b>D</b>,<b>G</b>,<b>J</b>,<b>M</b>) and 22–31 for (<b>B</b>,<b>C</b>,<b>E</b>,<b>F</b>,<b>H</b>,<b>I</b>,<b>K</b>,<b>L</b>,<b>N</b>,<b>O</b>). * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, and *** <span class="html-italic">p</span> &lt; 0.001 (independent <span class="html-italic">t</span>-test).</p>
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25 pages, 27207 KiB  
Article
From Data to Decision: Interpretable Machine Learning for Predicting Flood Susceptibility in Gdańsk, Poland
by Khansa Gulshad, Andaleeb Yaseen and Michał Szydłowski
Remote Sens. 2024, 16(20), 3902; https://doi.org/10.3390/rs16203902 - 20 Oct 2024
Viewed by 1028
Abstract
Flood susceptibility prediction is complex due to the multifaceted interactions among hydrological, meteorological, and urbanisation factors, further exacerbated by climate change. This study addresses these complexities by investigating flood susceptibility in rapidly urbanising regions prone to extreme weather events, focusing on Gdańsk, Poland. [...] Read more.
Flood susceptibility prediction is complex due to the multifaceted interactions among hydrological, meteorological, and urbanisation factors, further exacerbated by climate change. This study addresses these complexities by investigating flood susceptibility in rapidly urbanising regions prone to extreme weather events, focusing on Gdańsk, Poland. Three popular ML techniques, Support Vector Machine (SVM), Random Forest (RF), and Artificial Neural Networks (ANN), were evaluated for handling complex, nonlinear data using a dataset of 265 urban flood episodes. An ensemble filter feature selection (EFFS) approach was introduced to overcome the single-method feature selection limitations, optimising the selection of factors contributing to flood susceptibility. Additionally, the study incorporates explainable artificial intelligence (XAI), namely, the Shapley Additive exPlanations (SHAP) model, to enhance the transparency and interpretability of the modelling results. The models’ performance was evaluated using various statistical measures on a testing dataset. The ANN model demonstrated a superior performance, outperforming the RF and the SVM. SHAP analysis identified rainwater collectors, land surface temperature (LST), digital elevation model (DEM), soil, river buffers, and normalized difference vegetation index (NDVI) as contributors to flood susceptibility, making them more understandable and actionable for stakeholders. The findings highlight the need for tailored flood management strategies, offering a novel approach to urban flood forecasting that emphasises predictive power and model explainability. Full article
(This article belongs to the Special Issue Advances in GIS and Remote Sensing Applications in Natural Hazards)
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<p>Workflow of flood susceptibility mapping using topographical and environmental data, feature selection, machine learning classifiers, and SHAP analysis.</p>
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<p>The geographical location of the study area: map of Gdańsk, Poland (<b>bottom left</b>), Gdańsk in Pomeranian Voivodeship (<b>bottom right</b>), and a map of Gdańsk (<b>top</b>) showing flood event locations.</p>
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<p>Histograms and overlaid kernel density estimates illustrating the distribution of key features that are critical for flood susceptibility analyses at historical flood sites.</p>
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<p>Comparative analysis of feature rankings using four filter methods: ANOVA-F, gain ratio, mutual information, and correlation.</p>
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<p>Accuracy of ML classifier using different feature selection methods and EFFS.</p>
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<p>SHAP force plots for flood instances, showing the contribution of key features: (<b>a</b>) Contribution of key features for flood instance 1. (<b>b</b>) Contribution of key features for flood instance 2.</p>
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<p>SHAP force plots for non-flood instances, showing the contribution of key features: (<b>a</b>) Contribution of key features for non-flood instance 1. (<b>b</b>) Contribution of key features for non-flood instance 2.</p>
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<p>Explanation of models’ (<b>a</b>) SVM, (<b>b</b>) RF, and (<b>c</b>) ANN using SHAP. A cluster of data around the SHAP value of zero indicates a small impact on model output.</p>
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<p>ROC curves for training and test datasets for SVM, RF, and ANN under best parameter configuration.</p>
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<p>Flood susceptibility maps for SVM, RF, and ANN models.</p>
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<p>Flash flood-susceptible areas in Gdańsk; the top map shows the LULC with upper and lower terraces; the lower section features satellite images of specific areas (<b>A</b>–<b>D</b>), and a map indicating flood distribution across different districts, with colour gradients representing the number of floods.</p>
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<p>Spatial distribution of flood susceptibility factors: (<b>a</b>) DEM, (<b>b</b>) slope, (<b>c</b>) aspect, (<b>d</b>) TRI, (<b>e</b>) plan curvature, and (<b>f</b>) profile curvature.</p>
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<p>Spatial distribution of flood susceptibility factors: (<b>a</b>) SPI, (<b>b</b>) TWI, (<b>c</b>) NDVI, (<b>d</b>) NDWI, (<b>e</b>) LST, (<b>f</b>) distance from the coastline, (<b>g</b>) distance from the river network, and (<b>h</b>) distance from rainwater collectors.</p>
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<p>Spatial distribution of flood susceptibility factors: (<b>a</b>) LULC and (<b>b</b>) soil.</p>
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18 pages, 1609 KiB  
Article
Uncertainties of Economic Policy and Government Management Stability Played Important Roles in Increasing Suicides in Japan from 2009 to 2023
by Ruri Okubo, Ryusuke Matsumoto, Eishi Motomura and Motohiro Okada
Int. J. Environ. Res. Public Health 2024, 21(10), 1366; https://doi.org/10.3390/ijerph21101366 - 16 Oct 2024
Viewed by 743
Abstract
Standardized suicide mortality rates per 100,000 (SMRs) in Japan consistently decreased from 2009 to 2019 but increased from 2020. The causes of these temporal SMR fluctuations remain to be clarified. Therefore, this study was conducted to identify the causalities underlying the recently transformed [...] Read more.
Standardized suicide mortality rates per 100,000 (SMRs) in Japan consistently decreased from 2009 to 2019 but increased from 2020. The causes of these temporal SMR fluctuations remain to be clarified. Therefore, this study was conducted to identify the causalities underlying the recently transformed fluctuations of suicide mortality in Japan. Monthly suicide numbers disaggregated by sex and social standing, and political uncertainty indices, such as economic policy uncertainty (EPU) and government management instability (AENROP), were obtained from Japanese government databases. Interrupted time-series analysis was performed to analyze temporal fluctuations of SMRs disaggregated by sex/social standing associated with the three General Principles of Suicide Prevention Policy (GPSPP) periods and the COVID-19 pandemic. Panel data and vector autoregressive analyses were conducted to investigate causalities from political uncertainties to SMRs. During the first and second GPSPPs (2009–2017), all SMRs disaggregated by sex and social standing decreased, whereas those of unemployed females did not change. During the third GPSPP (2017–2022), decreasing trends in all SMRs were attenuated compared to previous periods. All female SMRs, except unemployed females, showed sharp increases synchronized with the pandemic outbreak. No male SMRs showed sharply increasing at the pandemic outbreak. SMRs of unemployed males/females drastically increased in the later periods of the pandemic, while SMRs of employed and multiple-person/single-person household males did not increase during the pandemic. SMR of unemployed males was positively related to AENROP but not EPU. Other male SMRs were positively related to EPU/AENROP. On the contrary, not all female SMRs were related to EPU/AENROP. Increasing AENROP generally contributed to increasing male SMRs throughout the observation period; however, susceptibility to AENROP and/or political information might have unexpectedly contributed to suppressing the sharply increasing male SMRs induced by large-scale social shocks (the COVID-19 pandemic outbreak) in Japan. Full article
(This article belongs to the Section Global Health)
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<p>Fluctuation in SDRs and uncertainty indices (EPU: economic policy uncertainty, and AENROP: government management instability) from January 2009 to June 2023 in Japan. Panels (<b>A</b>–<b>D</b>) indicated the trends and discontinuity of SDRs among males and females, EPU and AENROP, from January 2009 to June 2023 in Japan, respectively. Ordinates indicate the SDR (per 100,000 in the population) in panels (<b>A</b>,<b>B</b>) and EPU and AENROP indices in panels (<b>C</b>,<b>D</b>). Blue and red circles indicate the observed annualized monthly SDRs of males and females, respectively. Grey circles indicate the observed uncertainty indices value. Blue and red lines indicate the results calculated by ITSA with interventions from three GPSPP periods alone and GPSPP periods alongside the COVID-19 pandemic outbreak, respectively. Solid and dotted lines indicate the significant and non-significant trends or discontinuity detected by ITSA, respectively.</p>
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<p>Fluctuation in SMRs disaggregated by social standing from January 2009 to June 2023 in Japan. Panels (<b>A</b>–<b>D</b>) indicate the trends and discontinuity of SMRs of employed, unemployed individuals, multiple-person and single-person household residents from January 2009 to June 2023 in Japan, respectively. Panels (<b>A1</b>–<b>D1</b>) and (<b>A2</b>–<b>D2</b>) indicate male and female SMRs disaggregated by social standing, respectively. Ordinate and abscissa indicate the SMR (per 100,000 population) and years, respectively. Blue and red circles indicate the observed annualized monthly SMRs of males and females, respectively. Blue and red lines indicate the results calculated by ITSA with interventions of GPSPP alone and GPSPP with the COVID-19 pandemic outbreak, respectively. Solid and dotted lines indicate the significant and non-significant trends or discontinuity of SMRs detected by ITSA, respectively.</p>
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<p>Impulse responses of SDRs in males and females to AENROP and EPU indices. Impulse responses of SDRs in males (<b>A</b>,<b>B</b>) and females (<b>C</b>,<b>D</b>) to increasing one standard deviation (SD) of AENROP (<b>A</b>,<b>C</b>) and EPU (<b>B</b>,<b>D</b>) indices. Green lines and grey regions indicate the mean ± 95% confidence interval (CI) of responses, respectively.</p>
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