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36 pages, 3790 KiB  
Review
Hepatitis C Virus—Core Antigen: Implications in Diagnostic, Treatment Monitoring and Clinical Outcomes
by Duong Hoang Huy Le, Sitthichai Kanokudom, Ha Minh Nguyen, Ritthideach Yorsaeng, Sittisak Honsawek, Sompong Vongpunsawad and Yong Poovorawan
Viruses 2024, 16(12), 1863; https://doi.org/10.3390/v16121863 - 29 Nov 2024
Viewed by 36
Abstract
The hepatitis C virus (HCV) infection, a global health concern, can lead to chronic liver disease. The HCV core antigen (HCVcAg), a viral protein essential for replication, offers a cost-effective alternative to HCV RNA testing, particularly in resource-limited settings. This review explores the [...] Read more.
The hepatitis C virus (HCV) infection, a global health concern, can lead to chronic liver disease. The HCV core antigen (HCVcAg), a viral protein essential for replication, offers a cost-effective alternative to HCV RNA testing, particularly in resource-limited settings. This review explores the significance of HCVcAg, a key protein in the hepatitis C virus, examining its structure, function, and role in the viral life cycle. It also evaluates its clinical use in diagnosis and treatment monitoring, comparing its performance to the standard HCV RNA assay using data from PubMed and Google Scholar. HCVcAg assays show high pooled sensitivity (93.5%) and pooled specificity (99.2%) compared to HCV RNA assays, correlating closely (r = 0.87) with HCV RNA levels. Hence, HCVcAg testing offers a cost-effective way to diagnose active HCV infections and monitor treatment, especially in resource-limited settings, but its sensitivity can vary and standardization is needed. HCVcAg also predicts liver disease progression and assesses liver damage risk, aiding patient management. It helps to identify patients at risk for fibrosis or carcinoma, making it vital in hepatitis C care. HCVcAg testing can expand access to HCV care, simplify management, and contribute to global elimination strategies, especially in low- and middle-income countries. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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Figure 1

Figure 1
<p>Structure of HCV. E: envelope glycoprotein; ssRNA: single-stranded RNA. Created with <a href="https://www.biorender.com/" target="_blank">https://www.biorender.com/</a> (accessed on 8 September 2024).</p>
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<p>Phylogenetic tree of the eight HCV genotypes based on genomes from the NCBI Genbank. Sequences were aligned using MEGA v.11 software, and the tree was constructed with the maximum likelihood method based on the GTR+G+I substitution model (automatically determined by the software). The nomenclature used is genotype-subtype-accession number. The graphical representation was generated using the iTOL website.</p>
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<p>Structure of HCV genome depicting the structural and functional map of an HCV core protein. Created with <a href="https://www.biorender.com/" target="_blank">https://www.biorender.com/</a> (accessed on 15 September 2024).</p>
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<p>The HCV life cycle. Adapted from [<a href="#B17-viruses-16-01863" class="html-bibr">17</a>,<a href="#B21-viruses-16-01863" class="html-bibr">21</a>]. Created with <a href="https://www.biorender.com/" target="_blank">https://www.biorender.com/</a> (accessed on 12 October 2024).</p>
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<p>Summary of the algorithm for HCV testing and treatment according to WHO 2022 and recommendations when resources are limited. Adapted from [<a href="#B32-viruses-16-01863" class="html-bibr">32</a>,<a href="#B36-viruses-16-01863" class="html-bibr">36</a>]. Created with <a href="https://www.biorender.com/" target="_blank">https://www.biorender.com/</a> (accessed on 15 October 2024).</p>
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<p>The sensitivity, specificity, and correlation between HCVcAg and HCV RNA in various studies.</p>
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18 pages, 741 KiB  
Review
Salmonella enterica Serovar Infantis in Broiler Chickens: A Systematic Review and Meta-Analysis
by Alexandros Georganas, Giulia Graziosi, Elena Catelli and Caterina Lupini
Animals 2024, 14(23), 3453; https://doi.org/10.3390/ani14233453 - 28 Nov 2024
Viewed by 237
Abstract
Salmonella enterica subsp. enterica serovar Infantis poses a growing threat to public health, due to its increasing prevalence worldwide and its association with high levels of antimicrobial resistance. Among livestock, S. Infantis is especially isolated from broilers. Following the Preferred Reporting Items for [...] Read more.
Salmonella enterica subsp. enterica serovar Infantis poses a growing threat to public health, due to its increasing prevalence worldwide and its association with high levels of antimicrobial resistance. Among livestock, S. Infantis is especially isolated from broilers. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a systematic review was conducted by searching in three databases (Web of Science, Scopus, and PubMed) for English-language studies (1957–2023) that reported the prevalence of S. Infantis in broiler farms. Eligible studies included epidemiological investigations conducted in broiler chickens by sampling the house environment (flock-level prevalence) or the birds (individual-level prevalence). A random-effect model was applied to calculate S. Infantis pooled prevalence estimates with 95% confidence intervals (CIs). Furthermore, to assess between-study heterogeneity, the inconsistency index statistic (I2) was calculated. Among 537 studies retrieved, a total of 9 studies reporting flock-level prevalence of S. Infantis and 4 reporting individual-level prevalence were retained for analysis. The flock-level pooled prevalence was estimated to be 9% (95% CI: 1–26%) and a high between-study heterogeneity was found (I2 = 99%, p < 0.01). Concerning individual-level prevalence, a meta-analysis was not performed due to the scarcity of eligible studies. The data presented underscore the significant occurrence of S. Infantis in broilers at the farm level. By summarizing the existing literature, this work provides useful insights for conducting future surveys of Salmonella spp. in live broiler chickens as a preliminary step for developing more efficient control strategies. Full article
(This article belongs to the Section Poultry)
18 pages, 14095 KiB  
Article
Automated Stock Volume Estimation Using UAV-RGB Imagery
by Anurupa Goswami, Unmesh Khati, Ishan Goyal, Anam Sabir and Sakshi Jain
Sensors 2024, 24(23), 7559; https://doi.org/10.3390/s24237559 - 27 Nov 2024
Viewed by 155
Abstract
Forests play a critical role in the global carbon cycle, with carbon storage being an important carbon pool in the terrestrial ecosystem with tree crown size serving as a versatile ecological indicator influencing factors such as tree growth, wind resistance, shading, and carbon [...] Read more.
Forests play a critical role in the global carbon cycle, with carbon storage being an important carbon pool in the terrestrial ecosystem with tree crown size serving as a versatile ecological indicator influencing factors such as tree growth, wind resistance, shading, and carbon sequestration. They help with habitat function, herbicide application, temperature regulation, etc. Understanding the relationship between tree crown area and stock volume is crucial, as it provides a key metric for assessing the impact of land-use changes on ecological processes. Traditional ground-based stock volume estimation using DBH (Diameter at Breast Height) is labor-intensive and often impractical. However, high-resolution UAV (unmanned aerial vehicle) imagery has revolutionized remote sensing and computer-based tree analysis, making forest studies more efficient and interpretable. Previous studies have established correlations between DBH, stock volume and above-ground biomass, as well as between tree crown area and DBH. This research aims to explore the correlation between tree crown area and stock volume and automate stock volume and above-ground biomass estimation by developing an empirical model using UAV-RGB data, making forest assessments more convenient and time-efficient. The study site included a significant number of training and testing sites to ensure the performance level of the developed model. The findings underscore a significant association, demonstrating the potential of integrating drone technology with traditional forestry techniques for efficient stock volume estimation. The results highlight a strong exponential correlation between crown area and stem stock volume, with a coefficient of determination of 0.67 and mean squared error (MSE) of 0.0015. The developed model, when applied to estimate cumulative stock volume using drone imagery, demonstrated a strong correlation with an R2 of 0.75. These results emphasize the effectiveness of combining drone technology with traditional forestry methods to achieve more precise and efficient stock volume estimation and, hence, automate the process. Full article
(This article belongs to the Section Sensing and Imaging)
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Figure 1
<p>A flowchart of the methodology for automated stock volume estimation.</p>
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<p>Study area location map. This map shows the study area of the Indian Institute of Technology, which is situated in Indore city in the state of Madhya Pradesh.</p>
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<p>Drone data acquisition flowchart.</p>
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<p>Data collection using the drone. The figure (<b>a</b>) shows the setup of the communication box for the real-time tracking of the drone. Figure (<b>b</b>) shows the flight planning using BlueFire Touch software of v4.1.9047.1979 for the drone. During this stage, the waypoints for the drone flight were decided.</p>
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<p>Three different study sites were identified during this study. The locations where the drone imagery of the tree-covered areas was captured are shown here.</p>
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<p>Images of tree canopies captured by the drone at sites 1, 2, and 3.</p>
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<p>Field work performed for collecting DBH values. Figure (<b>a</b>) shows the geographic location data collection carried out using GARMIN eTrex 10, and Figure (<b>b</b>) depicts the DBH measurement of the tree trunks.</p>
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<p>Flowchart for tree crown delineation methodology.</p>
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<p>(<b>a</b>) and (<b>b</b>) show the measurement of DBH computed from the filed observations. (<b>a</b>) shows site 1, and (<b>b</b>) shows site 2.</p>
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<p>Tree crown delineation from the drone imagery for site 1 (<b>a</b>) and tree crown delineation from the drone imagery for site 2 (<b>b</b>).</p>
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<p>Tree crown delineation from the drone imagery for site 1 (<b>a</b>) and tree crown delineation from the drone imagery for site 2 (<b>b</b>).</p>
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<p>(<b>a</b>) shows the relationship between the tree trunk circumference and crown area. (<b>b</b>) shows the relationship between the DBH and tree crown.</p>
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<p>(<b>a</b>) shows the relationship between tree crown and stem volume. (<b>b</b>) shows the crown area data filtered. (<b>c</b>) shows the training data points for the model. (<b>d</b>) shows the testing data points of the model developed.</p>
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<p>(<b>a</b>) shows the values of stock volume from field measurements on the x-axis and for the model on the y-axis. (<b>b</b>) shows the values of the AGB from field measurements on the x-axis and for the model on the y axis. (<b>c</b>) shows the values of ton carbon from field measurements on the x-axis and the model in the y-axis (<b>d</b>) shows the values of tons/ha CO<sub>2</sub> emissions from field measurements on the x-axis and for the model on the y-axis.</p>
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<p>These plots show the accuracy assessment of the model by plotting the volumes computed by the model and the field measurements, respectively.</p>
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<p>These plots show the accuracy assessment of the model by plotting the AGB computed by the model and the field measurements, respectively.</p>
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<p>Validating the model for computing the cumulative stock volume.</p>
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29 pages, 2209 KiB  
Systematic Review
The Impact of Minerals on Female Fertility: A Systematic Review
by Celine Kapper, Patrick Stelzl, Peter Oppelt, Clara Ganhör, Ayberk Alp Gyunesh, Barbara Arbeithuber and Marlene Rezk-Füreder
Nutrients 2024, 16(23), 4068; https://doi.org/10.3390/nu16234068 - 27 Nov 2024
Viewed by 373
Abstract
Female fertility and reproductive system disorders are influenced by a complex interplay of biological, physiological, and environmental factors. Minerals have emerged as crucial yet often overlooked elements that impact fertility and the prevalence of reproductive system disorders. Background/Objectives: This review aims to provide [...] Read more.
Female fertility and reproductive system disorders are influenced by a complex interplay of biological, physiological, and environmental factors. Minerals have emerged as crucial yet often overlooked elements that impact fertility and the prevalence of reproductive system disorders. Background/Objectives: This review aims to provide a comprehensive overview of the multifaceted role of minerals in female fertility, focusing on key areas such as oocyte quality, ovulation, embryo development, oxidative stress, miscarriage, hormonal regulation, environmental exposure, and in-vitro fertilization (IVF) outcomes. Methods: A systematic review was conducted, focusing on randomized controlled trials (RCTs), prospective cohort studies, case-control studies, nested case-control, and observational studies examining mineral supplementation and nutrition in women planning pregnancy or utilizing assisted reproduction technologies (ARTs). Relevant literature was sourced from multiple electronic databases, including PubMed, Scopus, Google Scholar, Web of Science, and the Cochrane Library, using keywords related to minerals and female fertility. The quality of studies was assessed using the Newcastle–Ottawa Scale (NCO) for non-randomized studies and the Risk of Bias (RoB) tool for RCTs. This systematic review has been registered on PROSPERO (registration number is CDR 42024547656). Results: From an initial pool of 20,830 records, 39 articles met the inclusion criteria and were analyzed. The studies addressed various reproductive outcomes influenced by minerals: embryo development, oocyte quality, oxidative stress, miscarriage, hormonal regulation, IVF outcomes, environmental exposure, and minerals as biomarkers. The analysis revealed that minerals like selenium, zinc, and copper are essential for maintaining reproductive health, while exposure to toxic metals such as cadmium and lead is detrimental. Conclusions: This review highlights the crucial role of both mineral supplementation and serum mineral status in female fertility. The findings provide key insights for clinicians to improve reproductive health through targeted mineral intake and monitoring. Further research is needed to refine guidelines for supplementation and serum levels in women with fertility issues. Full article
(This article belongs to the Special Issue The Role of Nutrition in Gynecological Diseases)
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<p>Flowchart of the process to select and include studies for a systematic review of the impact of minerals on female fertility.</p>
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<p>Detailed Risk of Bias (RoB) assessment for randomized controlled trials.</p>
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<p>Aggregate Risk of Bias (RoB) as a percentage across bias domains.</p>
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<p>Frequency of study designs used (<span class="html-italic">n</span> = 39) and coefficients of fertility disorders included in the systematic review.</p>
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<p>Quality assessment using the Newcastle–Ottawa Scale in the systematic review of the impact of minerals on female fertility.</p>
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<p>Distribution of risk of bias for all studies included in the systematic review.</p>
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25 pages, 108807 KiB  
Article
SMEA-YOLOv8n: A Sheep Facial Expression Recognition Method Based on an Improved YOLOv8n Model
by Wenbo Yu, Xiang Yang, Yongqi Liu, Chuanzhong Xuan, Ruoya Xie and Chuanjiu Wang
Animals 2024, 14(23), 3415; https://doi.org/10.3390/ani14233415 - 26 Nov 2024
Viewed by 219
Abstract
Sheep facial expressions are valuable indicators of their pain levels, playing a critical role in monitoring their health and welfare. In response to challenges such as missed detections, false positives, and low recognition accuracy in sheep facial expression recognition, this paper introduces an [...] Read more.
Sheep facial expressions are valuable indicators of their pain levels, playing a critical role in monitoring their health and welfare. In response to challenges such as missed detections, false positives, and low recognition accuracy in sheep facial expression recognition, this paper introduces an enhanced algorithm based on YOLOv8n, referred to as SimAM-MobileViTAttention-EfficiCIoU-AA2_SPPF-YOLOv8n (SMEA-YOLOv8n). Firstly, the proposed method integrates the parameter-free Similarity-Aware Attention Mechanism (SimAM) and MobileViTAttention modules into the CSP Bottleneck with 2 Convolutions(C2f) module of the neck network, aiming to enhance the model’s feature representation and fusion capabilities in complex environments while mitigating the interference of irrelevant background features. Additionally, the EfficiCIoU loss function replaces the original Complete IoU(CIoU) loss function, thereby improving bounding box localization accuracy and accelerating model convergence. Furthermore, the Spatial Pyramid Pooling-Fast (SPPF) module in the backbone network is refined with the addition of two global average pooling layers, strengthening the extraction of sheep facial expression features and bolstering the model’s core feature fusion capacity. Experimental results reveal that the proposed method achieves a [email protected] of 92.5%, a Recall of 91%, a Precision of 86%, and an F1-score of 88.0%, reflecting improvements of 4.5%, 9.1%, 2.8%, and 6.0%, respectively, compared to the baseline model. Notably, the [email protected] for normal and abnormal sheep facial expressions increased by 3.7% and 5.3%, respectively, demonstrating the method’s effectiveness in enhancing recognition accuracy under complex environmental conditions. Full article
(This article belongs to the Section Small Ruminants)
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<p>Images of Eyes, Ears, and Nose compliant with SPFES.</p>
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<p>A selection of sheep facial expression images (<b>a</b>) for normal (<b>b</b>) for abnormal.</p>
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<p>Augmentation techniques for abnormal sheep facial expression image data.</p>
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<p>Annotation of sheep facial expression dataset.</p>
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<p>Architecture of the SMEA-YOLOv8n model for sheep facial expression recognition.</p>
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<p>Diagram of the YOLOv8n model architecture.</p>
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<p>Architecture of the SimAM Attention module.</p>
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<p>Architecture of the MobileViTAttention module.</p>
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<p>Architecture of the improved SPPF module: (<b>a</b>) SPPF structural diagram. (<b>b</b>) AA2_SPPF structural diagram.</p>
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<p>Comparative mAP@0.5 evaluation of enhanced sheep facial expression models.</p>
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<p>Comparison of P-R curves before and after model enhancement. (<b>a</b>) P-R curve in YOLOv8n. (<b>b</b>) P-R curve in SMEA-YOLOv8n.</p>
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<p>Comparison of F1-score curves before and after model enhancement. (<b>a</b>) F1-score curve in YOLOv8n. (<b>b</b>) F1-score curve in SMEA-YOLOv8n.</p>
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<p>Visual comparison of sheep facial expression recognition pre- and post-YOLOv8n model enhancements.</p>
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<p>Comparative analysis of mAP@0.5, Precision, and Recall across various YOLOv8n model enhancements.</p>
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27 pages, 5437 KiB  
Article
Multiple Myeloma Cells with Increased Proteasomal and ER Stress Are Hypersensitive to ATX-101, an Experimental Peptide Drug Targeting PCNA
by Camilla Olaisen, Lisa Marie Røst, Animesh Sharma, Caroline Krogh Søgaard, Tiffany Khong, Sigrid Berg, Mi Jang, Aina Nedal, Andrew Spencer, Per Bruheim and Marit Otterlei
Cancers 2024, 16(23), 3963; https://doi.org/10.3390/cancers16233963 - 26 Nov 2024
Viewed by 354
Abstract
Objectives: To examine the regulatory role of PCNA in MM, we have targeted PCNA with the experimental drug ATX-101 in three commercial cell lines (JJN3, RPMI 1660, AMO) and seven in-house patient-derived cell lines with a more primary cell-like phenotype (TK9, 10, [...] Read more.
Objectives: To examine the regulatory role of PCNA in MM, we have targeted PCNA with the experimental drug ATX-101 in three commercial cell lines (JJN3, RPMI 1660, AMO) and seven in-house patient-derived cell lines with a more primary cell-like phenotype (TK9, 10, 12, 13, 14, 16 and 18) and measured the systemic molecular effects. Methods: We have used a multi-omics untargeted approach, measuring the gene expression (transcriptomics), a subproteomics approach measuring mainly signalling proteins and proteins in complex with these (signallomics) and quantitative metabolomics. These results are supplemented with traditional analysis, e.g., viability, Western and ELISA analysis. Results: The sensitivity of the cell lines to ATX-101 varied, including between three cell lines derived from the same patient at different times of disease. A trend towards increased sensitivity to ATX-101 during disease progression was detected. Although with different sensitivities, ATX-101 treatment resulted in numerous changes in signalling and metabolite pools in all cell lines. Transcriptomics and signallomics analysis of the TK cell lines revealed that elevated endogenous expression of ribosomal genes, elevated proteasomal and endoplasmic reticulum (ER) stress and low endogenous levels of NAD+ and NADH were associated with ATX-101 hypersensitivity. ATX-101 treatment further enhanced the ER stress, reduced primary metabolism and reduced the levels of the redox pair GSH/GSSG in sensitive cells. Signallome analysis suggested that eleven proteins (TPD52, TNFRS17/BCMA, LILRB4/ILT3, TSG101, ZNRF2, UPF3B, FADS2, C11orf38/SMAP, CGREF1, GAA, COG4) were activated only in the sensitive MM cell lines (TK13, 14 and 16 and JJN3), and not in nine other cancer cell lines or in primary monocytes. These proteins may therefore be biomarkers of cells with activated proteasomal and ER stress even though the gene expression levels of these proteins were not elevated. Interestingly, carfilzomib-resistant cells were at least as sensitive to ATX-101 as the wild-type cells, suggesting both low cross-resistance between ATX-101 and proteasome inhibitors and elevated proteasomal stress in carfilzomib-resistant cells. Conclusions: Our multi-omics approach revealed a vital role of PCNA in regulation of proteasomal and ER stress in MM. Full article
(This article belongs to the Section Tumor Microenvironment)
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Figure 1
<p>Systemic changes after ATX-101 treatment of MM cells lead to reduced primary metabolism, increased ER stress and reduced redox capacity. (<b>A</b>) Log2 fold change in proteins detected by MIB assay performed on extract from JJN3 cells treated with ATX-101 (6 µM) for 4 h. Proteins in bold are mentioned specifically in the text. Data shown are mean of three repeated experiments relative to untreated control. Dark-coloured bars indicate significant change from untreated control (Wilcoxon sign rank test). (<b>B</b>) Top up- and downregulated STRING GO (KEGG) pathways based on significantly changed proteins in the MIB assays according to the Wilcoxon sign rank test. (<b>C</b>) Number of DE genes (upper panel) and up/downregulated DE genes in specific pathways (lower panel) in JJN3 cells after 24 h of APIM- or ATX-A (6 µM) treatment. M denotes that the gene product also was detected by the MIB assay. Average of three repeated experiments for 24 h and two repeated experiments for 4 and 8 h (included only if same trend in both) is shown. Dark-coloured circles are DE genes in three out of three replicates, while light-coloured circles are DE genes in two out of three replicates. (<b>D</b>) Average GSH levels after ATX-101 (6 µM: JJN3, RPMI 8226, HL60 and DU145 or 8 µM: HEK293) treatment for 4 and 24 h. Data based on triplicates from two (JJN3, HEK293 and RPMI 8226) or three (DU145 and HL60) repeated experiments. (<b>E</b>) Average HIF1A protein levels (fg/cell) in JJN3 cells 4, 8, 12 and 24 h after treatment with ATX-101 (8 µM) ± SD, <span class="html-italic">n</span> = 3. (<b>F</b>) Average viability relative to untreated control cells measured by the MTT assay in JJN3 cells treated with ATX-101 (6 µM) under atmospheric O<sub>2</sub> tension (normoxia) or 1% O<sub>2</sub> (hypoxia) at 24 h ± SD, <span class="html-italic">n</span> = 10. Data from one representative out of two repeated experiments are shown. * <span class="html-italic">p</span> ≤ 0.5, ** <span class="html-italic">p</span> ≤ 0.01, <span class="html-italic">t</span>-test. These results were previously published in [<a href="#B48-cancers-16-03963" class="html-bibr">48</a>].</p>
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<p>Sensitive TK cells have elevated expression of genes involved in translation (<b>A</b>) Viability measured by the MTT assay relative to untreated control presented for TK9, 10, 12, 13, 14, 16 and 18 cell lines on day 4 after treatment with ATX-101 (4 or 8 µM), melphalan (1 µM) and the combination of ATX-101 (8 µM) and melphalan. The average of 6 replicate wells from one representative out of two repeated experiments is shown. (<b>B</b>) Expression of genes in GO:0022626, cytosolic ribosome and cluster analysis for TK9, 10, 12, 13, 14, 16 and 18. Bolded italic genes have increased expression in TK13 and TK14 compared to TK12. (<b>C</b>) Selected biological processes (GO) of genes downregulated in sensitive (TK13, 14 and 16) relative to not sensitive (TK9, 10, 12 and 18) cells. GO network analysis revealed networks with 153 nodes/126 edges and a PPI enrichment <span class="html-italic">p</span>-value of 1.08 × 10<sup>–9</sup>. A subnetwork where proteins in VEGF (purple)/MAPK (green) and PI3K (yellow) signalling pathways is shown.</p>
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<p>Sensitivity to ATX-101 increases with increasing ER stress. (<b>A</b>) Hierarchical clustering of all quantified protein groups in controls (untreated) TK12, 13, 14 and 16 cells. Cell line over grey box is less sensitive to ATX-101. (<b>B</b>) Top KEGG pathways enriched in clusters 1, 2 and 3 shown in (<b>A</b>), identified by STRING GO analysis. (<b>C</b>) Top KEGG pathways found in the only cluster (same analysis as in (<b>A</b>)) with increasing pull-down of proteins from TK12-16- in ATX-101-treated cells. (<b>D</b>) Cluster analysis of all proteins in untreated and ATX-101-treated cells belonging to GO:003476, response to ER stress. Same heat maps with protein identifications are shown in <a href="#app1-cancers-16-03963" class="html-app">Supplementary Figure S3</a>. Data from 3–5 independent biological replica are shown.</p>
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<p>ATX-101 affects multiple signalling pathways differently in TK13, 14 and 16 versus TK12. (<b>A</b>) Venn diagram of proteins pulled down from ATX-101 (10 µM)-treated TK12, TK13, TK14 and TK16 cell extracts using MIB assay. Only proteins that are significantly changed from untreated control (changed in same direction in extracts from all three repeated experiments, Wilcoxon sign rank test) are shown. Full data set is deposit in PXD033510. (<b>B</b>) Enriched KEGG pathways (STRING) of proteins changed after ATX-101 treatment (10 µM) in in TK13, TK14 and TK16 (120 proteins) relative to untreated control. (<b>C</b>) Heat map of changes in proteins involved in metabolism (only including proteins significantly changed in more than 2 of the sensitive cell lines). Cell line over grey box is less sensitive to ATX-101. (<b>D</b>) Heat map of selected proteins involved in glycolysis, energy metabolism, proteasome, PI3K/AKT/mTOR, MAPK, STAT and apoptosis that changed in opposite directions in TK12 versus the sensitive cell lines (TK13, TK14 and TK16) (proteins significantly changed in more than 1 of the sensitive cell lines are included, for full pathway analysis see <a href="#app1-cancers-16-03963" class="html-app">Supplementary Figure S4</a>). Full data set is deposit in PXD033510.</p>
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<p>Reduced primary metabolism detected after ATX-101 treatment in ATX-101-sensitive cell lines. Log2 fold change (FC) of central carbon metabolites relative to untreated control measured in TK9, TK10, TK12, TK13, TK14 and TK16 cell lines treated with ATX-101 (10 µM) for 4 h. Average given relative to untreated control. Cell lines over grey boxes are less sensitive to ATX-101. Values are from <span class="html-italic">n</span> = 2–3 independent experiments. All sample concentrations are normalised to total protein in the extracts.</p>
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<p>The GSH/GSSG ratio is reduced after ATX-101 treatment in the TK cell lines that also respond to treatment with a metabolic shift. (<b>A</b>) Intracellular GSH levels (nmol/g protein) in untreated and ATX-101-treated (10 µM, 4 h) TK cell lines. Mean ± SD from three replicate cultures. (<b>B</b>) Change relative to untreated control (%) in GSH/GSSH ratio in ATX-101 treated (10 µM, 4 h) TK cell lines. Mean from three replicate cultures. (<b>C</b>) Endogenous intracellular NAD+ and NADH levels (nmol/g protein) in TK cell lines. Mean ± SD from three replicate cultures. TK16 levels &lt; limit of quantification (LOQ). (<b>D</b>) 6PGD activity in TK16 cells treated with ATX-101 (orange, 10 µM), ATX-A (brown, 10 µM) or the 6PGD-inhibitor ebselen (blue, 30 µM) for 4 h relative to activity in untreated control cells. Data displayed are mean ± SD (<span class="html-italic">n</span> = 3). (<b>E</b>) Protein levels of ENO1, 6PGD, GAPDH and PCNA in TK16 cells treated with ATX-101 (orange, 10 µM) or ATX-A (brown, 10 µM) for 24 h. Protein levels are normalised against H3 levels and relative to protein levels in untreated control cells. Data are displayed as mean ± SD (<span class="html-italic">n</span> = 3, ENO1 and 6PGD) or just mean (<span class="html-italic">n</span> = 2, GAPDH and PCNA). Representative Western blots are shown below the bars. (<b>F</b>) Protein levels of AKT and AKT-p in the panel of untreated TK cell lines arranged by increase in sensitivity towards ATX-101. Proteins are normalised to EIF2S1 levels and presented as relative to TK18 levels as mean ± SD (<span class="html-italic">n</span> = 3). * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001, unpaired two-tailed Student <span class="html-italic">t</span>-test. Representative Western blots are shown below the bars. Raw data and intensity measurements of Western blots in (<b>E</b>) and (<b>F</b>) are shown in <a href="#app1-cancers-16-03963" class="html-app">Supplementary Figures S8 and S9</a>, respectively.</p>
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<p>Potential biomarkers for ATX-101-sensitive MM cells. (<b>A</b>) Venn diagram of proteins pulled down from untreated TK12, TK13, TK14 and TK16 cell extracts using the MIB assay. Only proteins that are significantly changed from untreated control (similar change in extracts from all three repeated experiments, Wilcoxon sign rank test) are shown. Full data set is deposit in PXD033510. (<b>B</b>) Proteins out of the 39 proteins marked with red ring in A which are also detected in JJN3 but not in MCCAR, NB4, HL60, primary human monocytes from three donors [<a href="#B6-cancers-16-03963" class="html-bibr">6</a>], PXD028314, PXD017474), UmUc-3, T24 ([<a href="#B5-cancers-16-03963" class="html-bibr">5</a>] PXD011044), U2OS, H460, A549 [<a href="#B30-cancers-16-03963" class="html-bibr">30</a>] (PXD005286) or TK9 (PXD033531). Only proteins that are significantly changed from untreated control (similar change in extracts from all three repeated experiments, Wilcoxon sign rank test) are included.</p>
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<p>Proteasome inhibitor-resistant MM cells remain sensitive to ATX-101. Dose response of carfilzomib (0.032 to 2500 nM, blue) (<b>A</b>) and ATX-101 (2–12 μM, orange), (<b>B</b>) in sensitive (AMO-1, blank) and carfilzomib (CFZ)-resistant (AMO-CFZ, diagonal stripes) AMO-1 cells. (<b>C</b>) Single agent and combination treatments of CFZ and ATX-101; 0.8 nM CFZ and 6 μM ATX-101 on AMO-1 ((<b>left</b>) panel) and 250 nM CFZ and 2 μM ATX-101 on AMO-CFZ cells ((<b>right</b>) panel). All data presented are from the PrestoBlue assay on day 4 after treatment. The average of 4–6 replicate wells from one representative out of two repeated experiments is shown. Data are normalised to untreated control.</p>
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13 pages, 2618 KiB  
Review
Fecal Microbiota Transplantation for Chronic Pouchitis: A Systematic Review and Meta-Analysis
by Magnus Chun, Kyaw Min Tun, Tahne Vongsavath, Renuka Verma, Kavita Batra, David Limsui and Erin Jenkins
Microorganisms 2024, 12(12), 2430; https://doi.org/10.3390/microorganisms12122430 - 26 Nov 2024
Viewed by 314
Abstract
Pouchitis is a common complication after ileal-pouch anal anastomosis in patients with medically refractory ulcerative colitis. There has been a lack of high-level evidence focusing on the safety and efficacy outcomes of fecal microbiota transplantation (FMT). We aim to evaluate outcomes and complications [...] Read more.
Pouchitis is a common complication after ileal-pouch anal anastomosis in patients with medically refractory ulcerative colitis. There has been a lack of high-level evidence focusing on the safety and efficacy outcomes of fecal microbiota transplantation (FMT). We aim to evaluate outcomes and complications of fecal microbiota transplantation (FMT) for chronic pouchitis. Databases were systematically searched to retrieve English-only, original studies, published from inception to 31 March 2024, investigating chronic pouchitis only. Primary outcomes included overall remission, clinical response, remission, relapse, and complications. Seven studies with 94 patients were included. The pooled overall remission rate was 15% (95% CI: 0–29%, p < 0.001), the clinical response rate was 33% (95% CI: 19–46%, p = 0.14), the clinical remission rate was 14% (95% CI: 19–46%, p < 0.001), and the clinical relapse rate was 36% (95% CI: 16–55%, p = 0.11). The pooled proportion of patients with mild adverse events after FMT treatment was 39% (95% CI: 6–71%, p < 0.001). No severe adverse events or deaths were reported. Although FMT is an effective treatment for chronic pouchitis, there is still a high rate of mild adverse events. High-level evidence for FMT is still sparse, limiting recommendations for clinical use. Full article
(This article belongs to the Special Issue Advances in Viral Disease Epidemiology and Molecular Pathogenesis)
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<p>FMT treatment forest plots of (<b>A</b>) pooled proportion of overall remission, (<b>B</b>) pooled proportion of clinical response, (<b>C</b>) pooled proportion of clinical remission, and (<b>D</b>) pooled proportion of clinical relapse [<a href="#B5-microorganisms-12-02430" class="html-bibr">5</a>,<a href="#B13-microorganisms-12-02430" class="html-bibr">13</a>,<a href="#B14-microorganisms-12-02430" class="html-bibr">14</a>,<a href="#B15-microorganisms-12-02430" class="html-bibr">15</a>,<a href="#B16-microorganisms-12-02430" class="html-bibr">16</a>,<a href="#B17-microorganisms-12-02430" class="html-bibr">17</a>,<a href="#B18-microorganisms-12-02430" class="html-bibr">18</a>].</p>
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<p>Forest plot of pooled proportion of complications/adverse events for FMT treatment at 4 week follow-up [<a href="#B5-microorganisms-12-02430" class="html-bibr">5</a>,<a href="#B13-microorganisms-12-02430" class="html-bibr">13</a>,<a href="#B14-microorganisms-12-02430" class="html-bibr">14</a>,<a href="#B15-microorganisms-12-02430" class="html-bibr">15</a>,<a href="#B16-microorganisms-12-02430" class="html-bibr">16</a>,<a href="#B18-microorganisms-12-02430" class="html-bibr">18</a>].</p>
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<p>Forest plot of pooled proportion of (<b>A</b>) overall remission for FMT treatment at 4 week follow-up, moderated by country in which the study took place, and (<b>B</b>) clinical response for FMT treatment at 4 week follow-up, moderated by country in which the study took place [<a href="#B5-microorganisms-12-02430" class="html-bibr">5</a>,<a href="#B13-microorganisms-12-02430" class="html-bibr">13</a>,<a href="#B14-microorganisms-12-02430" class="html-bibr">14</a>,<a href="#B15-microorganisms-12-02430" class="html-bibr">15</a>,<a href="#B16-microorganisms-12-02430" class="html-bibr">16</a>,<a href="#B17-microorganisms-12-02430" class="html-bibr">17</a>,<a href="#B18-microorganisms-12-02430" class="html-bibr">18</a>].</p>
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<p>Forest plot of pooled proportion of (<b>A</b>) overall remission for FMT treatment at 4 week follow-up, moderated by donor source (single versus multiple donor subgroups) and (<b>B</b>) clinical response for FMT treatment at 4 week follow-up moderated by donor source (single versus multiple donor subgroups) [<a href="#B5-microorganisms-12-02430" class="html-bibr">5</a>,<a href="#B13-microorganisms-12-02430" class="html-bibr">13</a>,<a href="#B14-microorganisms-12-02430" class="html-bibr">14</a>,<a href="#B15-microorganisms-12-02430" class="html-bibr">15</a>,<a href="#B16-microorganisms-12-02430" class="html-bibr">16</a>,<a href="#B17-microorganisms-12-02430" class="html-bibr">17</a>,<a href="#B18-microorganisms-12-02430" class="html-bibr">18</a>].</p>
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13 pages, 1168 KiB  
Article
Dynamics of PCV2 and PCV3 in the Serum and Oral Fluids of Pigs After PCV2 Vaccination in a Commercial Farm
by Jesús Hernández, Yuly A. Henao-Díaz, Mónica Reséndiz-Sandoval, Angel Cota-Valdez, Verónica Mata-Haro and Luis G. Gimenez-Lirola
Vaccines 2024, 12(12), 1318; https://doi.org/10.3390/vaccines12121318 - 26 Nov 2024
Viewed by 376
Abstract
Objectives: This study investigated the dynamics of porcine circovirus type 2 (PCV2) and PCV3 on a commercial farm following PCV2 vaccination. Methods: Serum samples from 35 pigs, starting at 3 weeks of age, were collected weekly until 21 weeks of age. Oral fluids [...] Read more.
Objectives: This study investigated the dynamics of porcine circovirus type 2 (PCV2) and PCV3 on a commercial farm following PCV2 vaccination. Methods: Serum samples from 35 pigs, starting at 3 weeks of age, were collected weekly until 21 weeks of age. Oral fluids from six pens of pigs of the same age were also analyzed. Viral DNA was assessed in pooled sera and individual oral fluid samples, while antibodies (IgG and IgA) were measured in the serum and oral fluids. Productive parameters, including weekly mortality and cumulative mortality, were evaluated. Results: The results revealed that PCV2 and PCV3 co-infection was detected in pigs at 8 weeks of age, with PCV3 being detected in oral fluids two weeks earlier. PCV3 DNA was detected in oral fluids at 4 weeks of age. PCV2 IgG antibodies in the serum increased gradually after vaccination, peaking at 7 weeks of age, then declined and stabilized until 21 weeks of age. PCV3 IgG antibodies fluctuated early but were uniformly positive after 13 weeks of age. In oral fluids, PCV2 IgG and IgA antibodies showed a strong response only at 3 and 23 weeks of age. In contrast, a strong and consistent IgG response was observed in oral fluids in the absence of PCV2 and PCV3 co-infection of pigs at 3 to 11 weeks of age. The farm’s productive parameters remained stable throughout the study. Conclusions: These findings suggest that PCV2 and PCV3 co-infection, along with high PCV3 detection levels in serum and oral fluids, may have an impact on the efficacy of PCV2 vaccination. Full article
(This article belongs to the Special Issue Immunization Strategies for Animal Health)
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<p>Experimental design. This study comprised two separate investigations: a longitudinal study and a cross-sectional study. The longitudinal study evaluated PCV2 and PCV3 viremia, as well as the presence of IgG antibodies against PCV2 and PCV3 in the serum. Additionally, viral loads and IgG and IgA antibodies against PCV2 and PCV3 in oral fluids were quantified in pens of pigs aged 3 to 25 weeks. The cross-sectional study measured viral loads and IgG and IgA antibodies against PCV2 and PCV3 in oral fluids from pens of pigs aged 3 to 11 weeks.</p>
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<p>Cumulative mortality rates at Sites 2 and 3. Pigs were vaccinated against PCV2 at 3 weeks of age.</p>
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<p>Serum IgG antibodies against PCV2 and PCV3. Serum samples were collected weekly from 35 pigs aged 3 to 21 weeks and tested for IgG antibodies against the CAP protein of PCV2 and PCV3. Each data point represents an individual pig, with the dotted line indicating the test cutoff. The results are expressed as the absorbance at 450 nm. Significant differences between weeks are shown above the data points.</p>
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<p>PCV2 and PCV3 IgG and IgA antibodies in oral fluids. Oral fluid samples were collected weekly from six pens of pigs aged 3 to 21 weeks and tested for IgG and IgA antibodies against the CAP protein of PCV2 and PCV3. Each data point represents an individual oral fluid sample, with the dotted line indicating the test cutoff. The results are expressed as the absorbance at 450 nm.</p>
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<p>PCV2 and PCV3 IgG and IgA antibodies in oral fluids: cross-sectional study. Six oral fluid samples were collected weekly from pens of pigs aged 3 to 11 weeks and evaluated for the presence of IgG and IgA antibodies against the CAP protein of PCV2 or PCV3. Each data point represents an individual oral fluid sample, with the dotted line indicating the test cutoff. The results are expressed as the absorbance at 450 nm.</p>
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10 pages, 1745 KiB  
Review
Increased Leptin Levels in Plasma and Serum in Patients with Metabolic Disorders: A Systematic Review and Meta-Analysis
by Yazmín Hernández-Díaz, María de los Ángeles Ovando-Almeida, Ana Fresán, Isela Esther Juárez-Rojop, Alma Delia Genis-Mendoza, Humberto Nicolini, Thelma Beatriz González-Castro, Carlos Alfonso Tovilla-Zárate and María Lilia López-Narváez
Int. J. Mol. Sci. 2024, 25(23), 12668; https://doi.org/10.3390/ijms252312668 - 26 Nov 2024
Viewed by 265
Abstract
A large number of studies have reported the relationships between leptin levels and diabetes or obesity. However, the results are still controversial, and no consensus has been reached. Therefore, the purpose of the study was to collect data from various databases to perform [...] Read more.
A large number of studies have reported the relationships between leptin levels and diabetes or obesity. However, the results are still controversial, and no consensus has been reached. Therefore, the purpose of the study was to collect data from various databases to perform a meta-analysis and address the inconsistencies in these studies. A systematic literature search was conducted on PubMed, Web of Science, and EBSCO for relevant available articles. The pooled standard mean difference (SMD) with 95% confidence interval (CI) was used to estimate the association by a meta-analysis. Fifteen reports with 1,388 cases and 3,536 controls were chosen for the meta-analysis. First, an increase in leptin levels in serum (SMD 0.69; 95% CI 0.36–1.02 ng/mL) and plasma (SMD 0.46; 95% CI 0.18–0.74 ng/mL) was observed in individuals with diabetes compared to controls. This increased level was also observed by gender and population. Second, statistical analysis showed that leptin levels in serum were significantly increased in individuals with obesity (SMD 1.03; 95% CI 0.72–1.34 ng/mL). This meta-analysis analyzed leptin in individuals with diabetes or obesity and emphasized the importance of monitoring serum/plasma leptin levels in patients with these diseases. However, more comprehensive studies are necessary in order to draw firm conclusions. Full article
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<p>PRISMA flowchart of the inclusion process.</p>
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<p>Meta-analysis of leptin levels in patients with diabetes compared to healthy controls (I<sup>2</sup> = 21.72) [<a href="#B12-ijms-25-12668" class="html-bibr">12</a>,<a href="#B15-ijms-25-12668" class="html-bibr">15</a>,<a href="#B16-ijms-25-12668" class="html-bibr">16</a>,<a href="#B17-ijms-25-12668" class="html-bibr">17</a>].</p>
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<p>Meta-analysis of leptin levels in patients with obesity compared to healthy controls (I<sup>2</sup> = 00.00) [<a href="#B5-ijms-25-12668" class="html-bibr">5</a>,<a href="#B11-ijms-25-12668" class="html-bibr">11</a>,<a href="#B14-ijms-25-12668" class="html-bibr">14</a>].</p>
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<p>Funnel plot for studies in leptin levels for subjects with diabetes (<b>A</b>) or obesity (<b>B</b>) versus control subjects.</p>
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21 pages, 4501 KiB  
Article
A Deep Learning-Based Method for Bearing Fault Diagnosis with Few-Shot Learning
by Yang Li, Xiaojiao Gu and Yonghe Wei
Sensors 2024, 24(23), 7516; https://doi.org/10.3390/s24237516 - 25 Nov 2024
Viewed by 308
Abstract
To tackle the issue of limited sample data in small sample fault diagnosis for rolling bearings using deep learning, we propose a fault diagnosis method that integrates a KANs-CNN network. Initially, the raw vibration signals are converted into two-dimensional time-frequency images via a [...] Read more.
To tackle the issue of limited sample data in small sample fault diagnosis for rolling bearings using deep learning, we propose a fault diagnosis method that integrates a KANs-CNN network. Initially, the raw vibration signals are converted into two-dimensional time-frequency images via a continuous wavelet transform. Next, Using CNN combined with KANs for feature extraction, the nonlinear activation of KANs helps extract deep and complex features from the data. After the output of CNN-KANs, an FAN network module is added. The FAN module can employ various feature aggregation strategies, such as weighted averaging, max pooling, addition aggregation, etc., to combine information from multiple feature levels. To further tackle the small sample issue, data generation is performed on the original data through diffusion networks under conditions of fewer samples for bearings and tools, thereby increasing the sample size of the dataset and enhancing fault diagnosis accuracy. Experimental results demonstrate that, under small sample conditions, this method achieves higher accuracy compared to other approaches. Full article
(This article belongs to the Section Fault Diagnosis & Sensors)
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<p>Methodology of the proposed research work.</p>
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<p>The detailed differences between MLP and KAN.</p>
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<p>A schematic representation of a spline curve.</p>
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<p>Spline interpolation, showcasing different orders of spline interpolation. (<b>a</b>) for cubic interpolation, (<b>b</b>) for 7th-order interpolation, (<b>c</b>) for 5th-order interpolation, and (<b>d</b>) for linear spline.</p>
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<p>The noise addition process in the diffusion network (displayed every 20 steps).</p>
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<p>The structure of the KANs-CNN network.</p>
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<p>The fault diagnosis flowchart.</p>
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<p>Time-frequency diagram of the bearing after wavelet transform.</p>
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<p>Loss Function, Accuracy, and Confusion Matrix of the KANs-CNN Experiment on the Augmented Bearing Dataset Using DDPM.</p>
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<p>Comparison of time-frequency maps of the bearing dataset before and after using the diffusion network.</p>
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<p>In comparative experiments with other methods, KANs-CNN achieved the highest performance in terms of average accuracy.</p>
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<p>Comparison of confusion matrices for fault diagnosis accuracy among the DDPM, GAN, and VAE generative models.</p>
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<p>Time-frequency maps of the tool after wavelet transformation.</p>
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<p>Comparison of confusion matrices for fault diagnosis accuracy among the DDPM, GAN, and VAE generative models.</p>
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16 pages, 8003 KiB  
Article
Characterization of Cell Wall Compositions of Sodium Azide-Induced Brittle Mutant Lines in IR64 Variety and Its Potential Application
by Anuchart Sawasdee, Tsung-Han Tsai, Yi-Hsin Chang, Jeevan Kumar Shrestha, Meng-Chun Lin, Hsin-I Chiang and Chang-Sheng Wang
Plants 2024, 13(23), 3303; https://doi.org/10.3390/plants13233303 - 25 Nov 2024
Viewed by 267
Abstract
The rice brittle culm is a cell wall composition changed mutant suitable for studying mechanical strength in rice. However, a thorough investigation of brittle culm has been limited due to the lack of diverse brittle mutants on similar genetic backgrounds in cell walls. [...] Read more.
The rice brittle culm is a cell wall composition changed mutant suitable for studying mechanical strength in rice. However, a thorough investigation of brittle culm has been limited due to the lack of diverse brittle mutants on similar genetic backgrounds in cell walls. In this study, we obtained 45 various brittle mutant lines (BMLs) from the IR64 mutant pool induced by sodium azide mutagenesis using the finger-bending method and texture profile analysis. The first scoring method was established to differentiate the levels of brittleness in rice tissues. The variation of cell wall compositions of BMLs showed that the brittleness in rice primarily correlated with cellulose content supported by high correlation coefficients (R = −0.78) and principal component analysis (PCA = 81.7%). As demonstrated using PCA, lower correlation with brittleness, hemicellulose, lignin, and silica were identified as minor contributors to the overall balance of cell wall compositions and brittleness. The analysis of hydrolysis and feeding indexes highlighted the importance of diversities of brittleness and cell wall compositions of BMLs and their potential applications in ruminant animals and making bioenergy. These results contributed to the comprehension of brittleness and mechanical strength in rice and also extended the applications of rice straw. Full article
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<p>The breaking force of a fresh flag leaf of 45 BMLs and IR64 at the maturity stage. Breaking force (N/mm) was the highest force required to break the sample when using the texture profile analyzer (TPA) divided by its leaf width. The error bar is SD obtained by three repetitions (<span class="html-italic">n</span> = 3).</p>
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<p>Diverse phenotypes of the BMLs from the IR64 mutant pool. (<b>A</b>) Pigmentation diversity in different tissues. (<b>B</b>) Diversity of leaf character. (<b>C</b>) Diversity of leaf green intensity by IRRI’s leaf color chart. (<b>D</b>) Diversity of grain characters (Bar = 1 cm).</p>
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<p>Correlation coefficients of phenotypes of BMLs. Larger numerical values and sizes indicate a stronger correlation. LL, leaf length; LW, leaf width; TH, time to heading date; SL, stem length; PN, panicle number; TM, time to maturity; PL, panicle length; GL, grain length; GW, grain width; GR, grain L/W ratio; PF, percentage of fertility; BF, breaking force. The interpretation of coefficient intervals: 0–0.19 (very low), 0.2–0.39 (low), 0.4–0.59 (middle), 0.6–0.79 (strong), and 0.8–1.0 (very strong). The asterisk indicates a significance (* = <span class="html-italic">p</span> &lt; 0.05; ** = <span class="html-italic">p</span> &lt; 0.01; *** = <span class="html-italic">p</span> &lt; 0.001).</p>
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<p>Correlation coefficient and principal component analysis of the cell wall compositions, breaking force, and brittleness score. (<b>A</b>) Correlation between the cell wall compositions: cellulose, hemicellulose, lignin, silica, brittleness score, and the breaking force of the flag leaf of brittle culm mutant lines was illustrated. Larger numerical values and sizes indicate a stronger correlation. The interpretation of coefficient intervals: 0–0.19 (very low), 0.2–0.39 (low), 0.4–0.59 (middle), 0.6–0.79 (strong), and 0.8–1.0 (very strong). The asterisk indicates a significance (** = <span class="html-italic">p</span> &lt; 0.01; *** = <span class="html-italic">p</span> &lt; 0.001). (<b>B</b>) Principal component analysis (PCA) biplot of BMLs on the phenotypic variables (arrows). The first two (PC1 + PC2) components accounted for 81.7% of the variance.</p>
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<p>The practice of BMLs for rice farming machinery. (<b>A</b>) Bar chart showing the average percentage of leaf damage in each brittleness score group after the Megi typhoon in 2016. The red arrow pointed to the damaged leaves. (<b>B</b>) Seedling of the brittle mutant line (AZ1805) was transplanted using a transplanting machine. (<b>C</b>) The grain of the brittle mutant line was harvested using a combiner. (<b>D</b>) The degradation of stubble of the brittle mutant line (<b>Left</b>) was faster than the wild type (<b>Right</b>).</p>
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<p>The hydrolysis means the wild type (IR64, score 0) and BMLs (score 5) within 24 h of incubation. * = significant difference by t-test (<span class="html-italic">p</span>-value &lt; 0.05).</p>
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18 pages, 2815 KiB  
Article
Melatonin Attenuates Ferritinophagy/Ferroptosis by Acting on Autophagy in the Liver of an Autistic Mouse Model BTBR T+Itpr3tf/J
by Giorgia Cominelli, Claudio Lonati, Daniela Pinto, Fabio Rinaldi, Caterina Franco, Gaia Favero and Rita Rezzani
Int. J. Mol. Sci. 2024, 25(23), 12598; https://doi.org/10.3390/ijms252312598 - 23 Nov 2024
Viewed by 319
Abstract
Autism spectrum disorders (ASDs) are a pool of neurodevelopment disorders in which social impairment is the main symptom. Presently, there are no definitive medications to cure the symptoms but the therapeutic strategies that are taken ameliorate them. The purpose of this study was [...] Read more.
Autism spectrum disorders (ASDs) are a pool of neurodevelopment disorders in which social impairment is the main symptom. Presently, there are no definitive medications to cure the symptoms but the therapeutic strategies that are taken ameliorate them. The purpose of this study was to investigate the effects of melatonin (MLT) in treating ASDs using an autistic mouse model BTBR T+Itpr3tf/J (BTBR). We evaluated the hepatic cytoarchitecture and some markers of autophagy, ferritinophagy/ferroptosis, in BTBR mice treated and not-treated with MLT. The hepatic morphology and the autophagy and ferritinophagy/ferroptosis pathways were analyzed by histological, immunohistochemical, and Western blotting techniques. We studied p62 and microtubule-associated protein 1 light chain 3 B (LC3B) for evaluating the autophagy; nuclear receptor co-activator 4 (NCOA4) and long-chain-coenzyme synthase (ACSL4) for monitoring ferritinophagy/ferroptosis. The liver of BTBR mice revealed that the hepatocytes showed many cytoplasmic inclusions recognized as Mallory–Denk bodies (MDBs); the expression and levels of p62 and LC3B were downregulated, whereas ACSL4 and NCOA4 were upregulated, as compared to control animals. MLT administration to BTBR mice ameliorated liver damage and reduced the impairment of autophagy and ferritinophagy/ferroptosis. In conclusion, we observed that MLT alleviates liver damage in BTBR mice by improving the degradation of intracellular MDBs, promoting autophagy, and suppressing ferritinophagy/ferroptosis. Full article
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<p>Morphopathological evaluation of hepatocytes containing MDBs. Representative photomicrographs of hematoxylin–eosin staining of (<b>a</b>) BTBR mice, (<b>b</b>) MLT-treated BTBR mice, and (<b>c</b>) CTR mice. Original magnification: 200×; insert: 400×; bars = 50 µm. (<b>d</b>) Quantitative analysis of MDB-containing hepatocytes. * <span class="html-italic">p</span> &lt; 0.05 vs. BTBR mice; # <span class="html-italic">p</span> &lt; 0.05 vs. MLT-BTBR mice.</p>
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<p>Hepatic p62 and LC3B immunohistochemical evaluations. Representative photomicrographs of liver p62 (<b>a</b>–<b>c</b>) and LC3B (<b>d</b>–<b>f</b>); immunostainings of (<b>a</b>,<b>d</b>) BTBR mice, (<b>b</b>,<b>e</b>) BTBR mice treated with MLT, and (<b>c</b>,<b>f</b>) CTR mice. Black arrows indicate positivity in MDBs. Original magnification: 400×; insert: 1000× (<b>b</b>); bars = 20 µm.</p>
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<p>Hepatic p62 and LC3B Western blotting. Representative immunoblots of p62, LC3B I, and LC3B II of total liver samples from BTBR mice, BTBR mice treated with MLT, and CTR mice. β-actin was used as loading control. Relative expression quantification of Western blotting for p62 and LC3B. * <span class="html-italic">p</span> &lt; 0.05 vs. BTBR mice; # <span class="html-italic">p</span> &lt; 0.05 vs. MLT-BTBR mice.</p>
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<p>Hepatic NCOA4 and ACSL4 immunohistochemical evaluations. Representative photomicrographs of liver NCOA4 (<b>a</b>–<b>c</b>) and ACSL4 (<b>d</b>–<b>f</b>) immunostaining of (<b>a</b>,<b>d</b>) BTBR mice, (<b>b</b>,<b>e</b>) BTBR mice treated with MLT, and (<b>c</b>,<b>f</b>) CTR mice. Original magnification: 400×; bars = 20 µm.</p>
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<p>Schematic drawing of the experiment plan. (<b>A</b>) indicates the five mice per group transcardically perfused, whereas (<b>B</b>) indicates the other five mice per group which were euthanized by cervical dislocation. The black arrows indicate adequate liver samples collection; the blue arrows indicate the experimental treatment duration expressed in number of days (1 to 8); the white box indicates light exposition of mice and the black box indicates the dark exposition of mice. B-test: behavioral test; CTR: control; h: hour; MLT: melatonin; MLTV: melatonin vehicle.</p>
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19 pages, 4031 KiB  
Article
MSTrans: Multi-Scale Transformer for Building Extraction from HR Remote Sensing Images
by Fei Yang, Fenlong Jiang, Jianzhao Li and Lei Lu
Electronics 2024, 13(23), 4610; https://doi.org/10.3390/electronics13234610 - 22 Nov 2024
Viewed by 343
Abstract
Buildings are one of the most important goals of human transformation of the Earth’s surface. Therefore, building extraction (BE), such as in urban resource management and planning, is a task that is meaningful to actual production and life. Computational intelligence techniques based on [...] Read more.
Buildings are one of the most important goals of human transformation of the Earth’s surface. Therefore, building extraction (BE), such as in urban resource management and planning, is a task that is meaningful to actual production and life. Computational intelligence techniques based on convolutional neural networks (CNNs) and Transformers have begun to be of interest in BE, and have made some progress. However, the BE methods based on CNNs are limited by the difficulty in capturing global long-range relationships, while Transformer-based methods are often not detailed enough for pixel-level annotation tasks because they focus on global information. To conquer the limitations, a multi-scale Transformer (MSTrans) is proposed for BE from high-resolution remote sensing images. In the proposed MSTrans, we develop a plug-and-play multi-scale Transformer (MST) module based on atrous spatial pyramid pooling (ASPP). The MST module can effectively capture tokens of different scales through the Transformer encoder and Transformer decoder. This can enhance multi-scale feature extraction of buildings, thereby improving the BE performance. Experiments on three real and challenging BE datasets verify the effectiveness of the proposed MSTrans. While the proposed approach may not achieve the highest Precision and Recall accuracies compared with the seven benchmark methods, it improves the overall metrics F1 and mIoU by 0.4% and 1.67%, respectively. Full article
(This article belongs to the Special Issue Emerging Technologies in Computational Intelligence)
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<p>Overview of the proposed MSTrans BE framework.</p>
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<p>The architecture of the MST module.</p>
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<p>Dataset presentations: (<b>a</b>) WHU-CD dataset; (<b>b</b>) LEVIR-CD dataset; (<b>c</b>) GZ-CD dataset.</p>
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<p>The BE maps of different methods on the Massachusetts dataset: (<b>a</b>) image, (<b>b</b>) label, (<b>c</b>) U-Net [<a href="#B20-electronics-13-04610" class="html-bibr">20</a>], (<b>d</b>) SiU-Net [<a href="#B23-electronics-13-04610" class="html-bibr">23</a>], (<b>e</b>) Res2Unet [<a href="#B24-electronics-13-04610" class="html-bibr">24</a>], (<b>f</b>) CFENet [<a href="#B31-electronics-13-04610" class="html-bibr">31</a>], (<b>g</b>) CBRNet [<a href="#B32-electronics-13-04610" class="html-bibr">32</a>], (<b>h</b>) BBRNet [<a href="#B28-electronics-13-04610" class="html-bibr">28</a>], (<b>i</b>) AGPNet [<a href="#B29-electronics-13-04610" class="html-bibr">29</a>], and (<b>j</b>) proposed MSTrans.</p>
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<p>The BE maps of different methods on the EastAsia dataset: (<b>a</b>) image, (<b>b</b>) label, (<b>c</b>) U-Net [<a href="#B20-electronics-13-04610" class="html-bibr">20</a>], (<b>d</b>) SiU-Net [<a href="#B23-electronics-13-04610" class="html-bibr">23</a>], (<b>e</b>) Res2Unet [<a href="#B24-electronics-13-04610" class="html-bibr">24</a>], (<b>f</b>) CFENet [<a href="#B31-electronics-13-04610" class="html-bibr">31</a>], (<b>g</b>) CBRNet [<a href="#B32-electronics-13-04610" class="html-bibr">32</a>], (<b>h</b>) BBRNet [<a href="#B28-electronics-13-04610" class="html-bibr">28</a>], (<b>i</b>) AGPNet [<a href="#B29-electronics-13-04610" class="html-bibr">29</a>], and (<b>j</b>) proposed MSTrans.</p>
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<p>The BE maps of different methods on the Inria dataset: (<b>a</b>) image, (<b>b</b>) label, (<b>c</b>) U-Net [<a href="#B20-electronics-13-04610" class="html-bibr">20</a>], (<b>d</b>) SiU-Net [<a href="#B23-electronics-13-04610" class="html-bibr">23</a>], (<b>e</b>) Res2Unet [<a href="#B24-electronics-13-04610" class="html-bibr">24</a>], (<b>f</b>) CFENet [<a href="#B31-electronics-13-04610" class="html-bibr">31</a>], (<b>g</b>) CBRNet [<a href="#B32-electronics-13-04610" class="html-bibr">32</a>], (<b>h</b>) BBRNet [<a href="#B28-electronics-13-04610" class="html-bibr">28</a>], (<b>i</b>) AGPNet [<a href="#B29-electronics-13-04610" class="html-bibr">29</a>], and (<b>j</b>) proposed MSTrans.</p>
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<p>The BE maps of different submodule combinations on the Massachusetts dataset for ablation studies.</p>
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<p>The visual feature heatmaps of the proposed MSTrans on different submodules.</p>
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23 pages, 4802 KiB  
Review
Stromatolites and Their “Kin” as Living Microbialites in Contemporary Settings Linked to a Long Fossil Record
by Ed Landing and Markes E. Johnson
J. Mar. Sci. Eng. 2024, 12(12), 2127; https://doi.org/10.3390/jmse12122127 - 22 Nov 2024
Viewed by 591
Abstract
Organo-sedimentary deposits that result from fine-grained sediment trapping, binding, and likely precipitation (of carbonate) by microbes in flat-mat, branching, and dome-shaped constructions are termed microbialites. They were first identified as stromatolites by paleontologists well before the discovery of cyanobacteria that build the same [...] Read more.
Organo-sedimentary deposits that result from fine-grained sediment trapping, binding, and likely precipitation (of carbonate) by microbes in flat-mat, branching, and dome-shaped constructions are termed microbialites. They were first identified as stromatolites by paleontologists well before the discovery of cyanobacteria that build the same kinds of structures in contemporary settings around the world. Earth’s earliest life forms were prokaryotes (bacteria and bacteria-like forms) that reproduced under anaerobic conditions and later produced increasingly aerobic conditions. Stromatolites persisted through later Archean and Proterozoic times through the subsequent Phanerozoic to the present. At the start of the Cambrian Period 538 million years ago, stromatolites continued alongside rapidly diversifying plant and animal phyla during the Cambrian explosion of eukaryotic life, which have complex cells with internal structures and tissue-grade organization in multicellular taxa. The type locality exhibiting clear examples of stromatolite structures is conserved at Lester Park near Saratoga Springs in northeastern New York State. Paleontologist James Hall (1811–1898) was the first in 1884 to assign a Latin binomen (Cryptozoon proliferum) to stromatolite fossils from Lester Park. Thereafter, reports on formally named stromatolites proliferated, as did examples from virtually all subsequent geological time intervals including the Pleistocene Epoch. However, recognition that living cyanobacteria formed stromatolites identified as Cryptozoon took place much later in 1961 with the announcement by geologist Brian W. Logan (1933–2008) who described modern constructions in Hamlin Pool, Shark Bay, Western Australia. Initially, Shark Bay was regarded as a one-of-a-kind sanctuary for stromatolites living under restricted conditions with elevated levels of salinity that prohibited competition or grazing by eukaryotes. Most notably, among other settings with living stromatolites discovered and described since then are the Bahamas, East African rift lakes, Mexico’s Baja California, and saline lakes in Argentina. This report reviews the history of discoveries of modern-day stromatolites, more commonly called microbialites by biologists. All are predicated on the ground-breaking efforts of geologists and paleontologists who first described fossil stromatolites but were unaware of their living counterparts. The Lester Park locality is highlighted together with a master list of other North American localities that feature purported Cryptozoons. Full article
(This article belongs to the Special Issue Feature Review Papers in Geological Oceanography)
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<p>Global representation of today’s continents and oceans on a Mollweide projection showing major ocean spreading zones. Numerals on black triangles denote the locations of oligotrophic stromatolites living today in (1) Shark Bay, Western Australia; (2) Bahamas; (3) Lake Tanganyika, Africa; (4) saline lakes in northwestern Argentina; and (5) saline ponds in Mexico’s Baja California. The numbered black dot marks the location of fossil stromatolites from present-day Upper New York State (1).</p>
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<p>Maps showing the coast of Western Australia on the Indian Ocean: (<b>a</b>) Western Australia with a small arrow pointing to Shark Bay; and (<b>b</b>) enlargement showing the location of the Hamelin Pool Marine Nature Reserve (asterisk) within the UNESCO World Heritage zone protecting the greater Shark Bay.</p>
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<p>Examples of stromatolites shaped like large bread loaves oriented perpendicular to the shore at the Hamelin Pool Marine Nature Reserve, Shark Bay: (<b>a</b>) stromatolites exposed during low tide (pocket knife 9 cm long for scale); (<b>b</b>) stromatolites barely awash at high tide with narrow, open galleries from 10 to 20 cm wide.</p>
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<p>A field of living stromatolites in permanently subtidal seawater offshore Carbla Point near Hamelin Pool in Shark Bay. Junior author for scale.</p>
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<p>Maps showing Mexico’s Isla Ángel de la Guarda in relation to the Baja California peninsula: (<b>a</b>) the full peninsula adjacent to the Gulf of California off the Mexican mainland with the island’s location (asterisk) near the head of the gulf; (<b>b</b>) map of Isla Ángel de la Guarda marking the four localities (blue) where stromatolites occur in closed lagoons; and (<b>c</b>) topographic map enlarged from box in (<b>b</b>) showing the island’s southeast end, where thrombolites and mat-forming stromatolites were discovered in 2007.</p>
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<p>Photos showing living stromatolites from closed lagoons on the shores of southeast Isla Ángel de la Guarda (see <a href="#jmse-12-02127-f005" class="html-fig">Figure 5</a>c for location): (<b>a</b>) thrombolite assemblage of branched forms the size of small cauliflower heads from the small lagoon (coin 2.4 cm in diameter for scale); (<b>b</b>) matted microbialites dissected by desiccation polygons along the shore of the big lagoon (compass case 10 cm across for scale).</p>
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<p>Location of Lester Park in the Upper Cambrian–Upper Ordovician lowlands southeast of the Mesoproterozoic Adirondack Mountains massif, northeast of the upper Middle Devonian Catskill Highlands, and west from the terminal Ediacaran–lower Upper Ordovician Taconic Allochthon.</p>
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<p>Coalesced topotype specimens of the first-named stromatolite <span class="html-italic">Cryptozoon proliferum</span> Hall, 1884, at Lester Park, Saratoga County, eastern New York: (<b>a</b>) View of the top of a shoaling cycle abraded and truncated to show growth laminae by the movement of coarse quartz sand that weathers brownish; narrower, lower parts of domes (upper part of the figure) were exposed by glacial (Pleistocene) plucking of the upper part of domes. (<b>b</b>) Detail of clotted thrombolite structure surrounded by bedded limestone from Hoyt quarry, ca. 5 m above the <span class="html-italic">C</span>. <span class="html-italic">proliferum</span> surface at Lester Park. Hammer (30 cm) for scale in both pictures.</p>
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<p><span class="html-italic">Cryptozoon proliferum</span> from older Galway Formation (lower Upper Cambrian <span class="html-italic">Elvina</span> Zone) NE of Lester Park shows two generations of fracturing: (1) brownish carbonate mud-filled cracks in the lower part of the specimen that separate and also run transverse to growth laminae are syndepositional fractures (ca. 490 Ma) and reflect continued extension of the rifted margin of NE Laurentia; (2) thin white calcite veins parallel to growth laminae produced during the Taconic orogeny (ca. 460 Ma) [<a href="#B74-jmse-12-02127" class="html-bibr">74</a>]. Hypotype NYSM 19512 from the middle of the Galway Formation railroad cut above U.S. Route 9 just N of the intersection of U.S. Route 9 with Daniels Road [<a href="#B74-jmse-12-02127" class="html-bibr">74</a>], with a USD 25 cent coin (23 mm) for scale.</p>
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<p>Small <span class="html-italic">Crytozoon proliferum</span> dome at the north end of the Lester Park surface. This specimen was termed a “microatoll” [<a href="#B26-jmse-12-02127" class="html-bibr">26</a>], but it has an erosion-truncated top and lateral margins and is surrounded by a coarse-grained sandstone with light grey-colored <span class="html-italic">C. proliferum</span> clasts (yellow arrows).</p>
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18 pages, 742 KiB  
Article
The Development of a Zero Waste and Sustainable Waste Management Behavior Scale in Türkiye
by Bahar Ikizoglu
Sustainability 2024, 16(23), 10181; https://doi.org/10.3390/su162310181 - 21 Nov 2024
Viewed by 316
Abstract
Zero waste (ZW) and sustainable waste management (SWM) can vary based on environmental factors, economic and technological developments, social and cultural norms, and political and administrative differences across countries, as well as within rural or highly urbanized regions of the same country. The [...] Read more.
Zero waste (ZW) and sustainable waste management (SWM) can vary based on environmental factors, economic and technological developments, social and cultural norms, and political and administrative differences across countries, as well as within rural or highly urbanized regions of the same country. The research aims to obtain a valid and reliable scale that measures the multidimensional structure of ZW and SWM. Three hundred and thirty participants, including 213 women and 117 men, participated in the study. Participants had a mean age of 41.09 ± 12.31, with the majority (56.7%) holding a Bachelor’s degree. The study unfolded in two phases: initially, the item pool was reviewed, leading to the development of the final scale by eliminating unsuitable items. Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA) were conducted using IBM SPSS and IBM SPSS AMOS, and the scale provided construct validity with seven subdimensions and acceptable DFA parameters: χ2 = 933.249; df = 437; CMIN/DF = 2.136; CFI = 0.913; NFI = 0.905; RMSEA = 0.056; p = 0.010. The internal consistency of the scale was calculated using Cronbach’s alpha, and total scores and subdimensions ranged from 0.701 to 0.912, indicating an acceptable level of internal consistency. Thus, this new measurement tool can be used in various studies on ZW and SWM by facilitating the analysis of behavioral motivation, satisfaction, expectation, awareness, e-waste knowledge, and access to facilities regarding existing zero waste and sustainable waste management opportunities. Full article
(This article belongs to the Special Issue Waste Management and Recycling for Sustainability)
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<p>Multi-factor analysis model for final ZW-SWM Scale.</p>
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